Schmal, M., Kramer, L. T. S., Mach, R. L., Mach-Aigner, A., & Zimmermann, C. (2025). Providing a toolbox for genomic engineering of Trichoderma aggressivum. Microbiology Spectrum, 13(9), Article e0096625. https://doi.org/10.1128/spectrum.00966-25

Daza-Prieto, B., Raicevic, N., Hyden, P., Cabal, A., Ladstätter, J., Richter, S., Stoeger, A., Mach, R. L., Martinovic, A., & Ruppitsch, W. (2025). Ewingella docleensis sp. nov. isolated from artisanal Montenegrin komanski cheese. The Microbe, 8, Article 100449. https://doi.org/10.1016/j.microb.2025.100449

Hochenegger, N., Vignolle, G. A., Schmal, M., Mach, R. L., Mach-Aigner, A., Rahimi, M., Chan, C. M., Cai, F. M., Druzhinina, I., & Zimmermann, C. (2025). Genome sequencing and physiological characterization of three Neoarthrinium moseri strains. BMC Microbiology, 25(1), 1–18. https://doi.org/10.1186/s12866-025-04274-z

Steinbacher, S., Priselac, K., Kandler, W., Savio, D., Vierheilig, J., Mayer, R., Demeter, K., Linke, R. B., Mach, R. L., Sommer, R., Lindner, G., Zuser, K., Kolm, C., Stevenson, M. E., Blaschke, A. P., Kirschner, A. K. T., Leifels, M., & Farnleitner, A. H. (2025). Seasonally recurring patterns of dominant Crenothrix spp. in a European alluvial drinking water well: Significance and potential indicator role. Water Research, 279, Article 123406. https://doi.org/10.1016/j.watres.2025.123406

Ullah, S. F., Oreb, M., Boles, E., Srivastava, V., Seidl-Seiboth, V., Seiboth, B., & Kappel, L. (2025). N-acetylglucosamine sensing in the filamentous soil fungus Trichoderma reesei. FEBS Journal, 292(12), 3072–3090. https://doi.org/10.1111/febs.70015

Charest, J., Loebenstein, P., Mach, R. L., & Mach-Aigner, A. R. (2025). FunFEA: an R package for fungal functional enrichment analysis. BMC Bioinformatics, 26, Article 138. https://doi.org/10.1186/s12859-025-06164-7

Burger, I., Schmal, M., Peikert, K., Fourtis, L., Suster, C., Stanetty, C., Schnalzer, D., Hufnagel, B., Böttcher, T., Birner-Gruenberger, R., Mach, R. L., Mach-Aigner, A. R., Schittmayer-Schantl, M., & Zimmermann, C. (2025). Discovery of the antifungal compound ilicicolin K through genetic activation of the ilicicolin biosynthetic pathway in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS, 18(1), Article 32. https://doi.org/10.1186/s13068-025-02628-3

Danner, C., Machado Mello De Sousa, T., Mach, R. L., & Mach-Aigner, A. R. (2025). The Impact of DNA Methylation in Trichoderma reesei on Cellulase Production and Strain Degeneration. Microorganisms, 13(3), Article 584. https://doi.org/10.3390/microorganisms13030584

Zdouc, M. M., Blin, K., Louwen, N., Navarro, J., Loureiro, C., Bader, C., Bailey, C., Barra, L., Booth, T. J., Bozhüyük, K., Cediel Becerra, J. D. D., Charlop-Powers, Z., Chevrette, M., Chooi, Y.-H., D’Agostino, P. M., de Rond, T., Del Pup, E., Duncan, K. R., Gu, W., … Medema, M. H. (2025). MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration. Nucleic Acids Research, 53(D1), D678–D690. https://doi.org/10.1093/nar/gkae1115

Danner, C., Karpenko, Y., Mach, R. L., & Mach-Aigner, A. R. (2025). Act1 out of Action: Identifying Reliable Reference Genes in Trichoderma reesei for Gene Expression Analysis. Journal of Fungi, 11(5), Article 396. https://doi.org/10.3390/jof11050396

Dera, K. M., Barro, D. T., Kaboré, B. A., Gstöttenmayer, F., Dieng, M. M., Pagabeleguem, S., Weiss, B., Fiorenza, G., Piccinno, R., Malacrida, A. R., Aksoy, S., de Beer, C. J., Mach, R. L., Vreysen, M. J. B., & Abd‐Alla, A. M. M. (2025). Spiroplasma infection in colonized Glossina fuscipes fuscipes: impact on mass rearing and the sterile insect technique. Insect Science. https://doi.org/10.1111/1744-7917.70078

Derx, J., Valent, P., Steinbacher, S., Ameen, A., König, A.-M., Demeter, K., Linke, R., Sommer, R., Lindner, G., Schmalwieser, A. W., Walochnik, J., Kirschner, A., Mach, R. L., Cervero-Aragó, S., Zessner, M., Kittlaus, S., Blöschl, G., Stevenson, M., Blaschke, A. P., & Farnleitner, A. H. (2025). Resilience to Future Changes: Assessing the Impact of Human Wastewater Emissions on Microbiological Water Safety Along the Danube . In EGU General Assembly 2025. EGU General Assembly 2025, Wien, Austria. https://doi.org/10.5194/egusphere-egu25-8167

Daza-Prieto, B., Raicevic, N., Martinovic, A., Ladstätter, J., Zuber Bogdanovic, I., Anika Schorpp, Stoeger, A., Mach, R., Ruppitsch, W., & Cabal, A. (2024). Genetic diversity and distinction of Enterococcus faecium and Enterococcus lactis in traditional Montenegrin brine cheeses and salamis. Frontiers in Microbiology, 15, Article 1473938. https://doi.org/10.3389/fmicb.2024.1473938

Jodlbauer, J., Schmal, M., Waltl, C., Rohr, T., Mach-Aigner, A. R., Mihovilovic, M. D., & Rudroff, F. (2024). Unlocking the potential of cyanobacteria: a high-throughput strategy for enhancing biocatalytic performance through genetic optimization. Trends in Biotechnology, 42(12), 1795–1818. https://doi.org/10.1016/j.tibtech.2024.07.011

Daza Serna, L. V., Toussaint, V., Mach-Aigner, A., Mach, R., Kessler, P., Bachmann, S., Pöppler, A.-C., Friedl, A., & Delidovich, I. (2024). Assessment of the Recovery of Erythritol Using Boronic Acid Polymers. Industrial & Engineering Chemistry Research, 63(47), 20677–20687. https://doi.org/10.1021/acs.iecr.4c01224

Burger, I., Schmal, M., Fourtis, L., Peikert, K., Suster, C., Stanetty, C., Schnalzer, D., Birner-Grünberger, R., Mach, R., Mach-Aigner, A., Derntl, C., & Schittmayer-Schantl, M. (2024, September 23). Discovery of a novel antifungal compound, ilicicolin K, through genetic activation of the ilicicolin biosynthetic pathway in Trichoderma reesei. APMRS/CEEPC APMRS-CEEPC 2024, Wien, Austria.

Fritsche, S., Fronek, F., Mach, R., & Steiger, M. (2024, September 17). Applicability of non-invasive and live-cell holotomographic imaging on fungi. ÖGMBT Annual Meeting 2024, Graz, Austria. https://doi.org/10.34726/8502

Fritsche, S., Fronek, F., Mach, R., & Steiger, M. G. (2024). Applicability of non-invasive and live-cell holotomographic imaging on fungi. Journal of Microbiological Methods, 224, Article 106983. https://doi.org/10.1016/j.mimet.2024.106983

Burger, I., Schmal, M., Peikert, K., Fourtis, L., Suster, C., Stanetty, C., Schnalzer, D., Birner-Gruenberger, R., Mach, R. L., Mach-Aigner, A. R., Schittmayer, M., & Zimmermann, C. (2024). Discovery of a novel antifungal compound, ilicicolin K, through genetic activation of the ilicicolin biosynthetic pathway in Trichoderma reesei. bioRxiv. https://doi.org/10.1101/2024.06.20.599701

Burger, I., Schmal, M., Zimmermann, C., Birner-Grünberger, R., & Schittmayer-Schantl, M. (2024, June 18). Sherlocking with Multi-omics and a Dash of Molecular Networking Magic to Unravel Secondary Metabolites in Fungi. Metabolomics 2024, Japan.

Maier, I., Kontaxis, G., Zimmermann, C., & Steininger, C. (2024). Cyanovirin-N Binding to N-Acetyl-d-glucosamine Requires Carbohydrate-Binding Sites on Two Different Protomers. Biochemistry, 63(10), 1270–1277. https://doi.org/10.1021/acs.biochem.4c00113

Burger, I., Schmal, M., Zimmermann, C., Birner-Grünberger, R., & Schittmayer-Schantl, M. (2024, February 21). Unravelling Fungal RiPPs: Sherlocking with Proteomics, Metabolomics, and a Dash of Molecular Networking Magic. 34th Mass Spectrometry Forum 2024, Wien, Austria.

Daza-Prieto, B., Raicevic, N., Cabal, A., Hyden, P., Mösenbacher, T., Ladstätter, J., Richter, S., Stöger, A., Joao Cardoso, M., Chakeri, A., Hasenberger, P., Stadlbauer, S., Mach, R. L., Martinovic, A., & Ruppitsch, W. (2024). Enterococcus montenegrensis sp. nov., isolated from artisanal Montenegrin dry sausage. International Journal of Systematic and Evolutionary Microbiology, 74(1). https://doi.org/10.1099/ijsem.0.006206

Cabal, A., Prieto, B., Raicevic, N., Pietzka, A., Chakeri, A., Hyden, P., Kundi, M., Indra, A., Mach, R., Flores, J. E. P., Martinovic, A., & Ruppitsch, W. (2024). Whole Genome Sequencing for Food Safety, Clinical and Public Health Microbiology. In MEDICON’23 and CMBEBIH’23 : Proceedings of the Mediterranean Conference on Medical and Biological Engineering and Computing (MEDICON) and International Conference on Medical and Biological Engineering (CMBEBIH), September 14–16, 2023, Sarajevo, Bosnia and Herzegovina—Volume 1: Imaging, Engineering and Artificial Intelligence in Healthcare (pp. 865–873). Springer. https://doi.org/10.1007/978-3-031-49062-0_90

Daza-Prieto, B., Cabal Rosel, A., Raicevic, N., Stoeger, A., Ladstaetter, J., Mach, R. L., Ruppitsch, W., & Martinovic, A. (2024). The Many Faces of E. Faecium: From Probiotics to Pathogenesis. In MEDICON’23 and CMBEBIH’23 : Proceedings of the Mediterranean Conference on Medical and Biological Engineering and Computing (MEDICON) and International Conference on Medical and Biological Engineering (CMBEBIH), September 14–16, 2023, Sarajevo, Bosnia and Herzegovina—Volume 1: Imaging, Engineering and Artificial Intelligence in Healthcare (pp. 837–844). Springer. https://doi.org/10.1007/978-3-031-49062-0_87

Besleaga, M., Zimmermann, C., Ebner, K., Mach, R., Mach-Aigner, A., Geier, M., Glieder, A., Spadiut, O., & Kopp, J. (2024). Bi-directionalized promoter systems allow methanol-free production of hard-to-express peroxygenases with Komagataella Phaffii. Microbial Cell Factories, 23, Article 177. https://doi.org/10.1186/s12934-024-02451-9

Daza Prieto, B., Raicevic, N., Hyden, P., Mösenbacher, T., Ladstätter, J., Stöger, A., Cabal, A., Mach, R. L., Martinovic, A., & Ruppitsch, W. (2024). Complete genome of Microbacterium plantarum CoE-159-22, isolated from traditionally produced Montenegrin cheese. Microbiology Resource Announcements, Article e0003524. https://doi.org/10.1128/mra.00035-24

Dera, K. M., Pagabeleguem, S., Melachio Tanekou, T. T., Toé, A. I., Ouedraogo/Sanou, G. M. S., Belem, A. M. G., Ravel, S., Mach, R., Vreysen, M. J. B., & Abd-Alla, A. M. M. (2024). Impact of long-term mass-rearing on the genetic structure of tsetse fly Glossina palpalis gambiensis colonies. Insect Science. https://doi.org/10.1111/1744-7917.13479

Jadhav, R., Mach, R. L., & Mach-Aigner, A. R. (2024). Protein secretion and associated stress in industrially employed filamentous fungi. Applied Microbiology and Biotechnology, 108, Article 92. https://doi.org/10.1007/s00253-023-12985-4

Kaboré, B. A., Taqi, S. D., Mkinga, A., Morales Zambrana, A. E., Mach, R., Vreysen, M., & de Beer, C. J. (2024). Radiation dose fractionation and its potential hormetic effects on male Glossina palpalis gambiensis (Diptera: Glossinidae): a comparative study of reproductive and flight quality parameters. Parasite, 31, Article 4. https://doi.org/10.1051/parasite/2024001

Masi, A. L., Stark, G., Pfnier, J., Mach, R., & Mach-Aigner, A. (2024). Exploration of Trichoderma reesei as an alternative host for erythritol production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS, 17, Article 90. https://doi.org/10.1186/s13068-024-02537-x

Masi, A., Wögerbauer, K., Mach, R. L., & Mach-Aigner, A. R. (2024). Genomic deletions in Aureobasidium pullulans by an AMA1 plasmid for gRNA and CRISPR/Cas9 expression. Fungal Biology and Biotechnology, 11, Article 6. https://doi.org/10.1186/s40694-024-00175-4

Kaboré, B. A., Nawaj, A., Maiga, H., Soukia, O., Pagabeleguem, S., Ouédraogo/Sanon, M. S. G., Vreysen, M. J. B., Mach, R. L., & de Beer, C. J. (2023). X-rays are as effective as gamma-rays for the sterilization of Glossina palpalis gambiensis Vanderplank, 1911 (Diptera: Glossinidae) for use in the sterile insect technique. Scientific Reports, 13(1), Article 17633. https://doi.org/10.1038/s41598-023-44479-8

Burger, I., Schmal, M., Zimmermann, C., Birner-Grünberger, R., & Schittmayer-Schantl, M. (2023, October 12). Unravelling Fungal RiPPs Sherlocking with Proteomics, Metabolomics, and a Dash of Molecular Networking Magic. Munich Metabolomics Meeting 2023, München, Germany.

Knezevic, K., Daza Serna, L. V., Mach-Aigner, A., Mach, R., Friedl, A., Krampe, J., & Kreuzinger, N. (2023). Investigation of ion-exchange membranes and erythritol concentration for the desalination of erythritol culture broth by electrodialysis. Chemical Engineering and Processing: Process Intensification, 192, Article 109494. https://doi.org/10.1016/j.cep.2023.109494

Schneckenleitner, N., Mach, R., Mach-Aigner, A., & Zimmermann, C. (2023, September 22). Contribution of DHN melanin to survival and growth of Neoarthrinium moseri in extreme environments. IUBMB Focused Meeting on Extremophilic Fungi (FUN-EX 2023), Ljubljana, Slovenia.

Stadler, B., Haas, M., Leschanz, C., & Masi, A. L. (2023). The “PARENT” Initiative: PArents in REsearch aNd Technology: Study of the situation of parents at the Faculty of Technical Chemistry of TU WIEN. https://doi.org/10.34726/4822

Steiger, M. (2023, August 8). The Industrial Yeast Pichia pastoris Is Converted from a Heterotroph into an Autotroph Capable of Growth on CO2. Molecular Basis of Microbial One-Carbon Metabolism, Southbridge, MA, United States, United States of America (the).

Danner, C., Mach, R., & Mach-Aigner, A. R. (2023). The phenomenon of strain degeneration in biotechnologically relevant fungi. Applied Microbiology and Biotechnology, 107, 4745–4758. https://doi.org/10.1007/s00253-023-12615-z

Daza-Serna, L., Masi, A., Serna-Loaiza, S., Pfnier, J., Stark, G., Mach, R. L., Mach-Aigner, A. R., & Friedl, A. (2023). Detoxification strategy of wheat straw hemicellulosic hydrolysate for cultivating Trichoderma reesei: a contribution towards the wheat straw biorefinery. Biomass Conversion and Biorefinery, 13(18), 16495–16509. https://doi.org/10.1007/s13399-023-04099-8

Burger, I., Schmal, M., Zimmermann, C., Birner-Grünberger, R., & Schittmayer-Schantl, M. (2023, April 14). Proteomics, metabolomics and molecular networking as tools for the investigation of fungal RiPPs. MassSpec Forum 2023, Wien, Austria.

Burger, I., Schmal, M., Zimmermann, C., Birner-Grünberger, R., & Schittmayer-Schantl, M. (2023, April 12). Proteomics, metabolomics and molecular networking as tools for the identification of fungal RiPPs. ANAKON 2023, Wien, Austria.

Schmal, M. (2023, March 8). Phylogenetic analysis and investigation of RiPP cluster in 50 Trichoderma genomes. 16th European Conference on Fungal Genetics (ECFG16), Innsbruck, Austria.

Hochenegger, N., Mach, R., Mach-Aigner, A., & Zimmermann, C. (2023, March 7). On the interaction of SREBP Sah2 and the pleiotropic regulator Xpp1 in Trichoderma reesei. 16th European Conference on Fungal Genetics, Innsbruck, Austria.

Masi, A. L. (2023, March 7). Mannitol metabolism and osmotic stress answer: a comparative study on Trichoderma reesei and Aureobasidium pullulans. 16th European Conference on Fungal Genetics (ECFG16), Innsbruck, Austria.

Yamada, H., Kaboré, B. A., Bimbilé Somda, N. S., Ntoyi, N. L., de Beer, C. J., Bouyer, J., Caceres, C., Mach, R. L., & Gómez-Simuta, Y. (2023). Suitability of Raycell MK2 Blood X-ray Irradiator for the Use in the Sterile Insect Technique: Dose Response in Fruit Flies, Tsetse Flies and Mosquitoes. Insects, 14(1), Article 92. https://doi.org/10.3390/insects14010092

Besleaga, M., Vignolle, G. A., Kopp, J., Spadiut, O., Mach, R. L., Mach-Aigner, A. R., & Zimmermann, C. (2023). Evaluation of reference genes for transcript analyses in Komagataella phaffii (Pichia pastoris). Fungal Biology and Biotechnology, 10, Article 7. https://doi.org/10.1186/s40694-023-00154-1

Dera, K.-S. M., Dieng, M. M., Moyaba, P., Ouedraogo, G. M., Pagabeleguem, S., Njokou, F., Ngambia Freitas, F. S., de Beer, C. J., Mach, R. L., Vreysen, M., & Abd-Alla, A. M. (2023). Prevalence of Spiroplasma and interaction with wild Glossina tachinoides microbiota. Parasite, 30, Article 62. https://doi.org/10.1051/parasite/2023064

Gstöttenmayer, F., Moyaba, P., Rodriguez, M., Mulandane, F. C., Mucache, H. N., Neves, L., de Beer, C. J., Ravel, S., De Meeûs, T., Mach, R. L., Vreysen, M. J. B., & Abd-Alla, A. M. M. (2023). Development and characterization of microsatellite markers for the tsetse species Glossina brevipalpis and preliminary population genetics analyses. Parasite, 30, Article 34. https://doi.org/10.1051/parasite/2023038

Zimmermann, C., Till, P., Danner, C., & Mach-Aigner, A. R. (2022). Genetic Regulation Networks in Cellulase and Hemicellulase Production in an Industrially Applied Cellulase Producer Trichoderma reesei. In V. Bisaria (Ed.), Handbook of Biorefinery Research and Technology. Springer. https://doi.org/10.1007/978-94-007-6724-9_25-1

Dieng, M. M., Augustinos, A. A., Demirbas-Uzel, G., Doudoumis, V., Parker, A. G., Tsiamis, G., Mach, R., Bourtzis, K., & ABD-ALLA, A. (2022). Interactions between Glossina pallidipes salivary gland hypertrophy virus and tsetse endosymbionts in wild tsetse populations. Parasites and Vectors, 15, Article 447. https://doi.org/10.1186/s13071-022-05536-9

Vignolle, G. A., Mach, R., Mach-Aigner, A. R., & Zimmermann, C. (2022). FunOrder 2.0 – a method for the fully automated curation of co-evolved genes in fungal biosynthetic gene clusters. Frontiers in Fungal Biology. https://doi.org/10.3389/ffunb.2022.1020623

Masi, A. L., Stark, G., Pfnier, J., Daza Serna, L. V., Mach-Aigner, A., & Mach, R. (2022, September 22). Erythritol production by the saprobe Trichoderma reesei: screening and optimization using Design of Experiments to better understand the effect of nitrogen source, carbon source, pH and temperature.. 14th ÖGMBT Annual Meeting, Vienna, Austria.

Burger, I., Schmal, M., Zimmermann, C., Birner-Grünberger, R., & Schittmayer-Schantl, M. (2022, September 13). Proteomics, metabolomics and molecular networking as interplaying tools for identification and characterization of fungal RiPPs. SCP-APMRS 2022, Wien, Austria.

Schmal, M., Girod, C., Yaver, D., Mach, R., & Mach-Aigner, A. (2022). A bioinformatic-assisted workflow for genome-wide identification of ncRNAs. NAR Genomics and Bioinformatics, 4(3), lqac059. https://doi.org/10.1093/nargab/lqac059

Pflügl, S., Neuendorf, C. S., Vignolle, G. A., Novak, K., Zimmermann, C., Tomin, T., Mach, R., & Birner-Grünberger, R. (2022, August 11). Acetobacterium woodii as a flexible and robust host for formate-based bioproduction. Gordon Research Conference: Molecular Basis of Microbial One-Carbon Metabolism, Southbridge, MA, United States of America (the). https://doi.org/10.34726/3281

Burger, I., Schmal, M., Zimmermann, C., Birner-Grünberger, R., & Schittmayer-Schantl, M. (2022, July 31). Identification and Characterization of Fungal RiPPs, on the example of Aspergillus flavus. 14th European Summer School on Advanced Proteomics, Brixen, Italy.

Ellena, V., & Steiger, M. (2022). The importance of complete and high-quality genome sequences in Aspergillus niger research. Frontiers in Fungal Biology, 3. https://doi.org/10.3389/ffunb.2022.935993

Burger, I., Schmal, M., Zimmermann, C., Birner-Grünberger, R., & Schittmayer-Schantl, M. (2022, July 5). A journey into the unknown: proteomics and metabolomics as complementary techniques for the discovery of fungal RiPPs. 33rd MassSpec Forum 2022 Vienna, Wien, Austria.

Daza-Prieto, B., Raicevic, N., Ladstätter, J., Hyden, P., Jovanovic, A., Stöger, A., Cabal Rosel, A., Mach, R., Ruppitsch, W., & Martinovic, A. (2022). Draft Genome Sequence of Enterococcus dispar CoE-457-22, Isolated from Traditionally Produced Montenegrin Dry Sausage. Microbiology Resource Announcements, Article e0103822. https://doi.org/10.1128/mra.01038-22

Dieng, M. M., Dera, K. M., Moyaba, P., Ouedraogo, G. M. S., Demirbas-Uzel, G., Gstöttenmayer, F., Mulandane, F. C., Neves, L., Mdluli, S., Rayaisse, J.-B., Belem, A. M. G., Pagabeleguem, S., de Beer, C. J., Parker, A. G., Van Den Abbeele, J., March, R. L., Vreysen, M. J. B., & Abd-Alla, A. M. M. (2022). Prevalence of Trypanosoma and Sodalis in wild populations of tsetse flies and their impact on sterile insect technique programmes for tsetse eradication. Scientific Reports, 12(3322). https://doi.org/10.1038/s41598-022-06699-2

Ellena, V., Seekles, S. J., Vignolle, G. A., Ram, A. F. J., & Steiger, M. G. (2022). Genome sequencing of the neotype strain CBS 554.65 reveals the MAT1-2 locus of Aspergillus niger. BMC Genomics, 22(679). https://doi.org/10.1186/s12864-021-07990-8

Kreuter, J., Stark, G., Mach, R. L., Mach-Aigner, A. R., & Zimmermann, C. (2022). Fast and efficient CRISPR-mediated genome editing in Aureobasidium using Cas9 ribonucleoproteins. Journal of Biotechnology, 350, 11–16. https://doi.org/10.1016/j.jbiotec.2022.03.017

Oberhofer, M., Malfent, F., Zehl, M., Urban, E., Wackerlig, J., Reznicek, G., Vignolle, G. A., Rückert, C., Busche, T., Wibberg, D., & Zotchev, S. B. (2022). Biosynthetic Potential of the Endophytic Fungus Helotiales sp. BL73 Revealed via Compound Identification and Genome Mining. Applied and Environmental Microbiology, 88(6). https://doi.org/10.1128/aem.02510-21

Serna-Loaiza, S., Dias, M., Daza-Serna, L., de Carvalho, C. C. C. R., & Friedl, A. (2022). Integral Analysis of Liquid-Hot-Water Pretreatment of Wheat Straw: Evaluation of the Production of Sugars, Degradation Products, and Lignin. Sustainability, 14(1), 362. https://doi.org/10.3390/su14010362

Zimmermann, C., Bethge, O., Lutzer, B., & Bertagnolli, E. (2022). Platinum-assisted post deposition annealing of the n-Ge/Y₂O₃ interface. Semiconductor Science and Technology, 31(7), Article 075009. https://doi.org/10.1088/0268-1242/31/7/075009

Steinbacher, S., Savio, D. F., Demeter, K., Karl, M., Kandler, W., Kirschner, A. K. T., Reischer, G. H., Ixenmaier, S. K., Mayer, R., Mach, R. L. ., Derx, J., Sommer, R., Linke, R. B., & Farnleitner, A. (2021). Genetic microbial faecal source tracking: rising technology to support future water quality testing and safety management. Österreichische Wasser- Und Abfallwirtschaft, 73(11–12), 468–481. https://doi.org/10.1007/s00506-021-00811-y

Daza-Serna, L., Serna-Loaiza, S., Masi, A., Mach, R. L., Mach-Aigner, A. R., & Friedl, A. (2021). From the culture broth to the erythritol crystals: an opportunity for circular economy. Applied Microbiology and Biotechnology, 105(11), 4467–4486. https://doi.org/10.1007/s00253-021-11355-2

Masi, A., Mach, R. L., & Mach-Aigner, A. R. (2021). The pentose phosphate pathway in industrially relevant fungi: crucial insights for bioprocessing. Applied Microbiology and Biotechnology, 105(10), 4017–4031. https://doi.org/10.1007/s00253-021-11314-x

Agrimi, G., & Steiger, M. G. (2021). Metabolite transport and its impact on metabolic engineering approaches. FEMS Microbiology Letters, 368(1). https://doi.org/10.1093/femsle/fnaa211

Csarman, F., Obermann, T., Zanjko, M. C., Man, P., Halada, P., Seiboth, B., & Ludwig, R. (2021). Functional expression and characterization of two laccases from the brown rot Fomitopsis pinicola. Enzyme and Microbial Technology, 148(109801), 109801. https://doi.org/10.1016/j.enzmictec.2021.109801

Delabona, P. da S., Lima, D. J., Codima, C. A., Ramoni, J., Gelain, L., de Melo, V. S., Farinas, C. S., da Cruz Pradella, J. G., & Seiboth, B. (2021). Replacement of the carbon catabolite regulator (cre1) and fed-batch cultivation as strategies to enhance cellulase production in Trichoderma harzianum. Bioresource Technology Reports, 13(100634), 100634. https://doi.org/10.1016/j.biteb.2021.100634

Ellena, V. (2021). Towards sexual reproduction in an apparently asexual fungus: genome sequencing of the neotype strain CBS 554.65 reveals the MAT1 2 locus of Aspergillus niger. FemChem Scientific Workshop 2021, Wien, Austria.

Ellena, V., Bucchieri, D., Arcalis, E., Sauer, M., & Steiger, M. G. (2021). Sclerotia formed by citric acid producing strains of Aspergillus niger: Induction and morphological analysis. Fungal Biology, 125(6), 485–494. https://doi.org/10.1016/j.funbio.2021.01.008

Kolm, C., Reischer, G., Martzy, R., & Farnleitner, A. H. (2021). Molecular fecal pollution diagnostics and source tracking: New approaches and future possibilities for rapid, inexpensive and on-site applicable water quality test systems. In Abstracts of Lectures & Posters (p. 35).

Linke, R. B., Zeki, S., Mayer, R., Keiblinger, K., Savio, D., Kirschner, A. K. T., Reischer, G. H., Mach, R. L., Sommer, R., & Farnleitner, A. H. (2021). Identifying Inorganic Turbidity in Water Samples as Potential Loss Factor During Nucleic Acid Extraction: Implications for Molecular Fecal Pollution Diagnostics and Source Tracking. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.660566

Mach-Aigner, A. R. (2021). Die Rolle der Molekulargenetik bei der Entwicklung grüner Syntheseverfahren. 5. Fachdialog Grüne Chemie, Wien, Austria.

Martzy, R., Mello de Sousa, T. M., Mach, R. L., Yaver, D., & Mach-Aigner, A. R. (2021). The phenomenon of degeneration of industrial Trichoderma reesei strains. Biotechnology for Biofuels, 14(193). https://doi.org/10.1186/s13068-021-02043-4

Mayer, R., Linke, R., Vierheilig, J., Reischer, G., Mach, R. L., Kirschner, A. K. T., Zessner, M., Farnleitner, A. H., & Sommer, R. (2021). High persistence of genetic and cultivation-based bacterial fecal indicators in communal waste water at 5°C supports proportional autosampling procedures over 24h. In Abstracts (p. 2).

Neuendorf, C. S., Vignolle, G. A., Derntl, C., Tomin, T., Novak, K., Mach, R. L., Birner-Grünberger, R., & Pflügl, S. (2021). A quantitative metabolic analysis reveals Acetobacterium woodii as a flexible and robust host for formate-based bioproduction. Metabolic Engineering, 68, 68–85. https://doi.org/10.1016/j.ymben.2021.09.004

Primerano, P., Juric, M., Mach, R., Mach-Aigner, A., & Derntl, C. (2021). Expanding the toolbox: another auxotrophic marker for targeted gene integrations in Trichoderma reesei. Fungal Biology and Biotechnology, 8(9). https://doi.org/10.1186/s40694-021-00116-5

Serna-Loaiza, S., Dias, M., Daza-Serna, L., de Carvalho, C., & Friedl, A. (2021). Integral Analysis of Liquid-Hot-Water Pretreatment of Wheat Straw: Evaluation of the Production of Sugars, Degradation Products and Lignin. SDEWES - 16#^{th} Conference on Sustainable Development of Energy, Water and Environment Systems (Hybrid Conference), Dubrovnik, Croatia.

Steiger, M. (2021). Impact of transport processes on future organic acid production systems. In Abstracts (p. 8).

Steiger, M., Gassler, T., Egermeier, M., Baumschabl, M., & Mattanovich, D. (2021). Possibilities of carbon capture with methylotrophic yeasts. In Abstracts (p. 1).

Tomico Cuenca, I., Mach, R. L., Mach-Aigner, A. R., & Derntl, C. (2021). An overview on current molecular tools for heterologous gene expression in Trichoderma. Fungal Biology and Biotechnology, 8(11). https://doi.org/10.1186/s40694-021-00119-2

Vignolle, G. A., Mach, R. L., Mach-Aigner, A. R., & Derntl, C. (2021). Genome Sequence of the Black Yeast-Like Strain Aureobasidium pullulans var. aubasidani CBS 100524. Microbiology Resource Announcements, 10(12). https://doi.org/10.1128/mra.01293-20

Vignolle, G. A., Schaffer, D., Zehetner, L., Mach, R. L., Mach-Aigner, A. R., & Derntl, C. (2021). FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution. PLoS Computational Biology, 17(9), e1009372. https://doi.org/10.1371/journal.pcbi.1009372

Wohlschlager, L., Csarman, F., Chang, H., Fitz, E., Seiboth, B., & Ludwig, R. (2021). Heterologous expression of Phanerochaete chrysosporium cellobiose dehydrogenase in Trichoderma reesei. Microbial Cell Factories, 20(2). https://doi.org/10.1186/s12934-020-01492-0

Wohlschlager, L., Csarman, F., Zrilić, M., Seiboth, B., & Ludwig, R. (2021). Comparative characterization of glyoxal oxidase from Phanerochaete chrysosporium expressed at high levels in Pichia pastoris and Trichoderma reesei. Enzyme and Microbial Technology, 145(109748), 109748. https://doi.org/10.1016/j.enzmictec.2021.109748

Baumschabl, M., Prielhofer, R., Mattanovich, D., & Steiger, M. G. (2020). Fine-Tuning of Transcription in Pichia pastoris Using dCas9 and RNA Scaffolds. ACS Synthetic Biology, 9(12), 3202–3209. https://doi.org/10.1021/acssynbio.0c00214

Benocci, T., Aguilar-Pontes, M. V., Kun, R. S., Lubbers, R. J. M., Lail, K., Wang, M., Lipzen, A., Ng, V., Grigoriev, I. V., Seiboth, B., Daly, P., & de Vries, R. P. (2020). Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass. In ECFG15 - 15th European Conference on Fungal Genetics (Program and Abstracts). ECFG15 - 15th European Conference on Fungal Genetics, Rom, Italy.

Chenthamara, K., Druzhinina, I. S., Rahimi, M. J., Grujic, M., & Cai, F. (2020). Ecological Genomics and Evolution of Trichoderma reesei. In A. R. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 1–21). Springer Science + Business Media. https://doi.org/10.1007/978-1-0716-1048-0_1

Delabona, P. da S., Codima, C. A., Ramoni, J., Zubieta, M. P., de Araújo, B. M., Farinas, C. S., Pradella, J. G. da C., & Seiboth, B. (2020). The impact of putative methyltransferase overexpression on the Trichoderma harzianum cellulolytic system for biomass conversion. Bioresource Technology, 313(123616), 123616. https://doi.org/10.1016/j.biortech.2020.123616

Derntl, C., Hochenegger, N., Seidl, B. K., Kluger, B., Büschl, C., Schuhmacher, R., Mach, R. L., & Mach-Aigner, A. R. (2020). A pair of transcription factors regulates the switch between primary and secondary metabolism. In Program & Abstracts (p. 242).

Derntl, C., Mach, R., & Mach-Aigner, A. (2020). Application of the human estrogen receptor within a synthetic transcription factor in Trichoderma reesei. Fungal Biology and Biotechnology, 7(12). https://doi.org/10.1186/s40694-020-00102-3

Ellena, V., Bucchieri, D., Arcalis, E., Sauer, M., & Steiger, M. G. (2020). Sclerotia formed by citric acid producing strains of Aspergillus niger: Induction and morphological analysis. In Book of Abstracts. EFB -Microbial Stress Meeting. EFB -Microbial Stress Meeting (Online Conference), Rom, Italy.

