Publications archive

Valdivieso P., Vaughan D., Laczko E., Brogioli M., Waldron S., Rittweger J. and Flück M. external pageThe metabolic response of skeletal muscle to endurance exercise is modified by the ACE-I/D gene polymorphism and training state, Frontiers in Physiology, 8 (DEC), 2017.

J. Abplanalp, M. Leutert, E. Frugier, K. Nowak, R. Feurer, J. Kato, H. V. A. Kistemaker, D. V. Filippov, J. Moss, A. Caflisch and M. O. Hottiger, external pageProteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase. Nat Commun, 8 (1): 2055, 2017/12/12.

Massimiliano Manzo, Joël Wirz, Christina Ambrosi, Rodrigo Villaseñor, Bernd Roschitzki and Tuncay Baubec, external pageIsoform-specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands. EMBO Journal, 36 (23): 3421-3434, Weinheim: Wiley, 2017.

György Sipos, Arun N. Prasanna, Mathias C. Walter, Eoin O’Connor, Balázs Bálint, Krisztina Krizsán, Brigitta Kiss, Jaqueline Hess, Torda Varga, Jason Slot, Robert Riley, Bettina Bóka, Daniel Rigling, Kerrie Barry, Juna Lee, Sirma Mihaltcheva, Kurt LaButti, Anna Lipzen, Rose Waldron, Nicola M. Moloney, Christoph Sperisen, László Kredics, Csaba Vágvölgyi, Andrea Patrignani, David Fitzpatrick, István Nagy, Sean Doyle, James B. Anderson, Igor V. Grigoriev, Ulrich Güldener, Martin Münsterkötter and László G. Nagy, external pageGenome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nature Ecology and Evolution, 1: 1931-1941, London: Springer Nature, 2017.

Marc Bachofner, Tobias Speicher, Roman L. Bogorad, Sukalp Muzumdar, Carina P. Derrer, Fabrizio Hürlimann, Friederike Böhm, Paolo Nanni, Tobias Kockmann, Ekaterina Kachaylo, Michael Meyer, Susagna Padrissa-Altés, Rolf Graf, Daniel G. Anderson, Victor Koteliansky, Ulrich Auf dem Keller and Sabine Werner, external pageLarge-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration. Developmental Cell, 42 (6): 616-625.e8, Cambridge, MA: Cell Press; Elsevier, 2017.

Karin Moelling, Felix Broecker, Giancarlo Russo and Shinichi Sunagawa, external pageRNase H As Gene Modifier, Driver of Evolution and Antiviral Defense. Frontiers in Microbiology, 8, Lausanne: Frontiers, 2017.

Sunil Kumar Dogga, Budhaditya Mukherjee, Damien Jacot, Tobias Kockmann, Luca Molino, Pierre-Mehdi Hammoudi, Ruben C. Hartkoorn, Adrian B. Hehl and Dominique Soldati-Favre, external pageA druggable secretory protein maturase of Toxoplasma essential for invasion and egress. eLife, 6: e27480, Cambridge: eLife Sciences Publications, 2017.

Yannick Boege, Mohsen Malehmir, Marc E. Healy, Kira Bettermann, Anna Lorentzen, Mihael Vucur, Akshay K. Ahuja, Friederike Böhm, Joachim C. Mertens, Yutaka Shimizu, Lukas Frick, Caroline Remouchamps, Karun Mutreja, Thilo Kähne, Devakumar Sundaravinayagam, Monika J. Wolf, Hubert Rehrauer, Christiane Koppe, Tobias Speicher, Susagna Padrissa-Altésse, Renaud Maire, Jörn M. Schattenberg, Ju-Seong Jeong and Lei Liu, external pageA Dual Role of Caspase-8 in Triggering and Sensing Proliferation-Associated DNA Damage, a Key Determinant of Liver Cancer Development. Cancer Cell, 32 (3): 342-359.e10, Cambridge, MA; Amsterdam: Cell Press; Elsevier, 2017.

Parisa Amini, Julia Ettlin, Lennart Opitz, Elena Clementi, Alexandra Malbon and Enni Markkanen, external pageAn optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing. BMC Molecular biology, 18: 22, London: BioMed Central, 2017.

Kapil D. Singh, Xue Zheng, Stuart Milstein, Martin Keller, Bernd Roschitzki, Jonas Grossmann and Michael O. Hengartner, external pageDifferential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans. PLoS ONE, 12 (7): e0182270, San Francisco, CA: Public Library of Science, 2017.