Ellena, V., Sauer, M., & Steiger, M. G. (2020). The fungal sexual revolution continues: discovery of sexual development in members of the genus Aspergillus and its consequences. Fungal Biology and Biotechnology, 7(17). https://doi.org/10.1186/s40694-020-00107-y

Frick, C., Vierheilig, J., Nadiotis-Tsaka, T., Ixenmaier, S., Linke, R., Reischer, G. H., Komma, J., Kirschner, A. K. T., Mach, R. L., Savio, D., Seidl, D., Blaschke, A. P., Sommer, R., Derx, J., & Farnleitner, A. H. (2020). Elucidating fecal pollution patterns in alluvial water resources by linking standard fecal indicator bacteria to river connectivity and genetic microbial source tracking. Water Research, 184(116132), 116132. https://doi.org/10.1016/j.watres.2020.116132

Fritsche, S., & Steiger, M. (2020). Marker-free live cell imaging of Aspergillus niger. EFB -Microbial Stress Meeting (Online Conference), Rom, Italy.

Gassler, T., Sauer, M., Gasser, B., Egermeier, M., Troyer, C., Causon, T., Hann, S., Mattanovich, D., & Steiger, M. G. (2020). The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO₂. Nature Biotechnology, 38(2), 210–216. https://doi.org/10.1038/s41587-019-0363-0

Gupta, V. K., Zeilinger, S., Singh, H. B., & Druzhinina, I. (2020). New and Future Developments in Microbial Biotechnology and Bioengineering - Recent Developments in Trichoderma Research. Elsevier.

Hochenegger, N., Vignolle, G. A., Mach, R. L., Druzhinina, I., Mach-Aigner, A. R., & Derntl, C. (2020). Bioprospecting a newly identified fungus from the Borneo rain forest regarding its bioactive properties. In Program & Abstracts (p. 222).

Jovanović, B. (2020). Batch Cultivation of Trichoderma reesei. In A. R. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 113–118). Springer Science + Business Media. https://doi.org/10.1007/978-1-0716-1048-0_10

Kilic, H. S., Cervero-Aragó, S., Frick, C., Linke, R., Schijven, J., Kirschner, A., Lindner, G., Walochnik, J., Sommer, R., Blaschke, A. P., Farnleitner, A. H., & Derx, J. (2020). Identifying faecal pollution sources in urban surface water resources to support water safety management. In First International Conference on Urban Water Interfaces (UWI) (p. 1).

Kolm, C., Cervenka, I., Aschl, U. J., Baumann, N., Jakwerth, S., Krska, R., Mach, R. L., Sommer, R., DeRosa, M. C., Kirschner, A. K. T., Farnleitner, A. H., & Reischer, G. H. (2020). DNA aptamers against bacterial cells can be efficiently selected by a SELEX process using state‑of‑the art qPCR and ultra‑deep sequencing. Scientific Reports, 10(20917). https://doi.org/10.1038/s41598-020-77221-9

Kolm, C., Reischer, G., Martzy, R., & Farnleitner, A. H. (2020). Molecular fecal pollution diagnostics for water quality testing: From polymerase chain reaction to rapid isothermal amplification to detect genetic fecal markers. Analytica Virtual 2020 (Online Konferenz), München, Germany.

Köber, A., & Steiger, M. (2020). Utilization of Saccharomyces cerevisiae for the production of HIV1 Gag virus-like particles. EFB -Microbial Stress Meeting (Online Conference), Rom, Italy.

Linke, R. B. (2020). Sexual Crossing of Trichoderma reesei. In A. R. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 79–85). Springer Science + Business Media. https://doi.org/10.1007/978-1-0716-1048-0_7

Mach-Aigner, A. R., & Martzy, R. (2020). Preface. In A. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 5–5). Springer Science + Business Media.

Mach-Aigner, A. R., & Martzy, R. (Eds.). (2020). Trichoderma reesei - Methods and Protocols. Springer Science + Business Media.

Martzy, R., & Mach-Aigner, A. R. (2020). The Potential of Synthetic Biology for Trichoderma reesei. In A. R. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 45–54). Springer Science + Business Media. https://doi.org/10.1007/978-1-0716-1048-0_3

Masi, A., Mach, R. L., & Mach-Aigner, A. R. (2020). Understanding parameters enhancing erythritol consumption, a prerequisite to the development of an efflcient erythritol production process in T. reesei. In Program & Abstracts (p. 234).

Moreno-Ruiz, D., Fuchs, A., & Zeilinger, S. (2020). The effects of light on Trichoderma atroviride conidiation and mycoparasitic activity are partially dependent on the strain and the Tmk3 MAP kinase. In Program & Abstracts (pp. 357–358).

Moreno-Ruiz, D., Lichius, A., Turra, D., Di Pietro, A., & Zeilinger, S. (2020). Mycoparasitism-related chemotropic sensing in Trichoderma atroviride germlings and hyphae. In Program & Abstracts (pp. 358–359).

Rahimi, M. J., Cai, F., Grujic, M., Chenthamara, K., & Druzhinina, I. S. (2020). Molecular Identification of Trichoderma reesei. In A. R. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 157–175). Springer Science + Business Media. https://doi.org/10.1007/978-1-0716-1048-0_14

Regnat, K., Masi, A., Mach, R. L., & Mach-Aigner, A. R. (2020). Erythritol in Trichoderma reesei - Construction of a multirecombinant production strain. In Program & Abstracts (p. 241).

Schmoll, M., & Zeilinger, S. (2020). Resistance Marker- and Gene Gun-Mediated Transformation of Trichoderma reesei. In A. R. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 55–62). Springer Science + Business Media. https://doi.org/10.1007/978-1-0716-1048-0_4

Segreto, R., Bazafkan, H., Millinger, J., Doppler, M., Blueschl, C., Schuhmacher, R., Atanasova, L., & Zeilinger, S. (2020). Trichoderma atroviride mycoparasitism and its regulation by the TOR signaling pathway. In Program & Abstracts (pp. 178–179).

Seiboth, B. (2020). In Silico Gene Analysis and Oligonucleotide Design for the Construction of Expression Vectors. In A. R. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 297–309). Springer Science + Business Media. https://doi.org/10.1007/978-1-0716-1048-0_20

Speckbacher, V., Ruszsanyi, V., Hinterdobler, W., Schuhmacher, R., & Zeilinger, S. (2020). The lipoxygenase gene lox1 is involved in light- and injury-response as weil as volatile secondary metabolite production in Trichoderma atroviride. In Program & Abstracts (pp. 75–76).

Steiger, M. G. (2020). Flow Cytometry for Filamentous Fungi. In A. R. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 147–155). Springer Science + Business Media. https://doi.org/10.1007/978-1-0716-1048-0_13

Till, P. (2020). RNA Characterization in Trichoderma reesei. In A. R. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 191–235). Springer Science + Business Media. https://doi.org/10.1007/978-1-0716-1048-0_16

Till, P., Derntl, C., Kiesenhofer, D. P., Mach, R. L., Yaver, D., & Mach-Aigner, A. R. (2020). Regulation of gene expression by the action of a fungal lncRNA on a transactivator. RNA Biology, 17(1), 47–61. https://doi.org/10.1080/15476286.2019.1663618

Till, P., Martzy, R., Derntl, C., Kiesenhofer, D., Mach, R. L., Yaver, D., & Mach-Aigner, A. R. (2020). lnteraction of a fungal lncRNA with a transactivator enhances cellulase production in Trichoderma reesei. In Program & Abstracts (pp. 257–258).

Till, P., Toepel, J., Bühler, B., Mach, R. L., & Mach-Aigner, A. R. (2020). Regulatory systems for gene expression control in cyanobacteria. Applied Microbiology and Biotechnology, 104(5), 1977–1991. https://doi.org/10.1007/s00253-019-10344-w

Tomico Cuenca, I., & Derntl, C. (2020). Use of Auxotrophic Markers for Targeted Gene Insertions in Trichoderma reesei. In A. R. Mach-Aigner & R. Martzy (Eds.), Trichoderma reesei (pp. 63–72). Springer Science + Business Media. https://doi.org/10.1007/978-1-0716-1048-0_5

Tomico Cuenca, I., Derntl, C., Seidl, B. K., Mach, R. L., Schuhmacher, R., & Mach-Aigner, A. R. (2020). Fusion transcription factors as a tool for controlled gene overexpression in Trichoderma reesei. In Program & Abstracts (p. 76).

Totaro, D., Radoman, B., Schmelzer, B., Rothbauer, M., Steiger, M. G., Mayr, T., Sauer, M., Ertl, P., & Mattanovich, D. (2020). Microscale Perfusion‐Based Cultivation for Pichia pastoris Clone Screening Enables Accelerated and Optimized Recombinant Protein Production Processes. Biotechnology Journal, 16(3), 2000215. https://doi.org/10.1002/biot.202000215

V. D. dos Santos, A. C., Heydenreich, R., Derntl, C., Mach-Aigner, A. R., Mach, R. L., Ramer, G., & Lendl, B. (2020). Nanoscale Infrared Spectroscopy and Chemometrics Enable Detection of Intracellular Protein Distribution. Analytical Chemistry, 92(24), 15719–15725. https://doi.org/10.1021/acs.analchem.0c02228

Vignolle, G. A., Mach, R. L., Mach-Aigner, A. R., & Derntl, C. (2020). Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp. BMC Genomics, 21(258). https://doi.org/10.1186/s12864-020-6653-6

Vignolle, G. A., Mach, R. L., Mach-Aigner, A. R., & Derntl, C. (2020). Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp. In ECFG15 - 15th European Conference on Fungal Genetics (Program and Abstracts). ECFG15 - 15th European Conference on Fungal Genetics, Rom, Italy.

Wierckx, N., Agrimi, G., Lübeck, P. S., Steiger, M. G., Mira, N. P., & Punt, P. J. (2020). Metabolic specialization in itaconic acid production: a tale of two fungi. Current Opinion in Biotechnology, 62, 153–159. https://doi.org/10.1016/j.copbio.2019.09.014

Youngblut, N. D., de la Cuesta-Zuluaga, J., Reischer, G. H., Dauser, S., Schuster, N., Walzer, C., Stalder, G., Farnleitner, A. H., & Ley, R. E. (2020). Large-Scale Metagenome Assembly Reveals Novel Animal- Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity. MSystems, 5(6). https://doi.org/10.1128/msystems.01045-20

dos Santos, A. C. V. D., Heydenreich, R., Derntl, C., Mach-Aigner, A. R., Mach, R. L., Ramer, G., & Lendl, B. (2020). Near-field IR detection enables nanoscale computational staining. SciX 2020, Online, Unknown.

Benocci, T., Aguilar-Pontes, M. V., Kun, R. S., Lubbers, R. J. M., Lail, K., Wang, M., Lipzen, A., Ng, V., Grigoriev, I. V., Seiboth, B., Daly, P., & de Vries, R. P. (2019). Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass. Biotechnology for Biofuels, 12(81). https://doi.org/10.1186/s13068-019-1422-y

Derntl, C., Hochenegger, N., Seidl, B. K., Kluger, B., Büschl, C., Schuhmacher, R., Mach, R. L., & Mach-Aigner, A. R. (2019). Regulation of the Primary and Secondary Metabolism in Fungi by a pair of Transcription Factors. In 18. Österreichische Chemietage (p. 1).

Derntl, C., Mach, R. L., & Mach-Aigner, A. R. (2019). Fusion transcription factors for strong, constitutive expression of cellulases and xylanases in Trichoderma reesei. Biotechnology for Biofuels, 12(231). https://doi.org/10.1186/s13068-019-1575-8

Derntl, C., Mach, R. L., & Mach-Aigner, A. R. (2019). Usage of an estradiol-inducible fusion transactivation domain for controlled gene expression in Trchoderma reesei. In Abstract Book (p. 1).

Fitz, E., Gamauf, C., Seiboth, B., & Wanka, F. (2019). Morphogenetic switch: rac1 deletion in Trichoderma reesei. In esib/2019 (p. 103).

Gupta, V. K., Mach, R. L., & Sreenivasaprasad, S. (2019). Fungal Biomolecules - Sources, Applications and Recent Developments. Wiley - Blackwell.

Gupta, V. K., Mach, R. L., & Sreenivasaprasad, S. (2019). Preface. In Fungal Biomolecules - Sources, Applications and Recent Developments (p. xvii). Wiley - Blackwell.

Hochenegger, N., Mach, R. L., Druzhinina, I., Mach-Aigner, A. R., & Derntl, C. (2019). Bioprospecting of fungi from the Borneo rain forest regarding their bioactive properties. In 18. Österreichische Chemietage (p. 1).

Kilic, H. S., Cervero-Aragó, S., Frick, C., Linke, R., Schijven, J., Kirschner, A., Lindner, G., Sommer, R., Blaschke, A. P., Farnleitner, A. H., & Derx, J. (2019). Impact of Waterborne Pathogens on Infection Risks in Viennese Recreational Waters. HydroCarpath 2019, Wien, Austria.

Kilic, H. S., Cervero-Aragó, S., Frick, C., Linke, R., Schijven, J., Kirschner, A., Lindner, G., Sommer, R., Blaschke, A. P., Farnleitner, A. H., & Derx, J. (2019). Sources, Transport PathwaysandInfectionRisksofWaterbornePathogens in Viennese Surface Water Bodies. Annual Symposium of the Doctoral programme on Water Resource Systems, Zeillern, Austria.

Kirschner, A. K. T., Reischer, G., Jakwerth, S., Savio, D. F., Ixenmaier, S., Toth, E., Sommer, R., Mach, R. L., Linke, R., Eiler, A., Kolarevic, S., & Farnleitner, A. H. (2019). Source tracking of microbial faecal pollution along a 2600 km stretch of the River Danube. In Abstractbook (p. 1).

Kolm, C., Martzy, R., Führer, M., Mach, R. L., Krska, R., Baumgartner, S., Farnleitner, A. H., & Reischer, G. (2019). Detection of a microbial source tracking marker by isothermal helicasedependent amplification and a nucleic acid lateralflow strip test. In Abstractbook (p. 2).

Kolm, C., Martzy, R., Führer, M., Mach, R. L., Krska, R., Baumgartner, S., Farnleitner, A. H., & Reischer, G. H. (2019). Detection of a microbial source tracking marker by isothermal helicase-dependent amplification and a nucleic acid lateral-flow strip test. Scientific Reports, 9(393). https://doi.org/10.1038/s41598-018-36749-7

Lepuschitz, S., Baron, S., Larvor, E., Granier, S. A., Pretzer, C., Mach, R. L., Farnleitner, A. H., Ruppitsch, W., Pleininger, S., Indra, A., & Kirschner, A. K. T. (2019). Phenotypic and Genotypic Antimicrobial Resistance Traits of Vibrio cholerae Non-O1/Non-O139 Isolated From a Large Austrian Lake Frequently Associated With Cases of Human Infection. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.02600

Lepuschitz, S., Schill, S., Stoeger, A., Pekard-Amenitsch, S., Huhulescu, S., Inreiter, N., Hartl, R., Kerschner, H., Sorschag, S., Springer, B., Brisse, S., Allerberger, F., Mach, R. L., & Ruppitsch, W. (2019). Whole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella pneumoniae isolates from Austrian rivers and clinical isolates from hospitals. Science of the Total Environment, 662, 227–235. https://doi.org/10.1016/j.scitotenv.2019.01.179

Linke, R., Stadler, P., Reischer, G. H., Savio, D., Kollanur, D., Mayer, R., Mach, R. L., Kirschner, A. K. T., Sommer, R., Derx, J., Stadler, H., & Farnleitner, A. (2019). Using genetic microbial source tracking (MST) markers to identify fecal pollution sources in spring water of a large alpine karst catchment. In J. Rose & B. Jiménez-Cisneros (Eds.), Water and Sanitation for the 21st Century: Health and Microbiological Aspects of Excreta and Wastewater Management (Global Water Pathogen Project). Unesco. https://doi.org/10.14321/waterpathogens.82

Linke, R., Zeki, S., Mayer, R., Keiblinger, K., Mach, R. L., Derx, J., Sommer, R., Reischer, G., & Farnleitner, A. H. (2019). Loss of DNA to surface-reactive matrix compounds during extraction - the need for comprehensive process controls in molecular diagnostics ofwater samples. In Abstractbook (p. 1).

Martzy, R., Bica-Schröder, K., Pálvölgyi, Á. M., Kolm, C., Jakwerth, S., Kirschner, A. K. T., Sommer, R., Krska, R., Mach, R. L., Farnleitner, A. H., & Reischer, G. H. (2019). Simple lysis of bacterial cells for DNA-based diagnostics using hydrophilic ionic liquids. Scientific Reports, 9(13994). https://doi.org/10.1038/s41598-019-50246-5

Novy, V., Nielsen, F., Seiboth, B., & Nidetzky, B. (2019). The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles. Biotechnology for Biofuels, 12(238). https://doi.org/10.1186/s13068-019-1571-z

Regnat, K., Beisl, S., Friedl, A., Mach, R. L., & Mach-Aigner, A. R. (2019). Erythritol from straw A multilevel feasibility study in Trichoderma reesei. In 18. Österreichische Chemietage (p. 1).

Reischer, G., Youngblut, N. D., Walters, W., Schuster, N., Walzer, C., Stalder, G. L., Ley, R. E., & Farnleitner, A. H. (2019). Factors shaping the intestinal microbiome of vertebrate faecal sources: unravelling the role of diet and host phylogeny. In Abstractbook (p. 2).

Savio, D. F., Karl, M., Stadler, P., Reischer, G., Demeter, K., Linke, R., Blaschke, A. P., Mach, R. L., Kirschner, A. K. T., Stadler, H., & Farnleitner, A. H. (2019). Highthroughput 16S rRNA gene amplicon sequencing for the characterisation of the drinking water microbiome from an alpine karst spring. In Abstractbook (p. 1).

Savio, D., Stadler, P., Reischer, G. H., Demeter, K., Linke, R. B., Blaschke, A. P., Mach, R. L., Kirschner, A. K. T., Stadler, H., & Farnleitner, A. H. (2019). Spring Water of an Alpine Karst Aquifer Is Dominated by a Taxonomically Stable but Discharge-Responsive Bacterial Community. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.00028

Seidl, B. K., Derntl, C., Mach, R. L., Mach-Aigner, A. R., & Schuhmacher, R. (2019). An LC-HRMS Based Metabolomics Workflow to Investigate the Sorbicillinoid Biosynthesis in Trichoderma reesei. In 18. Österreichische Chemietage (p. 1).

Steiger, M. G., Rassinger, A., Mattanovich, D., & Sauer, M. (2019). Engineering of the citrate exporter protein enables high citric acid production in Aspergillus niger. Metabolic Engineering, 52, 224–231. https://doi.org/10.1016/j.ymben.2018.12.004

Tallian, C., Rumpler, V., Skopek, L., Russmayer, H., Steiger, M. G., Vielnascher, R., Weinberger, S., Pellis, A., Vecchiato, S., & Guebitz, G. M. (2019). Glutathione from recovered glucose as ingredient in antioxidant nanocapsules for triggered flavor delivery. Journal of Materials Chemistry B: Materials for Biology and Medicine, 7(25), 3958–3969. https://doi.org/10.1039/c9tb00473d

Till, P., Kiesenhofer, D., Mach, R. L., Yaver, D., & Mach-Aigner, A. R. (2019). LncRNA and transactivator meet for regulation of cellulase-encoding gene expression. In Abstract Book (p. 1).

Till, P., Pucher, M., Kiesenhofer, D., Mach, R. L., Yaver, D., & Mach-Aigner, A. R. (2019). Transactivator and long non-coding RNA meet for regulation of cellulase formation in Trichoderma reesei. In 18. Österreichische Chemietage (p. 1).

Tomico Cuenca, I., Derntl, C., Seidl, B. K., Mach, R. L., Schuhmacher, R., & Mach-Aigner, A. R. (2019). Development of synthetic transcription factors to activate biosynthetic gene clusters. In 18. Österreichische Chemietage (p. 1).

Vignolle, G. A., Seidl, B. K., Mach, R. L., Schuhmacher, R., Mach-Aigner, A. R., & Derntl, C. (2019). New approaches in genome mining reveal conserved RiPPs in Trichoderma reesei. In 18. Österreichische Chemietage (p. 1).

Wanka, F., Bischof, R., Metz, B., Gamauf, C., Schirmacher, G., Kubicek, C. P., & Seiboth, B. (2019). Fine-tuning gene expression: Pantothenic acid inducible promoters in Trichoderma reesei. In Abstract Book (p. 1).

Wanka, F., Bischof, R., Metz, B., Gamauf, C., Schirrmacher, G., Kubicek, C. P., & Seiboth, B. (2019). Fine-tuning gene expression: Pantothenic acid inducible promoters in Trichoderma reesei. In The 16#^{th} International Aspergillus Meeting (p. 61).

Youngblut, N. D., Reischer, G. H., Walters, W., Schuster, N., Walzer, C., Stalder, G., Ley, R. E., & Farnleitner, A. H. (2019). Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nature Communications, 10(2200). https://doi.org/10.1038/s41467-019-10191-3

Zeilinger, S. (2019). Peptaibiotics and peptaibols from fungi. In Fungal Biomolecules - Sources, Applications and Recent Developments (pp. 101–113). Wiley - Blackwell.

Reismann, A. W. A. F., Atanasova, L., Schrangl, L., Zeilinger, S., & Schütz, G. J. (2018). Temporal Filtering to Improve Single Molecule Identification in High Background Samples. Molecules, 23(12), Article 3338. https://doi.org/10.3390/molecules23123338

Fitz, E., Wanka, F., Bischof, R., & Seiboth, B. (2018). Optimising nature for industry: Design of synthetic promoters for strain engineering of Trichoderma reesei. New Biotechnology, 44, S52. https://doi.org/10.1016/j.nbt.2018.05.075

Zeilinger, S., Atanasova, L., Lichius, A., Bazafkan, H., Speckbacher, V., Schenk, M., Schuhmacher, R., Doppler, M., & Marchetti-Deschmann, M. (2018). Unraveling the mycoparasitic interaction between Trichoderma atroviride and a fungal prey. 11#^{th} International Mycological Congress, San Juan, United States of America (the).

Ata, Ö., Rebnegger, C., Tatto, N. E., Valli, M., Mairinger, T., Hann, S., Steiger, M. G., Çalık, P., & Mattanovich, D. (2018). A single Gal4-like transcription factor activates the Crabtree effect in Komagataella phaffii. Nature Communications, 9(4911). https://doi.org/10.1038/s41467-018-07430-4

Atanasova, L., & Zeilinger, S. (2018). lnterplay between GPI-anchored a-1,6-mannanase DfgS and MAPK signaling in cell wall remodefing of the mycoparasite Trichoderma atroviride. In Program & Abstracts (p. 123).

Atanasova, L., Gruber, S., Lichius, A., Radebner, T., Abendstein, L., Münsterkötter, M., Stralis-Pavese, N., Labaj, P., Kreil, D., & Zeilinger, S. (2018). The Gpr1-regulated Sur7 family protein Sfp2 is required for hyphal growth and cell wall stability in the mycoparasite Trichoderma atroviride. Scientific Reports, 8(12064). https://doi.org/10.1038/s41598-018-30500-y

Demirbas-Uzel, G., De Vooght, L., Parker, A. G., Vreysen, M. J. B., Mach, R. L., Van Den Abbeele, J., & Abd-Alla, A. M. M. (2018). Combining paratransgenesis with SIT: impact of ionizing radiation on the DNA copy number of Sodalis glossinidius in tsetse flies. BMC Microbiology, 18(160). https://doi.org/10.1186/s12866-018-1283-8

Demirbas-Uzel, G., Kariithi, H. M., Parker, A. G., Vreysen, M. J. B., Mach, R. L., & Abd-Alla, A. M. M. (2018). Susceptibility of Tsetse Species to Glossina pallidipes Salivary Gland Hypertrophy Virus (GpSGHV). Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.00701

Demirbas-Uzel, G., Parker, A. G., Vreysen, M. J. B., Mach, R. L., Bouyer, J., Takac, P., & Abd-Alla, A. M. M. (2018). Impact of Glossina pallidipes salivary gland hypertrophy virus (GpSGHV) on a heterologous tsetse fly host, Glossina fuscipes fuscipes. BMC Microbiology, 18(161). https://doi.org/10.1186/s12866-018-1276-7

Derntl, C., Kluger, B., Büschl, C., Schuhmacher, R., Mach, R. L., & Mach-Aigner, A. R. (2018). lnducible expression of secondary metabolites using a synthetic transcription factor in an essentially background-free system. In http://www.ecfg14.org/scientific-program/ (p. 1).

Derntl, C., Mello de Sousa, T. M., Regnat, K., Rassinger, A., Mach, R. L., & Mach-Aigner, A. R. (2018). Synthetic transcription factors and expression system in Trichoderma reesei. In Abstract Book (p. 222).

Farnleitner, A. H., Savio, D. F., Jakwerth, S., Ixenmaier, S., Toth, E., Sommer, R., Linke, R., Mach, R. L., Kolarevic, S., Reischer, G., & Kirschner, A. K. T. (2018). Elucidating the extent and sources of faecal pollution along the whole Danube River: when Robert Koch meets Kary Mullis. In Abstracts (p. 10).

Fitz, E., Wanka, F., & Seiboth, B. (2018). The Promoter Toolbox for Recombinant Gene Expression in Trichoderma reesei. Frontiers in Bioengineering and Biotechnology, 6. https://doi.org/10.3389/fbioe.2018.00135

Fitz, E., Wanka, F., Bischof, R., & Seiboth, B. (2018). Expand the biotechnological toolbox for Trichoderma reesei: design of synthetic promoters. TG2018 - 15#^{th} International Trichoderma & Gliocladium Workshop, Salamanca, Spain.

Fitz, E., Wanka, F., Bischof, R., & Seiboth, B. (2018). Optimising nature for industry: Design of synthetic promoters for strain engineering of Trichoderma reesei. 18#^{th} European Congress On Biotechnology, Genf, Switzerland.

Fitz, E., Wanka, F., Bischof, R., & Seiboth, B. (2018). Expand the biotechnological toolbox for Trichoderma reesei: design of synthetic promoters. In R. Hermosa, M. B. Rubio, & E. Monte (Eds.), Opportunism and Conversations with the Environment. TG2018: Proceedings of the 15#^{th} International Trichoderma & Gliocladium Workshop (p. 91). University of Salamanca, 2018, Salamanca, Spain.

Frei, J., Wanka, F., Bischof, R., Haarmann, T., Puranen, T., Lorenz, P., & Seiboth, B. (2018). Exploring codon usage preferences in Trichoderma reesei. TG2018 - 15#^{th} International Trichoderma & Gliocladium Workshop, Salamanca, Spain.

Frei, J., Wanka, F., Bischof, R., Haarmann, T., Puranen, T., Lorenz, P., & Seiboth, B. (2018). Exploring codon usage preferences in Trichoderma reesei. In R. Hermosa, M. B. Rubio, & E. Monte (Eds.), Opportunism and Conversations with the Environment. TG2018: Proceedings of the 15#^{th} International Trichoderma & Gliocladium Workshop (p. 93). University of Salamanca, 2018, Salamanca, Spain.

Kiesenhofer, D. P., Mach, R. L., & Mach-Aigner, A. R. (2018). Influence of cis Element Arrangement on Promoter Strength in Trichoderma reesei. Applied and Environmental Microbiology, 84(1). https://doi.org/10.1128/aem.01742-17

Kolm, C., Martzy, R., Führer, M., Mach, R. L., Krska, R., Baumgartner, S., Farnleitner, A. H., & Reischer, G. (2018). Tracking ruminant fecal pollution in water by isothermal amplification and a disposable strip test. In Abstracts (p. 11).

Lepuschitz, S., Huhulescu, S., Hyden, P., Springer, B., Rattei, T., Allerberger, F., Mach, R. L., & Ruppitsch, W. (2018). Characterization of a communityacquired- MRSA USA300 isolate from a river sample in Austria and whole genome sequence based comparison to a diverse collection of USA300 isolates. Scientific Reports, 8(9467). https://doi.org/10.1038/s41598-018-27781-8

Lepuschitz, S., Pekard-Amenitsch, S., Haunold, R., Schill, S., Schriebl, A., Mach, R., Allerberger, F., Ruppitsch, W., & Forsythe, S. J. (2018). Draft Genome Sequence of the First Documented Clinical Siccibacter turicensis Isolate in Austria. Genome Announcements, 6(18). https://doi.org/10.1128/genomea.00380-18

Lepuschitz, S., Ruppitsch, W., Pekard-Amenitsch, S., Forsythe, S. J., Cormican, M., Mach, R. L., Piérard, D., & Allerberger, F. (2018). Multicenter Study of Cronobacter sakazakii Infections in Humans, Europe, 2017. Emerging Infectious Diseases, 25(3), 515–522. https://doi.org/10.3201/eid2503.181652

Mach, R. (2018). Alternative Süßungsmittel. Aktuelle Ernaehrungsmedizin, 43(S 01), S50–S54. https://doi.org/10.1055/a-0660-4579

Mach-Aigner, A. R. (2018). Partner search and relationship: how university meets industry. Vienna Knowledge Exchange Conference, Wien, Austria.

Mairinger, T., Wegscheider, W., Peña, D. A., Steiger, M. G., Koellensperger, G., Zanghellini, J., & Hann, S. (2018). Comprehensive assessment of measurement uncertainty in ¹³C-based metabolic flux experiments. Analytical and Bioanalytical Chemistry, 410(14), 3337–3348. https://doi.org/10.1007/s00216-018-1017-7

Martzy, R., Kolm, C., Mach, R. L., Krska, R., Jakwerth, S., Kirschner, A. K. T., Sommer, R., Farnleitner, A. H., & Reischer, G. (2018). A field-deployable concept for the rapid molecular detection of fecal contamination in water. In Abstracts (p. 58).

Mayer, R., Reischer, G., Ixenmaier, S., Derx, J., Blaschke, A. P., Ebdon, J. E., Linke, R., Egle, L., Ahmed, W., Blanch, A. R., Byamukama, D., Savill, M., Mushi, D., Cristóbal, H. A., Edge, T. A., Schade, M. A., Aslan, A., Brooks, Y. M., Sommer, R., … Farnleitner, A. (2018). Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents. Environmental Science and Technology, 52(9), 5076–5084. https://doi.org/10.1021/acs.est.7b04438

Mello de Sousa, T. M., Derntl, C., Mach, R. L., Yaver, D., & Mach-Aigner, A. R. (2018). Strain degeneration in Trichoderma reesei is triggered by high protein productivity and influenced by DNA methylation. In http://www.ecfg14.org/scientific-program/ (p. 1).

Peña, D. A., Gasser, B., Zanghellini, J., Steiger, M. G., & Mattanovich, D. (2018). Metabolic engineering of Pichia pastoris. Metabolic Engineering, 50, 2–15. https://doi.org/10.1016/j.ymben.2018.04.017

Radebner, T., Wanka, F., Gasser, B., & Seiboth, B. (2018). Elucidation of the regulatory network of Trichoderma reesei operating under cellulose-degrading conditions. In http://www.ecfg14.org/scientific-program/ (p. 309).

Ramoni, J., Marchetti-Deschmann, M., Seidl-Seiboth, V., & Seiboth, B. (2018). Optimization of the industrial workhorse Trichoderma reesei towards improved xylanase production. In Abstract Book (p. 89).

Rassinger, A., Gacek‑Matthews, A., Strauss, J., Mach, R. L., & Mach-Aigner, A. R. (2018). Truncation of the transcriptional repressor protein Cre1 in Trichoderma reesei Rut‑C30 turns it into an activator. Fungal Biology and Biotechnology, 5(15). https://doi.org/10.1186/s40694-018-0059-0

Regnat, K., Mach, R. L., & Mach-Aigner, A. R. (2018). Erythritol as sweetener-wherefrom and whereto? Applied Microbiology and Biotechnology, 102(2), 587–595. https://doi.org/10.1007/s00253-017-8654-1

Savio, D., Stadler, P., Reischer, G. H., Kirschner, A. K. T., Demeter, K., Linke, R., Blaschke, A. P., Sommer, R., Szewzyk, U., Wilhartitz, I. C., Mach, R. L., Stadler, H., & Farnleitner, A. H. (2018). Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management. WILEY INTERDISCIPLINARY REVIEWS-WATER, 5(3). https://doi.org/10.1002/wat2.1282

Till, P., Mach, R. L., & Mach-Aigner, A. R. (2018). A current view on long noncoding RNAs in yeast and filamentous fungi. Applied Microbiology and Biotechnology, 102(17), 7319–7331. https://doi.org/10.1007/s00253-018-9187-y

Till, P., Pucher, M. E., Mach, R. L., & Mach-Aigner, A. R. (2018). A long noncoding RNA promotes cellulase expression in Trichoderma reesei. Biotechnology for Biofuels, 11(78). https://doi.org/10.1186/s13068-018-1081-4

Till, P., Pucher, M., Kiesenhofer, D., Mach, R. L., Yaver, D., & Mach-Aigner, A. R. (2018). Regulatory interplay of a long non-coding RNA and a transactivator in a filamentous fungus. In https://rnasociety.dk/events/4th-annual-rna-meeting (p. 1).

Till, P., Pucher, M., Mach, R. L., Yaver, D., & Mach-Aigner, A. R. (2018). A long noncoding RNA promotes cellulase expression in Trichoderma reesei. In http://www.ecfg14.org/scientific-program/ (p. 1).

Till, P., Pucher, M., Mach, R. L., Yaver, D., & Mach-Aigner, A. R. (2018). Long non-coding RNA meets transactivator for regulation of cellulase expression. In http://www.ecfg14.org/scientific-program/ (p. 1).

Wanka, F., Bischof, R., Beinhauer, A., Metz, B., Koger, C., Steiger, M., Gamauf, C., Schirrmacher, G., Kubicek, C. P., & Seiboth, B. (2018). Fine-tuning gene expression: pantothenic acid inducible promoters in Trichoderma reesei. In http://www.ecfg14.org/scientific-program/ (p. 308).

Wohlschlager, L., Csarman, F., Obermann, T., Kropatsch, K., Seiboth, B., & Ludwig, R. (2018). Recombinant expression and characterization of fungal extracellular enzymes involved in lignocellulose degradation. In Abstract Book (p. 173).

Wohlschlager, L., Csarman, F., Obermann, T., Seiboth, B., & Ludwig, R. (2018). Recombinant expression and characterization of lignocelluloseactive enzymes from Phanerochaete chrysosporium. In Lignobiotech 2018 (p. 34).

Zeilinger-Migsich, S. (2018). Trichoderma atroviride secondary metabolism and its regulation by signaling pathways. TG2018 - 15#^{th} International Trichoderma & Gliocladium Workshop, Salamanca, Spain.

Benocci, T., Aguilar-Pontes, M. V., Kun, R. S., Seiboth, B., de Vries, R. P., & Daly, P. (2017). ARA1 regulates not only L-arabinose but also D-galactose catabolism in Trichoderma reesei. FEBS Letters, 592(1), 60–70. https://doi.org/10.1002/1873-3468.12932

Przylucka, A., Bayram Akcapinar, G., Bonazza, K., Machado Mello De Sousa, T., Mach-Aigner, A. R., Lobanov, V., Grothe, H., Kubicek, C. P., Reimhult, E., & Druzhinina, I. (2017). COMPARATIVE PHYSIOCHEMICAL ANALYSIS OF HYDROPHOBINS PRODUCED IN ESCHERICHIA COLI AND PICHIA PASTORIS. Colloids and Surfaces B: Biointerfaces, 159, 913–923. https://doi.org/10.1016/j.colsurfb.2017.08.058

De Vries, R., Riley, R., Wiebenga, A., Aguilar-Osorio, G., Amillis, S., Akemi Uchima, C., Anderluh, G., Asadollahi, M., Askin, M., Barry, K., Battaglia, E., Bayram, Ö., Benocci, T., Braus-Stromeyer, S. A., Caldana, C., Canovas, D., Cerqueira, G., Chen, F., Wanping Chen, … Grigoriev, I. V. (2017). Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology, 18(28). https://doi.org/10.1186/s13059-017-1151-0

Akcapinar, G. B., Camposeo, T., Berezhinskiy, V., Przylucka, A., Cai, F., Mello de Sousa, T. M., Grothe, H., Reimhult, E., Mach-Aigner, A. R., Shen, Q., & Druzhinina, I. (2017). Learning from fungi: new applications of the natural and engineered surfaceactive proteins from fungi. In Book of Abstracts (p. 1).

Akcapinar, G. B., Przylucka, A., Cai, F., Mello de Sousa, T. M., Grothe, H., Reimhult, E., Mach-Aigner, A. R., Shen, Q., & Druzhinina, I. (2017). Learning from nature: establishment of a library of natural and rationally designed hydrophobins from Trichoderma spp. with diverse surface activity. In Abstract Book (p. 64).

Benocci, T., Aguilar-Pontes, M. V., Seiboth, B., & De Vries, R. (2017). Regulation of plant biomass degradation in Ascomycete fungi. In Abstracts (p. 52).

Benocci, T., Aguilar-Pontes, M. V., Zhou, M., Seiboth, B., & de Vries, R. P. (2017). Regulators of plant biomass degradation in ascomycetous fungi. Biotechnology for Biofuels, 10(152). https://doi.org/10.1186/s13068-017-0841-x

Bischof, R., Wanka, F., Beinhauer, A., Metz, B., Koger, C., Steiger, M., Gamauf, C., Schirmacher, G., Kubicek, C. P., & Seiboth, B. (2017). Fine-tuning gene expression: Pantothenic acid inducible promoters in Trichoderma reesei. In Book of Abstracts (p. 135).

Bischof, R., Wanka, F., Beinhauer, A., Metz, B., Koger, C., Valentini, I., Steiger, M., Gamauf, C., Schirrmacher, G., Kubicek, C. P., & Seiboth, B. (2017). Carbohydrate- active enzyme independent inducible gene expression in Trichoderma reesei. In Abstracts (p. 51).

Demeter, K., Linke, R., Ixenmaier, S., Lindner, G., Frick, C., Kirschner, A., Derx, J., Blaschke, A. P., & Farnleitner, A. H. (2017). Linking faecal indicators, microbial source tracking markers and pathogens to characterise an urban stretch of the Danube River at Vienna as a water resource. Vienna Doctoral Programme on Water Resource Systems Annual Symposium 2017, Payerbach-Reichenau, Austria.

Demeter, K., Linke, R., Ixenmaier, S., Mayer, R., Sommer, R., Lindner, G., Frick, C., Kirschner, A., Derx, J., Blaschke, A. P., & Farnleitner, A. H. (2017). Characterisation of the microbial water quality of the Danube River at Vienna. Vienna Young Scientists Symposium 2017 (VSS 2017), Vienna, Austria, Austria.

Demeter, K., Linke, R., Ixenmaier, S., Mayer, R., Sommer, R., Lindner, G., Frick, C., Savio, D. F., Kirschner, A., Derx, J., Farnleitner, A. H., & Blaschke, A. P. (2017). Nachhaltige Managementmaßnahmen bei Veränderung der Rohwasserqualität mittels genetischer Herkunftsbestimmung fäkaler Einträge und quantitativer mikrobieller Risikoabschätzung. Vienna Doctoral Programme on Water Resource Systems Annual Symposium 2017, Payerbach-Reichenau, Austria.

Demeter, K., Linke, R., Ixenmaier, S., Mayer, R., Sommer, R., Lindner, G., Frick, C., Savio, D., Kirschner, A., Derx, J., Farnleitner, A. H., & Blaschke, A. P. (2017). Nachhaltige Managementmaßnahmen bei Veränderung der Rohwasserqualität mittels genetischer Herkunftsbestimmung fäkaler Einträge und quantitativer mikrobieller Risikoabschätzung. Österreichische Wasserwirtschaftstagung 2017 “Die Zukunft der Abwasserwirtschaft in Österreich,” Linz, Austria.

Demeter, K., Vierheilig, J., Baumgartner, C., Bucher, C., Blaschke, A. P., Derx, J., Kirschner, A., Ryzinska-Paier, G., Mayer, R., Sommer, R., Farnleitner, A. H., & Frick, C. (2017). Poikilothermic Animals as a Previously Unrecognized Source of Fecal Indicator Bacteria. In International Symposium on Health-Related Water Microbiology 2017 Abstract Book (p. 1).

Derntl, C., Guzmán-Chávez, F., Machado Mello De Sousa, T., Busse, H.-J., Driessen, A. J. M., Mach, R. L., & Mach-Aigner, A. R. (2017). In Vivo Study of the Sorbicillinoid Gene Cluster in Trichoderma reesei. Frontiers in Microbiology, 8. https://doi.org/10.3389/fmicb.2017.02037

Derntl, C., Kluger, B., Büschl, C., Schuhmacher, R., Mach, R. L., & Mach-Aigner, A. R. (2017). A pleiotropic regulator of the Primary and Secondary Metabolism in Fungi. In Book of Abstracts (p. 1).

Derntl, C., Kluger, B., Büschl, C., Schuhmacher, R., Mach, R. L., & Mach-Aigner, A. R. (2017). Transcription factor Xpp1 is a switch between primary and secondary fungal metabolism. Proceedings of the National Academy of Sciences, 114(4), 560–569.

Derx, J., Schijven, J., Sommer, R., Reischer, G., Kirschner, A., Frick, C., Farnleitner, A. H., & Blaschke, A. P. (2017). Predicting levels of microorganisms and viruses in river Danube water resources with a lumped hydrological water quality and infection risk model. International Conference RIVER BASINS 2017, Wien, Austria.

Druzhinina, I., Laminger, T., Kamravamanesh, D., Pflügl, S., Mauschitz, G., Mach, R. L., Herwig, C., & Friedl, A. (2017). Less plastic waste in the future. Open Access Government, 16, 312–313.

Fitz, E., Bischof, R., & Seiboth, B. (2017). Establishing a box structure for the design of synthetic promoters for Trichoderma reesei. In Programme & Abstracts (p. 117).

Fitz, E., Bischof, R., & Seiboth, B. (2017). Optimising nature for industry: design of synthetic promoters for strain engineering of Trichoderma reesei. In Book of Abstracts (pp. 56–57).

Fitz, E., Wanka, F., Bischof, R., & Seiboth, B. (2017). Establishing a box structure for the design of synthetic promoters for Trichoderma reesei. In Book of Abstracts. 17. Österreichische Chemietage, Salzburg, Austria.

Fitz, E., Wanka, F., Bischof, R., & Seiboth, B. (2017). Optimising Nature for Industry: Design of Synthetic Promoters for Trichoderma reesei. In esib/2017 (p. 188).

Frei, J., Wanka, F., Bischof, R., Steiger, M., Haarmann, T., Puranen, T., Lorenz, P., & Seiboth, B. (2017). Unraveling the codon usage in Trichoderma reesei. In Book of Abstracts. 17. Österreichische Chemietage, Salzburg, Austria.

Frei, J., Wanka, F., Bischof, R., Steiger, M., Haarmann, T., Puranen, T., Lorenz, P., & Seiboth, B. (2017). Unraveling the codon usage in Trichoderma reesei. In Programme & Abstracts (p. 118).

Gaderer, R., Seidl-Seiboth, V., de Vries, R. P., Seiboth, B., & Kappel, L. (2017). N-acetylglucosamine, the building block of chitin, inhibits growth of Neurospora crassa. Fungal Genetics and Biology, 107, 1–11. https://doi.org/10.1016/j.fgb.2017.07.005

Holzlechner, M., Reitschmidt, S., Gruber, S., Zeilinger-Migsich, S., & Marchetti-Deschmann, M. (2017). Visualizing Fungal Metabolites during Mycoparasitic Interaction by MALDI MSI. 28th Mass Spec Forum Vienna, Vienna, Austra, Austria.

Ivanova, C., Ramoni, J., Aouam, T., Frischmann, A., Seiboth, B., Baker, S. E., Le Crom, S., Lemoine, S., Margeot, A., & Bidard, F. (2017). Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction. Biotechnology for Biofuels, 10, Article 209. https://doi.org/10.1186/s13068-017-0897-7

Kiesenhofer, D. P., Mach, R. L., & Mach-Aigner, A. R. (2017). Glucose Oxidase Production from Sustainable Substrates. Current Biotechnology, 6(3). https://doi.org/10.2174/2211550105666160712225517

Kirschner, A. K. T., Reischer, G. H., Jakwerth, S., Savio, D., Ixenmaier, S., Toth, E., Sommer, R., Mach, R. L., Linke, R., Eiler, A., Kolarevic, S., & Farnleitner, A. H. (2017). Multiparametic monitoring of microbial faecal pollution reveals the dominance of human contamination along the whole Danube River. Water Research, 124, 543–555. https://doi.org/10.1016/j.watres.2017.07.052

Kolm, C., Martzy, R., Brunner, K., Mach, R. L., Krska, R., Heinze, G., Sommer, R., Reischer, G. H., & Farnleitner, A. H. (2017). A Complementary Isothermal Amplification Method to the U.S. EPA Quantitative Polymerase Chain Reaction Approach for the Detection of Enterococci in Environmental Waters. Environmental Science and Technology, 51(12), 7028–7035. https://doi.org/10.1021/acs.est.7b01074

Kolm, C., Martzy, R., Brunner, K., Mach, R. L., Krska, R., Heinze, G., Sommer, R., Reischer, G., & Farnleitner, A. H. (2017). A complementary isothermal amplification method to the U.S EPA qPCR approach for the detection of enterococci in environmental waters. In Book of Abstracts (pp. 46–47).

Kolm, C., Martzy, R., Brunner, K., Mach, R. L., Krska, R., Heinze, G., Sommer, R., Reischer, G., & Farnleitner, A. H. (2017). An Isothermal Amplification Method Complementary to US EPA qPCR for the Detection of Enterococci in Environmental Waters. In Water Microbiology 2017 (p. 1).

Lepuschitz, S., Mach, R. L., Springer, B., Allerberger, F., & Ruppitsch, W. (2017). Draft Genome Sequence of a Community-Acquired Methicillin- Resistant Staphylococcus aureus USA300 Isolate from a River Sample. Genome Announcements, 5(42), 2.

Linke, R., Zeki, S., Mayer, R., Keiblinger, K., Mach, R. L., Sommer, R., Reischer, G., & Farnleitner, A. H. (2017). Opening Pandora’s box Unmasking the Need for a Continuous Sample Processing Control for PCR Based Fecal Marker Analysis. In Water Microbiology 2017 (p. 1).

Linke, R., Zeki, S., Mayer, R., Keiblinger, K., Mach, R. L., Sommer, R., Reischer, G., & Farnleitner, A. H. (2017). Quantitative PCR tools for cultivation-independent analysis of microbial faecal pollution in water - the need for a continuous sample processing control. In Book of Abstracts (p. 47).

Lobanov, V., Przylucka, A., Akcapinar, G. B., Bonazza, K., Mello de Sousa, T. M., Mach-Aigner, A. R., Grothe, H., Reimhult, E., & Druzhinina, I. (2017). Production of Fungal Surface-Active Proteins in Three Microbial Cell Factories. In Book of Abstracts (p. 1).

Ma, S., Preims, M., Piumi, F., Kappel, L., Seiboth, B., Record, E., Kracher, D., & Ludwig, R. (2017). Molecular and catalytic properties of fungal extracellular cellobiose dehydrogenase produced in prokaryotic and eukaryotic expression systems. Microbial Cell Factories, 16(37). https://doi.org/10.1186/s12934-017-0653-5

Mach, R. L. (2017). Alternative Süßungsmittel. 21. Heidelberger Ernährungsforum, Heidelberg, Germany.

Mach, R. L. (2017). Imagineering Nature - Closing Cycles: Beispiele für eine biobasierte Ökonomie. Science Breakfast, Wien, Austria.

Mach, R. L. (2017). Imagineering Nature - Closing Cycles: Examples for a bio-based industry. IEA Bioenergy Task 42 Biorefining Vernetzungstreffen und Stakeholder Workshop, Wien, Austria.

Mach-Aigner, A. R. (2017). Regulation of secondary metabolism in Trichoderma reesei. Jahrestagung der Deutschen Gesellschaft für Genetik, Bochum, Germany.

Martzy, R., Kolm, C., Brunner, K., Mach, R. L., Krska, R., Sinkovec, H., Sommer, R., Farnleitner, A. H., & Reischer, G. (2017). A Loop-Mediated Isothermal Amplification (LAMP) Assay for the Rapid Detection of Enterococcus spp. in Water. In Water Microbiology 2017 (p. 2).

Martzy, R., Kolm, C., Brunner, K., Mach, R. L., Krska, R., Sinkovec, H., Sommer, R., Farnleitner, A. H., & Reischer, G. (2017). A loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Enterococcus spp. in water. In Book of Abstracts (pp. 60–61).

Martzy, R., Kolm, C., Brunner, K., Mach, R. L., Krska, R., Šinkovec, H., Sommer, R., Farnleitner, A. H., & Reischer, G. H. (2017). A loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Enterococcus spp. in water. Water Research, 122, 62–69. https://doi.org/10.1016/j.watres.2017.05.023

Mello de Sousa, T. M., Derntl, C., Mach, R. L., Yaver, D., & Mach-Aigner, A. R. (2017). When more is less: high productivity contributes to strain degeneration in Trichoderma reesei. In Book of Abstracts (p. 1).

Przylucka, A., Akcapinar, G. B., Bonazza, K., Mello de Sousa, T. M., Mach-Aigner, A. R., Reimhult, E., Grothe, H., Kubicek, C. P., & Druzhinina, I. (2017). Expression platforms impact the surface modulating properties of Trichoderma class II hydrophobins. In Abstract Book (p. 113).

Radebner, T., Wanka, F., Gasser, B., & Seiboth, B. (2017). Shedding light on the regulatory network of the fungus Trichoderma reesei operating under cellulose- degrading conditions. In Book of Abstracts (p. 129).

Radebner, T., Wanka, F., Gasser, B., & Seiboth, B. (2017). Shedding light on the regulatory network of the fungus Trichoderma reesei operating under cellulose-degrading conditions. In Abstracts (p. 46).

Radebner, T., Wanka, F., Gasser, B., & Seiboth, B. (2017). The Regulatory Network of Trichoderma reesei Present under Cellulase Expressing Conditions. In esib/2017 (p. 210).

Ramoni, J., Marchetti-Deschmann, M., Seidl-Seiboth, V., & Seiboth, B. (2017). Trichoderma reesei xylanase 5 is defective in the reference strain QM6a but functional alleles are present in other wild-type strains. Applied Microbiology and Biotechnology, 101(10), 4139–4149. https://doi.org/10.1007/s00253-017-8161-4

Rassinger, A., Machado Mello De Sousa, T., Regnat, K., Derntl, C., Mach, R. L., & Mach-Aigner, A. R. (2017). Impact of xylanase expression-inducing compounds on DNA accessibility in Trichoderma reesei. MYCOSPHERE, 8(3), 432–444. https://doi.org/10.5943/mycosphere/8/3/5

Rassinger, A., Mello de Sousa, T. M., Regnat, K., Derntl, C., Mach, R. L., & Mach-Aigner, A. R. (2017). Impact of inducer molecules on DNA accessibility in cellulase and xylanase expression in Trichoderma reesei. In Book of Abstracts (pp. 76–77).

Sarkari, P., Marx, H., Blumhoff, M. L., Mattanovich, D., Sauer, M., & Steiger, M. G. (2017). An efficient tool for metabolic pathway construction and gene integration for Aspergillus niger. Bioresource Technology, 245, 1327–1333. https://doi.org/10.1016/j.biortech.2017.05.004

Seiboth, B. (2017). Recombinant protein production in Trichoderma reesei by tunable and CAZyme independent promoters. 5#^{th} Central European Forum for Microbiology, Keszthely, Hungary.

Seiboth, B. (2017). Recombinant protein production in Trichoderma reesei by tunable and CAZyme independent promoters. In Acta Microbiologica et Immunologica Hungarica (Issue Supplement-1). https://doi.org/10.1556/030.64.2017.102

Seiboth, B. (2017). Tunable Promoters for Recombinant Protein Production in Trichoderma Reesei. In Proceedings (p. 58).

Steiger, M. G., Mattanovich, D., & Sauer, M. (2017). Microbial organic acid production as carbon dioxide sink. FEMS Microbiology Letters, 364(21). https://doi.org/10.1093/femsle/fnx212

Steiger, M. G., Patzschke, A., Holz, C., Lang, C., Causon, T., Hann, S., Mattanovich, D., & Sauer, M. (2017). Impact of glutathione metabolism on zinc homeostasis in Saccharomyces cerevisiae. FEMS Yeast Research, 17(4). https://doi.org/10.1093/femsyr/fox028

Steiger, M., Wierckx, N., Blank, L., Mattanovich, D., & Sauer, M. (2017). Itaconic Acid - An Emerging Building Block. In C. Wittmann & J. Liao (Eds.), Industrial Biotechnology: Products and Processes (pp. 453–472). Wiley-VCH.

Till, P., Pucher, M., Mach, R. L., & Mach-Aigner, A. R. (2017). A new activator of cellulase expression in Trichoderma reesei. In Book of Abstracts (p. 1).

da Silva Delabona, P., Rodrigues, G. N., Zubieta, M. P., Ramoni, J., Codima, C. A., Lima, D. J., Farinas, C. S., da Cruz Pradella, J. G., & Seiboth, B. (2017). The relation between xyr1 overexpression in Trichoderma harzianum and sugarcane bagasse saccharification performance. Journal of Biotechnology, 246, 24–32. https://doi.org/10.1016/j.jbiotec.2017.02.002

Schosserer, M., Minois, N., Angerer, T. B., Amring, M., Dellago, H., Harreither, E., Calle-Perez, A., Pircher, A., Gerstl, M. P., Pfeifenberger, S., Brandl, C., Sonntagbauer, M., Kriegner, A., Linder, A., Weinhäusel, A., Mohr, T., Steiger, M., Mattanovich, D., & Rinnerthaler, M. (2016). Correction: Corrigendum: Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan. Nature Communications, 7(11530). https://doi.org/10.1038/ncomms11530

Akcapinar, G. B., Przylucka, A., Cai, F., Mello de Sousa, T. M., Grothe, H., Reimhult, E., Mach-Aigner, A. R., Shen, Q., & Druzhinina, I. (2016). Rational design of novel Trichoderma hydrophobins for industrial applications. In Abstract Book (p. 424).

Bellasio, M., Peymann, A., Steiger, M. G., Valli, M., Sipiczki, M., Sauer, M., Graf, A. B., Marx, H., & Mattanovich, D. (2016). Complete genome sequence and transcriptome regulation of the pentose utilizing yeast Sugiyamaella lignohabitans. FEMS Yeast Research, 16(4), fow037. https://doi.org/10.1093/femsyr/fow037

Benocci, T., Benoit, I., Seiboth, B., & De Vries, R. (2016). The influence of regulatory mutations on growth of Trichoderma reesei on plant biomass related carbon sources. In Abstract Book (p. 378).

Benocci, T., Klaubauf, S., Battaglia, E., Benoit, I., Seiboth, B., & De Vries, R. (2016). Comparative study of L-arabinose responsive regulators AraR and Ara1. In Book of Abstracts (p. 7).

Bischof, R. H., Ramoni, J., & Seiboth, B. (2016). Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei. Microbial Cell Factories, 15(106). https://doi.org/10.1186/s12934-016-0507-6

Bischof, R., Horejs, J., Metz, B., Kubicek, C. P., & Seiboth, B. (2016). Repressible promoters as tools for Trichoderma reesei synthetic biology. In Programme and Abstract Book (p. 78).

Bischof, R., Seiboth, B., Horejs, J., & Kubicek, C. P. (2016). L-Methionine responsive dioxygenase genes provide promoters for conditional gene expression in Trichoderma reesei. 17#^{th} European Congress on Biotechnology, Krakau, Poland.

Bischof, R., Seiboth, B., Horejs, J., & Kubicek, C. P. (2016). L-Methionine responsive dioxygenase genes provide promoters for conditional gene expression in Trichoderma reesei. New Biotechnology, 33, S2. https://doi.org/10.1016/j.nbt.2016.06.735

Delabona, P., Rodrigues Nunes, G., Zubieta, M., Lima Deise, J., Crucello, A., Horta Crivelente, M. A., Farinas Sanchez, C., Pradella Da Cruz, J. G., & Seiboth, B. (2016). Expression of biomass-degrading enzymes by xyr1 overexpression in T. harzianum. In Abstract Book (p. 602).

Derntl, C., Kluger, B., Büschl, C., Schuhmacher, R., Mach, R. L., & Mach-Aigner, A. R. (2016). The transcription factor Xpp1 is a repressor of the fungal secondary metabolism. In Abstract Book (p. 546).

Derntl, C., Rassinger, A., Srebotnik, E., Mach, R. L., & Mach-Aigner, A. R. (2016). Identification of the Main Regulator Responsible for Synthesis of the Typical Yellow Pigment Produced by Trichoderma reesei. Applied and Environmental Microbiology, 82(20), 6247–6257.

Derx, J., Schijven, J., Sommer, R., van Driezum, I. H., Reischer, G., Ixenmaier, S., Kirschner, A., Frick, C., Farnleitner, A. H., & Blaschke, A. P. (2016). QMRAcatch: Human-associated faecal pollution and infection risk modelling for a river/floodplain environment. Journal of Environmental Quality, 45(4), 1205–1214.

Eibinger, M., Sigl, K., Ganner, T., Sattelkow, J., Plank, H., Ramoni, J., Seiboth, B., & Nidetzky, B. (2016). On the roles of auxiliary proteins and enzymes in cellulose surface degradation: swollenin and lytic polysaccharide monooxygenase. In Abstracts (p. 1).

Eibinger, M., Sigl, K., Sattelkow, J., Ganner, T., Ramoni, J., Seiboth, B., Plank, H., & Nidetzky, B. (2016). Functional characterization of the native swollenin from Trichoderma reesei: study of its possible role as C₁ factor of enzymatic lignocellulose conversion. Biotechnology for Biofuels, 9(178). https://doi.org/10.1186/s13068-016-0590-2

Fitz, E., Bischof, R., & Seiboth, B. (2016). Engineering an artificial core promoter for protein production in Trichoderma reesei. In Abstract Book 2016 (p. 160).

Frei, J., Bischof, R., Steiger, M., Haarmann, T., Puranen, T., Lorenz, P., & Seiboth, B. (2016). Optimizat ion of heterologous protein production in Trichoderma reesei by improving the mRNA sequence. In ESIB 2016 (p. 115).

Frick, C., Zoufal, W., Zoufal-Hruza, C. M., Kirschner, A. K. T., Seidl, D., Derx, J., Sommer, R., Blaschke, A. P., Nadiotis-Tsaka, T., & Farnleitner, A. H. (2016). The microbiological water quality of Vienna’s River Danube section and its associated water bodies. Österreichische Wasser- Und Abfallwirtschaft, 69(1–2), 76–88. https://doi.org/10.1007/s00506-016-0349-9

Fritz, E. A., Bischof, R., & Seiboth, B. (2016). Rational design of a promotor for Trichoderma reesei. In ESIB 2016 (p. 114).

Gaderer, R., Flipphi, M., Seidl-Seiboth, V., & Kappel, L. (2016). RON1, an Ndt80-like transcription factor, is a key regulator of the final steps of chitin catabolism in filamentous fungi. In Abstract Book (p. 363).

Gaderer, R., Flipphi, M., Seidl-Seiboth, V., & Kappel, L. (2016). The Ndt80-like transcription factor RON1 is a key regulator of the final steps of chitin degradation in Trichoderma reesei. In Book of Abstracts (p. 4).

Gaderer, R., Hanzl, E., Flipphi, M., Seidl-Seiboth, V., & Kappel, L. (2016). Degradation of the biopolymer chitin and its monomeric subunit N-acetylglucosamine in fungi is regulated by the novel NDT80-like transcription factor RON1. In Abstract Book 2016 (p. 37).

Garcia, E. G., Farnleitner, A. H., Mach, R. L., Krska, R., & Brunner, K. (2016). A rapid genomic DNA extraction method and its combination with helicase dependent amplification for the detection of genetically modified maize. Analytical Methods, 8(1), 136–141. https://doi.org/10.1039/c5ay02628h

Gupta, V. K., Stecca Steindorff, A., Graciano de Paula, R., Silva-Rocha, R., Mach-Aigner, A. R., Mach, R. L., & Silva, R. N. (2016). The Post-genomic Era of Trichoderma reesei: What’s Next? Trends in Biotechnology, 34(12), 970–982. https://doi.org/10.1016/j.tibtech.2016.06.003

Holzlechner, M., Reitschmidt, S., Gruber, S., Zeilinger, S., & Marchetti-Deschmann, M. (2016). Visualizing fungal metabolites during mycoparasitic interaction by MALDI mass spectrometry imaging. Proteomics, 16(11–12), 1742–1746.

Holzlechner, M., Zoratto, S., Reitschmidt, S., Zeilinger-Migsich, S., & Marchetti-Deschmann, M. (2016). Mass Spectrometry Imaging To Better Understand The Mycoparasitic Interaction Of Biocontrol Agents. 64th American Society of Mass Spectrometry Conference, San Antonio, Texas, United States of America (the).

Ivanova, C., Aouam, T., Ramoni, J., Frischmann, A., Seiboth, B., Baker, S. E., Le Crom, S., Margeot, A., & Bidard, F. (2016). Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 reveals vib1 to be essential for cellulase induction. In Book of Abstracts (p. 5).

Ivanova, C., Aouam, T., Seiboth, B., Ramoni, J., Frischmann, A., Margeot, A., Baker, S. E., Le Crom, S., & Bidard, F. (2016). Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 reveals vib1 to be essential for cellulase induction. In Abstract Book (p. 364).

Kappel, L., Gaderer, R., Flipphi, M., & Seidl-Seiboth, V. (2016). The N-acetylglucosamine catabolic gene cluster in Trichoderma reesei is controlled by the Ndt80-like transcription factor RON1. Molecular Microbiology, 99(4), 640–657.

Kiesenhofer, D., Mach, R. L., & Mach-Aigner, A. R. (2016). GoxA production from wheat straw using an engineered Trichoderma reesei strain. In Abstract Book (p. 403).

Kiesenhofer, D., Mach-Aigner, A. R., & Mach, R. L. (2016). Understanding the Mechanism of Carbon Catabolite Repression to Increase Protein Production in Filamentous Fungi. In M. Schmoll & C. Dattenböck (Eds.), Gene Expression Systems in Fungi: Advancements and Applications (pp. 275–288). Springer International Publishing Switzerland 2016. https://doi.org/10.1007/978-3-319-27951-0_12

Kolm, C., Martzy, R., Brunner, K., Mach, R. L., Krska, R., Sommer, R., Reischer, G., & Farnleitner, A. H. (2016). A novel approach for the molecular detection of enterococci in water for resource-limited settings - via helicase-dependent amplification. In Abstracts (p. 60).

Kolm, C., Martzy, R., Brunner, K., Mach, R. L., Krska, R., Sommer, R., Reischer, G., & Farnleitner, A. H. (2016). A novel approach for the molecular detection of faecal enterococci in water via helicasedependent amplification for resource-limited settings. In Abstracts of Lectures and Posters (pp. 79–80).

Linke, R., Thallinger, G. G., Haarmann, T., Eidner, J., Schreiter, M., Lorenz, P., Kubicek, C. P., & Seiboth, B. (2016). Introduction of a functional ham5 into Trichoderma reesei QM6a restores female fertility and provides the basis for classical strain breeding. In Abstract Book (p. 436).

Linke, R., Thallinger, G. G., Haarmann, T., Eidner, J., Schreiter, M., Lorenz, P., Kubicek, C. P., & Seiboth, B. (2016). Sexual reproduction in the industrial strain line of Trichoderma reesei QM6a. In Book of Abstracts (p. 14).

Linke, R., Zeki, S., Mayer, R., Keiblinger, K., Mach, R. L., Reischer, G., & Farnleitner, A. H. (2016). Pitfalls in DNA-based diagnostics in environmental water samples- tools for validation and optimisation of filtration/extraction procedures. In Abstracts (pp. 61–62).

Martzy, R., Kolm, C., Brunner, K., Mach, R. L., Krska, R., Sommer, R., Farnleitner, A. H., & Reischer, G. (2016). Using loop-mediated isothermal amplification (LAMP) technique for the rapid detection of Enterococcus spp. 235 rDNA as a marker for faecal pollution in water resources. In Abstracts (pp. 60–61).

Martzy, R., Kolm, C., Brunner, K., Mach, R. L., Krska, R., Sommer, R., Farnleitner, A. H., & Reischer, G. (2016). Using loop-mediated isothermal amplification (LAMP) technique for the rapid detection of the Enterococcus spp. 238 rRNA gene as a marker for faecal pollution in water resources. In Abstracts of Lectures and Posters (pp. 82–83).

Mayer, R. E., Bofill-Mas, S., Egle, L., Reischer, G. H., Schade, M., Fernandez-Cassi, X., Fuchs, W., Mach, R. L., Lindner, G., Kirschner, A., Gaisbauer, M., Piringer, H., Blaschke, A. P., Girones, R., Zessner, M., Sommer, R., & Farnleitner, A. H. (2016). Occurrence of human-associated Bacteroidetes genetic source tracking markers in raw and treated wastewater of municipal and domestic origin and comparison to standard and alternative indicators of faecal pollution. Water Research, 90, 265–276. https://doi.org/10.1016/j.watres.2015.12.031

Mayer, R., Egle, L., Reischer, G., Mach, R. L., Zessner, M., & Farnleitner, A. H. (2016). Weltweites Auftreten von human-assoziierten genetischen Fäkalmarkern in hohen Konzentrationen in ungereinigtem und mechanisch-biologisch gereinigtem kommunalen Abwasser. In Abstracts (pp. 62–63).

Mello de Sousa, T. M., Derntl, C., Gorsche, R., Regnat, K., Jovanovic, B., Marchetti-Deschmann, M., Pocas-Fonseca, M., Mach, R. L., & Mach-Aigner, A. R. (2016). The transactivator Xyr1 of Trichoderma reesei functions in a nuclear receptorlike way. In Abstract Book (p. 428).

Mello-de-Sousa, T. M., Rassinger, A., Derntl, C., Poças-Fonseca, M. J., Mach, R. L., & Mach-Aigner, A. R. (2016). The Relation Between Promoter Chromatin Status, Xyr1 and Cellulase Expression in Trichoderma reesei. Current Genomics, 17(2), 145–152. https://doi.org/10.2174/1389202917666151116211812

Nocon, J., Steiger, M., Mairinger, T., Hohlweg, J., Rußmayer, H., Hann, S., Gasser, B., & Mattanovich, D. (2016). Increasing pentose phosphate pathway flux enhances recombinant protein production in Pichia pastoris. Applied Microbiology and Biotechnology, 100(13), 5955–5963. https://doi.org/10.1007/s00253-016-7363-5

Omony, J., Mach-Aigner, A. R., van Straten, G., & van Boxtel, A. J. B. (2016). Quantitative modeling and analytic assessment of the transcription dynamics of the XlnR regulon in Aspergillus niger. BMC Systems Biology, 10(13). https://doi.org/10.1186/s12918-016-0257-4

Radebner, T., Bischof, R., Gasser, B., & Seiboth, B. (2016). Cellular mechanisms of regulation during enzyme production in Trichoderma reesei. In ESIB 2016 (p. 118).

Ramoni, J., & Seiboth, B. (2016). 6 Degradation of Plant Cell Wall Polymers by Fungi. In I. Druzhinina & P. C. Kubicek (Eds.), Environmental and Microbial Relationships (Vol. 4, pp. 127–148). Springer International Publishing Switzerland 2016. https://doi.org/10.1007/978-3-319-29532-9_6

Ramoni, J., Brown, N. A., Goldman, G. H., & Seiboth, B. (2016). The Trichoderma reesei mucin MSB2: a signalling protein involved in cellulase production. In Book of Abstracts (p. 18).

Ramoni, J., Brown, N. A., Goldmann, G. H., & Seiboth, B. (2016). The Trichoderma reesei mucin MSB2: characterization of a multifunctional signalling protein. In Abstract Book 2016 (p. 135).

Ramoni, J., Seidl-Seiboth, V., Bischof, R. H., & Seiboth, B. (2016). Gene Expression Systems in Industrial Ascomycetes: Advancements and Applications. In M. Schmoll & C. Dattenböck (Eds.), Gene Expression Systems in Fungi: Advancements and Applications (pp. 3–22). Springer International Publishing Switzerland 2016. https://doi.org/10.1007/978-3-319-27951-0_1

Ramoni, J., Seidl-Seiboth, V., Marchetti-Deschmann, M., & Seiboth, B. (2016). Targeted improvement of Trichoderma reesei xylanase activity by the restoration of its full genome capacities. In Abstract Book (p. 415).

Rassinger, A., Mello de Sousa, T. M., Regnat, K., Derntl, C., Mach, R. L., & Mach-Aigner, A. R. (2016). Impact of inducer molecules on DNA accessibility in cellulase and xylanase gene expression in Trichoderma reesei. In Abstract Book (p. 370).