Angelo Gámez-Pozo, Lucía Trilla-Fuertes, Guillermo Prado-Vázquez, Cristina Chiva, Rocío López-Vacas, Paolo Nanni, Julia Berges-Soria, Jonas Grossmann, Mariana Díaz-Almirón, Eva Ciruelos, Eduard Sabidó, Enrique Espinosa and Juan Á. Fresno Vara, external pagePrediction of adjuvant chemotherapy response in triple negative breast cancer with discovery and targeted proteomics. PLoS ONE, 12 (6): e0178296, San Francisco, CA: Public Library of Science, 2017.

Vera Bilan, Nathalie Selevsek, Hans A.V. Kistemaker, Jeanette Abplanalp, Roxane Feurer, Dmitri V. Filippov and Michael O. Hottiger, external pageNew Quantitative Mass Spectrometry Approaches Reveal Different ADP-ribosylation Phases Dependent On the Levels of Oxidative Stress. Molecular & Cellular Proteomics, 16 (5): 949-958, Bethesda, MD: American Society for Biochemistry and Molecular Biology, 2017.

Ruben Casanova, Daniel Xia, Undine Rulle, Paolo Nanni, Jonas Grossmann, Bart Vrugt, Reto Wettstein, Rafael Ballester, Alberto Astolfo, Walter Weder, Holger Moch, Marco Stampanoni, Andrew H. Beck and Alex Soltermann, external pageMorphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness. Cancer research, 77 (10): 2585-2593, Philadelphia, PA: American Association for Cancer Research, 2017.

Xiaorong Wang, Peter Cimermancic, Clinton Yu, Andreas Schweitzer, Nikita Chopra, James L. Engel, Charles Greenberg, Alexander S. Huszagh, Florian Beck, Eri Sakata, Yingying Yang, Eric J. Novitsky, Alexander Leitner, Paolo Nanni, Abdullah Kahraman, Xing Guo, Jack E. Dixon, Scott D. Rychnovsky, Ruedi Aebersold, Wolfgang Baumeister, Andrej Sali and Lan Huang, external pageMolecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Molecular & Cellular Proteomics, 16 (5): 840-854, Bethesda, MD: American Society for Biochemistry and Molecular Biology, 2017.

Jacqueline Neubauer, Maria Rita Lecca, Giancarlo Russo, Christine Bartsch, Argelia Medeiros-Domingo, Wolfgang Berger and Cordula Haas, external pagePost-mortem whole-exome analysis in a large sudden infant death syndrome cohort with a focus on cardiovascular and metabolic genetic diseases. European journal of human genetics, 25 (4): 404-409, Houndmills, Basingstoke: Nature, 2017.

Minerva S. Trejo-Arellano, Walid Mahrez, Miyuki Nakamura, Jordi Moreno-Romero, Paolo Nanni, Claudia Köhler and Lars Hennig, external pageH3K23me1 is an evolutionarily conserved histone modification associated with CG DNA methylation in Arabidopsis. Plant Journal, 90 (2): 293-303, Oxford: Wiley-Blackwell, 2017.

Etienne Caron, Romain Roncagalli, Takeshi Hase, Witold E. Wolski, Meena Choi, Marisa G. Menoita, Stephane Durand, Antonio García-Blesa, Ivo Fierro-Monti, Tatjana Sajic, Moritz Heusel, Tobias Weiss, Marie Malissen, Ralph Schlapbach, Ben C. Collins, Samik Ghosh, Hiroaki Kitano, Ruedi Aebersold, Bernard Malissen and Matthias Gstaiger, external pagePrecise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Reports, 18 (13): 3219-3226, Amsterdam: Elsevier, 2017.

Mojca Frank-Bertoncelj, Michelle Trenkmann, Kerstin Klein, Emmanuel Karouzakis, Hubert Rehrauer, Anna Bratus, Christoph Kolling, Maria Armaka, Andrew Filer, Beat A. Michel, Renate E. Gay, Christopher D. Buckley, George Kollias, Steffen Gay and Caroline Ospelt, external pageEpigenetically-driven anatomical diversity of synovial fibroblasts guides joint-specific fibroblast functions. Nature Communications, 8: 14852, London: Nature Publishing Group, 2017.

Ayako Izuno, Kanehiro Kitayama, Yusuke Onoda, Tetsuya Tsujii, Masaomi Hatakeyama, Atsushi J. Nagano, Mie N. Honjo, Rie Shimizu-Inatsugi, Hiroshi Kudoh, Kentaro K. Shimizu and Yuji Isagi, external pageThe population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae). Molecular Ecology, 26 (6): 1515-1532, Oxford: Wiley-Blackwell, 2017.