Reischer, G., Schuster, N., Mossler, P., Ley, R. E., & Farnleitner, A. H. (2016). Novel Bioinformatic Tools for the Discovery and Evaluation of Genetic Faecal Markers. In Abstracts (p. 24).

Ressmann, A., Gonzalez Garcia, E., Zirbs, R., Gärtner, P., Mach, R. L., Brunner, K., & Schröder, K. (2016). From genetically modified maize to horse meat: New ionic liquid solutions in food control. COST CM1206 Meeting, Poznan, Poland.

Savio, D. F., Reischer, G., Sinclair, L., Parajka, J. D., Stadler, P., Blaschke, A. P., Mach, R. L., Kirschner, A. K. T., Blöschl, G., Eiler, A., & Farnleitner, A. H. (2016). Evaluating the applicability of metagenemies for the monitaring of microbiological water quality in natural water resources. In Abstracts (pp. 63–64).

Schmoll, M., Dattenböck, C., Carreras-Villasenor, N., Mendoza-Mendoza, A., Tisch, D., Aleman, M. I., Baker, S. E., Frischmann, A., Seidl-Seiboth, V., & Zeilinger, S. (2016). The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiology and Molecular Biology Reviews, 80(1), 205–327.

Sloothaak, J., Tamayo-Ramos, J. A., Odoni, D. I., Laothanachareon, T., Derntl, C., Mach-Aigner, A. R., Martins dos Santos, V. A. P., & Schaap, P. J. (2016). Identification and functional characterization of novel xylose transporters from the cell factories Aspergillus niger and Trichoderma reesei. Biotechnology for Biofuels, 9(148). https://doi.org/10.1186/s13068-016-0564-4

Steiger, M. G., Punt, P. J., Ram, A. F. J., Mattanovich, D., & Sauer, M. (2016). CharacterizingMttAasamitochondrial cis-aconitic acidtransporter bymetabolicengineering. Metabolic Engineering, 35, 95–104. https://doi.org/10.1016/j.ymben.2016.02.003

Till, P., Pucher, M., Mach, R. L., & Mach-Aigner, A. R. (2016). A hitherto unknown hydrolase activator in Trichoderma reesei. In Abstract Book (p. 352).

Zeilinger, S., Gruber, S., Lichius, A., Radebner, T., Labaj, P., & Kreil, D. (2016). Host sensing and attack in the mycoparasite Trichoderma atroviride: the 7-TM receptor Gpr1 and its putative interactor, a Sur7 -family protein. In Abstract Book (p. 53).

Zeilinger, S., Gupta, V. K., Dahms, T. E. S., Silva, R. N., Singh, H. B., Upadhyay, R. S., Gomes, E. V., Tsui, C. K.-M., & Nayak S, C. (2016). Friends or foes? Emerging insights from fungal interactions with plants. FEMS Microbiology Reviews, 40(2), 182–207. https://doi.org/10.1093/femsre/fuv045

Vierheilig, J., Savio, D. F., Ley, R. E., Mach, R. L., Farnleitner, A. H., & Reischer, G. (2015). Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring. Water Science & Technology, 72(11), 1962–1972. https://doi.org/10.2166/wst.2015.407

Akcapinar, G. B., Kappel, L., Sezerman, O. U., & Seidl-Seiboth, V. (2015). Molecular diversity of LysM carbohydrate‑binding motifs in fungi. Current Genetics, 61(2), 103–113. https://doi.org/10.1007/s00294-014-0471-9

Bichler, M., Felgitsch, L., Seidl-Seiboth, V., & Grothe, H. (2015). Biological Ice Nucleation. 16. Österreichische Chemietage 2015, Innsbruck, Austria.

Bichler, M., Felgitsch, L., Seidl-Seiboth, V., & Grothe, H. (2015). Biological Ice Nucleation. Workshop - Microphysics of ice clouds, Wien, Austria.

Bichler, M., Felgitsch, L., Seidl-Seiboth, V., & Grothe, H. (2015). Ice Nucleation Triggered by Biological Substances. In EGU General Assembly 2015. EGU General Assembly 2015, Vienna, Austria. Copernicus Publishing.

Bischof, R. H., Horejs, J., Metz, B., Gamauf, C., Kubicek, C. P., & Seiboth, B. (2015). L‑Methionine repressible promoters for tuneable gene expression in Trichoderma reesei. Microbial Cell Factories, 14(120). https://doi.org/10.1186/s12934-015-0308-3

Bischof, R., & Seiboth, B. (2015). Systems biology of carbohydrate active enzyme production in Trichoderma reesei. In P. C. Hallenbeck (Ed.), Advances in Enzymatic Conversion of Biomass to Biofuels (pp. 6–19). Future Science Ltd. https://doi.org/10.4155/fseb2013.14.166

Bischof, R., Horejs, J., Metz, B., Gamauf, C., Kubicek, C. P., & Seiboth, B. (2015). Novel repressible promoters for tuneable gene expression in Trichoderma reesei. In 11#^{th} VAAM Conference (p. 166).

Blanch, A. R., Balleste, E., Muniesa, M., Stange, C., Tiehm, A., Schuster, N., Farnleitner, A. H., Sommer, R., Lindner, G., Nunes-Monteiro, S. P., Santos, R., Oristo, S., Maunula, L., & Lucena, F. (2015). Selection of workable combinations of microbial source tracking markers to distinguish faecal pollution from more than two origins: an ongoing EU project. In Proceedings (pp. 42–44).

Blaschke, A. P., Farnleitner, A. H., Derx, J., Reiner, P., Sommer, R., Kirschner, A., & Frick, C. (2015). Gewässervernetzung (Neue) Donau - Untere Lobau (Nationalpark Doanu-Auen) - Endbericht.

Bonazza, K., Gaderer, R., Neudl, S., Przylucka, A., Allmaier, G., Druzhinina, I. S., Grothe, H., Friedbacher, G., & Seidl-Seiboth, V. (2015). The fungal cerato-platanin protein EPL1 forms highly ordered layers at hydrophobic/hydrophilic interfaces. Soft Matter, 11(9), 1723–1732. https://doi.org/10.1039/c4sm02389g

Brunner, K. (2015). DNA analysis goes on site: the combination of isothermal amplification methods with ionic liquid based rapid extraction protocols. In Abstracts of Lectures and Posters. RME 2015 Rapid Methods for Food, Feed and Water Analysis, Noordwijkerhout, Netherlands (the).

Derntl, C., Kiesenhofer, D., Mach, R. L., & Mach-Aigner, A. R. (2015). Novel Strategies for Genomic Manipulation of Trichoderma reesei with the Purpose of Strain Engineering. Applied and Environmental Microbiology, 81(18), 6314–6323.

Derntl, C., Mello de Sousa, T. M., Kiesenhofer, D., Rassinger, A., Pocas-Fonseca, M., Mach, R. L., & Mach-Aigner, A. R. (2015). How to modify regulatory proteins for desired gene expression? In Abstract Book (p. 22).

Derntl, C., Rassinger, A., Srebotnik, E., Mach, R. L., & Mach-Aigner, A. R. (2015). Xpp1 regulates the expression of xylanases, but not of cellulases in Trichoderma reesei. Biotechnology for Biofuels, 8(112). https://doi.org/10.1186/s13068-015-0298-8

Farnleitner, A. H., Blaschke, A. P., Sommer, R., Kirschner, A., Derx, J., & Frick, C. (2015). Jahresbericht 2015: GWRS - Groundwater Resource Systems Vienna.

Gaderer, R., Kappel, L., & Seidl-Seiboth, V. (2015). Metabolism of the chitin monomer N-acetylglucosamine in Neurospora crassa. In Abstract Book (pp. 87–88).

Gaderer, R., Lamdan, N. L., Frischmann, A., Sulyok, M., Krska, R., Horwitz, B. A., & Seidl-Seiboth, V. (2015). Sm2, a paralog of the Trichoderma cerato-platanin elicitor Sm1, is also highly important for plant protection conferred by the fungal-root interaction of Trichoderma with maize. BMC Microbiology, 15(2). https://doi.org/10.1186/s12866-014-0333-0

Gasser, B., Steiger, M. G., & Mattanovich, D. (2015). Methanol regulated yeast promoters: production vehicles and toolbox for synthetic biology. Microbial Cell Factories, 14(196). https://doi.org/10.1186/s12934-015-0387-1

Ghassemi, S., Lichius, A., Bidard, F., Lemoine, S., Rossignol, M.-N., Herold, S., Seidl-Seiboth, V., Seiboth, B., Espeso, E. A., Margeot, A., & Kubicek, C. P. (2015). The ß-importin KAP8 (Pse1/Kap121) is required for nuclear import of the cellulase transcriptional regulator XYR1, asexual sporulation and stress resistance in Trichoderma reesei. Molecular Microbiology, 96(2), 405–418.

Kappel, L., Gaderer, R., & Seidl-Seiboth, V. (2015). Regulation of the N-acetylglucosamine catabolism gene cluster by an NDT80-like transcription factor in filamentous fungi. In Abstract Book (p. 193).

Kiesenhofer, D., Mach-Aigner, A. R., & Mach, R. L. (2015). Fungal Metabolic Engineering for Biofuel Production. In R. Nascimento Silva (Ed.), Mycology: Current and Future Developments (pp. 128–147). Bentham Science Publishers. https://doi.org/10.2174/9781681080741115010008

Kirschner, A., Kavka, G., Reischer, G., Sommer, R., Blaschke, A. P., Stevenson, M., Vierheilig, J., Mach, R. L., & Farnleitner, A. H. (2015). Microbiological Water Quality of the Danube River: Status Quo and Future Perspectives. In The Handbook of Environmental Chemistry - The Danube River Basin (pp. 439–468). Springer.

Kolm, C., Mach, R. L., Krska, R., & Brunner, K. (2015). A rapid DNA lateral flow test for the detection of transgenic maize by isothermal amplification of the 35S promoter. Analytical Methods, 7(1), 129–134. https://doi.org/10.1039/c4ay01997k

Lichius, A., Bidard, F., Buchholz, F., Le Crom, S., Martin, J., Schackwitz, W., Austerlitz, T., Grigoriev, I. V., Baker, S. E., Margeot, A., Seiboth, B., & Kubicek, C. P. (2015). Erratum to: Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics, 16(725). https://doi.org/10.1186/s12864-015-1917-2

Lichius, A., Bidard, F., Buchholz, F., Le Crom, S., Martin, J., Schackwitz, W., Austerlitz, T., Grigoriev, I. V., Baker, S. E., Margeot, A., Seiboth, B., & Kubicek, C. P. (2015). Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics, 16(326). https://doi.org/10.1186/s12864-015-1526-0

Linke, R., Thallinger, G. G., Haarmann, T., Eidner, J., Schreiter, M., Lorenz, P., Kubicek, C. P., & Seiboth, B. (2015). Restoration of female fertility in Trichoderma reesei QM6a provides the basis for inbreeding in this industrial enzyme producer. In 11#^{th} VAAM Conference (p. 158).

Linke, R., Thallinger, G. G., Haarmann, T., Eidner, J., Schreiter, M., Lorenz, P., Seiboth, B., & Kubicek, C. P. (2015). Restoration of female fertility in Trichoderma reesei QM6a provides the basis for inbreeding in this industrial cellulase producing fungus. Biotechnology for Biofuels, 8(155). https://doi.org/10.1186/s13068-015-0311-2

Machado Mello De Sousa, T., Rassinger, A., Pucher, M. E., dos Santos Castro, L., Persinoti, G. F., Silva-Rocha, R., Poças-Fonseca, M. J., Mach, R. L., Nascimento Silva, R., & Mach-Aigner, A. R. (2015). The impact of chromatin remodelling on cellulase expression in Trichoderma reesei. BMC Genomics, 16(588). https://doi.org/10.1186/s12864-015-1807-7

Mairinger, T., Steiger, M., Nocon, J., Mattanovich, D., Koellensperger, G., & Hann, S. (2015). Gas Chromatography-Quadrupole Time-of-Flight Mass Spectrometry-Based Determination of Isotopologue and Tandem Mass Isotopomer Fractions of Primary Metabolites for ¹³C-Metabolic Flux Analysis. Analytical Chemistry, 87(23), 11792–11802. https://doi.org/10.1021/acs.analchem.5b03173

Mayer, R., Vierheilig, J., Egle, L., Reischer, G., Saracevic, E., Mach, R. L., Kirschner, A. K. T., Zessner, M., Sommer, R., & Farnleitner, A. H. (2015). Automated Sampling Procedures Supported by High Persistence of Bacterial Fecal Indicators and Bacteroidetes Genetic Microbial Source Tracking Markers in Municipal Wastewater during Short-Term Storage at 5°C. Applied and Environmental Microbiology, 81(15), 5134–5143.

Mello de Sousa, T. M., Mach, R. L., & Mach-Aigner, A. R. (2015). A Recyclable and Bidirectionally Selectable Marker System for Transformation of Trichoderma. In M. A. van den Berg & K. Maruthachalam (Eds.), Genetic Transformation Systems in Fungi, Volume 2 (pp. 169–174). Springer International Publishing. https://doi.org/10.1007/978-3-319-10503-1_14

Nemes, A., Bruckner, B., Zeilinger-Migsich, S., & Marchetti-Deschmann, M. (2015). (Phospho-)proteome changes during mycoparasitism in the fungus Trichoderma atroviride. In Book of Abstracts (p. 30).

Nemes, A., Reitschmidt, S., Hartmanova, M., Lemr, K., Zeilinger-Migsich, S., & Marchetti-Deschmann, M. (2015). From Proteomics to Mass Spectrometry Imaging - The Study of Mycoparasitic Interactions. 14th International Congress on Amino Acids, Peptides and Proteins, Wien, Austria.

Nemes, A., Reitschmidt, S., Hartmanova, M., Lemr, K., Zeilinger-Migsich, S., & Marchetti-Deschmann, M. (2015). From Proteomics to Mass Spectrometry Imaging - The Study of Mycoparasitic Interactions. IX Annual Congress - EuPA, Mailand, Italy.

Neumann, N. K., Stoppacher, N., Zeilinger-Migsich, S., Degenkolb, T., Brückner, H., & Schuhmacher, R. (2015). The Peptaibiotics Database - A Comprehensive Online Resource. Chemistry and Biodiversity, 12, 743–751.

Nunes-Monteiro, S. P., Schuster, N., Moreira, B., Balleste, E., Stange, C., Tiehm, A., Reischer, G., Oristo, S., Blanch, A. R., Farnleitner, A. H., & Santos, R. (2015). Quantitative occurance of genetic microbial source tracking markers in target and non-target fecal sources across Europe. In Proceedings (pp. 508–510).

Patzschke, A., Steiger, M., Holz, C., Lang, C., Mattanovich, D., & Sauer, M. (2015). Enhanced glutathione production by evolutionary engineering of Saccharomyces cerevisiae strains. Biotechnology Journal, 10(11), 1719–1726. https://doi.org/10.1002/biot.201400809

Preiser, V., Goetsch, D., Sulyok, M., Krska, R., Mach, R. L., Farnleitner, A., & Brunner, K. (2015). The development of a multiplex real-time PCR to quantify Fusarium DNA of trichothecene and fumonisin producing strains in maize. Analytical Methods, 7(4), 1358–1365. https://doi.org/10.1039/c4ay02581d

Ramoni, J., Herold, S., Marchetti-Deschmann, M., Seidl-Seiboth, V., & Seiboth, B. (2015). Trichoderma reesei XYN5, the flawed sibling of XYN1. In 11#^{th} VAAM Conference (p. 191).

Ramoni, J., Marchetti-Deschmann, M., Seidl-Seiboth, V., & Seiboth, B. (2015). Trichoderma reesei XYNS, the flawed sibling of XYN1. In Abstract Book 2015 (p. 56).

Reischer, G., Kirschner, A. K. T., Schnitzer, G., Savio, D. F., Mach, R. L., Bahlmann, A., Schulze, T., Brack, W., & Farnleitner, A. H. (2015). Microbial Faecal Source Tracking. In Joint Danube Survey 3 - A Comprehensive Analysis of Danube Water Quality (pp. 162–168). ICPDR-International Commission for the Protection of the Danube River.

Reischer, G., Schuster, N., Mossler, P., Ley, R. E., & Farnleitner, A. H. (2015). Bioinformatic processes using a tailored metagenomic sequence database for discovery and evaluation of genetic faecal markers. In Proceedings (pp. 235–237).

Reitschmidt, S., Zeratto, S., Hartmanova, M., Lemr, K., Allmaier, G., Zeilinger-Migsich, S., & Marchetti-Deschmann, M. (2015). Studying fungal proteome and surface changes during host-pathogen interaction. 9th Central and Eastern European Proteomics Conference, Poznan, Poland.

Ressmann, A., Gonzales Garcia, E., Khlan, D., Gärtner, P., Mach, R. L., Krska, R., Brunner, K., & Schröder, K. (2015). Fast and efficient extraction of DNA from meat and meat derived products using aqueous ionic liquid buffer systems. New Journal of Chemistry, 39(6), 4994–5002. https://doi.org/10.1039/c5nj00178a

Russmayer, H., Troyer, C., Neubauer, S., Steiger, M. G., Gasser, B., Hann, S., Koellensperger, G., Sauer, M., & Mattanovich, D. (2015). Metabolomics sampling of Pichia pastoris revisited: rapid filtration prevents metabolite loss during quenching. FEMS Yeast Research, 15(6), fov049. https://doi.org/10.1093/femsyr/fov049

Savio, D. F., Reischer, G., Sinclair, L., Parajka, J. D., Stadler, P., Blaschke, A. P., Mach, R. L., Kirschner, A. K. T., Blöschl, G., Eiler, A., & Farnleitner, A. H. (2015). Meta-genomics for water resources monitoring: Bacterial 16S RRNA gene communities along 2600 km of the Danube river. In Proceedings (pp. 436–437).

Savio, D. F., Sinclair, L., Ijaz, U. Z., Parajka, J. D., Reischer, G., Stadler, P., Blaschke, A. P., Blöschl, G., Mach, R. L., Kirschner, A. K. T., Farnleitner, A. H., & Eiler, A. (2015). Bacterial diversity along a 2600 km river continuum. Environmental Microbiology, 17(12), 4994–5007.

Savio, D. F., Sinclair, L., Parajka, J. D., Reischer, G., Stadler, P., Blaschke, A. P., Mach, R. L., Kirschner, A. K. T., Blöschl, G., Farnleitner, A. H., & Eiler, A. (2015). Bacterial diversity along a 2,600 km river continuum. In Proceedings (p. 2).

Seiboth, B. (2015). Systems Biology approaches for Trichoderma reesei strain engineering. 17#^{th} International Congress of the Hungarian Society for Microbiology, Budapest, Hungary.

Seiboth, B. (2015). The secrets of cellulase hyperproducing and non-producing Trichoderma reesei mutants. Symposium Plant Biomass Utilization by Fungi, Utrecht, Netherlands (the).

Seiboth, B. (2015). Systems Biology approaches for Trichoderma reesei strain engineering. Acta Microbiologica et Immunologica Hungarica, 62(Supplement), 213.

Zeilinger, S., Garcia-Estrada, C., & Martin, J.-F. (2015). Fungal Secondary Metabolites in the “OMICS” Era. In S. Zeilinger, J.-F. Martin, & C. Garcia-Estrada (Eds.), Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites (Vol. 2, pp. 1–12). Springer Science + Business Media. https://doi.org/10.1007/978-1-4939-2531-5_1

Zeilinger, S., Martin, J.-F., & Garcia-Estrada, C. (Eds.). (2015). Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites, Volume 2. Springer Science + Business Media. https://doi.org/10.1007/978-1-4939-2531-5

Zeilinger-Migsich, S. (2015). From Genes to Biocontrol: Molecular Mechanisms of a Mycoparasitic Fungus. In Abstracts (p. 1).

Zeki, S., Mayer, R., Keiblinger, K., Schuster, N., Kiesenhofer, D., Mach-Aigner, A. R., Mach, R. L., Reischer, G., & Farnleitner, A. H. (2015). Design and application of a genetically modified E. coli strain for assessment of DNA extraction and recovery efficiencies in Bacteroidetes based MST studies. In Proceedings (pp. 77–79).

Nocon, J., Steiger, M., Pfeffer, M., Sohn, S. B., Kim, T. Y., Maurer, M., Rußmayer, H., Pflügl, S., Ask, M., Haberhauer-Troyer, C., Ortmayr, K., Hann, S., Koellensperger, G., Gasser, B., Lee, S. Y., & Mattanovich, D. (2014). Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production. Metabolic Engineering, 24, 129–138. https://doi.org/10.1016/j.ymben.2014.05.011

Benocci, T., Sahar, M., Benoit, I., Seiboth, B., & De Vries, R. (2014). The influence of regulatory and metabolic mutations on growth of Trichoderma reesei on plant biomass related carbon sources. In Book of Abstracts (p. 101).

Bischof, R., & Seiboth, B. (2014). Molecular Tools for Strain Improvement of Trichoderma spp. In V. K. Gupta, M. Schmoll, A. Herrera-Estrella, R. S. Upadhyay, I. Druzhinina, & M. G. Tuohy (Eds.), Biotechnology and Biology of Trichoderma (pp. 179–191). Elsevier B.V. https://doi.org/10.1016/b978-0-444-59576-8.00012-6

Bischof, R., Frischmann, A., Ivanova, C., Lichius, A., Kubicek, C. P., & Seiboth, B. (2014). Elucidation of novel targets for Trichoderma reesei strain improvement towards better enzyme production. In 16th European Congress on Biotechnology. ECB 16 - 16th European Congress on Biotechnology, Edinburgh, United Kingdom of Great Britain and Northern Ireland (the).

Blaschke, A. P., Sommer, R., Vierheilig, J., Reischer, G., Derx, J., Mach, R. L., Kirschner, A., & Farnleitner, A. H. (2014). Vorstellung des ICC Water & Health - Interdisziplinäre Wissenschaft und Forschung. Lange Nacht der Forschung 2014, Wien, Austria.

Blaschke, A. P., Sommer, R., Vierheilig, J., Reischer, G., Derx, J., Mach, R. L., Kirschner, A., & Farnleitner, A. H. (2014). Vorstellung des ICC Water & Health - Interdisziplinäre Wissenschaft und Forschung. TU-Galaabend der Forschung 2014, Wien, Austria.

Brunner, K. (2014). Isothermal amplification of DNA as a novel approach for the rapid detection of DNA in food samples: a simple test for the food allergen celery. Rapid Methods for Food Feed and Water analysis. In Abstracts of Lectures and Posters (p. 70).

Derntl, C., Mach-Aigner, A. R., & Mach, R. L. (2014). Trichoderma Proteins with Disruption Activity on Cellulosic Substrates. In V. K. Gupta, M. Schmoll, A. Herrera-Estrella, R. S. Upadhyay, I. Druzhinina, & M. G. Tuohy (Eds.), Biotechnology and Biology of Trichoderma (pp. 309–317). Elsevier B.V. https://doi.org/10.1016/b978-0-444-59576-8.00021-7

Derntl, C., Ortner, K., Mach, R. L., & Mach-Aigner, A. R. (2014). Identification of Crucial Motifs in the Transcription Factors Ace1 and Xyr1 in Trichoderma reesei. In Book of Abstracts (p. 210).

Farnleitner, A. H., Reischer, G., Savio, D., Frick, C., Schuster, N., Schilling, K., Mach, R. L., Derx, J., Kirschner, A. K. T., Blaschke, A. P., & Sommer, R. (2014). Diagnostik mikrobiologischer Fäkalkontaminationen in Wasser und Gewässern - Status Quo und gegenwärtige Entwicklungen. In J. Krampe (Ed.), Abwasserreinigung - Werte erhalten, Effizienz steigern und Ressourcen schonen : ÖWAV-Seminar Wien 2014, TU Wien, 25. - 26. Februar 2014 (Vol. 230, pp. 157–184). Institut für Wassergüte/ TU Wien.

Farnleitner, A. H., Reischer, G., Savio, D., Mach, R. L., Stadler, P., Kirschner, A. K. T., Stadler, H., Blaschke, A. P., Sommer, R., & Zerobin, W. (2014). Microbial water quality management at all time scales: from molecuar source tracking to near real-time water abstraction at alpine karst water resources. In Abstracts (pp. 30–31).

Farnleitner, A. H., Reischer, G., Stadler, H., Derx, J., Kirschner, A. K. T., Mach, R. L., Cervero-Arago, S., Blaschke, A. P., & Sommer, R. (2014). Opening the Black Box of Microbial Faecal Pollution in (Ground) Water Resources. Joint CONFERENCE PROMISE and BacFood Net Persistent lifestyles of food - borne pathogens and its consequence, Wien, Austria.

Farnleitner, A. H., Stadler, H., Reischer, G., Sommer, R., Ryzinska-Paier, G., Mach, R. L., Kirschner, A. K. T., Schuster, N., Savio, D., & Zerobin, W. (2014). New Framework for Microbial Faecal Pollution Analysis Supports Water Resource Management at all Time Scales. IWA World Water Congress & Exhibition, Lissabon, Portugal.

Fink, M., Iqbal, N., Derntl, C., Feroz, S., Rudroff, F., & Mihovilovic, M. D. (2014). Dynamic Kinetic Asymmetric Transformations Catalyzed by the Enoate Reductase YqjM. Gordon Research Seminar Biocatalysis 2014, Smithfield, United States of America (the).

Fink, M., Iqbal, N., Feroz, S., Derntl, C., Rudroff, F., & Mihovilovic, M. D. (2014). Dynamic Kinetic Asymmetric Transformations Catalyzed by the Enoate Reductase YqjM. Gordon Research Conference Biocatalysis 2014, Smithfield, United States of America (the).

Frick, C., Vierheilig, J., Kirschner, A., Blaschke, A. P., Sommer, R., & Farnleitner, A. H. (2014). Microbial water quality at alluvial backwaters can be influenced by internal and external faecal pollution sources. 34. Jahrestagung der Österreichischen Gesellschaft für Hygiene, Mikrobiologie und Präventivmedizin, Bad Ischl, Austria.

Gaderer, R., Bonazza, K., & Seidl-Seiboth, V. (2014). Cerato-platanins: a fungal protein family with intriguing properties and application potential. Applied Microbiology and Biotechnology, 98(11), 4795–4803. https://doi.org/10.1007/s00253-014-5690-y

Gaderer, R., Bonazza, K., Lamdan, N. L., Horwitz, B. A., & Seidl-Seiboth, V. (2014). CPPs in Trichoderma: Properties of protein layers and analysis of cerato-platanin gene knockout strains. In Book of Abstracts (p. 87).

Gaderer, R., Bonazza, K., Lamdan, N. L., Horwitz, B. A., & Seidl-Seiboth, V. (2014). Cerato-platanin proteins: Induction of plant defense responses and formation of self-assembled hybrid protein layers with hydrophobins. In Abstract Book (p. 190).

Garcia Basallote, M., Tysklind, M., Seiboth, B., Mihok, I., & Laurenczy, G. (2014). Comments on the results of the ENVIKUT research project (01.01.2013 - 30.04.2015) “Basic chemical and biological research for elimination of environmentally hazardous chemicals”, given by the International Advisory Board.

Ghassemi, S., Lichius, A., Seiboth, B., Seidl-Seiboth, V., & Kubicek, C. P. (2014). Nuclear transport and cellulase production in Trichoderma reesei. In Abstract Book (p. 177).

Ghassemi, S., Lichius, A., Seidl-Seiboth, V., Seiboth, B., & Kubicek, C. P. (2014). Nuclear transport and cellulase production in Trichoderma reesei. In Book of Abstracts (p. 136).

Gonzalez Garcia, E., Kolm, C., Mach, R. L., Krska, R., & Brunner, K. (2014). A rapid DNA extraction method and its combination with isothermal DNA amplification for the determination of genetically modified maize. In Book of Abstracts (p. 53).

Gonzalez Garcia, E., Ressmann, A., Gärtner, P., Zirbs, R., Mach, R. L., Krska, R., Bica, K., & Brunner, K. (2014). Direct extraction of genomic DNA from maize with aqueous ionic liquid buffer systems for applications in genetically modified organisms analysis. Analytical and Bioanalytical Chemistry, 406(30), 7773–7784. https://doi.org/10.1007/s00216-014-8204-y

Gruber, S., & Zeilinger, S. (2014). The Transcription Factor Ste12 Mediates the Regulatory Role of the Tmk1 MAP Kinase in Mycoparasitism and Vegetative Hyphal Fusion in the Filamentous Fungus Trichoderma atroviride. PLoS ONE, 9(10), e111636. https://doi.org/10.1371/journal.pone.0111636

Jovanović, B., Mach, R. L., & Mach-Aigner, A. R. (2014). Erythritol production on wheat straw using Trichoderma reesei. AMB Express, 4(34). https://doi.org/10.1186/s13568-014-0034-y

Kappel, L., Gaderer, R., & Seidl-Seiboth, V. (2014). Characterization of the N-acetylglucosamine catabolism gene cluster in filamentous fungi. In Abstract Book (p. 202).

Kappel, L., Gaderer, R., & Seidl-Seiboth, V. (2014). Characterization of the N-acetylglucosamine catabolism gene cluster in filamentous fungi. In Book of Abstracts (p. 199).

Karimi Aghcheh, R., Bredeweg, E. L., Seiboth, B., Lichius, A., Kubicek, C. P., & Freitag, M. (2014). Heterochromatin protein 1 of Trichoderma reesei is required for transcription of CAZyme genes and conidiation. In Book of Abstracts (p. 208).

Karimi Aghcheh, R., Nemeth, Z., Atanasova, L., Ghassemi, S., Aquino, B., Druzhinina, I., Fekete, E., Seiboth, B., Karaffa, L., & Kubicek, C. P. (2014). Vel1 of Trichoderma reesei has an auxiliary role in in cellulase gene expression and is required for sexual and asexual development. In Book of Abstracts (p. 152).

Kittinger, C., Reischer, G., Jakwerth, S., Kolarevic, S., Baumert, R., Folli, B., Lipp, M., Zarfel, G., Galler, H., Grisold, A., Savio, D., Schnitzer, G., Sommer, R., Farnleitner, A. H., & Kirschner, A. K. T. (2014). The JOINT DANUBE SURVEY 2013 - An overview of the microbiological program and a first glance at the patterns of faecal pollution, ecotoxicological status and antibiotic resistance. In Abstracts (p. 32).

Klaubauf, S., Narang, H. M., Post, H., Zhou, M., Brunner, K., Mach-Aigner, A. R., Mach, R. L., Heck, A. J. R., Altelaar, A. F. M., & de Vries, R. P. (2014). Similar is not the same: Differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi. Fungal Genetics and Biology, 72, 73–81. https://doi.org/10.1016/j.fgb.2014.07.007

Lichius, A., & Lord, K. M. (2014). Chemoattractive Mechanisms in Filamentous Fungi. The Open Mycology Journal, 8(1), 28–57. https://doi.org/10.2174/1874437001408010028

Lichius, A., Seidl-Seiboth, V., Seiboth, B., & Kubicek, C. P. (2014). Nucleo-cytoplasmic shuttling dynamics of the transcriptional regulators XYR1 and CRE1 under conditions of cellulase and xylanase gene expression in Trichoderma reesei. Molecular Microbiology, 94(5), 1162–1178.

Mach, R. L., Mach-Aigner, A. R., Derntl, C., Mello de Sousa, T. M., Rassinger, A., Till, P., & Kiesenhofer, D. (2014). Complex, Multilevel Mechanisms Regulate Expression of Hydrolase Encoding Genes in Trichoderma. In TG2014 Programme & Abstracts (p. 17).

Mach-Aigner, A. R., Gorsche, R., Mello de Sousa, T. M., Pocas-Fonseca, M., & Mach, R. L. (2014). What Makes Rut-C30 an Appealing Parent of Industry Strains? In Book of Abstracts (p. 231).

Martin, J.-F., Garcia-Estrada, C., & Zeilinger, S. (2014). Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites. Springer. https://doi.org/10.1007/978-1-4939-1191-2

Mayer, R., Egle, L., Reischer, G., Piringer, H., Gaisbauer, M., Mach, R. L., Zessner, M., Sommer, R., & Farnleitner, A. H. (2014). Are genetic faecal markers a valuable tool to monitor sewage associated contamination at water resources? In Abstracts (p. 31).

Mello de Sousa, T. M., Gorsche, R., Pocas-Fonseca, M., Mach, R. L., & Mach-Aigner, A. R. (2014). Characterization of a Nuclear Receptor-like Domain of the Xylanase Regulator 1. In Book of Abstracts (p. 198).

Mello de Sousa, T. M., Gorsche, R., Rassinger, A., Pocas-Fonseca, M., Mach, R. L., & Mach-Aigner, A. R. (2014). A truncation of Cre1 from T. reesei leads to a different functionality. In TG2014 Programme & Abstracts (p. 23).

Mello de Sousa, T. M., Gorsche, R., Rassinger, A., Poças-Fonseca, M. J., Mach, R. L., & Mach-Aigner, A. R. (2014). A truncated form of the Carbon catabolite repressor 1 increases cellulase production in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS, 7(129). https://doi.org/10.1186/s13068-014-0129-3

Nemes, A., Bruckner, B., Gruber, S. G., Rehulka, P., Allmaier, G., Zeilinger, S., & Marchetti-Deschmann, M. (2014). Phosphoproteome changes during mycoparasitism in the fungus Trichoderma atroviride. In Abstractbook (p. 1).

Neumann, N. K., Stoppacher, N., Zeilinger, S., Degenkolb, T., Brückner, H., & Schuhmacher, R. (2014). The Peptaibiotics Database Directory. 33#^{rd} European Peptide Symposium, Sofia, Bulgaria.

Pazzagli, L., Seidl-Seiboth, V., Barsottini, M., Vargas, W. A., Scala, A., & Mukherjee, P. K. (2014). Cerato-platanins: Elicitors and effectors. Plant Science, 228, 79–87. https://doi.org/10.1016/j.plantsci.2014.02.009

Poggi-Parodi, D., Bidard, F., Pirayre, A., Portnoy, T., Blugeon, C., Seiboth, B., Kubicek, C. P., Le Crom, S., & Margeot, A. (2014). Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain. Biotechnology for Biofuels, 7(173). https://doi.org/10.1186/s13068-014-0173-z

Preiser, V., Mach, R. L., & Brunner, K. (2014). Selection and characterization of aptamers for the rapid detection of aflatoxin in maize. The World Mycotoxin Forum, 8th Conference, Vienna, Austria, Austria.

Ramoni, J., Herold, S., Kubicek, C. P., & Seiboth, B. (2014). A genome wide analysis of xylanases in Trichoderma reesei. In Abstract Book (p. 62).

Rebnegger, C., Graf, A., Valli, M., Steiger, M., Gasser, B., Maurer, M., & Mattanovich, D. (2014). In Pichia pastoris, growth rate regulates protein synthesis and secretion, mating and stress response. Biotechnology Journal, 9, 511–525.

Reischer, G., Schuster, N., Ley, R. E., & Farnleitner, A. H. (2014). A DNA Sequence Database Of Vertebrate Faecal Communities As A Basis For Molecular Faecal Indication. IWA World Water Congress & Exhibition, Lissabon, Portugal.

Reischer, G., Schuster, N., Stalder, G. L., Walzer, C., Ley, R. E., & Farnleitner, A. H. (2014). Deciphering the Diversity of Vertebrate Faecal Microbiota as a Solid Basis for Molecular Faecal Indication and Source Tracking. In Abstracts (pp. 31–32).

Reischer, G., Schuster, N., Stalder, G. L., Walzer, C., Ley, R. E., & Farnleitner, A. H. (2014). Finding the drivers of intestinal community composition in vertebrate animals - the role of host phylogeny, physiology and diet. In Proceedings (pp. 311–312).

Reithner, B., & Mach, R. L. (2014). Genes from Trichoderma as a Source for Improving Plant Resistance to Fungal Pathogen. In V. K. Gupta, M. Schmoll, A. Herrera-Estrella, R. S. Upadhyay, I. Druzhinina, & M. G. Tuohy (Eds.), Biotechnology and Biology of Trichoderma (pp. 505–513). Elsevier B.V.

Reithner, B., Mach-Aigner, A. R., Herrera-Estrella, A., & Mach, R. L. (2014). Trichoderma atroviride Transcriptional Regulator Xyr1 Supports the Induction of Systemic Resistance in Plants. Applied and Environmental Microbiology, 80(17), 5274–5281.

Ressmann, A., Gonzales Garcia, E., Gärtner, P., Mach, R. L., Brunner, K., & Schröder, K. (2014). An ionic liquid-buffer system for the enhancement of DNA extraction from maize. 15th EUCHEM on Ionic Liquids and Molten Salts 2014, Tallinn, Estonia.

Ryzinska-Paier, G., Lendenfeld, T., Correa, K., Stadler, P., Blaschke, A. P., Mach, R. L., Stadler, H., Kirschner, A. K. T., & Farnleitner, A. H. (2014). A sensitive and robust method for automated on-line monitoring of enzymatic activities in water and water resources. Water Science & Technology, 69(6), 1349–1358. https://doi.org/10.2166/wst.2014.032

Sauer, M., Steiger, M., Mattanovich, D., & Marx, H. (2014). Biorefineries-Conceptsfor Sustainability. In V. S. Bisaria & A. Kondo (Eds.), Bioprocessing of Renewable Resources to Commodity Bioproducts (pp. 2–27). John Wiley & Sons, Ltd.

Schmoll, M., Seiboth, B., Druzhinina, I., & Kubicek, C. P. (2014). Genomics Analysis of Biocontrol Species and Iudustrial Enzyme Producers from the Genus Trichoderma. In Fungal Genomics, The Mycota, Vol. XIII (pp. 233–264). Springer-Verlag.

Schnitzer, G., Kirschner, A. K. T., Mach, R. L., Farnleitner, A. H., & Reischer, G. (2014). Integration of internal amplification control in quantitative PCR methods for microbial faecal source tracking. In Abstracts (p. 82).

Seiboth, B. (2014). Cellulase and hemicellulase regulation and production in Trichoderma reesei. In Book of Abstracts (p. 53).

Seiboth, B. (2014). Foreword. In V. K. Gupta, M. G. Tuohy, C. P. Kubicek, J. Saddler, & F. Xu (Eds.), Bioenergy Research: Advances and Applications (p. xi). Elsevier B.V.

Seiboth, B. (2014). Systems biological approaches to analyze cellulase production processes in Trichoderma reesei. In Programme and Abstract Book (p. 25).

Seidl-Seiboth, V., Ihrmark, K., Druzhinina, I., & Karlsson, M. (2014). Molecular Evolution of Trichoderma Chitinases. In V. K. Gupta, M. Schmoll, A. Herrera-Estrella, R. S. Upadhyay, I. Druzhinina, & M. G. Tuohy (Eds.), Biotechnology and Biology of Trichoderma (pp. 67–78). Elsevier B.V. https://doi.org/10.1016/b978-0-444-59576-8.00005-9

Stadler, P., Lendenfeld, T., Ryzinska-Paier, G., Blaschke, A. P., Stadler, H., Mach, R. L., Brunner, K., Appels, J., Zessner, M., & Farnleitner, A. H. (2014). A sensitive and robust method for automated on-line monitoring of enzymatic activities in water and water resources. In Abstracts of Lectures and Posters (p. 97).

Vierheilig, J., Reischer, G., Frick, C., Sommer, R., Blaschke, A. P., Derx, J., Kirschner, A. K. T., Muniesa, M., Mach, R. L., & Farnleitner, A. H. (2014). Comparative analyses of the genetic bacterial population structures in intestinal and non-intestinal habitats using an innovative multi-compartment approach. In Proceedings (pp. 432–433).

Vierheilig, J., Reischer, G., Savio, D., Frick, C., Blaschke, A. P., Derx, J., Sommer, R., Mach, R. L., & Farnleitner, A. H. (2014). Bacterial population structure analysis in a complex backwater area by next generation sequencing (NGS) to support the development of faecal pollution detection in the future. In Abstracts (pp. 32–33).

Zahradnik, C., Kolm, C., Martzy, R., Mach, R. L., Farnleitner, A. H., Krska, R., & Brunner, K. (2014). Isothermal DNA amplification approaches for the detection of genetically modofied maize. In Abstracts of Lectures and Posters (p. 96).

Zahradnik, C., Kolm, C., Martzy, R., Mach, R. L., Krska, R., Farnleitner, A. H., & Brunner, K. (2014). Detection of the 35S promoter in transgenic maize via various isothermal amplification techniques: a practical approach. Analytical and Bioanalytical Chemistry, 406(27), 6835–6842. https://doi.org/10.1007/s00216-014-7889-2

Zahradnik, C., Martzy, R., Mach, R. L., Krska, R., Farnleitner, A. H., & Brunner, K. (2014). A Simple Method for the Detection of Horsemeat in Food. In Book of Abstracts (p. 62).

Zahradnik, C., Martzy, R., Mach, R. L., Krska, R., Farnleitner, A. H., & Brunner, K. (2014). Detection of the food allergen celery via loop-mediated isothermal amplification technique. Analytical and Bioanalytical Chemistry, 406(27), 6827–6833. https://doi.org/10.1007/s00216-014-7873-x

Zeilinger, S. (2014). Insights into MAP kinase signaling in the mycoparasitic fungus Trichoderma atroviride. In Joint International Symposium on Mechanisms of Cellular Compartmentalization (p. 30).

Zeilinger, S., & Gruber, S. (2014). Insights into Signaling Pathways of Antagonistic Trichoderma Species. In V. K. Gupta, M. Schmoll, A. Herrera-Estrella, R. S. Upadhyay, I. Druzhinina, & M. G. Tuohy (Eds.), Biotechnology and Biology of Trichoderma (pp. 465–476). Elsevier B.V. https://doi.org/10.1016/b978-0-444-59576-8.00034-5

Zeilinger, S., & Gruber, S. G. (2014). The transcription factor TaSte12 mediates the regulatory role of the Tmk1 MAP kinase in mycoparasitism and vegetative hyphal fusion in Trichoderma atroviride. VAAM-Jahrestagung 2014 und 66. Jahrestagung der DGHM, Dresden, Germany.

Zeilinger, S., & Gruber, S. G. (2014). The transcription factor TaSte12 mediates the regulatory role of the Tmk1 MAP kinase in mycoparasitism and vegetative hyphal fusion in Trichoderma atroviride. BIOspektrum, 20, 99.

Zeilinger, S., Gruber, S. G., Escobar Rodriguez, C., Labaj, P., & Kreil, D. (2014). Dissecting the role of the 7-transmembrane receptor Gpr1 in the biocontrol fungus Trichoderma atroviride using a transcriptomics approach. 5#^{th} World Congress on Biotechnology, Valencia, Spain.

Zeilinger, S., Gruber, S. G., Escobar Rodriguez, C., Labaj, P., & Kreil, D. (2014). Dissecting the role of the 7-transmembrane receptor Gpr1 in the biocontrol fungus Trichoderma atroviride using a transcriptomics approach. Journal of Biotechnology & Biomaterials, 3(5), 249.

Zeilinger, S., Nemes, A., Labaj, P., Marchetti-Deschmann, M., Kreil, D., & Gruber, S. G. (2014). How MAP kinase signaling regulates the transcriptomic and proteomic response of the biocontrol fungus Trichoderma atroviride. 5#^{th} World Congress on Biotechnology, Valencia, Spain.

Zeilinger, S., Nemes, A., Labaj, P., Marchetti-Deschmann, M., Kreil, D., & Gruber, S. G. (2014). How MAP kinase signaling regulates the transcriptomic and proteomic response of the biocontrol fungus Trichoderma atroviride. Journal of Biotechnology & Biomaterials, 3(5), 107–107.

Zeilinger-Migsich, S., & Mukherjee, P. K. (2014). Fungus-Fungus Interactions. The Open Mycology Journal, 8(1), 27–27. https://doi.org/10.2174/1874437001408010027

Reischer, G., Ebdon, J. E., Bauer, J. M., Schuster, N., Ahmed, W., Aström, J., Blanch, A. R., Blöschl, G., Byamukama, D., Coakley, T., Ferguson, C., Goshu, G., Ko, G., de Roda Husman, A. M., Mushi, D., Poma, R., Pradhan, B., Rajal, V., Schade, M. A., … Farnleitner, A. (2013). Performance Characteristics of qPCR Assays Targeting Human- and Ruminant-Associated Bacteroidetes for Microbial Source Tracking across Sixteen Countries on Six Continents. Environmental Science and Technology, 47(15), 8548–8556. https://doi.org/10.1021/es304367t

Frischmann, A., Neudl, S., Gaderer, R., Bonazza, K., Zach, S., Gruber, S. G., Spadiut, O., Friedbacher, G., Grothe, H., & Seidl-Seiboth, V. (2013). Self-assembly at Air/Water Interfaces and Carbohydrate Binding Properties of the Small Secreted Protein EPL1 from the fungus Trichoderma atroviride. Journal of Biological Chemistry, 288(6), 4278–4287. https://doi.org/10.1074/jbc.m112.427633

Karimi Aghcheh, R., Bok, J. W., Phatale, P., Smith, K. M., Baker, S. E., Lichius, A., Omann, M., Zeilinger, S., Seiboth, B., Rhee, C., Keller, N. P., Freitag, M., & Kubicek, C. P. (2013). Functional Analyses of Trichoderma reesei LAE1 Reveal Conserved and Contrasting Roles of This Regulator. G3: Genes | Genomes | Genetics, 3(2), 369–378. https://doi.org/10.1534/g3.112.005140

Atanasova, L., Crom, S. L., Gruber, S., Coulpier, F., Seidl-Seiboth, V., Kubicek, C. P., & Druzhinina, I. S. (2013). Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism. BMC Genomics, 14(121). https://doi.org/10.1186/1471-2164-14-121

Bischof, R. (2013). Systems analysis of cellulase expression in Trichoderma reesei. Bio-Alternatives 2013, Graz, Austria.

Bischof, R., Fourtis, L., Gamauf, C., Seiboth, B., & Kubicek, C. P. (2013). Differences of the lactose and lignocelluloses induced transcriptome of T. reesei. In PYFF5 Symposium Book (p. 27).

Bischof, R., Fourtis, L., Limbeck, A., Gamauf, C., Seiboth, B., & Kubicek, C. P. (2013). Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose. Biotechnology for Biofuels, 6(127). https://doi.org/10.1186/1754-6834-6-127

Blumhoff, M. L., Steiger, M. G., Mattanovich, D., & Sauer, M. (2013). Targeting enzymes to the right compartment: Metabolic engineering for itaconic acid production by Aspergillus niger. Metabolic Engineering, 19, 26–32. https://doi.org/10.1016/j.ymben.2013.05.003

Blumhoff, M., Steiger, M. G., Marx, H., Mattanovich, D., & Sauer, M. (2013). Six novel constitutive promoters for metabolic engineering of Aspergillus niger. Applied Microbiology and Biotechnology, 97(1), 259–267. https://doi.org/10.1007/s00253-012-4207-9

Brunner, K. (2013). Magnetic Attraction - Aptamers as a New Alternative to Antibodies. Labor & More, 9(2), 20–23.

Brunner, K. (2013). Magnetisierende Wirkung - Aptamere als neue Alternative zu Antikörpern. Labor & More, 9(3), 50–54.

Brunner, K., Zahradnik, C., Krska, R., & Mach, R. L. (2013). Isothermale DNA Amplifikation zum Nachweis von Allergenen und gentechnisch veränderten Pflanzen in Lebensmitteln. ANAKON 2013, Essen, Germany.

Brunner, K., Zahradnik, C., Martzy, R., Krska, R., & Mach, R. L. (2013). Detection of Celery by Isothermal Amplification of DNA. In Book of Abstracts (p. 170).

Crutcher, F. K., Parich, A., Schuhmacher, R., Mukherjee, P. K., Zeilinger, S., & Kenerley, C. M. (2013). A putative terpene cyclase, vir4, is responsible for the biosynthesis of volatile terpene compounds in the biocontrol fungus Trichoderma virens. Fungal Genetics and Biology, 56, 67–77. https://doi.org/10.1016/j.fgb.2013.05.003

Dashtban, M., Kepka, G., Seiboth, B., & Qin, W. (2013). Xylitol production by genetically engineered Trichoderma reesei strains using barley straw as feedstock. Applied Biochemistry and Biotechnology, 169(2), 554–569. https://doi.org/10.1007/s12010-012-0008-y

Derntl, C., Gudynaite-Savitch, L., Calixte, S., White, T., Mach, R. L., & Mach-Aigner, A. R. (2013). Mutation of the Xylanase regulator 1 causes a glucose blind hydrolase expressing phenotype in industrially used Trichoderma strains. Biotechnology for Biofuels, 6(62). https://doi.org/10.1186/1754-6834-6-62

Derntl, C., Gudynaite-Savitch, L., Calixte, S., White, T., Mach-Aigner, A. R., & Mach, R. L. (2013). A point mutation in Xyr1 causes a glucose-blind, inducer independent enzyme production phenotype in Trichoderma reesei. In XI International Fungal Biology Conference (p. 235).

Farnleitner, A. H., Reischer, G., Kirschner, A. K. T., Blaschke, A. P., Stadler, H., Mach, R. L., & Sommer, R. (2013). Untersuchung und Bewertung der mikrobiologischen Qualität von Wasserressourcen: von der Hazard-Detektion zur Risikoabschätzung. Mikrobiologische Qualität von Trinkwasser - neue Herausforderungen, Wien, Austria.

Farnleitner, A. H., Reischer, G., Sommer, R., Mach, R. L., Kirschner, A. K. T., Vierheilig, J., Stadler, H., & Zerobin, W. (2013). Microbial Water Quality Management at All Time Scales: From Faecal Source Tracking to Near Real-Time Water Abstraction at Karstic Groundwater Resources. In Abstracts - 17#^{th} International Symposium on Health-Related Water Microbiology (p. 3).

Farnleitner, A. H., Reischer, G., Sommer, R., Mach, R. L., Ryzinska-Paier, G., Kirschner, A. K. T., Stadler, H., & Zerobin, W. (2013). Microbiological Quality Management of Drinking Water Resources at all Time Scales: from Molecular Microbial Source Tracking to Near-Real-Time Water Abstraction Management. In Delegate Program Booklet. 2#^{nd} Water Research Conference (IWA), Singapore, Singapore.

Gaderer, R., & Seidl-Seiboth, V. (2013). Biochemical characterization of fungal chitinases. In Abstract Book (p. 78).

Gasser, B., Prielhofer, R., Marx, H., Maurer, M., Nocon, J., Steiger, M., Puxbaum, V., Sauer, M., & Mattanovich, D. (2013). Pichia pastoris: protein production host and model organism for biomedical research. Future Microbiology, 8(2), 191–208. https://doi.org/10.2217/fmb.12.133

Gonzalez Garcia, E., Mach, R. L., Krska, R., & Brunner, K. (2013). A Rapid DNA Extraction Method Suitable For On-Site Application. In Book of Abstracts (p. 283).

Gorsche, R., Jovanovic, B., Gudynaite-Savitch, L., Mach, R. L., & Mach-Aigner, A. R. (2013). A highly sensitive in vivo footprinting technique for condition-dependent identifcation of cis elements. Nucleic Acids Research, 42(1), e1–e1. https://doi.org/10.1093/nar/gkt883

Gorsche, R., Mach-Aigner, A. R., & Mach, R. L. (2013). Trichoderma as Cell Factories. In Trichoderma Biology and Applications (pp. 280–291). CABI.

Gruber, S. G., Escobar Rodriguez, C., Labaj, P., Kreil, D., & Zeilinger, S. (2013). The Gpr1 7-transmembrane receptor from the mycoparasite Trichoderma atroviride, its targets and interactors. In XI International Fungal Biology Conference (p. 105).

Gruber, S., Omann, M., & Zeilinger, S. (2013). Comparative analysis of the repertoire of G protein-coupled receptors of three species of the fungal genus Trichoderma. BMC Microbiology, 13(108). https://doi.org/10.1186/1471-2180-13-108

Guerrasio, R., Haberhauer-Troyer, C., Steiger, M., Sauer, M., Mattanovich, D., Koellensperger, G., & Hann, S. (2013). Measurement uncertainty of isotopologue fractions in fluxomics determined via mass spectrometry. Analytical and Bioanalytical Chemistry, 405(15), 5133–5146. https://doi.org/10.1007/s00216-013-6910-5

Herold, S., Bischof, R., Metz, B., Seiboth, B., & Kubicek, C. P. (2013). Prepared for the possible: xylanase gene transcription in Trichoderma reesei is triggered by different inducers representing different hemicellulosic pentose polymers. Eukaryotic Cell, 12(3), 390–398.

Ivanova, C., Baath, J. A., Seiboth, B., & Kubicek, C. P. (2013). Identification of a lactose permease of Trichoderma reesei that is required for cellulase gene expression. In 27#^{th} Fungal Genetics Conference (p. 136).

Ivanova, C., Bååth, J. A., Seiboth, B., & Kubicek, C. P. (2013). Systems analysis of lactose metabolism in Trichoderma reesei identifies a lactose permease that is essential for cellulase induction. PLoS ONE, 8(5), e62631. https://doi.org/10.1371/journal.pone.0062631

Jovanović, B., Mach, R. L., & Mach-Aigner, A. R. (2013). Characterization of erythrose reductases from filamentous fungi. AMB Express, 3(43). https://doi.org/10.1186/2191-0855-3-43

Karaffa, L., Coulier, L., Fekete, E., Overkamp, K. M., Druzhinina, I. S., Mikus, M., Seiboth, B., Novák, L., Punt, P. J., & Kubicek, C. P. (2013). The intracellular galactoglycome in Trichoderma reesei during growth on lactose. Applied Microbiology and Biotechnology, 97(12), 5447–5456. https://doi.org/10.1007/s00253-012-4667-y

Karaffa, L., Coulier, L., Fekete, E., Overkamp, K. M., Druzhinina, I., Mikus, M., Seiboth, B., Novak, L., Punt, P. J., & Kubicek, C. P. (2013). Analysis of the intracellular galactoglycom of Trichoderma reesei grown on lactose. In 27#^{th} Fungal Genetics Conference (p. 78).

Karaffa, L., Fekete, E., Novak, L., Punt, P. J., Seiboth, B., & Kubicek, C. P. (2013). Mechanisms of the induction of cellulase genes in Trichoderma reesei grown on lactose: A Metabolomics Approach. 4#^{th} Central European Forum for Microbiology, Keszthely, Hungary.

Karaffa, L., Fekete, E., Novak, L., Punt, P. J., Seiboth, B., & Kubicek, C. P. (2013). Mechanisms of the induction of cellulase genes in Trichoderma reesei grown on lactose: A Metabolomics Approach. Acta Microbiologica et Immunologica Hungarica, 60(Supplement), 156–157.

Kluger, B., Zeilinger, S., Wiesenberger, G., Schöfbeck, D., & Schuhmacher, R. (2013). Detection and Identification of Fungal Microbial Volatile Organic Compounds by HS-SPME-GC–MS. In V. K. Gupta, M. G. Tuohy, M. Ayychamy, K. M. Turner, & A. Donovan (Eds.), Laboratory Protocols in Fungal Biology (pp. 455–465). Springer Science + Business Media. https://doi.org/10.1007/978-1-4614-2356-0_42

Kulcsar, L., Kun, R. S., Fekete, E., Vasasne Jonas, A., Seiboth, B., & Karaffa, L. (2013). Isolation, overexpression and purification of the major intracellular beta-galactosidase (BGAD) from Penicillium chrysogenum. 4#^{th} Central European Forum for Microbiology, Keszthely, Hungary.

Kulcsar, L., Kun, R. S., Fekete, E., Vasasne Jonas, A., Seiboth, B., & Karaffa, L. (2013). Isolation, overexpression and purification of the major intracellular beta-galactosidase (BGAD) from Penicillium chrysogenum. Acta Microbiologica et Immunologica Hungarica, 60(Supplement), 170–171.

Lang, M., Wolf, B., Honecker, A., Balents, L., Tutsch, U., Cong, T., Hofmann, G., Krüger, N., Ritter, F., Assmus, W., & Prokofiev, A. (2013). Field-induced quantum criticality - application to magnetic cooling. PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS, 250(3), 457–463.

Lang, M., Wolf, B., Honecker, A., Tsui, Y., Jaiswal-Nagar, D., Tutsch, U., Hofmann, G., Prokofiev, A., Cong, P. T., Krüger, N., Ritter, F., & Assmus, W. (2013). Magnetic cooling through quantum criticality. Journal of Physics: Conference Series, 400(3), 032043. https://doi.org/10.1088/1742-6596/400/3/032043

Lichius, A., Kubicek, C. P., & Seidl-Seiboth, V. (2013). Transcription factor shuttling during cellulase induction in Trichoderma reesei. In 27#^{th} Fungal Genetics Conference (p. 63).

Lichius, A., Seidl-Seiboth, V., Seiboth, B., & Kubicek, C. P. (2013). Nucleo-cytoplasmic shuttling dynamics of the transcriptional regulators XYR1 and CRE1 under conditions of cellulase and xylanase gene expression in Trichoderma reesei. 4#^{th} Central European Forum for Microbiology, Keszthely, Hungary.

Lichius, A., Seidl-Seiboth, V., Seiboth, B., & Kubicek, C. P. (2013). Nucleo-cytoplasmic shuttling dynamics of the transcriptional regulators XYR1 and CRE1 under conditions of cellulase and xylanase gene expression in Trichoderma reesei. Acta Microbiologica et Immunologica Hungarica, 60(Supplement), 179.

Mello de Sousa, T. M., Rassinger, A., Mach, R. L., & Mach-Aigner, A. R. (2013). Chromatin rearrangement analysis of Xyr1 regulon genes in Trichoderma reesei. In XI International Fungal Biology Conference (p. 237).

Metz, B., Mojzita, D., Herold, S., Kubicek, C. P., Richard, P., & Seiboth, B. (2013). A novel L-xylulose reductase essential for L-arabinose catabolism in Trichoderma reesei. ADVANCES IN CARBOHYDRATE CHEMISTRY AND BIOCHEMISTRY, 52(14), 2453–2460. https://doi.org/10.1021/bi301583u

Nemes, A., Bruckner, B., Allmaier, G., Kreil, D., Zeilinger-Migsich, S., & Marchetti-Deschmann, M. (2013). Identification of Regulators of Mycoparasitism of the Fungus Trichoderma atroviride. In 11th Austrian Proteomic Research Symposium (p. 43).

Nemes, A., Bruckner, B., Gruber, S. G., Allmaier, G., Zeilinger-Migsich, S., & Marchetti-Deschmann, M. (2013). Identification of Regulators of Mycoparasitism of the Fungus Trichoderma atroviride by Phosphoproteomics. In Book of Abstract (p. 41).

Nemes, A., Gruber, S. G., Labaj, P., Marchetti-Deschmann, M., Kreil, D., & Zeilinger, S. (2013). A transcriptomic and proteomic approach to dissect MAP kinase signaling in the mycoparasitic fungus Trichoderma atroviride. In XI International Fungal Biology Conference (p. 31).

Nemes, A., Gruber, S. G., Marchetti-Deschmann, M., & Zeilinger, S. (2013). MAPK signaling and mycoparasitism: transcriptomic and proteomic approaches to dissect the mycoparasitic interaction of the biocontrol fungus Trichoderma with phytopathogenic host fungi. In BIOspektrum - Tagungsband zur Jahrestagung fer VAAM 2013 (p. 88). Springer Spektrum.

Nemes, A., Kreil, D., Allmaier, G., Zeilinger-Migsich, S., & Marchetti-Deschmann, M. (2013). TRICHODERMA ATROVIRIDE - A Proteomic And Genomic Approach To Identify Regulators Of Mycoparasitism In A Biocontrol Fungus. In EUPA 2013 Scientific Meeting (pp. 335–336).

Nemes, A., Marchetti-Deschmann, M., & Zeilinger, S. (2013). Identification of Regulators of Mycoparasitism in the Biocontrol Fungus Trichoderma atroviride by Phosphoproteomics and Reverse Genetics (Endbericht).

Portnoy, T., Bidard-Michelot, F., Seiboth, B., Blanquet, S., Monot, F., Baker, S. E., Kubicek, C. P., Le Crom, S., & Margeot, A. (2013). A genome-wide approach to understand the roots of cellulase hypersecretion in the filamentous fungus Trichoderma reesei. In 34#^{th} SBFC (p. 76).

Preiser, V., Mach, R. L., Krska, R., & Brunner, K. (2013). Development of Aptamers For a Rapid Detection of Aflatoxin in Maize. In Book of Abstracts (p. 353).

Reischer, G., Schuster, N., Ley, R. E., & Farnleitner, A. H. (2013). Towards a Unified System for the Molecular Faecal Indication and Source Tracking. In Abstracts - 17#^{th} International Symposium on Health-Related Water Microbiology (p. 3).

Reischer, G., Schuster, N., Vierheilig, J., Ley, R. E., & Farnleitner, A. H. (2013). The Co-Evolution of Host and Intestinal Microbiota? - Towards a Unified System for Molecular Faecal Indication and Source Tracking. Second International IWA Conference on Water Research, Singapore.

Ryzinska-Paier, G., Lendenfeld, T., Correa, K., Stadler, H., Blaschke, A. P., Mach, R. L., & Farnleitner, A. H. (2013). Field testing of a novel concept for automated on-line monitoring of β-D-glucuronidase activity in water resources. In Abstracts - 17#^{th} International Symposium on Health-Related Water Microbiology (p. 2).

Savio, D., Reischer, G., Stadler, H., Vierheilig, J., Wilhartitz, I., & Farnleitner, A. H. (2013). Elucidating the prokaryotic population structure/dynamics in water resources for water quality monitoring-perspectives by high-throughput sequencing. 3rd Meeting Fresh Blood for Fresh Water - Young Aquatic Science, Lunz am See, Austria.

Seiboth, B. (2013). Strategies to improve (hemi) cellulolytic enzyme production in Trichoderma reesei. Documentos 15 - Anais Do Simpósio Microrganismos Em Agroenergia: Da Prospecção Aos Bioprocessos, #?, 88–93.

Seiboth, B. (2013). Systems Analysis of Cellulase Production in Trichoderma reesei. In Second Generation Bioethanol 2013 - Enzymatic Hydrolysis (p. 14).

Seiboth, B. (2013). Systems biology approaches to understand cellulase production in Trichoderma reesei. In Abstract Book (p. 172).

Seiboth, B., Ivanova, C., Baath, J. A., & Kubicek, C. P. (2013). Systems analysis of lactose metabolism in Trichoderma reesei. Acta Microbiologica et Immunologica Hungarica, 60(Supplement), 78–79.

Steiger, M. G. (2013). Molecular tools in Trichoderma genetic studies. In P. Mukherjee, B. A. Horwitz, U. S. Singh, M. Mukherjee, & M. Schmoll (Eds.), Trichoderma: biology and applications (pp. 128–143). CABI. https://doi.org/10.1079/9781780642475.0128

Steiger, M. G., Blumhoff, M. L., Mattanovich, D., & Sauer, M. (2013). Biochemistry of microbial itaconic acid production. Frontiers in Microbiology, 4. https://doi.org/10.3389/fmicb.2013.00023

Stoppacher, N., Neumann, N. K., Burgstaller, L., Zeilinger, S., Degenkolb, T., Brückner, H., & Schuhmacher, R. (2013). The Comprehensive Peptaibiotics Database. Chemistry and Biodiversity, 10, 734–743.

Vierheilig, J., Frick, C., Mayer, R., Kirschner, A., Reischer, G., Derx, J., Mach, R. L., Sommer, R., & Farnleitner, A. H. (2013). Clostridium perfringens Is Not Suitable for the Indication of Fecal Pollution from Ruminant Wildlife but Is Associated with Excreta from Nonherbivorous Animals and Human Sewage. Applied and Environmental Microbiology, 79(16), 5089–5092.

Vierheilig, J., Reischer, G., Sommer, R., Frick, C., Blaschke, A. P., Derx, J., Mach, R. L., & Farnleitner, A. H. (2013). Elucidating the genetic population structures of fecal bacteria in intestinal and non-intestinal habitats within a complex backwater system of a large river. In Abstracts - 17#^{th} International Symposium on Health-Related Water Microbiology (p. 3).

Wilhartitz, I., Kirschner, A. K. T., Brussaard, C. P. D., Fischer, U. R., Wieltschnig, C., Stadler, H., & Farnleitner, A. H. (2013). Dynamics of natural prokaryotes, viruses, and heterotrophic nanoflagellates in alpine karstic groundwater. MicrobiologyOpen, 2(4), 633–643.

Zeilinger, S., & Schuhmacher, R. (2013). Volatile Organic Metabolites of Trichoderma spp. : Biosynthesis, Biology and Analytics. In P. Mukherjee, B. A. Horwitz, U. S. Singh, M. Mukherjee, & M. Schmoll (Eds.), Trichoderma Biology and Applications (pp. 110–127). CABI.

Zeilinger, S., Kreil, D., & Marchetti-Deschmann, M. (2013). BIOGEN: From genes to biocontrol (Endbericht).

Zeilinger-Migsich, S., Marchetti-Deschmann, M., & Kreil, D. (2013). BIOGEN: From genes to biocontrol.

Gruber, S., Omann, M., Rodrìguez, C. E., Radebner, T., & Zeilinger, S. (2012). Generation of Trichoderma atroviride mutants with constitutively activated G protein signaling by using geneticin resistance as selection marker. BMC Research Notes, 5(641). https://doi.org/10.1186/1756-0500-5-641

Atanasova, L., Le Crom, S., Gruber, S. G., Coulpier, F., Seidl-Seiboth, V., Druzhinina, I., & Kubicek, C. P. (2012). Functional diversity of Trichoderma mycoparasitism. In Meeting Abstracts (p. 129).

Bischof, R., Kubicek, C. P., & Seiboth, B. (2012). New technologies for strain engineering in Trichoderma reesei (1st interim report 2012).

Bischof, R., Kubicek, C. P., & Seiboth, B. (2012). New technologies for strain engineering in Trichoderma reesei (2nd interim report 2012).

Bischof, R., Kubicek, C. P., & Seiboth, B. (2012). New technologies for strain engineering in Trichoderma reesei (3rd interim report 2012).

Bischof, R., Kubicek, C. P., & Seiboth, B. (2012). New technologies for strain engineering in Trichoderma reesei (th interim report 2012).

Bruckner, B., Gaderer, R., Nemes, A., Allmaier, G., Zeilinger, S., & Marchetti-Deschmann, M. (2012). Identification of phosphoproteins expressed during mycoparasitism: evaluation of sample preparatio methods for MALDI-RTOF-MS analysis of phosphopeptides. 10th Austrian Proteomic Research Symposium, Graz, Austria.

Brunner, K., Farnleitner, A. H., & Mach, R. L. (2012). Novel Methods for the Quantification of Pathogenic Fungi in Crop Plants : Quantitative PCR and ELISA Accurately Determine Fusarium Biomass. In Plant Pathology (pp. 203–218). In Tech Rijeka, Croatia.

Brunner, K., Preiser, V., Götsch, D., Krska, R., & Mach, R. L. (2012). A real-time triplex assay for the accurate quantification of trichothecene and fumonisin producing Fusarium species in maize. 7#^{th} Conference of the World Mycotoxin Forum, Rotterdam, Netherlands (the).

Derntl, C., Mach-Aigner, A. R., & Mach, R. L. (2012). Regulation of (Hemi-) Cellulases in Trichoderma reesei. In Topcial Issues of Rational Use of Natural Resources Vol. II (pp. 116–117).

Derntl, C., Steiger, M., Gorsche, R., Mach-Aigner, A. R., & Mach, R. L. (2012). A novel utilisation of the biopolymer chitin : Generation of a pharmaceutically relevant fine chemical by a whole-cell catalyst approach in Trichoderma. In TG 2012 Programme and Abstracts (p. 39).

Escobar Rodriguez, C., Omann, M., & Zeilinger, S. (2012). Identification of novel interactors of the Trichoderma atroviride Gpr1 7-transmembrane receptor. In Meeting Abstracts (p. 202).

Farnleitner, A. H., Stadler, H., Vierheilig, J., Sommer, R., Mach, R. L., Kirschner, A. K. T., & Reischer, G. (2012). Integrating molecular source tracking into target-oriented microbial water quality management and catchment protection. 33. Jahrestagung der Österreichischen Gesellschaft für Hygiene, Mikrobiologie und Präventivmedizin, Salzburg, Austria.

Fekete, E., De Vries, R., Seiboth, B., vanKuyk, P., Sandor, E., Fekete, E., Metz, B., Kubicek, C. P., & Karaffa, L. (2012). D-Galactose uptake is nonfunctional in the conidiospores of Aspergillus niger. FEMS Microbiology Letters, 329(2), 198–203. https://doi.org/10.1111/j.1574-6968.2012.02524.x

Fekete, E., Karaffa, L., Seiboth, B., Fekete, E., Kubicek, C. P., & Flipphi, M. (2012). Identification of a permease gene involved in lactose utilisation in Aspergillus nidulans. Fungal Genetics and Biology, 49(6), 415–425. https://doi.org/10.1016/j.fgb.2012.03.001

Fekete, E., Kubicek, C. P., De Vries, R., Seiboth, B., Sandor, E., vanKuyk, P., & Karaffa, L. (2012). D-galactose uptake of Aspergillus niger. In Meeting Abstracts (p. 256).