Anuli C. Uzozie, Nathalie Selevsek, Asa Wahlander, Paolo Nanni, Jonas Grossmann, Achim Weber, Federico Buffoli and Giancarlo Marra, external pageTargeted proteomics for multiplexed verification of markers of colorectal tumorigenesis. Molecular and Cellular Proteomics, 16 (3): 407-427, Bethesda, MD: American Society for Biochemistry and Molecular Biology, 2017.

Vera Bilan, Mario Leutert, Paolo Nanni, Christian Panse and Michael O. Hottiger, external pageCombining Higher-Energy Collision Dissociation and Electron-Transfer/Higher-Energy Collision Dissociation Fragmentation in a Product-Dependent Manner Confidently Assigns Proteomewide ADP-Ribose Acceptor Sites. Analytical Chemistry, 89 (3): 1523-1530, Washington, DC: American Chemical Society, 2017.

Christian Gerspach, Sandro Imhasly, M. Gubler, Hanspeter Naegeli, Maja Ruetten and Endre Laczkó, external pageAltered plasma lipidome profile of dairy cows with fatty liver disease. Research in Veterinary Science, 110: 47-59, Oxford: Elsevier, 2017.

André M. Almeida, Paolo Nanni, Ana M. Ferreira, Claudia Fortes, Jonas Grossmann, Rui J.B. Bessa and Paolo Costa, external pageThe longissimus thoracis muscle proteome in Alentejana bulls as affected by growth path. Journal of Proteomics, 152: 206-215, Amsterdam: Elsevier, 2017.

Martin Fluck, Severin Ruoss, Christoph B. Mohl, Paola Valdivieso, Mario C. Benn, Brigitte Von Rechenberg, Endre Laczko, Junmin Hu, Karl Wieser, Dominik C. Meyer and Christian Gerber, Genomic and lipidomic actions of nandrolone on detached rotator cuff muscle in sheep. Journal of Steroid Biochemistry and Molecular Biology, 165: 382-395, Amsterdam: Elsevier, 2017.

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Matthias Rosenwald, Vissarion Efthymiou, Lennart Opitz and Christian Wolfrum, SRF and MKL1 independently inhibit brown adipogenesis. PLoS ONE, 12 (1): e0170643, San Francisco, CA: Public Library of Science, 2017.

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Michael Walser, Christoph A. Umbricht, Erika Fröhli, Paolo Nanni and Alex Hajnal, beta-Integrin de-phosphorylation by the Density-Enhanced Phosphatase DEP-1 attenuates EGFR signaling in C. elegans. PLoS Genetics, 13 (1): e1006592, San Francisco, CA: Public Library of Science, 2017.

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Ravi B. Anjanappa, Devang Mehta, Michal J. Okoniewski, Alicja Szabelska-Berȩsewicz, Wilhelm Gruissem and Hervé Vanderschuren, Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response. Molecular Plant Pathology, Oxford: Wiley-Blackwell, 2017.

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M. Bachofner, T. Speicher, R. L. Bogorad, S. Muzumdar, C. P. Derrer, F. Hurlimann, F. Bohm, P. Nanni, T. Kockmann, E. Kachaylo, M. Meyer, S. Padrissa-Altes, R. Graf, D. G. Anderson, V. Koteliansky, U. Auf dem Keller and S. Werner, Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration. Dev Cell, 42 (6): 616-625 e8, 2017.

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K. Bao, N. Bostanci, T. Thurnheer and G. N. Belibasakis, Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus. Sci Rep, 7 (1): 4409, 2017.

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E. Becker, S. Bengs, S. Aluri, L. Opitz, K. Atrott, C. Stanzel, P. A. Castro, G. Rogler and I. Frey-Wagner, Doxycycline, metronidazole and isotretinoin: Do they modify microRNA/mRNA expression profiles and function in murine T-cells?. Sci Rep, 6: 37082, 2017.

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E. Becker, T. S. B. Schmidt, S. Bengs, L. Poveda, L. Opitz, K. Atrott, C. Stanzel, L. Biedermann, A. Rehman, D. Jonas, C. von Mering, G. Rogler and I. Frey-Wagner, Effects of oral antibiotics and isotretinoin on the murine gut microbiota. Int J Antimicrob Agents, 50 (3): 342-351, 2017.

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K. Becker, K. Haldimann, P. Selchow, L. M. Reinau, M. Dal Molin and P. Sander, Lipoprotein Glycosylation by Protein-O-Mannosyltransferase (MAB_1122c) Contributes to Low Cell Envelope Permeability and Antibiotic Resistance of Mycobacterium abscessus. Front Microbiol, 8: 2123, 2017.

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L. Bisceglie, G. Bartolomei and M. O. Hottiger, ADP-ribose-specific chromatin-affinity purification for investigating genome-wide or locus-specific chromatin ADP-ribosylation. Nat Protoc, 12 (9): 1951-1961, 2017.