Frischmann, A., Neudl, S., Zach, S., & Seidl-Seiboth, V. (2012). Surface-activity and carbohydrate-binding properties of the small secreted protein EPL1 from the fungus Trichoderma atroviride. In Abstract Book 2012 (p. 96).

Frischmann, A., Zach, S., Gruber, S. G., Spadiut, O., Rodler, A., & Seidl-Seiboth, V. (2012). Self-assembly at air/water interfaces and chitin-binding properties of the small cell wall protein EPL1 from Trichoderma atroviride. In Meeting Abstracts. ECFG 11 - 11#^{th} European Conference on Fungal Genetics, Marburg, Germany.

Gaderer, R., Zach, S., Frischmann, A., & Seidl-Seiboth, V. (2012). Functional analysis of cerato-platanin genes in the biocontrol fungus Trichoderma atroviride. In Abstract Book 2012 (p. 96).

Ghassemi, S., Lichius, A., Kubicek, C. P., & Seidl-Seiboth, V. (2012). Nuclear transport and cellulase production in Trichoderma reesei. In Abstract Book 2012 (p. 100).

Gorsche, R., Derntl, C., Mach, R. L., & Mach-Aigner, A. R. (2012). Improving in vivo Footprinting - finding a more sensitive way to detect Protein-DNA Interactions. In TG 2012 Programme and Abstracts (p. 81).

Gorsche, R., Mach, R. L., & Mach-Aigner, A. R. (2012). High Throughput in vivo Footprinting - an improved Method to detect Protein-DNA Interactions. In Meeting Abstracts (p. 109).

Gorsche, R., Mello de Sousa, T. M., Derntl, C., Mach, R. L., & Mach-Aigner, A. R. (2012). Partner search and relationship: how to find regulatory elements and proteins and to monitor their interaction. In www.furb.br (p. 1).

Gruber, S., & Seidl-Seiboth, V. (2012). Self versus non-self : fungal cell wall degradation in Trichoderma. MICROBIOLOGY-SGM, 158(1), 26–34. https://doi.org/10.1099/mic.0.052613-0

Hartl, L., Zach, S., & Seidl-Seiboth, V. (2012). Fungal chitinases : diversity, mechanistic properties and biotechnological potential. Applied Microbiology and Biotechnology, 93(2), 533–543. https://doi.org/10.1007/s00253-011-3723-3

Herold, S., Seiboth, B., & Kubicek, C. P. (2012). Regulation of xylanase expression in the biomass degrading fungus Trichoderma reesei. In Topcial Issues of Rational Use of Natural Resources Vol. II (p. 123).

Ivanova, C. (2012). Molecular strain breeding towards improved biomass hydrolysis in Trichoderma reesei. In Topcial Issues of Rational Use of Natural Resources Vol. II (pp. 123–124).

Ivanova, C., Baath, J. A., Seiboth, B., & Kubicek, C. P. (2012). Lactose induces all genes related to plant biomass hydrolysis and corresponding mono- and oligosaccharide transporters in Trichoderma reesei. In Meeting Abstracts (p. 62).

Karimi Aghcheh, R., Phatale, P., Smith, K. M., Baker, S. E., Bok, J. W., Seiboth, B., Keller, N. P., Freitag, M., & Kubicek, C. P. (2012). Genome wide insights into the targets and mechanism of function of LAE1 in Trichoderma reesei. In Meeting Abstracts (p. 93).

Klaubauf, S., Narang, H. M., Battaglia, E., Kobayashi, T., Brunner, K., Mach-Aigner, A. R., Mach, R. L., & De Vries, R. (2012). Similar Is Not The Same : Differences In The Function Of The (Hemi -) Cellulolytic Regulator XlnR (Xlr1/Xyr1) In Filamentous Fungi. In Meeting Abstracts (p. 122).

Lichius, A., Kubicek, C. P., & Seidl-Seiboth, V. (2012). Monitoring nucleo-cytoplasmic shuttling of CRE1 and XYR1 during cellulase induction in Trichoderma reesei. In Abstract Book 2012 (p. 97).

Linke, R., Kubicek, C. P., & Seiboth, B. (2012). 3.6.2. Project Report, 1st interim report 2012.

Linke, R., Kubicek, C. P., & Seiboth, B. (2012). 3.6.2. Project Report, 2nd interim report 2012.

Linke, R., Kubicek, C. P., & Seiboth, B. (2012). 3.6.2. Project Report, 3rd interim report 2012.

Linke, R., Kubicek, C. P., & Seiboth, B. (2012). 3.6.2. Project Report, 4th interim report 2012.

Mach-Aigner, A. R. (2012). Burnout in der Biotechnologie: Stammdegeneration mit epigenetischen Ursachen? Workshop Kulturelle Faktoren der Vererbung III: Verfahren, Berlin, Germany.

Mach-Aigner, A. R., Omony, J., Jovanovic, B., van Boxtel, A. J. B., & De Graaff, L. (2012). D-Xylose Concentration-Dependent Hydrolase Expression Profiles and the Function of CreA and XlnR in Aspergillus niger. Applied and Environmental Microbiology, 78(9), 3145–3155.

Mach-Aigner, A. R., Omony, J., Jovanovic, B., van Boxtel, A. J. B., & De Graaff, L. (2012). D-Xylose Concentration-dependent Hydrolase Expression Profiles and the According Role of CreA and XlnR in Aspergillus niger. In Meeting Abstracts (p. 224).

Matarese, F., Sarrocco, S., Gruber, S., Seidl-Seiboth, V., & Vannacci, G. (2012). Biocontrol of Fusarium head blight : interactions between Trichoderma and mycotoxigenic Fusarium. MICROBIOLOGY-SGM, 158(1), 98–106. https://doi.org/10.1099/mic.0.052639-0

Mello de Sousa, T. M., Gorsche, R., Derntl, C., Mach-Aigner, A. R., & Mach, R. L. (2012). Complex, multilevel mechanisms regulate expression of hydrolase encoding genes in Trichoderma. In www.furb.br (p. 1).

Mello de Sousa, T. M., Paes, B. G., Mach-Aigner, A. R., Mach, R. L., & Pocas-Fonseca, M. (2012). DNA methylation influence on glycoside hydrolase genes expression in Humicola grisea var. thermoidea. IV Encontro Nacional de Epigenética, Sao Paulo, Brazil.

Mojzita, D., Herold, S., Metz, B., Seiboth, B., & Richard, P. (2012). L-xylo-3-Hexulose Reductase Is the Missing Link in the Oxidoreductive Pathway for D-Galactose Catabolism in Filamentous Fungi. Journal of Biological Chemistry, 287(31), 26010–26018. https://doi.org/10.1074/jbc.m112.372755

Mukherjee, M., Mukherjee, P. K., Horwitz, B. A., Zachow, C., Berg, G., & Zeilinger, S. (2012). Trichoderma-Plant-Pathogen Interactions: Advances in Genetics of Biological Control. Indian Journal of Microbiology, 52(4), 522–529. https://doi.org/10.1007/s12088-012-0308-5

Mushi, D., Byamukama, D., Kirschner, A. K. T., Mach, R. L., Brunner, K., & Farnleitner, A. H. (2012). Sanitary inspection of wells using risk-of-contamination scoring indicates a high predictive ability for bacterial faecal pollution in the peri-urban tropical lowlands of Dar es Salaam,Tanzania. Journal of Water & Health, 10(2), 236–243. https://doi.org/10.2166/wh.2012.117

Nemes, A., Bruckner, B., Rehulka, P., Zeilinger, S., Allmaier, G., & Marchetti-Deschmann, M. (2012). Trichoderma atroviridiae identifying regulators of mycoparasitism in a biocontrol fungus. In 6th Central and Eastern European Proteomic Conference - Book of Abstracts (p. 58).

Neubauer, S., Haberhauer-Troyer, C., Klavins, K., Rußmayer, H., Steiger, M., Gasser, B., Sauer, M., Mattanovich, D., Hann, S., & Köllensperger, G. (2012). U¹³C cell extract of Pichia pastoris - a powerful tool for evaluation of sample preparation in metabolomics. Journal of Separation Science, 35(22), 3091–3105.

Omann, M. R., Lehner, S., Escobar Rodríguez, C., Brunner, K., & Zeilinger, S. (2012). The seven-transmembrane receptor Gpr1 governs processes relevant for the antagonistic interaction of Trichoderma atroviride with its host. Microbiology, 158(1), 107–118. https://doi.org/10.1099/mic.0.052035-0

Omony, J., Mach-Aigner, A. R., Jovanovic, B., van Straten, G., van Boxtel, A. J. B., & De Graaff, L. (2012). Modeling the XlnR regulon of Aspergillus niger. In Meeting Abstracts (p. 61).

Omony, J., Mach-Aigner, A. R., de Graaff, L. H., van Straten, G., & van Boxtel, A. J. B. (2012). Evaluation of Design Strategies for Time Course Experiments in Genetic Networks : Case Study of the XlnR Regulon in Aspergillus niger. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5), 1316–1325. https://doi.org/10.1109/tcbb.2012.59

Portnoy, T., Bidard-Michelot, F., Seiboth, B., Monot, F., Baker, S. E., Kubicek, C. P., Le Crom, S., & Margeot, A. (2012). Transcriptomic and Genomic Approaches to Understand Cellulase Hyper-production in the Filamentous Fungus Trichoderma reesei. In Meeting Abstracts (p. 242).

Reischer, G., Schuster, N., Vierheilig, J., & Farnleitner, A. H. (2012). Potential of Next Generation Sequencing (NGS) Methods for Water Quality Monitoring. 33. Jahrestagung der Österreichischen Gesellschaft für Hygiene, Mikrobiologie und Präventivmedizin, Salzburg, Austria.

Reithner, B., & Mach, R. L. (2012). Trichoderma atroviride xylanase regulator 1 (Xyr1) and its role in mycoparasitism. In TG 2012 Programme and Abstracts (p. 23).

Schuster, A., Bruno, K. S., Collett, J. R., Baker, S. E., Seiboth, B., Kubicek, C. P., & Schmoll, M. (2012). A versatile toolkit for high throughput functional genomics with Trichoderma reesei. Biotechnology for Biofuels, 5(1). https://doi.org/10.1186/1754-6834-5-1

Seiboth, B., Herold, S., & Kubicek, C. P. (2012). Metabolic Engineering of Inducer Formation for Cellulase and Hemicellulase Gene Expression in Trichoderma reesei. In X. Wang, J. Chen, & P. J. Quinn (Eds.), Subcellular Biochemistry (pp. 367–390). Springer. https://doi.org/10.1007/978-94-007-5055-5_18

Seiboth, B., Ivanova, C., Baath, J. A., & Kubicek, C. P. (2012). Systems analysis of lactose metabolism in Trichoderma reesei identifies a lactose permease that is essential for cellulase induction. In Eurofung Meeting (p. 5).

Seiboth, B., Ivanova, C., Baath, J. A., & Kubicek, C. P. (2012). Systems analysis of lactose metabolism in Trichoderma reesei. In Absztraktfüzet (p. 48).

Seiboth, B., Karimi Aghcheh, R., Phatale, P., Linke, R., Hartl, L., Sauer, D. G., Smith, K. M., Baker, S. E., Freitag, M., & Kubicek, C. P. (2012). The putative protein methyltransferase LAE1 controls cellulase gene expression in Trichoderma reesei. Molecular Microbiology, 84(6), 1150–1164.

Seidl-Seiboth, V., Zach, S., Frischmann, A., Spadiut, O., Dietzsch, C., Herwig, C., & Kubicek, C. P. (2012). Functional analysis and structural features of fungal LysM chitin-binding proteins. In Abstract Book 2012 (p. 91).

Stadler, H., Sommer, R., Kirschner, A. K. T., Reischer, G., Mach, R. L., & Farnleitner, A. H. (2012). Neue Erkenntnisse zur mikrobiologischen Qualitätsdynamik an ausgewählten Karstquellen der Nördlichen Kalkalpen mittels automatisierter und feldtauglicher Untersuchungsmethoden. Beiträge Zur Hydrogeologie, 59, 95–108.

Uzbas, F., Sezerman, U., Hartl, L., Kubicek, C. P., & Seiboth, B. (2012). A homologous production system for Trichoderma reesei secreted proteins in a cellulase-free background. Applied Microbiology and Biotechnology, 93(4), 1601–1608. https://doi.org/10.1007/s00253-011-3674-8

Vierheilig, J., Farnleitner, A. H., Kollanur, D., Blöschl, G., & Reischer, G. (2012). Lack in fecal specificity of genetic bacteroidetes assays for fecal pollution monitoring of water resources. 33. Jahrestagung der Österreichischen Gesellschaft für Hygiene, Mikrobiologie und Präventivmedizin, Salzburg, Austria.

Vierheilig, J., Farnleitner, A. H., Kollanur, D., Blöschl, G., & Reischer, G. (2012). Importance of evaluating genetic markers for faecal pollution applied in water quality management. In Topical Issues of Rational Use of Natural Resources Vol. II (pp. 146–148).

Vierheilig, J., Farnleitner, A. H., Kollanur, D., Blöschl, G., & Reischer, G. H. (2012). High abundance of genetic Bacteroidetes markers for total fecal pollution in pristine alpine soils suggests lack in specificity for feces. Journal of Microbiological Methods, 88(3), 433–435. https://doi.org/10.1016/j.mimet.2012.01.009

Zeilinger-Migsich, S. (2012). From Genes to Biocontrol: Elucidating Trichoderma atroviride mycoparasitism at the entrance to the post-genomic era (Zwischenbericht).

Zeinzinger, J., Pietzka, A. T., Stöger, A., Kornschober, C., Kunert, R., Allerberger, F., Mach, R. L., & Ruppitsch, W. (2012). One-Step Triplex High-Resolution Melting Analysis for Rapid Identification and Simultaneous Subtyping of Frequently Isolated Salmonella Serovars. Applied and Environmental Microbiology, 78(9), 3352–3360.

Alcazar-Fuoli, L., Clavaud, C., Lamarre, C., Aimanianda, V., Seidl-Seiboth, V., Mellado, E., & Latgé, J.-P. (2011). Functional analysis of the fungal/plant class chitinase family in Aspergillus fumigatus. Fungal Genetics and Biology, 48(4), 418–429. https://doi.org/10.1016/j.fgb.2010.12.007

Atanasova, L., Le Crom, S., Gruber, S. G., Coulpier, F., Seidl, V., Druzhinina, I., & Kubicek, C. P. (2011). The transcriptional profile of Trichoderma mycoparasitism. In Conference Series (p. 102).

Brunner, K. (2011). Untersuchung des Fusariumbefalls an fünf deutschen Standorten mittels quantitativer PCR. Tagung der Gruppe Züchtung, Deutsches Maiskomitee, Würzburg, Germany.

Brunner, K., Preiser, V., Kovalsky- Paris, M. P., & Mach, R. L. (2011). Quantifizierung von toxinproduzierenden Arten des pflanzenpathogenen Pilzes Fusarium in Getreide und Mais mittels duplex-real -time PCR. In Anakon 2011 - Kurzreferate (p. 270).

Catalano, V., Vergara, M., Hauzenberger, J. R., Seiboth, B., Sarrocco, S., Vannacci, G., Kubicek, C. P., & Seidl-Seiboth, V. (2011). Use of a non-homologous end-joining-deficient strain (delta-ku70) of the biocontrol fungus Trichoderma virens to investigate the function of the laccase gene lcc1 in sclerotia degradation. Current Genetics, 57(1), 13–23. https://doi.org/10.1007/s00294-010-0322-2

Druzhinina, I. S., Seidl-Seiboth, V., Herrera-Estrella, A., Horwitz, B. A., Kenerley, C. M., Monte, E., Mukherjee, P. K., Zeilinger, S., Grigoriev, I. V., & Kubicek, C. P. (2011). Trichoderma : the genomics of opportunistic success. Nature Reviews Microbiology, 9(10), 749–759. https://doi.org/10.1038/nrmicro2637

Fackler, K., Srebotnik, E., Friedl, A., Ters, T., Zikeli, F., Bischof, R., Dybov, A., Fuqaha, A. H., Weinwurm, F., & Drljo, A. (2011). Biomimetischer Lignocellulose-Aufschluss.

Farnleitner, A. H., Reischer, G. H., Stadler, H., Kollanur, D., Sommer, R., Zerobin, W., Blöschl, G., Barrella, K. M., Truesdale, J. A., Casarez, E. A., & Di Giovanni, G. D. (2011). Agricultural and Rural Watersheds. In Microbial Source Tracking: Methods, Applications, and Case Studies (pp. 399–431). Springer Science + Business Media. https://doi.org/10.1007/978-1-4419-9386-1_18

Farnleitner, A. H., Sommer, R., Mach, R. L., Kirschner, A. K. T., & Reischer, G. (2011). Molecular microbial source tracking : Was kann es derzeit leisten? DVGW Symposium Potential und Grenzen molekularbiologischer Methoden in der Wasserwirtschaft, Karlsruhe, Germany.

Farnleitner, A. H., Vierheilig, J., Sommer, R., Mach, R. L., Kirschner, A. K. T., & Reischer, G. (2011). Integrating faecal source tracking into target-oriented microbial water quality management and catchment protection. 16#^{th} International Symposium on Health-Related Water Microbiology, Rotorua, New Zealand, Non-EU.

Fekete, E., Karaffa, L., Fekete, E., Szentirmai, A., Seiboth, B., Kubicek, C. P., & Flipphi, M. (2011). Identification of a Beta-galactosidase/lactose permease gene couple and the characterisaton of lactose transport in Aspergillus nidulans. 16#^{th} International Congress of the Hungarian Society for Microbiology, Budapest, Hungary.

Fekete, E., Karaffa, L., Fekete, E., Szentirmai, A., Seiboth, B., Kubicek, C. P., & Flipphi, M. (2011). Identification of a Beta-galactosidase/lactose permease gene couple and the characterisaton of lactose transport in Aspergillus nidulans. Acta Microbiologica et Immunologica Hungarica, 58(Supplement), 142–143.

Gorsche, R., Mach-Aigner, A. R., & Mach, R. L. (2011). A High Throughput in vivo Footprinting Technique to detect Protein-DNA Interactions. In Abstract Booklet. 2011 Einsteins in the City, New York, USA, Non-EU.

Gorsche, R., Mach-Aigner, A. R., & Mach, R. L. (2011). Transcriptional regulation of cellulolytic and hemicellulolytic enzymes in Trichoderma reesei. In Proceedings Probleme der Ausnutzung von Bodenschätzen, Band II (pp. 120–121).

Gruber, S. G., Kubicek, C. P., & Seidl-Seiboth, V. (2011). Differential Regulation of Orthologous Chitinase Genes in Mycoparasitic Tricoderma Species. Applied and Environmental Microbiology, 77(20), 7217–7226.

Gruber, S. G., Kubicek, C. P., & Seidl-Seiboth, V. (2011). The multifunctional roles of chitinases in mycoparasitism and cell wall remodelling in the fungus Trichoderma. In BIOspektrum (p. 136). Spektrum.

Gruber, S., Vaaje-Kolstad, G., Matarese, F., López-Mondéjar, R., Kubicek, C. P., & Seidl-Seiboth, V. (2011). Analysis of subgroup C of fungal chitinases containing chitin-binding and LysM modules in the mycoparasite Trichoderma atroviride. Glycobiology, 21(1), 122–133. https://doi.org/10.1093/glycob/cwq142

Hartl, L., Gastebois, A., Aimanianda, V., & Latgé, J.-P. (2011). Characterization of the GPI-anchored endo β-1,3-glucanase Eng2 of Apergillus fumigatus. Fungal Genetics and Biology, 48(2), 185–191. https://doi.org/10.1016/j.fgb.2010.06.011

Herold, S., Kubicek, C. P., & Seiboth, B. (2011). Xylanase induction in Trichoderma reesei by D-xylose. In Eurofung Meeting (p. 15).

Karimi Aghcheh, R., Bok, J. W., Omann, M., Zeilinger, S., Linke, R., Seiboth, B., Baker, S. E., Keller, N. P., & Kubicek, C. P. (2011). The Trichoderma LaeA orthologue LAE1 identifies new targets of epigenetic regulation in fungi. In Fungal Genetics Report (p. 174).

Kubicek, C. P., Herrera-Estrella, A., Seidl-Seiboth, V., Martinez, D. A., Druzhinina, I., Thon, M., Zeilinger, S., Casas-Flores, S., Horwitz, B. A., Mukherjee, P. K., Mukherjee, M., Kredics, L., Alcaraz, L. D., Aerts, A., Antal, Z., Atanasova, L., Cervantes-Badillo, M. G., Challacombe, J., Chertkov, O., … Grigoriev, I. V. (2011). Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biology, 12, Article R40. https://doi.org/10.1186/gb-2011-12-4-r40

Mach-Aigner, A. R., Gudynaite-Savitch, L., & Mach, R. L. (2011). L-Arabitol Is the Actual Inducer of Xylanase Expression in Hypocrea jecorina (Trichoderma reesei). Applied and Environmental Microbiology, 77(17), 5988–5994.

Mach-Aigner, A. R., Steiger, M., & Mach, R. L. (2011). From the biopolymer chitin to a highly valuable, pharmaceutically relevant fine chemical : applying an integrated bioprocess technology approach to Trichoderma. In 19#^{th} Annual Meeting of the BioEnvironmental Polymer Society. 19#^{th} Annual Meeting of the BioEnvironmental Polymer Society (BEPS), Wien, Austria.

Metz, B., Seidl-Seiboth, V., Haarmann, T., Kopchinskiy, A., Lorenz, P., Seiboth, B., & Kubicek, C. P. (2011). Expression of Biomass-Degrading Enzymes Is a Major Event during Conidium Development in Trichoderma reesei. Eukaryotic Cell, 10(11), 1527–1535.

Nemes, A., Radebner, T., Omann, M., Rehulka, P., Allmaier, G., Zeilinger, S., & Marchetti-Deschmann, M. (2011). The biocontrol fungus Trichoderma atroviride : a first approach to target proteome changes during mycoparasitism. 9th Austrian Proteomics Research Symposium - Special focus on clinical proteomics, Wien, Austria.

Omann, M., Escobar Rodriguez, C., & Zeilinger, S. (2011). Signal Transduction in the Biocontrol Agent Trichoderma Atroviride : News and Highlights. In BIT’s 1#^{st} Annual World Congress of Microbes-2011 (p. 261).

Parich, A., Kluger, B., Zeilinger, S., Mukherjee, P., Crutcher, F., Kenerley, C., & Schuhmacher, R. (2011). Study of the volatile metabolome of different species of the filamentous fungus Trichoderma. In metabomeeting 2011 (pp. 117–118).

Portnoy, T., Margeot, A., Linke, R., Atanasova, L., Fekete, E., Sándor, E., Hartl, L., Karaffa, L., Druzhinina, I. S., Seiboth, B., Le Crom, S., & Kubicek, C. P. (2011). The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei : a master regulator of carbon assimilation. BMC Genomics, 12(269). https://doi.org/10.1186/1471-2164-12-269

Portnoy, T., Margeot, A., Seidl-Seiboth, V., Le Crom, S., Ben Chaabane, F., Linke, R., Seiboth, B., & Kubicek, C. P. (2011). Differential Regulation of the Cellulase Transcription Factors XYR1, ACE2, and ACE1 in Trichoderma reesei Strains Producing High and Low Levels of Cellulase. Eukaryotic Cell, 10(2), 262–271.

Pucher, M. E., Steiger, M. G., Mach, R. L., & Mach-Aigner, A. R. (2011). A modified expression of the major hydrolase activator in Hypocrea jecorina (Trichoderma reesei) changes enzymatic catalysis of biopolymer degradation. Catalysis Today, 167(1), 122–128. https://doi.org/10.1016/j.cattod.2010.12.038

Reischer, G. H., Kollanur, D., Vierheilig, J., Wehrspaun, C., Mach, R. L., Sommer, R., Stadler, H., & Farnleitner, A. H. (2011). Hypothesis-Driven Approach for the Identification of Fecal Pollution Sources in Water Resources. Environmental Science and Technology, 45(9), 4038–4045. https://doi.org/10.1021/es103659s

Reithner, B., Ibarra-Laclette, E., Mach, R. L., & Herrera-Estrella, A. (2011). Identification of Mycoparasitism-Related Genes in Trichoderma atroviride. Applied and Environmental Microbiology, 77(13), 4361–4370.

Richie, D. L., Feng, X., Hartl, L., Aimanianda, V., Krishnan, K., Powers-Fletcher, M. V., Watson, D. S., Galande, A. K., White, S. M., Willett, T., Latgé, J.-P., Rhodes, J. C., & Askew, D. S. (2011). The virulence of the opportunistic fungal pathogen Aspergillus fumigatus requires cooperation between the endoplasmic reticulum-associated degradation pathway (ERAD) and the unfolded protein response (UPR). Virulence, 2(1), 12–21. https://doi.org/10.4161/viru.2.1.13345

Ryzinska-Paier, G., Sommer, R., Haider, J. M., Knetsch, S., Frick, C., Kirschner, A. K. T., & Farnleitner, A. H. (2011). Acid phosphatase test proves superior to standard phenotypic identification procedure for Clostridium perfringens strains isolated from water. Journal of Microbiological Methods, 87(2), 189–194. https://doi.org/10.1016/j.mimet.2011.08.006

Schmoll, M., Tisch, D., & Schuster, A. (2011). Signal Transduction Processes Connecting Light Response to Cellulase Gene Regulation in Trichoderma reesei. In BIT’s 1#^{st} Annual World Congress of Microbes-2011 (p. 241).

Schuster, A., Kubicek, C. P., & Schmoll, M. (2011). Dehydrogenase GRD1 Represents a Novel Component of the Cellulase Regulon in Trichoderma reesei (Hypocrea jecorina). Applied and Environmental Microbiology, 77(13), 4553–4563.

Seiboth, B. (2011). New targets for genetic strain improvement in the cellulase producer Trichoderma reesei. In Acta Microbiologica et Immunologica Hungarica (p. 211).

Seiboth, B., & Metz, B. (2011). Fungal arabinan and L-arabinose metabolism. Applied Microbiology and Biotechnology, 89(6), 1665–1673. https://doi.org/10.1007/s00253-010-3071-8

Seiboth, B., Bischof, R., & Kubicek, C. P. (2011). New technologies for strain engineering in Trichoderma reesei (4th interim report).

Seiboth, B., Ivanova, C., & Seidl-Seiboth, V. (2011). Trichoderma reesei : A Fungal Enzyme Producer for Cellulosic Biofuels. In M. A. dos Santos Bernardes (Ed.), Biofuel Production-Recent Developments and Prospects (pp. 310–340). InTech.

Seiboth, B., Karimi Aghcheh, R., Linke, R., Sauer, D. G., Baker, S. E., & Kubicek, C. P. (2011). Epigenetic regulation of cellulase gene expression by Trichoderma reesei. In Abstract Book (p. 58).

Seiboth, B., Linke, R., & Kubicek, C. P. (2011). 3.6.1. Project Report, 1st interim report.

Seiboth, B., Linke, R., & Kubicek, C. P. (2011). 3.6.1. Project Report, 2nd interim report.

Seiboth, B., Linke, R., & Kubicek, C. P. (2011). 3.6.1. Project Report, 3rd interim report.

Seiboth, B., Linke, R., & Kubicek, C. P. (2011). 3.6.1. Project Report, 4th interim report.

Seiboth, B., Metz, B., & Kubicek, C. P. (2011). New technologies for strain engineering in Trichoderma reesei (1st interim report).

Seiboth, B., Metz, B., & Kubicek, C. P. (2011). New technologies for strain engineering in Trichoderma reesei (2nd interim report).

Seiboth, B., Metz, B., Bischof, R., & Kubicek, C. P. (2011). New technologies for strain engineering in Trichoderma reesei (3rd interim report).

Seidl-Seiboth, V. (2011). Self vs. non-self : Fungal cell wall degradation in Trichoderma. GRC Conference Cellulosomes, Cellulases & Other Carbohydrate Modifying Enzymes, Stonehill, MA,USA, Non-EU.

Seidl-Seiboth, V. (2011). Fungal cell wall and chitin degradation in mycoparasites. In The Second International Fungal Cell Wall Meeting (p. 87).

Seidl-Seiboth, V., & Kubicek, C. P. (2011). New avenues for fungal strain improvement towards enzymatic degradation of cellulosic biomass for biofuel production. In Highlights der Bioenergieforschung, Nationale und Internationale Ergebnisse zu den IEA Schwerpunkten (pp. 141–144).

Seidl-Seiboth, V., Gruber, S., Sezerman, U., Schwecke, T., Albayrak, A., Neuhof, T., von Döhren, H., Baker, S. E., & Kubicek, C. P. (2011). Novel Hydrophobins from Trichoderma Define a New Hydrophobin Subclass : Protein Properties, Evolution, Regulation and Processing. Journal of Molecular Evolution, 72(4), 339–351. https://doi.org/10.1007/s00239-011-9438-3

Stalder, G. L., Sommer, R., Walzer, C., Mach, R. L., Beiglböck, C., Blaschke, A. P., & Farnleitner, A. H. (2011). Gefährdungs- und risikobasierende Konzepte zur Bewertung der mikrobiologischen Wasserqualität - Teil 1. WIENER TIERARZTLICHE MONATSSCHRIFT, 98(1–2), 9–24.

Steiger, M. G., Mach-Aigner, A. R., Gorsche, R., Rosenberg, E. E., Mihovilovic, M. D., & Mach, R. L. (2011). Synthesis of an antiviral drug precursor from chitin using a saprophyte as a whole-cell catalyst. Microbial Cell Factories, 10(102). https://doi.org/10.1186/1475-2859-10-102

Steiger, M., Vitikainen, M., Uskonen, P., Brunner, K., Adam, G., Pakula, T., Penttilä, M. E., Saloheimo, M., Mach, R. L., & Mach-Aigner, A. R. (2011). Transformation System for Hypocrea jecorina (Trichoderma reesei) That Favors Homologous Integration and Employs Reusable Bidirectionally Selectable Markers. Applied and Environmental Microbiology, 77(1), 114–121.

Wilhartitz, I., Kirschner, A. K. T., Stadler, H., Sommer, R., Reischer, G., & Farnleitner, A. H. (2011). Elucidating the Microbiology of Alpine Karst Spring Aquifers. 8#^{th} International Symposium on Subsurface Microbiology (ISSM), Garmisch-Partenkirchen, Germany.

Zeilinger, S. (2011). New insights into the mycoparasitic lifestyle of Trichoderma and the involvement of G protein signalling therein. In Conference Book of the 10#^{th} VAAM Symposium “Molecular Biology of Fungi” (p. 57).

Zembek, P., Perlińska-Lenart, U., Brunner, K., Reithner, B., Palamarczyk, G., Mach, R. L., & Kruszewska, J. S. (2011). Elevated Activity of Dolichyl Phosphate Mannose Synthase Enhances Biocontrol Abilities of Trichoderma atroviride. Molecular Plant-Microbe Interactions, 24(12), 1522–1529. https://doi.org/10.1094/mpmi-02-11-0025

Aguilar-Osorio, G., vanKuyk, P. A., Seiboth, B., Blom, D., Solomon, P. S., Vinck, A., Kindt, F., Wösten, H. A. B., & de Vries, R. P. (2010). Spatial and Developmental Differentiation of Mannitol Dehydrogenase and Mannitol-1-Phosphate Dehydrogenase in Aspergillus niger. Eukaryotic Cell, 9(9), 1398–1402. https://doi.org/10.1128/ec.00363-09

Brunner, K., Preiser, V., Farnleitner, A. H., & Mach, R. L. (2010). Neueste Entwicklungen in der Resistenzbestimmung von Getreide und Mais : Nachweis der DNA als Schlüssel zur präzisen Messung von Fusarium-Befall. In Tagungsband (pp. 131–133).

Druzhinina, I. S., Komoń-Zelazowska, M., Atanasova, L., Seidl, V., & Kubicek, C. P. (2010). Evolution and Ecophysiology of the Industrial Producer Hypocrea jecorina (Anamorph Trichoderma reesei) and a New Sympatric Agamospecies Related to It. PLoS ONE, 5(2), e9191. https://doi.org/10.1371/journal.pone.0009191

Farnleitner, A. H., Ryzinska-Paier, G., Reischer, G. H., Burtscher, M. M., Knetsch, S., Kirschner, A. K. T., Dirnböck, T., Kuschnig, G., Mach, R. L., & Sommer, R. (2010). Escheria coli and enterococci are sensitive and reliable indicators for human, livestock and wildlife faecal pollution in alpine mountainous water resources. Journal of Applied Microbiology, no-no. https://doi.org/10.1111/j.1365-2672.2010.04788.x

Fekete, E., De Vries, R., Seiboth, B., vanKuyk, P., Kubicek, C. P., & Karaffa, L. (2010). The Galactose-negative Phenotype of Aspergillus niger is Restricted to the Inability of the Conidiospores to Germinate on this Sugar. In IMC9 The Biology of Fungi. 9#^{th} International Mycological Congress, Edinburgh, UK, EU.

Fekete, E., Karaffa, L., Fekete, E., Seiboth, B., Kubicek, C. P., & Flipphi, M. (2010). Identification of a beta-galactosidase/lactose permease gene couple and the characterisation of lactose transport in Aspergillus nidulans. In IMC9 The Biology of Fungi. 9#^{th} International Mycological Congress, Edinburgh, UK, EU.

Gruber, S. G., Vaaje-Kolstad, G., Matarese, F., Kubicek, C. P., & Seidl-Seiboth, V. (2010). Fungal chitinases : regulation of subgroup C-chitinases containing multiple carbohydrate binding domains by internal and external inducers in Trichoderma atroviride. In IMC9 The Biology of Fungi. 9#^{th} International Mycological Congress, Edinburgh, UK, EU.

Gruber, S. G., Vaaje-Kolstad, G., Matarese, F., Lopez-Mondejar, R., Kubicek, C. P., & Seidl-Seiboth, V. (2010). Analysis of subgroup C of fungal chitinases containing chitin-binding and LysM modules in the mycoparasite Trichoderma atroviride. In Molecular and Applied Biosciences Austria 2010 (pp. 83–84).

Gruber, S. G., Vaaje-Kolstad, G., Matarese, F., Lopez-Mondejar, R., Kubicek, C. P., & Seidl-Seiboth, V. (2010). Regulation of fungal chitinases containing LysM motifs and adjacent LysM-proteins in Trichoderma atroviride. In Book of Abstracts (p. 86).

Guangtao, Z., Seiboth, B., Wen, C., Yaohua, Z., Xian, L., & Wang, T. (2010). A novel carbon source-dependent genetic transformation system for the versatile cell factory Hypocrea jecorina (anamorph Trichoderma reesei). FEMS Microbiology Letters, 303(1), 26–32. https://doi.org/10.1111/j.1574-6968.2009.01851.x

Gyalai-Korpos, M., Nagy, G., Mareczky, Z., Schuster, A., Réczey, K., & Schmoll, M. (2010). Relevance of the light signaling machinery for cellulase expression in trichoderma reesei (hypocrea jecorina). BMC Research Notes, 3(330). https://doi.org/10.1186/1756-0500-3-330

Kasper, D. C., Mechtler, T. P., Reischer, G. H., Witt, A., Langgartner, M., Pollak, A., Herkner, K. R., & Berger, A. (2010). The bacterial load of Ureaplasma parvum in amniotic fluid is correlated with an increased intrauterine inflammatory response. Diagnostic Microbiology and Infectious Disease, 67(2), 117–121. https://doi.org/10.1016/j.diagmicrobio.2009.12.023

Kollanur, D., Reischer, G., Wehrspaun, C., Sommer, R., Stadler, H., Zerobin, W., & Farnleitner, A. H. (2010). Quantitative Assessment of Faecal Pollution Sources in Alpine Spring Catchments as a Basis for Microbial Hazard- and Risk Assessment. In Young Water Professionals (p. 11).

Kubicek, C. P., Ivanova, C., & Seiboth, B. (2010). Trichoderma technology development DTT : 2nd interim report.

Kubicek, C. P., Ivanova, C., & Seiboth, B. (2010). Trichoderma technology development DTT : 3rd interim report.

Kubicek, C. P., Seidl, V., & Seiboth, B. (2010). Plant Cell Wall and Chitin Degradation. In Cellular and Molecular Biology of Filamentous Fungi (pp. 396–413). ASM Press.

Mach, R. L., Pucher, M., & Mach-Aigner, A. R. (2010). New generation of strain improvement for hydrolase production via genetic engineering : a case study Trichoderma. In Book of Abstracts (p. 22).

Mach, R. L., Steiger, M., & Mach-Aigner, A. R. (2010). Engineering an N-acetylneuraminic acid Pathway into Trichoderma spp. : From Chitin to the Zanamivir Precursor N-acetylneuraminic Acid by Whole. In ibio 2010 (p. 205).

Mach-Aigner, A. R., Grosstessner-Hain, K., Pocas-Fonseca, M., Mechtler, K., & Mach, R. L. (2010). From an electrophoretic mobility shift assay to isolated transcription factors : a fast genomic-proteomic approach. BMC Genomics, 11, 644–653.

Mach-Aigner, A. R., Pucher, M. E., & Mach, R. L. (2010). D-Xylose as a Repressor or Inducer of Xylanase Expression in Hypocrea jecorina (Trichoderma reesei). Applied and Environmental Microbiology, 76(6), 1770–1776. https://doi.org/10.1128/aem.02746-09

Mach-Aigner, A. R., Pucher, M., Gorsche, R., & Mach, R. L. (2010). Deregulating Hydrolase Production in the Industrial Important Fungus Trichoderma Reesei - from Gene Regulation to Strain Improvement. In ibio 2010 (p. 234).

Mach-Aigner, A. R., Steiger, M., & Mach, R. L. (2010). From chitin to a highly valuable, pharmaceutically relevant fine chemical : inserting a multi-step enzyme cascade into Trichoderma. In Meeting Abstracts (p. 159).

Mach-Aigner, A. R., Steiger, M., Gorsche, R., & Mach, R. L. (2010). Synthesis of N-acetyl neuraminic acid from Chitin using Trichoderma as whole-cell catalyst. In Book of Abstracts (p. 48).

Messner, K., Fackler, K., Srebotnik, E., Ters, T., Karabec, M., Zikeli, F., Bischof, R., & Kroismayr, R. (2010). Biomimetischer Lignocelluloseaufschluss (Halbjahresbericht Juni 2010).

Metz, B., Akel, E., Kubicek, C. P., & Seiboth, B. (2010). Arabinan and L-arabinose metabolism in Trichoderma reesei. In Meeting Abstracts (p. 36).

Mushi, D., Byamukama, D., Kivaisi, A. K., Mach, R. L., & Farnleitner, A. H. (2010). Sorbitol-fermenting Bifidobacteria are indicators of very recent human faecal pollution in streams and groundwater habitats in urban tropical lowlands. Journal of Water & Health, 8(3), 466–478. https://doi.org/10.2166/wh.2010.116

Omann, M., & Zeilinger, S. (2010). How a Mycoparasite Employs G-Protein Signaling : Using the Example of Trichoderma. Journal of Signal Transduction, 2010, 1–8. https://doi.org/10.1155/2010/123126

Omann, M., Escobar Rodriguez, C., & Zeilinger, S. (2010). Host recognition and mycoparasitism in the biocontrol agent Trichoderma atroviride : the role of G protein signaling. In IMC9 The Biology of Fungi. 9#^{th} International Mycological Congress, Edinburgh, UK, EU.

Omann, M., Escobar Rodriguez, C., & Zeilinger, S. (2010). The role of G-Protein signaling in the biocontrol agent Trichoderma atroviride. In Book of Abstracts (p. 21).

Omann, M., Lehner, S., Escobar Rodriguez, C., Stoppacher, N., & Zeilinger, S. (2010). Role of G protein signalling in host sensing of the mycoparasite Trichoderma atroviride. In IOBC/WPRS Working Group (p. 46).

Perkhofer, S., Mrazek, C., Hartl, L., & Lass-Flörl, C. (2010). In Vitro Susceptibility Testing in Fungi : What is its Role in Clinical Practice. Current Infectious Disease Reports, 12(6), 401–408. https://doi.org/10.1007/s11908-010-0134-z

Pisanelli, I., Kujawa, M., Gschnitzer, D., Spadiut, O., Seiboth, B., & Peterbauer, C. (2010). Heterologous expression of an Agaricus meleagris pyranose dehydrogenase-encoding gene in Aspergillus spp. and characterization of the recombinant enzyme. Applied Microbiology and Biotechnology, 86(2), 599–606. https://doi.org/10.1007/s00253-009-2308-x

Portnoy, T., Margeot, A., Seidl, V., Le Crom, S., Ben Chaabane, F., Seiboth, B., & Kubicek, C. P. (2010). Transcriptional response is a limiting factor in cellulase overproduction by Trichoderma reesei. In Meeting Abstracts (p. 88).

Pucher, M., Mach-Aigner, A. R., & Mach, R. L. (2010). D-xylose : repressor or inducer of xylanase expression in Hypocrea jecorina (Trichoderma reesei). In Meeting Abstracts (p. 74).

Pucher, M., Mach-Aigner, A. R., & Mach, R. L. (2010). Improvement of cultivation conditions for high enzyme production in the industrially important fungus Trichoderma reesei. In Proceedings (pp. 383–384).

Reischer, G., Kollanur, D., Wehrspaun, C., Sommer, R., Stadler, H., & Farnleitner, A. H. (2010). Hypothesis-driven identification of faecal pollution sources in mountainous water resources used for recreational purposes. The Water Research Conference, Lissabon, Portugal, EU.

Ryzinska-Paier, G., Farnleitner, A. H., Haider, J., Knetsch, S., & Sommer, R. (2010). Testing genotypic PCR methods for the straightforward identification of Clostridium perfringens isolates from water and faeces. In ÖGHMP 2010 Abstracts (pp. 116–117).

Ryzinska-Paier, G., Haider, J., Knetsch, S., Stadler, H., Reischer, G., Kirschner, A. K. T., Mach, R. L., Sommer, R., & Farnleitner, A. H. (2010). Investigating the potential of Clostridium perfringens as a conservative faecal marker in alpine water resources. In ÖGHMP 2010 Abstracts (pp. 30–31).

Ryzinska-Paier, G., Sommer, R., Reischer, G., Burtscher, M. M., Mach, R. L., Knetsch, S., & Farnleitner, A. H. (2010). Evaluating the sensitivity of standard faecal indicator bacteria (SFIB) for water resource monitoring in human and animal faecal excreta at alpine catchments. In ÖGHMP 2010 Abstracts (pp. 117–118).

Schuhmacher, R., Lehner, S., Zeilinger, S., Stoppacher, N., & Krska, R. (2010). Determination of Extracellular Siderophores of Trichoderma atroviride by High Resolution Liquid Chromatography - Mass Spectrometry. In Book of Abstracts (p. 56).

Schuster, A., & Schmoll, M. (2010). Biology and biotechnology of Trichoderma. Applied Microbiology and Biotechnology, 87(3), 787–799. https://doi.org/10.1007/s00253-010-2632-1

Schuster, A., Tisch, D., Kubicek, C. P., & Schmoll, M. (2010). Targets of the cAMP signaling pathway in Trichoderma reesei (Hypocrea jecorina). In Molecular and Applied Biosciences Austria 2010 (p. 80).

Seiboth, B. (2010). Approaches towards understanding enzyme production by Trichoderma reesei. In IMC9 The Biology of Fungi. 9#^{th} International Mycological Congress, Edinburgh, UK, EU.

Seiboth, B., Karimi Aghcheh, R., Linke, R., Sauer, D. G., Baker, S. E., & Kubicek, C. P. (2010). Epigenetic regulation of (hemi)cellulase gene expression in Trichoderma reesei. In Eurofung Meeting (p. 14).

Seidl, V., & Seiboth, B. (2010). Trichoderma reesei : genetic approaches to improving strain efficiency. Biofuels, 1(2), 343–354.

Seidl, V., Gruber, S. G., Sezerman, O. U., Baker, S. E., & Kubicek, C. P. (2010). Fungal hydrophobins are regulated by differtial splicing. In Molecular and Applied Biosciences Austria 2010 (pp. 44–45).

Seidl, V., Seibel, C., Kubicek, C. P., & Schmoll, M. (2010). Sexual development in the industrial workhorse Trichoderma reesei. In Molecular and Applied Biosciences Austria 2010 (pp. 23–24).

Seidl-Seiboth, V., & Kubicek, C. P. (2010). Fungal hydrophobic proteins : how fungi protect and disguise themselves in their environment and biotechnological applications of these proteins. In ÖGHMP 2010 Abstracts (p. 89).

Seidl-Seiboth, V., Coutinho, P., Henrissat, B., & Kubicek, C. P. (2010). Trichoderma CAZomes : the carbohydrate degradation potential of mycoparasites. In Book of Abstracts (p. 13).

Stadler, H., Klock, E., Skritek, P., Mach, R. L., Zerobin, W., & Farnleitner, A. H. (2010). The spectral absorption coefficient at 254 nm as a real-time early warning proxy for detecting faecal pollution events at alpine karst water resources. WATER SCIENCE AND TECHNOLOGY, 62(8), 1898–1906.

Steiger, M. G., Mach, R. L., & Mach-Aigner, A. R. (2010). An accurate normalization strategy for RT-qPCR in Hypocrea jecorina (Trichoderma reesei). Journal of Biotechnology, 145(1), 30–37. https://doi.org/10.1016/j.jbiotec.2009.10.012

Steiger, M., Mach, R. L., & Mach-Aigner, A. R. (2010). Engineering an N-acetylneuraminic acid synthesis pathway into Trichoderma. In Meeting Abstracts (p. 160).

Steiger, M., Mach, R. L., & Mach-Aigner, A. R. (2010). Reference genes for Hypocrea jecorina. In Proceedings (pp. 415–416).

Steiger, M., Vitikainen, M., Brunner, K., Adam, G., Saloheimo, M., Mach, R. L., & Mach-Aigner, A. R. (2010). A transformation system for Hypocrea (Trichoderma) that favours homologous integration and that uses reusable bi-directionally selectable markers. In Book of Abstracts. Trichoderma - Molecular mechanisms and applications of biocontrol in agriculture, Technion, Haifa, Israel, Non-EU.

Stoppacher, N., Kluger, B., Zeilinger, S., Krska, R., & Schuhmacher, R. (2010). Identification and profiling of volatile metabolites of the biocontrol fungus Trichoderma atroviride by HS-SPME-GC-MS. Journal of Microbiological Methods, 81(2), 187–193. https://doi.org/10.1016/j.mimet.2010.03.011

Stoppacher, N., Kluger, B., Zeilinger, S., Krska, R., & Schuhmacher, R. (2010). Volatile secondary metabolites of the biocontrol fungus Trichoderma atroviride : Profiling by HS-SPME-GC-MS. In IOBC/WPRS Working Group (p. 47).

Stoppacher, N., Schwarzböck, M., Zeilinger, S., Krska, R., & Schuhmacher, R. (2010). The Peptaibiotics Database - a valuable tool for the research on Aib-peptides. In Book of Abstracts (p. 57).

Stoppacher, N., Zeilinger, S., Krska, R., & Schuhmacher, R. (2010). Screening for peptaibiotics in commercially available Trichoderma biocontrol products by LC-MS/MS. In IOBC/WPRS Working Group (p. 143).

Wilhartitz, I. C., & Farnleitner, A. H. (2010). Comment on “Non-permanent shallow halocline in a fractured carbonate aquifer, southern Italy” by E.Petrella, G. Naclerio, A. Falasca, A. Bucci, P. Capuano, V.De Felice and F.Celico [J. Hydrol. 373 (2009) 267-272]. Journal of Hydrology, 391(3–4), 387–388. https://doi.org/10.1016/j.jhydrol.2010.07.029

Zeilinger, S., & Omann, M. (2010). The G protein-coupled receptor Gpr1 is required for host recognition and mycoparasitism in the biocontrol agent Trichoderma atroviride. In Meeting Abstracts (p. 64).

Akel, E., Metz, B., Seiboth, B., & Kubicek, C. P. (2009). Molecular Regulation of Arabinan and L-Arabinose Metabolism in Hypocrea jecorina (Trichoderma reesei). Eukaryotic Cell, 8(12), 1837–1844. https://doi.org/10.1128/ec.00162-09

Brunner, K. (2009). Mykotoxine in Lebens- und Futtermitteln - Entwicklung verbesserter Testmethoden. In Optimierung des Futterwertes von Mais und Maisprodukten (p. 7).

Brunner, K., Kovalsky Paris, M. P., Paolino, G., Bürstmayr, H., Lemmens, M., Berthiller, F., Schuhmacher, R., Krska, R., & Mach, R. L. (2009). A reference-gene-based quantitative PCR method as a tool to determine Fusarium resistance in wheat. Analytical and Bioanalytical Chemistry, 395(5), 1385–1394. https://doi.org/10.1007/s00216-009-3083-3

Brunner, K., Kovalsky- Paris, M. P., Paolino, G., Bürstmayr, H., Lemmens, M., Berthiller, F., Schuhmacher, R., Krska, R., & Mach, R. L. (2009). Die Entwicklung einer quantitativen PCR Methode zur Beurteilung der Fusarium-Resistenz von Weizen. In Tagungsband 59.Tagung der Pflanzenzüchter und Saatgutkaufleute Österreichs (pp. 27–30). Lehr- und Forschungszentrum für Landwirtschaft Raumberg-Gumpenstein.

Brunner, K., Kovalsky- Paris, M. P., Paolino, G., Bürstmayr, H., Lemmens, M., Berthiller, F., Schuhmacher, R., Krska, R., & Mach, R. L. (2009). Eine quantitativen PCR Methode zur Fusarium Resistenzbestimmung. In ALVA Mitteilungen 7 (pp. 35–40). ALVA Mitteilungen.

Brunner, K., Zeilinger, S., Reithner, B., Omann, M., & Mach, R. L. (2009). Trichoderma as Biocontrol Agent: Potentials and Limitations of Strain Improvement. In Agriculturally Important Microorganisms (pp. 153–164). Academic World International.

Burtscher, M. M., Zibuschka, F., Mach, R. L., Lindner, G., & Farnleitner, A. H. (2009). Heterotrophic plate count vs. in situ bacterial 16S rRNA gene amplicon profiles from drinking water reveal completely different communities with distinct spatial and temporal allocations in a distribution net. Water SA, 35(4), 495–504.

Coutinho, P., Andersen, M. R., Kolenova, K., vanKuyk, P., Benoit, I., Gruben, B., Trejo-Aguilar, B., Visser, H., van Solingen, P., Pakula, T., Seiboth, B., Battaglia, E., Aguilar-Osorio, G., de Jong, J., Ohm, R., Aguilar, M., Henrissat, B., Nielsen, J., Stalbrand, H., & De Vries, R. (2009). Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus oryzae. Fungal Genetics and Biology, 46(1), S161–S169. https://doi.org/10.1016/j.fgb.2008.07.020

Farnleitner, A. H., Haider, J., Ryzinska-Paier, G., Knetsch, S., Stadler, H., Reischer, G., Kirschner, A. K. T., Mach, R. L., & Sommer, R. (2009). Clostridium perfringens as a faecal indicator: a polyphasic evaluation by standard- and molecular methods for a large Austrian catchment. In 15th Health Related Water Microbiology Symposium (pp. 101–103).

Gherbawy, Y., Mach, R. L., & Rai, M. (Eds.). (2009). Current Advances in Molecular Mycology. Nova Science Publishers, Inc.

Gruber, S. G., Kubicek, C. P., & Seidl, V. (2009). Regulation of fungal chitinases by cell wall fragments and their relevance for biocontrol. In EUCHIS 2009 Conference Book (p. 86).

Guangtao, Z., Hartl, L., Schuster, A., Polak, S., Schmoll, M., Wang, T., Seidl, V., & Seiboth, B. (2009). Gene targeting in a nonhomologous end joining deficient Hypocrea jecorina. Journal of Biotechnology, 139(2), 146–151. https://doi.org/10.1016/j.jbiotec.2008.10.007

Haider, J., Ryzinska-Paier, G., Sommer, R., Knetsch, S., & Farnleitner, A. H. (2009). Phospholipase C gene PCR: a straightforward tool for the genotypic identification of presumptive Clostridium perfringens isolates from water. In 15th Health Related Water Microbiology Symposium (pp. 210–212).

Hartl, L., Kubicek, C. P., & Seiboth, B. (2009). Role of hexokinases in carbon catabolite repression and induction in Hypocrea jecorina. In Fungal Genetics Reports (p. 97).

Kemptner, J., Marchetti-Deschmann, M., Mach, R., Druzhinina, I. S., Kubicek, C. P., & Allmaier, G. (2009). Evaluation of matrix-assisted laser desorption/ionization (MALDI) preparation techniques for surface characterization of intact Fusarium spores by MALDI linear time-of-flight mass spectrometry. Rapid Communications in Mass Spectrometry, 23(6), 877–884. https://doi.org/10.1002/rcm.3949

Kirschner, A. K. T., Kavka, G. G., Mach, R. L., Sommer, R., & Farnleitner, A. H. (2009). Microbiological water quality along the Danube River : Integrating data from two whole-river surveys and a transnational monitoring network. In 15th Health Related Water Microbiology Symposium (pp. 220–222).

Kirschner, A. K. T., Kavka, G. G., Velimirov, B., Mach, R. L., Sommer, R., & Farnleitner, A. H. (2009). Microbiological water quality along the Danube River : Integrating data from two whole-river surveys and a transnational monitoring network. Water Research, 43(15), 3673–3684. https://doi.org/10.1016/j.watres.2009.05.034

Kirschner, A. K. T., Schauer, S., Steinberger, B., Wilhartitz, I., Grim, C. J., Huq, A., Colwell, R. R., Herzig, A., & Sommer, R. (2009). Interaction of Vibrio cholerae non01/non0139 with copepods, cladocerans and competing bacteria. In 15th Health Related Water Microbiology Symposium (pp. 116–118).

Kluger, B., Lehner, S., Stoppacher, N., Zeilinger, S., Krska, R., & Schuhmacher, R. (2009). Determination of volatile metabolites of the biocontrol fungus Trichoderma atroviride by GC/MS. In IOBC/WPRS Bulletin (pp. 145–148). IOBC/WPRS.

Kubicek, C. P., & Seiboth, B. (2009). New technologies for Trichoderma strain improvement (1.Zwischenbericht).

Kubicek, C. P., Allmaier, G., Mach, R. L., & Druzhinina, I. (2009). Multidisziplinäre Detektion und Beurteilung einheimischer Fusarien (Endbericht).

Kubicek, C. P., Mikus, M., Schuster, A., Schmoll, M., & Seiboth, B. (2009). Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina. Biotechnology for Biofuels, 2(1), 19. https://doi.org/10.1186/1754-6834-2-19

Kubicek, C. P., Seiboth, B., & Linke, R. (2009). Increase of cellulase production in Trichoderma reesei by integrated molecular and classical strain improvement (Endbericht).

Le Crom, S., Schackwitz, W., Pennacchio, L., Magnuson, J. K., Culley, D. E., Collett, J. R., Martin, J., Druzhinina, I. S., Mathis, H., Monot, F., Seiboth, B., Cherry, B., Rey, M., Berka, R., Kubicek, C. P., Baker, S. E., & Margeot, A. (2009). Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proceedings of the National Academy of Sciences, 106(38), 16151–16156. https://doi.org/10.1073/pnas.0905848106

Le Crom, S., Schackwitz, W., Pennacchio, L., Magnuson, J., Culley, D., Collett, J., Martin, J., Druzhinina, I., Mathis, H., Monot, F., Seiboth, B., Cherry, B., Rey, M., Berka, R. M., Kubicek, C. P., Baker, S. E., & Margeot, A. (2009). Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. In Eurofung Meeting (p. 24).

Lopez-Mondejar, R., Catalano, V., Kubicek, C. P., & Seidl, V. (2009). Beta-N-acetylglucosaminidases are essential for growth of filamentous fungi on chitin. In EUCHIS 2009 Conference Book (p. 76).

López-Mondéjar, R., Catalano, V., Kubicek, C. P., & Seidl, V. (2009). The β-N-acetylglucosaminidases NAG1 and NAG2 are essential for growth of Trichoderma atroviride on chitin. The FEBS Journal, 276(18), 5137–5148. https://doi.org/10.1111/j.1742-4658.2009.07211.x

Mach, R. L., Steiger, M., & Mach-Aigner, A. R. (2009). Heterologous expression of the GlcNAc 2-epimerase and neuNAc-synthase in Trichoderma to construct a N-Acetylneuraminic acid synthesis pathway. In The Third Annual Workshop of COST FP0620 - Abstract Book (p. 40).

Mach-Aigner, A. R., Steiger, M., & Mach, R. L. (2009). From the biopolymer chitin to a highly valuable, pharmaceutically relevant fine chemical : Applying an integrated bioprocess technology approach to Trichoderma. In The Third Annual Workshop of COST FP0620 - Abstract Book (p. 54).

Manandhar, S. A., Byamukama, D., Shrestha, R. R., Haberl, R., Mach, R. L., & Farnleitner, A. H. (2009). Use of faecal pollution indicators to estimate pathogen die off conditions in source separated faeces in Kathmandu Valley, Nepal. Journal of Water & Health, 7(1), 97–107. https://doi.org/10.2166/wh.2009.149

Marchetti-Deschmann, M., Winkler, W., Kemptner, J., Raptakis, E., Druzhinina, I., Mach, R. L., Kubicek, C. P., & Allmaier, G. (2009). Classification of mycotoxin-producing Fusarium species based on MALDI-TOF MS analyses of their intact spores. In Proceedings of the 57th ASMS conference on mass spectrometry and allied topics (p. 3).

Metz, B., Akel, E., Kubicek, C. P., & Seiboth, B. (2009). Arabinan and L-arabinose metabolism in Trichoderma reesei (Hypocrea jecorina) : Components, regulation and other surprises. In Acta Microbiologica et Immunologica Hungarica (pp. 203–204).

Metz, B., de Vries, R. P., Polak, S., Seidl, V., & Seiboth, B. (2009). The Hypocrea jecorina (syn.Trichoderma reesei) lxr1 gene encodes a D-mannitol dehydrogenase and is not involved in L-arabinose catabolism. FEBS Letters, 583(8), 1309–1313. https://doi.org/10.1016/j.febslet.2009.03.027

Mikus, M., Fekete, E., Karaffa, L., van der Werf, M. J., Seiboth, B., & Kubicek, C. P. (2009). Lactose induction of cellulase gene expression in Hypocrea jecorina : a role for galactosyl-transferases? In Acta Microbiologica et Immunologica Hungarica (pp. 205–206).

Mushi, D., Mach, R. L., Byamukama, D., & Farnleitner, A. H. (2009). An integral approach in estimating the risk of contamination associated with unprotected groundwater in peri-urban area of tropical developing country. In 15th Health Related Water Microbiology Symposium (pp. 57–58).

Omann, M., & Zeilinger, S. (2009). The G protein-coupled receptor Gpr1 is involved in mycoparasitism of Trichoderma atroviride. In MAPK Signalling during Fungal Pathogenesis - Book of Abstracts. SIGNALPATH Final Network Meeting, Berlin, Deutschland, EU.

Omann, M., Lehner, S., Brunner, K., Delic, M., Stoppacher, N., Schuhmacher, R., Pucher, M., & Zeilinger, S. (2009). A cAMP receptor-like GPCR is involved in Trichoderma atroviride mycoparasitism. In IOBC/WPRS Bulletin (pp. 105–108). IOBC/WPRS.

Pucher, M., Mach-Aigner, A. R., & Mach, R. L. (2009). Towards hydrolase production on pentose sugars : the xylose dependent interplay of the two key opponents Xyr1 and Cre1 in Trichoderma reesei. In 9#^{th} VAAM Symposium -Molecular Biology of Fungi - Conference Book. 9#^{th} VAAM Symposium -Molecular Biology of Fungi, Münster, Deutschland, EU.

Reischer, G., Haider, J., Pokorny, N., Roda Husman, A. M. D., Wuertz, S., Pradhan, B., Ferguson, C., Byamukama, D., Mushi, D., Goshu, G., Ko, G., Ebdon, J. E., Aström, J., Coakley, T., Poma, R., Ahmed, W., Vrajmasu, V., Toth, E., Schade, M. A., … Farnleitner, A. H. (2009). A global assessment of the source specificity, sensitivity and geographical stability of Bacteroidetes qPCR assays for microbial source tracking. In 15th Health Related Water Microbiology Symposium (pp. 66–68).

Ryzinska-Paier, G., Sommer, R., Reischer, G., Rudnicki, S., Burtscher, M. M., Mach, R. L., Knetsch, S., & Farnleitner, A. H. (2009). Presence of Escherichia coli, Enterococci and Clostridium perfringens in human-, livestock- and wildlife faecal pollution sources at alpine / mountainous catchments: basic implications for sound water quality monitoring. In 15th Health Related Water Microbiology Symposium (pp. 267–269).

Schmoll, M., Schuster, A., Silva, R. do N., & Kubicek, C. P. (2009). The G-Alpha Protein GNA3 of Hypocrea jecorina (Anamorph Trichoderma reesei) Regulates Cellulase Gene Expression in the Presence of Light. Eukaryotic Cell, 8(3), 410–420. https://doi.org/10.1128/ec.00256-08

Schuhmacher, R., Stoppacher, N., Reithner, B., Omann, M., Zeilinger, S., & Krska, R. (2009). Antifungal peptides of the biocontrol fungus Trichoderma atroviride-detection and structure characterisation by LC-MS/MS. In IOBC/WPRS Bulletin (pp. 45–48). IOBC/WPRS.

Schuster, A., & Schmoll, M. (2009). Heterotrimeric G-protein signaling and light response : Two signaling pathways coordinated for optimal adjustment to nature. Communicative & Integrative Biology, 2(4), 308–310. https://doi.org/10.4161/cib.2.4.8223

Schuster, A., Kubicek, C. P., & Schmoll, M. (2009). A cellulase related dehydrogenase of Hypocrea jecorina (Trichoderma reesei) specifically responsive to soluble inducing compounds. In 31#^{st} Symposium on Biotechnology for Fuels and Chemicals (p. 113).

Schuster, A., Kubicek, C. P., & Schmoll, M. (2009). A cellulase related dehydrogenase of Hypocrea jecorina (Trichoderma reesei) specifically responsive to soluble inducing compounds. In 9#^{th} VAAM Symposium -Molecular Biology of Fungi - Conference Book. 9#^{th} VAAM Symposium -Molecular Biology of Fungi, Münster, Deutschland, EU.

Seibel, C., Gremel, G., do Nascimento Silva, R., Schuster, A., Kubicek, C. P., & Schmoll, M. (2009). Light-dependent roles of the G-protein α subunit GNAI of Hypocrea jecorina (anamorph Trichoderma reesei). BMC Biology, 7(58). https://doi.org/10.1186/1741-7007-7-58

Seidl, V., Seibel, C., Kubicek, C. P., & Schmoll, M. (2009). Sex and the Trichoderma : New perspectives for industrial strain improvement. In Fungal Genetics Reports (p. 221).

Seidl, V., Seibel, C., Kubicek, C. P., & Schmoll, M. (2009). Sex and the Trichoderma : New perspectives for industrial strain improvement. In Fungal Genetics Reports (p. 80).

Seidl, V., Seibel, C., Kubicek, C. P., & Schmoll, M. (2009). Sexual development in the industrial workhorse Trichoderma reesei. Proceedings of the National Academy of Sciences, 106(33), 13909–13914. https://doi.org/10.1073/pnas.0904936106

Seidl, V., Song, L., Lindquist, E., Gruber, S. G., Koptchinskiy, A., Zeilinger, S., Schmoll, M., Martínez, P., Sun, J., Grigoriev, I., Herrera-Estrella, A., Baker, S. E., & Kubicek, C. P. (2009). Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey. BMC Genomics, 10(567). https://doi.org/10.1186/1471-2164-10-567

Stadler, H., Klock, E., Skritek, P., Mach, R. L., Zerobin, W., & Farnleitner, A. H. (2009). Real-time Characterization of Microbial Faecal Pollution Dynamics at Alpine Karstic Water Resources. In 15th Health Related Water Microbiology Symposium (pp. 276–278).

Steiger, M., Mach, R. L., & Mach-Aigner, A. R. (2009). Defining the norm : reference genes for RT-qPCR in Trichoderma. In 9#^{th} VAAM Symposium -Molecular Biology of Fungi - Conference Book. 9#^{th} VAAM Symposium -Molecular Biology of Fungi, Münster, Deutschland, EU.

Stricker, A. R., & Mach, R. L. (2009). Gene Regulation of Hydrolase Expression: Lessons from the Industrially Important Fungus Trichoderma reesei (Hypocrea jecorina). In Current Advances in Molecular Mycology (pp. 205–222). Nova Science Publishers, Inc.

Wilhartitz, I. C., Kirschner, A. K. T., Stadler, H., Herndl, G. J., Dietzel, M., Latal, C., Mach, R. L., & Farnleitner, A. H. (2009). Heterotrophic prokaryotic production in ultraoligotrophic alpine karst aquifers and ecological implications. FEMS Microbiology Ecology, 68(3), 287–299. https://doi.org/10.1111/j.1574-6941.2009.00679.x

Wortman, J., Gilsenan, J., Joardar, V., Deegan, J., Clutterbuck, J., Andersen, M. R., Archer, D., Bencina, M., Braus, G., Coutinho, P., von Döhren, H., Doonan, J., Driessen, A. J. M., Durek, P., Espeso, E. A., Fekete, E., Flipphi, M., Garcia-Estrada, C., Geysens, S., … Turner, G. (2009). The 2008 update of the Aspergillus nidulans genome annotation : A community effort. Fungal Genetics and Biology, 46(1), S2–S13. https://doi.org/10.1016/j.fgb.2008.12.003

Zach, S., Kubicek, C. P., & Seidl, V. (2009). Development of a reusable selection marker system for multiple gene knockouts in Trichoderma atroviride. In 9#^{th} VAAM Symposium -Molecular Biology of Fungi - Conference Book. 9#^{th} VAAM Symposium -Molecular Biology of Fungi, Münster, Deutschland, EU.

Zeilinger, S., Reithner, B., Brunner, K., & Omann, M. (2009). Signal Transduction in Host Sensing and Mycoparasitism of Trichoderma Biocontrol Strains. In Agriculturally Important Microorganisms (pp. 165–175). Academic World International.

Reischer, G., Haider, J., Sommer, R., Stadler, H., Keiblinger, K., Hornek, R., Zerobin, W., Mach, R. L. ., & Farnleitner, A. (2008). Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics. Environmental Microbiology, 10(10), 2598–2608. https://doi.org/10.1111/j.1462-2920.2008.01682.x

Stricker, A. R., Trefflinger, P., Aro, N., Penttilä, M., & Mach, R. L. (2008). Role of Ace2 (Activator of Cellulases 2) within the xyn2 transcriptosome of Hypocrea jecorina. Fungal Genetics and Biology, 45(4), 436–445. https://doi.org/10.1016/j.fgb.2007.08.005

Brunner, K. (2008). Die Resistenzbewertung von 20 Weizensorten mittels quantitative PCR. Mold Meeting, Gars am Kamp, Austria.

Brunner, K. (2008). Die Resistenzbewertung von 20 Weizensorten mittels quantitative PCR. Züchtertagung Gumpenstein, Raumberg, Austria.

Brunner, K. (2008). Real-time PCR analysis of samples in agriculture: Detection of toxin producing Fusarium species. In www.copenmind.com. Copenmind 2008, Copenhagen, Dänemark, EU.

Brunner, K., Omann, M., Pucher, M. E., Delic, M., Lehner, S. M., Domnanich, P., Kratochwill, K., Druzhinina, I., Denk, D., & Zeilinger, S. (2008). Trichoderma G protein-coupled receptors : functional characterisation of a cAMP receptor-like protein from Trichoderma atroviride. Current Genetics, 54(6), 283–299. https://doi.org/10.1007/s00294-008-0217-7

Brunner, K., Pucher, M., Delic, M., Domnanich, P., Omann, M., & Zeilinger, S. (2008). Trichoderma atroviride G protein-coupled receptors of the cAMP receptor-like class : isolation, transcriptional regulation and involvement in host sensing. In 9#^{th} European Conference on Fungal Genetics - Meeting Abstracts (p. 121).

Farnleitner, A. H., Stadler, H., Reischer, G., Sommer, R., Kirschner, A. K. T., Burtscher, M. M., Ryzinska, G., Wilhartitz, I., Kuschnig, G., Mach, R. L., & Zerobin, W. (2008). Methods and Strategies for Alpine Karstic Water Resource Management: Opening Pollution Microbiology’s “Black Box.” In World Water Congress and Exhibition (pp. 169–171). International Water Association.

Fekete, E., Karaffa, L., Seiboth, B., Szentirmai, A., & Kubicek, C. P. (2008). Lactose metabolism in Aspergillus nidulans requires a lactose permease and an intracellular beta-galactosidase. In 9#^{th} European Conference in Fungal Genetics - Meeting Abstracts (p. 167).

Fekete, E., Seiboth, B., Kubicek, C. P., Szentirmai, A., & Karaffa, L. (2008). Lack of aldose 1-epimerase in Hypocrea jecorina (anamorph Trichoderma reesei) : A key to cellulase gene expression on lactose. Proceedings of the National Academy of Sciences, 105(20), 7141–7146.

Fekete, E., Seiboth, B., Kubicek, C. P., Szentirmai, A., & Karaffa, L. (2008). Lack of aldose 1-epimerase in Hypocrea jecorina is a key to cellulase gene expression on lactose. In 9#^{th} European Conference in Fungal Genetics - Meeting Abstracts (p. 38).

Güldener, U., Peruci, M., Berthiller, F., Cziferszky, A., Wiesenberger, G., Erhart, C., Drexler, J., Brunner, K., Schuhmacher, R., Krska, R., Lemmens, M., Mitterbauer, R., & Adam, G. (2008). Genomforschung an Fusarium graminearum: relevant für zukünftige Bekämpfungsstrategien? In ALVA Mitteilungen 6 (pp. 31–35). ALVA Mitteilungen.

Haider, J., Ryzinska-Paier, G., Knetsch, S., Rudnicki, S., Farnleitner, A. H., & Sommer, R. (2008). Standard- und Alternativmethoden zur Identifizierung von Clostridium perfringens in der mikrobiologischen Wasseruntersuchung. In 31.Jahrestagung der Österreichischen Gesellschaft für Hygiene, Mikrobiologie und Präventivmedizin (pp. 83–84).

Hirschmann, J., Marchetti, M., Mach, R. L., Kubicek, C. P., & Allmaier, G. (2008). Intact spore mass spectrometry (ISMS) - vacuum MALDI TOF mass spectrometry of spores of the fungi Fusarium. MassSpec-Forum Vienna 2008, Wien, Austria.

Kasper, D. C., Sadeghi, K., Prusa, A.-R., Reischer, G. H., Kratochwill, K., Förster-Waldl, E., Gerstl, N., Hayde, M., Pollak, A., & Herkner, K. R. (2008). Quantitative real-time polymerase chain reaction for the accurate detection of Toxoplasma gondii in amnotic fluid. Diagnostic Microbiology and Infectious Disease, 63(1), 10–15. https://doi.org/10.1016/j.diagmicrobio.2008.09.009

Kavka, G. G., Kirschner, A. K. T., Velimirov, B., Reischer, G., Haider, J., Mach, R. L., & Farnleitner, A. H. (2008). Mikrobiologische Wassergüte der Donau unter Einbeziehung einer DNA-basierenden Methode zur Herkunftbestimmung fäkaler Verunreinigungen. In Das Leben im Donaustrom (pp. 7–23). Bundesamt für Wasserwirtschaft.

Kirschner, A. K. T., Kavka, G. G., Velimirov, B., Reischer, G., Mach, R. L., & Farnleitner, A. H. (2008). Microbiological water quality and DNA-based quantitative microbial source tracking. In IKSD short form report on JDS2 (pp. 86–95). ICPDR-International Commission for the Protection of the Danube River.

Kluger, B., Lehner, S., Stoppacher, N., Zeilinger, S., Krska, R., & Schuhmacher, R. (2008). Determination of volatile metabolites of the biocontrol fungus Trichoderma atroviride by GC/MS. In Molecular Tools for Understanding and Improving Biocontrol - Abstract Book (p. 64).

Lendenfeld, T., Mach, R. L., & Farnleitner, A. H. (2008). Basic Considerations for the Development of an Online- Measurement Device for Faecal Pollution Monitoring in Water. In World Water Congress and Exhibition (p. 40). International Water Association.

Mach-Aigner, A. R., Pucher, M. E., Steiger, M. G., Bauer, G. E., Preis, S. J., & Mach, R. L. (2008). Transcriptional regulation of xyr1 , encoding the main regulator of the xylanolytic and cellulolytic enzyme system in Hypocrea jecorina. Applied and Environmental Microbiology, 74(21), 6554–6562. https://doi.org/10.1128/aem.01143-08

Mach-Aigner, A. R., Pucher, M., Steiger, M., & Mach, R. L. (2008). From Gene Regulation to Strain Improvement - lessons from the Industrial Important Fungus Trichoderma reesei. In ENZITEC 2008 - VIII Seminario Brasileiro de Tecnologia Enzimatica (p. 20).

Mach-Aigner, A. R., Pucher, M., Steiger, M., & Mach, R. L. (2008). Xyr1 is a major target to genetically engineer the Hydrolase Profile of Trichoderma reesei. In ENZITEC 2008 - VIII Seminario Brasileiro de Tecnologia Enzimatica (p. 21).

Omann, M., Lehner, S., Brunner, K., Delic, M., Stoppacher, N., Schuhmacher, R., Pucher, M., & Zeilinger, S. (2008). A cAMP receptor-like GPCR is involved in Trichoderma atroviride mycoparasitism. In Molecular Tools for Understanding and Improving Biocontrol - Abstract Book (p. 18).

Omann, M., Lehner, S., Delic, M., Stoppacher, N., Schuhmacher, R., Brunner, K., & Zeilinger, S. (2008). Involvement of the G protein-coupled receptor Gpr1 in mycoparasitism of Trichoderma atroviride. In First German/ French/ European/ Meeting on Yeast and Filamentous Fungi (p. 19).

Pucher, M., Bauer, G., Steiger, M., Mach, R. L., & Mach-Aigner, A. R. (2008). Investigations of Xyr1 (Xylanase regulator 1), the main transcriptional regulator of the xylanaolytic and cellulolytic enzymes in Hypocrea jecorina (Trichoderma reesei). In Enzymatic fiber modification and hydrolysis (p. 38).

Pucher, M., Bauer, G., Steiger, M., Mach, R. L., & Mach-Aigner, A. R. (2008). Investigations of Xyr1 (Xylanase regulator 1), the main transcriptional regulator of the xylanaolytic and cellulolytic enzymes in Hypocrea jecorina (Trichoderma reesei). In Junior Scientist Conference 2008 - Proceedings (pp. 161–162).

Pucher, M., Pocas-Fonseca, M., Mach, R. L., & Stricker, A. R. (2008). Identification and isolation of the xylanase repressor protein (Xrp1) of Hypocrea jecorina (Trichoderma reesei). In 9#^{th} European Conference on Fungal Genetics - Meeting Abstracts (p. 159).

Reischer, G., Haider, J., Keiblinger, K., Sommer, R., Stadler, H., Mach, R. L., & Farnleitner, A. H. (2008). Tracking the Source of Faecal Pollution in Water : Quantitative Microbial Source Tracking of Genetic Markers from Human and Ruminant Origin. In World Water Congress and Exhibition (pp. 247–248). International Water Association.

Reischer, G., Haider, J., Kirschner, A. K. T., Sommer, R., Mach, R. L., & Farnleitner, A. H. (2008). Quantitative PCR Methoden zum spezifischen Nachweis fäkaler Verunreinigungen durch den Menschen und durch Wiederkäuer in Wasserressourcen. In 31.Jahrestagung der Österreichischen Gesellschaft für Hygiene, Mikrobiologie und Präventivmedizin (pp. 59–60).

Reischer, G., Kavka, G. G., Kasper, D., Winter, C., Mach, R. L., & Farnleitner, A. H. (2008). Applicability of DNA based quantitative microbial source tracking (QMST) evaluated on a large scale in the Danube River and its important tributaries. Fundamental and Applied Limnology, 162 / SUPPL.LARGE RIVERS VOL.18(1–2), 117–125.

Reischer, G., Kirschner, A. K. T., Velimirov, B., Kavka, G. G., Mach, R. L., & Farnleitner, A. H. (2008). Faecal Polution Monitoring and DNA Based Quantitative Microbial Source Tracking (QMST) On A Large Scale In The Danube River Catchment Area. In World Water Congress and Exhibition (pp. 14–16). International Water Association.

Schuster, A., Tisch, D., Seidl, V., Kubicek, C. P., & Schmoll, M. (2008). The cAMP-protein kinase A pathway is dispensable for cellulase gene expression in Hypocrea jecorina (=Trichoderma reesei). In 9#^{th} European Conference in Fungal Genetics - Meeting Abstracts (p. 119).

Seiboth, B. (2008). Lactose metabolism and cellulase induction in Trichoderma reesei (Hypocrea jecorina). In Eurofung (p. 23).

Seidl, V. (2008). Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions. Fungal Biology Reviews, 22, 36–42.

Seidl, V., Gamauf, C., Druzhinina, I., Seiboth, B., Hartl, L., & Kubicek, C. P. (2008). The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome. BMC Genomics, 9, 1–15.

Seidl, V., Kubicek, C. P., & Schmoll, M. (2008). Sexual development and morphological consequences of mating partner recognition in Hypocrea jecorina. In 9#^{th} European Conference in Fungal Genetics - Meeting Abstracts (p. 208).

Stadler, H., Skritek, P., Mach, R. L., Zerobin, W., & Farnleitner, A. H. (2008). Elucidating Faecal Indicator Dynamics in Alpine Karstic Spring Water at a High Resolution Scale: LEO - Satellite Based Automatic Event Sampling and E.coli Field Analysis. In World Water Congress and Exhibition (p. 40). International Water Association.

Stadler, H., Skritek, P., Sommer, R., Mach, R. L., Zerobin, W., & Farnleitner, A. H. (2008). Microbiological monitoring and automated event sampling at karst springs using LEO-satellites. Water Science & Technology, 58(4), 899–909. https://doi.org/10.2166/wst.2008.442

Steiger, M., Pucher, M., Mach-Aigner, A. R., & Mach, R. L. (2008). Learning more about the Gene Regulation of Hydrolytic enzyme - encoding Genes in an industrial relevant Fungus. In Enzymatic fiber modification and hydrolysis (p. 37).

Steiger, M., Pucher, M., Mach-Aigner, A. R., & Mach, R. L. (2008). Learning more about the Gene Regulation of Hydrolytic enzyme - encoding Genes in an industrial relevant Fungus. In Junior Scientist Conference 2008 - Proceedings (pp. 159–160).

Stoppacher, N., Zeilinger, S., Omann, M., Krska, R., & Schuhmacher, R. (2008). Antifungal peptides of the biocontrol fungus Trichoderma atroviride-detection and structure characterisation by LC-MS/MS. In Molecular Tools for Understanding and Improving Biocontrol - Abstract Book (p. 13).

Stoppacher, N., Zeilinger, S., Omann, M., Lassahn, P.-G., Roitinger, A., Krska, R., & Schuhmacher, R. (2008). Characterisation of the peptaibiome of the biocontrol fungus Trichoderma atroviride by liquid chromatography/tandem mass spectrometry. Rapid Communications in Mass Spectrometry, 22(12), 1889–1898. https://doi.org/10.1002/rcm.3568

Stricker, A. R., & Mach, R. L. (2008). Transcriptional regulation of hydrolase expression : lessons from the industrially important fungus Trichoderma reesei. In 9#^{th} European Conference on Fungal Genetics - Meeting Abstracts (p. 31).

Stricker, A. R., Mach, R. L., & de Graaff, L. H. (2008). Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei). Applied Microbiology and Biotechnology, 78(2), 211–220. https://doi.org/10.1007/s00253-007-1322-0

Stricker, A. R., Steiger, M., Pucher, M., & Mach, R. L. (2008). Modified hydrolase profiles in Hypocrea jecorina by changing the expression of the general activator protein Xylanase regulator 1 (Xyr1). In 9#^{th} European Conference on Fungal Genetics - Meeting Abstracts (p. 183).

Stricker, A. R., Wilhartitz, I., Farnleitner, A. H., & Mach, R. L. (2008). Development of a scorpion probe-based real-time PCR for the sensitive quantification of Bacteroides sp.ribosomal DNA from evaluation in spring water matrices. Microbiological Research, 163(2), 140–147. https://doi.org/10.1016/j.micres.2006.03.012

Wilhartitz, I., Kirschner, A. K. T., Stadler, H., Herndl, G., Szewzyk, U., Mach, R. L., & Farnleitner, A. H. (2008). Ecological Significance of Microbial Endokarst Communities in Groundwater from Alpine Karst Aquifers. In ISME 12. ISME 12 - 12th International Symposium on Microbial Ecology, Cairns, Australien, Non-EU.

Wilhartitz, I., Kirschner, A. K. T., Stadler, H., Szewzyk, U., Herndl, G., Mach, R. L., & Farnleitner, A. H. (2008). Ecological Significance and Applied Aspects of Microbial Endokarst Communities in Alpine Karstic Groundwater Resources. In World Water Congress and Exhibition (pp. 24–26). International Water Association.

Gamauf, C., Marchetti, M., Kallio, J., Puranen, T., Vehmaanperä, J., Allmaier, G., Kubicek, P. C., & Seiboth, B. (2007). Characterization of the bga1- encoded glycosyl hydrolase family 35 β-galactosidase of Hypocrea jecorina with galacto-β-ᴅ-galactanase activity. FEBS Journal, 274(7), 1691–1700. https://doi.org/10.1111/j.1742-4658.2007.05714.x

Pel, H. J., de Winde, J. H., Archer, D., Dyer, P. S., Hofmann, G., Schaap, P. J., Turner, G., De Vries, R., Albang, R., Albermann, K., Andersen, M. R., Bendtsen, J. D., Benen, J. A. E., van den Berg, M., Breestraat, S., Caddick, M., Contreras, R., Cornell, M., Coutinho, P., … Stam, H. (2007). Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology, 25(2), 221–231. https://doi.org/10.1038/nbt1282

Brunner, K., Kasper, D., Köllner, Krista. E., Lemmens, M., Adam, G., & Mach, R. L. (2007). Reduzierte Virulenz eines Glucoseoxidase produzierenden Fusarium graminearum Stammes. In ALVA - Mitteilungen (pp. 44–49). Springer-Verlag.

Brunner, K., Lichtenauer, A. M., Kratochwill, K., Delic, M., & Mach, R. L. (2007). Xyr1 regulates xylanase but not cellulase formation in the head blight fungus Fusarium graminearum. Current Genetics, 52, 213–220.

Brunner, K., Zeilinger, S., & Mach, R. L. (2007). Molecular Approaches for Studying Fungi in the Environment. In Environmental and Microbial Relationships,2nd Edition The Mycota (pp. 18–27). Springer-Verlag.

Farnleitner, A. H., Mach, R. L., Reischer, G., & Kavka, G. G. (2007). Mikrobiologisch - hygienische Risiken trotz Abwasserentsorgung nach dem Stand der Technik? In Wiener Mitteilingen (pp. 209–242). Institut für Wassergüte/ TU Wien.

Farnleitner, A. H., Stadler, H., Haider, J., Sommer, R., Kirschner, A. K. T., Ryzinska, G., Reischer, G., Burtscher, M. M., Keiblinger, K., Fischer, U. R., Wieltschnig, C., & Mach, R. L. (2007). Establishing the basic links between hydrological conditions and microbial quality parameters in alpine karstic spring water under increased discharge. In WaterMicro 2007 (pp. 216–218).

Fekete, E., Karaffa, L., Kubicek, C. P., Szentirmai, A., & Seiboth, B. (2007). Induction of extracellular ß-galactosidase (Bga1) formation by D-galactose in Hypocrea jecorina is mediated by galactitol. Microbiology, 153, 507–512.

Gamauf, C., Metz, B., & Seiboth, B. (2007). Degradation of plant cell wall polymers by fungi. In The Mycota IV: Envinronmental and Microbial Relationship (pp. 325–340). Springer-Verlag.

Hartl, L., Kubicek, C. P., & Seiboth, B. (2007). Induction of the Leloir pathway in the fungus Hypocrea jecorina involves no transcriptional inducer function of the galactokinase. Biological Chemistry, 282, 18654–18659.

Hirschmann, J., Marchetti, M., Mach, R. L., Belgacem, O., Raptakis, E., Kubicek, C. P., & Allmaier, G. (2007). Comparison of different sample preparation techniques for differentiation of mycotoxin-producing Fusarium species by MALDI-TOF/RTOF mass spectrometry. In Proceedings of the 55th ASMS Conference. 55th Annual Conference of the American Society of Mass Spectrometry, Inndianapolis, USA, Non-EU.

Kubicek, C. P., & Seiboth, B. (2007). Regulation of lactose induction of cellulase formation in Trichoderma reesei, Final report.

Mach, R. L., Stricker, A. R., Rauscher, R., Würleitner, E., & Trefflinger, P. (2007). Differential regulation of xylanase gene expression in Hypocrea jecorina is due to the interplay of the general activator Xyr1 and the fine tuning transcription factors Ace1 and Ace2. In Fungal Genetics Newsletter (p. 114).

Metz, B., Polak, S., Kubicek, C. P., & Seiboth, B. (2007). Functional analysis of the Hypocrea jecorina lxr1 encodes a D-mannitol dehydrogenase and is not involved in L-arabinose catabolism. In Fungal Genetics Newsletter (p. 106).

Mushi, D., Kivaisi, A., Mach, R. L., Byamukama, D., & Farnleitner, A. H. (2007). Sources of sorbitol-fermenting Bifidobacteria and their incidence and survival in streams and ground water habitats in urban tropical lowland of Dar es Salaam,Tanzania. In WaterMicro 2007 (pp. 22–24).

Nagy, V., Seidl, V., Szakacs, G., Komon-Zelazowska, M., Kubicek, C. P., & Druzhinina, I. (2007). Application of DNA BarCodes for screening of industrially important fungi: the haplotype of Trichoderma harzianum sensu stricto indicates superior chitinase formation. Applied and Environmental Microbiology, 73, 7048–7058.

Reischer, G., Kasper, D., Haider, J., Sommer, R., Mach, R. L., & Farnleitner, A. H. (2007). DNA-based human- and ruminant-specific quantitative microbial source tracking (QMST) in a karstic spring catchment area: development and application. In WaterMicro 2007 (pp. 26–27).

Reischer, G., Kasper, D., Steinborn, R., Farnleitner, A. H., & Mach, R. L. (2007). A quantitative real-time PCR assay for the hihgly sensitive and specific detection of human faceal influence in spring water from a large alpine catement area. Letters in Applied Microbiology, 44, 351–356.

Reischer, G., Kasper, D., Steinborn, R., Mach, R. L., & Farnleitner, A. H. (2007). Tracing the source of faecal pollution in water by qPCR: quantitative microbial source tracking (QMST). In Proceedings qPCR 2007 Event (p. 33).

Reithner, B., Schuhmacher, R., Stoppacher, N., Pucher, M., Brunner, K., & Zeilinger, S. (2007). Signaling via the Trichoderma atroviride mitogen-activated protein kinase Tmk 1 differntially affects mycoparasitism and plant protection. Fungal Genetics and Biology, 44, 1123–1133.

Schuhmacher, R., Stoppacher, N., & Zeilinger, S. (2007). Peptaibols of Trichoderma atroviride: screening, identification, and structur elucidation by liquid chromatography-tandem mass spectrometry. In Communicating Current Research and Education Topics and Trends in Applied Microbiology (pp. 609–617). FORMATEX.

Schuhmacher, R., Stoppacher, N., Reithner, B., Omann, M., Zeilinger, S., & Krska, R. (2007). Peptaibol profiles in cultures of Trichoderma atroviride: Detection and characterization by LC-MS/MS. 15th International Reinhardsbrunn Symposium - Modern Fungicides and Antifungal Compounds, Friedrichroda, Germany, EU.

Schuster, A., Kubicek, C. P., Friedl, M. A., Druzhinina, I. S., & Schmoll, M. (2007). Impact of light on Hypocrea jecorina and the multiple cellular roles of ENVOY in this process. BMC Genomics, 8(449). https://doi.org/10.1186/1471-2164-8-449

Schuster, A., Kubicek, C. P., Friedl, M., Druzhinina, I., & Schmoll, M. (2007). Novel functions of the light response regulatory protein Envoy in Hypocrea jecorina. In Molecular Biology of Fungi (p. 128).

Seiboth, B. (2007). pyr4 Blasterkassetten: Ein essentielles Werkzeug für funkrionelle Genomik in Hypocrea jecorina (Trichoderma reesei).

Seiboth, B., & Kubicek, C. P. (2007). 2nd interim report on New Genes and Proteins of Trichoderma GEPROMA 2.

Seiboth, B., & Kubicek, C. P. (2007). 3rd Interim Report on New Genes Protein of Trichoderma GEPROMA 2.

Seiboth, B., Gamauf, C., Pail, M., Hartl, L., & Kubicek, C. P. (2007). The major D-xylose reductase of Hypocrea jecorina is necessary for efficient pentose and lactose catabolism and for cellulase induction by lactose. Molecular Microbiology, 66, 890–900.

Seiboth, B., Pakdaman, B. S., Hartl, L., & Kubicek, C. P. (2007). Lactose metabolism in filamentous fungi: how to deal with an unknown substrate. Fungal Biology Reviews, 21, 42–48.

Seidl, V., Kubicek, C. P., & Read, N. D. (2007). Cell biology of the mode of action on Neurospora crassa of an antifungal agent from Hypocrea atroviridis. In Fungal Genetics (p. 49).

Seidl, V., Kubicek, C. P., & Read, N. D. (2007). Mycoparasitism and competition for living space by Trichoderma. In Ecology of Fungal Communities (p. 30).

Seidl, V., Read, N. D., & Kubicek, C. P. (2007). The chinitolytic enzyme machinery of filamentous fungi. In Cell Wall Polysaccarides of fungi and plants (p. 68).

Stadler, H., Skritek, P., Mach, R. L., & Farnleitner, A. H. (2007). Microbiological Monitoring and Automated Event Sampling at Karst Springs using Leo-Satellites. In WaterMicro 2007 (pp. 270–271).

Stoppacher, N., Reithner, B., Omann, M., Zeilinger, S., Brunner, K., Mach, R. L., Krska, R., & Schuhmacher, R. (2007). Detection and Characterization of Peptaibols in Trichoderma atroviride Culture Samples by LC-MS/MS. MassSpec - Forum - Vienna, Wien, Austria.

Stoppacher, N., Reithner, B., Omann, M., Zeilinger, S., Brunner, K., Mach, R. L., Krska, R., & Schuhmacher, R. (2007). Identification and sequencing of Trichorzianines produced by Trichoderma atroviride. 15th International Reinhardsbrunn Symposium - Modern Fungicides and Antifungal Compounds, Friedrichroda, Germany, EU.

Stoppacher, N., Reithner, B., Omann, M., Zeilinger, S., Krska, R., & Schuhmacher, R. (2007). Profiling of trichorzianines in culture samples of Trichoderma atroviride by liquid chromatography/tandem mass spectrometry. Rapid Communications in Mass Spectrometry, 21, 3963–3970.

Stoppacher, N., Reithner, B., Zeilinger, S., Krska, R., & Schuhmacher, R. (2007). Detection and Structure Characterization of Novel Peptaibols in Trichoderma Atroviride Culture Samples. In Proc. of XIII International Congress on Molecular Plant - Microbe Interactions. XIII International Congress on Molecular Plant - Microbe Interactions, Sorrento, Italy, EU.

Stricker, A. R., Steiger, M., & Mach, R. L. (2007). Xyr1 receives the lactose induction signal and regulates lactose metabolism in Hypocrea jecorina. FEBS Letters, 581, 3915–3920.

Stricker, A. R., Trefflinger, P., Aro, N., Penttila, M. E., & Mach, R. L. (2007). Involvement of Ace2(Activator of Cellulases 2) in the architecture of the yxn2 transcriptosome of Hypocrea jecorina. In Fungal Genetics Newsletter (p. 114).

Wilhartitz, I., Kirschner, A. K. T., & Farnleitner, A. H. (2007). Insitu determination of bacterial populations and corresponding activities by CARD-FISH, microautoradiography(MAR) and heterotrophic bacterial production (BP) in ground- and mineral water. In WaterMicro 2007 (pp. 374–375).

Wilhartitz, I., Mach, R. L., Teira, E., Herndl, G., & Farnleitner, A. H. (2007). Prokaryotic community analysis with CARD-FISH IN comparsion with FISH in ultra-oligotropic ground- and drinking water. Journal of Applied Microbiology, 103, 871–881.

Winter, C., Hein, T., Kavka, G. G., Mach, R. L., & Farnleitner, A. H. (2007). Longitudinal Changes in the Bacterial Community Composition of the Danube River: a Whole-River Approach. Applied and Environmental Microbiology, 73(2), 421–431.

Zeilinger, S., & Omann, M. (2007). Trichoderma Biocontrol: Signal Transduction Pathways Involved in Host Sensing and Mycoparasitism. Gene Regulation and Systems Biology, 1, 227–234.

Adam, G., Hauser, M. T., Strauss, J., Mach, R. L., & Krska, R. (2006). GEN-AU pilot project: FUSARIUM, Virulence mechanisms of the plant patogenic fungus Fusarium graminearum and resistance mechanisms in host plants, Final Report January 2003 - May 2006.

Brunner, K., Lemmens, M., Kaspar, D., Köllner, Krista. E., Adam, G., & Mach, R. L. (2006). Reduced virulence of a glucose oxidase producing strain of Fusarium graminearum on wheat. In Book of Abstracts (p. 308).

Burtscher, M. M., Köllner, Krista. E., Ryzinska, G., Sommer, R., Keiblinger, K., & Farnleitner, A. H. (2006). Identifizierung von Verursachern fäkaler Einträge mittels Profildatenbanken-basierender Methoden. In Abstracts der 30. Jahrestagung der österreichischen Gesellschaft für Hygiene, Mikrobiologie und Präventivmedizin. 30. Jahrestagung der österreichischen Gesellschaft für Hygiene, Mikrobiologie und Präventivmedizin, Linz, Austria.

Burtscher, M. M., Köllner, Krista. E., Sommer, R., Keiblinger, K., Farnleitner, A. H., & Mach, R. L. (2006). Development of a novel amplified fragment length polymorphism (AFLP) typing method for enterococci isolates from cattle faecces and evaluation of the single versus pooled faecal sampling approach. Journal of Microbiological Methods, 67, 281–293.

Ciliento, R., Woo, S. L., Brunner, K., Marra, R., Vinale, F., Ferraioli, S., Ambrosino, P., Soriente, I., Ruocco, M., Turra, D., Lanzuise, S., Gigante, S., Mach, R. L., Zeilinger, S., & Lorito, M. (2006). Genetic improvement of Trichoderma harzianum strain T22 using an inducible promoter and the Aspergillus niger goxA gene. In Book of Abstracts. 9#^{th} International Workshop on Trichoderma and Gliocladium, Wien, Austria.

Druzhinina, I., Schmoll, M., Seiboth, B., & Kubicek, C. P. (2006). Global Carbon Utilization Profiles of Wild Type, Mutant and Transformant Strains of Hypocrea jecorina. Applied and Environmental Microbiology, 72(3), 2126–2132.

Epr1 an elicitor of phytoalexin production in plants, is constitutively expressed in Hypocrea atroviridis. (2006). In Book of Abstracts. 9#^{th} International Workshop on Trichoderma and Gliocladium, Wien, Austria.

Farnleitner, A. H., Kavka, G. G., Blaschke, A. P., Strelec, H., Kirnbauer, R., Zessner, M., Schilling, C., Hassler, C., Tentschert, E.-H., Mach, R. L., & Kroiss, H. (2006). Ausmaß der Beeinträchtigung von Grundwasser als Trinkwassertresource durch Versickerung von biologisch gereinigtem häuslichem Abwasser anhand mikrobiologischer Risikoabschhätzung und Transportmodellierung. In Abstracts der 30. Jahrestagung der Österreichischen Gesellschaft für Hygiene, Mikrobiologie und Präventivmedizin (p. 52).

Farnleitner, A. H., Reischer, G., Winter, C., Hein, T., Mach, R. L., & Kavka, G. G. (2006). Progress in aquatic microbiology: introducing molecular biological approaches on a whole River Danube scale from Germany to the Black Sea. In Danube News (pp. 8–12). International Association of the Danube Research.

Farnleitner, A. H., Wilhartitz, I., Burtscher, M. M., Reischer, G., Ryzinska, G., Sommer, R., Kirschner, A. K. T., Stadler, H., Swezyk, U., & Mach, R. L. (2006). Microbiology of alpine karst aquifer springs - current view and future perspectives. In All about karst an water: decision making in a sensitive environment (pp. 183–188). European Regional Development Funds (ERDF).

Farnleitner, A. H., Wilhartitz, I., Burtscher, M. M., Reischer, G., Ryzinska, G., Sommer, R., Kirschner, A. K. T., Stadler, H., Swezyk, U., & Mach, R. L. (2006). Microbiology of alpine karst aquifer springs - current view and future perspectives. In Proc.of International Conference: All about Karst & Water. International Conference: All about Karst & Water Vienna 2006, Wien, Austria.

Farnleitner, A. H., Winter, C., Hein, T., Mach, R. L., & Kavka, G. G. (2006). Longitudinal Changes in the Bacterial Community of the Danube: A Whole River Approach. In Proceedings 36th International Conference of IAD (pp. 326–331). Austrian Committee Danube Research / IAD, Vienna.

Gamauf, C., Pail, M., Hartl, L., Kubicek, C. P., & Seiboth, B. (2006). The D-xylose reductase of Hypocrea jecorina is a general aldose reductase involved in cellulase induction on lactose. In Book of Abstracts (p. 240).

Gamauf, C., Pail, M., Hartl, L., Kubicek, C. P., & Seiboth, B. (2006). The metabolic role of Hypocrea jecorina D-xylose reductase and its influence on cellulase gene induction on lactose. In Book of Abstracts. 9#^{th} International Workshop on Trichoderma and Gliocladium, Wien, Austria.

Hartl, L., & Seiboth, B. (2006). Pyr4 blaster cassettes: a tool for functional genomics in Hypocrea jecorina. In Book of Abstracts. 9#^{th} International Workshop on Trichoderma and Gliocladium, Wien, Austria.

Hartl, L., Seiboth, B., & Kubicek, C. P. (2006). Sequential deletion of the Hypocrea jecorina glucokinase and hexokinase genes. In Book of Abstracts (p. 246).

Hornek, R., Pommerening-Röser, A., Koops, H.-P., Farnleitner, A. H., Kreuzinger, N., Kirschner, A., & Mach, R. L. (2006). Primers containing universal bases reduce multiple amoA gene specific DGGE band patterns when analysing the diversity of beta - ammonia oxidizers in the environment. Journal of Microbiological Methods, 66, 147–155.

Karaffa, L., Fekete, E., Gamauf, C., Szentirmai, A., Kubicek, C. P., & Seiboth, B. (2006). D-Galactose induces cellulase gene expression in Hypocrea jecorina at low growth rates. Microbiology, 152, 1507–1514.

Marchetti, M., Schandl, R., Allmaier, G., & Kubicek, C. P. (2006). Epl1 , the major secreted protein of Hypocrea atroviridis on glucose is a member of a strongly conserved protein family comprising plant defense response elicitors. In Stress in Yeasts and Filamentous Fungi (p. 79).

Marchetti, M., Seidl, V., Schandl, R., Kubicek, C. P., & Allmaier, G. (2006). EST databases for massspectrometric-basedprotein identification: requirement of PSD and CID (MS/MS)experiments for successful identification of aplant defense elicitor. In Book of Abstracts (p. 288).

Rauscher, R., Würleitner, E., Wacenovsky, C., Aro, N., Stricker, A. R., Zeilinger, S., Kubicek, C. P., Penttilä, M. E., & Mach, R. L. (2006). Transciptional Regulation of xyn1, Encoding Xylanase I, in Hypocrea jecorina. Eukaryotic Cell, 5(7), 447–456.

Reischer, G., Kasper, D., Mach, R. L., & Farnleitner, A. H. (2006). Zwei real-time PCR Methoden für den Nachweis von genetischen Fäkalmarkern zur Differenzierung und Quantifizierung von fäkalem Eintrag durch den Menschen und durch Wiederkäuer. In Abstracts (pp. 54–55).

Reischer, G., Kasper, D., Steinborn, R., Mach, R. L., & Farnleitner, A. H. (2006). Quantitative PCR Method for Sensitive Detection of Ruminant Fecal Pollution in Freshwater and Evaluations of This Method in Alpine Karstic Regions. Applied and Environmental Microbiology, 72(8), 5610–5614.

Reischer, G., Mach, R. L., Kasper, D., Winter, C., Kavka, G. G., & Farnleitner, A. H. (2006). Testing the applicability of DNA based microbial faecal source tracking methods on a large scale in the River Danube and its important tributaries. In Proceedings 36th International Conference of IAD (pp. 332–337). Austrian Committee Danube Research / IAD, Vienna.

Reithner, B., Schuhmacher, R., & Zeilinger, S. (2006). The mitogen-activated protein kinase Tmk1 is involved in Trichoderma atroviride mycoparasitism. In Book of Abstracts (p. 184).

Reithner, B., Schuhmacher, R., & Zeilinger, S. (2006). Tmk1, a Trichoderma atroviride MAP-kinase, and its role in the mycoparasitic response. In Book of Abstracts. 9#^{th} International Workshop on Trichoderma and Gliocladium, Wien, Austria.

Seiboth, B. (2006). Monosaccharide catabolic pathways controlling extracellular enzyme induction in Hypocrea jecorina. In Book of Abstracts (p. 14).

Seiboth, B., Hartl, L., Gamauf, C., Metz, B., & Kubicek, C. P. (2006). Metabolic engineering of utilization of lactose, a renewable carbon source for cell factory Hypocrea jecorina (Trichoderma reesei). In Industrielle Biotechnologie - Eine Chance für Österreich? (pp. 27–28).

Seidl, V., & Druzhinina, I. (2006). A screening system for carbon sources enhancing β-N-acetylglucosaminidase formation in Hypocrea atroviridis (Trichoderma atroviride). In Book of Abstracts (p. 202).

Seidl, V., Marchetti, M., Schandl, R., Allmaier, G., & Kubicek, C. P. (2006). Epl1, the major secreted protein of Hypocrea atroviridis on glucose, is a member of a strong conserved protein family comparsing plant defense response elicitors. The FEBS Journal, 273, 4346–4359.

Stadler, H., Skritek, P., Mach, R. L., & Farnleitner, A. H. (2006). Event sampling and monitoring for microbiological investigations at karstic springs by networking via leo-satellites. In Proc.of International Conference: All about Karst & Water. International Conference: All about Karst & Water Vienna 2006, Wien, Austria.

Stoppacher, N., Reithner, B., Zeilinger, S., Brunner, K., Mach, R. L., Krska, R., & Schuhmacher, R. (2006). Screening for Atroviridins, Neoatroviridins and Harzianins in Culture Samples of Trichoderma atroviride using LC-MS/MS. In Book of Abstracts. 9#^{th} International Workshop on Trichoderma and Gliocladium, Wien, Austria.