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Felix Broecker, Giancarlo Russo, Jochen Klumpp and Karin Moelling, Stable core virome despite variable microbiome after fecal transfer. Gut Microbes, 8 (3): 214-220, Philadelphia, PA: Taylor & Francis, 2017.

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E. Caron, R. Roncagalli, T. Hase, W. E. Wolski, M. Choi, M. G. Menoita, S. Durand, A. Garcia-Blesa, I. Fierro-Monti, T. Sajic, M. Heusel, T. Weiss, M. Malissen, R. Schlapbach, B. C. Collins, S. Ghosh, H. Kitano, R. Aebersold, B. Malissen and M. Gstaiger, Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Rep, 18 (13): 3219-3226, 2017.

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Ruben Casanova, Daniel Xia, Undine Rulle, Paolo Nanni, Jonas Grossmann, Bart Vrugt, Reto Wettstein, Rafael Ballester, Alberto Astolfo, Walter Weder, Holger Moch, Marco Stampanoni, Andrew H. Beck and Alex Soltermann, Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness. CANCER RESEARCH, 77 (10): 2585-2593, American Association for Cancer Research (AACR), 2017.

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Ben C. Collins, Christie L. Hunter, Yansheng Liu, Birgit Schilling, George Rosenberger, Samuel L. Bader, Daniel W. Chan, Bradford W. Gibson, Anne-Claude Gingras, Jason M. Held, Mio Hirayama-Kurogi, Guixue Hou, Christoph Krisp, Brett Larsen, Liang Lin, Siqi Liu, Mark P. Molloy, Robert L. Moritz, Sumio Ohtsuki, Ralph Schlapbach, Nathalie Selevsek, Stefani N. Thomas, Hui Zhang and Ruedi Aebersold, Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nature Communications, 8: 291, London: Nature Publishing Group, 2017.

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Ana M. Ferreira, Jonas Grossmann, Claudia Fortes, Tanya Kilminster, Tim Scanlon, John Milton, Johan Greeff, Chris Oldham, Paolo Nanni and André M. Almeida, The sheep (Ovis aries) muscle proteome: Decoding the mechanisms of tolerance to Seasonal Weight Loss using label-free proteomics. Journal of Proteomics, 161: 57-67, Amsterdam: Elsevier, 2017.

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U. Graf, E. A. Casanova, S. Wyck, D. Dalcher, M. Gatti, E. Vollenweider, M. J. Okoniewski, F. A. Weber, S. S. Patel, M. W. Schmid, J. Li, J. Sharif, G. A. Wanner, H. Koseki, J. Wong, P. Pelczar, L. Penengo, R. Santoro and P. Cinelli, Pramel7 mediates ground-state pluripotency through proteasomal-epigenetic combined pathways. Nat Cell Biol, 19 (7): 763-773, 2017.

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Angelo Gámez-Pozo, Lucia Trilla-Fuertes, Julia Berges-Soria, Nathalie Selevsek, Rocío López-Vacas, Mariana Díaz-Almirón, Paolo Nanni, Jorge M. Arevalillo, Hilario Navarro, Jonas Grossmann, Francisco G. Moreno, Rubén Gómez Rioja, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Paloma Main, Jaime Feliú, Purificación Martínez del Prado, Pilar Zamora, Eva Ciruelos, Enrique Espinosa and Juana A. Fresno Vara, Functional proteomics outlines the complexity of breast cancer molecular subtypes. Scientific Reports, 7: 10100, London: Nature Publishing Group, 2017.

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M. Hatakeyama, S. Aluri, M. T. Balachadran, S. R. Sivarajan, A. Patrignani, S. Gruter, L. Poveda, R. Shimizu-Inatsugi, J. Baeten, K. J. Francoijs, K. N. Nataraja, Y. A. N. Reddy, S. Phadnis, R. L. Ravikumar, R. Schlapbach, S. M. Sreeman and K. K. Shimizu, Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. DNA Res, 2017.

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F. Item, S. Wueest, V. Lemos, S. Stein, F. C. Lucchini, R. Denzler, M. C. Fisser, T. D. Challa, E. Pirinen, Y. Kim, S. Hemmi, E. Gulbins, A. Gross, L. A. O'Reilly, M. Stoffel, J. Auwerx and D. Konrad, Fas cell surface death receptor controls hepatic lipid metabolism by regulating mitochondrial function. Nat Commun, 8 (1): 480, 2017.

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A. Javed, N. Leuchte, G. Salinas, L. Opitz, C. Stahl-Hennig, S. Sopper and U. Sauermann, Pre-infection transcript levels of FAM26F in peripheral blood mononuclear cells inform about overall plasma viral load in acute and post-acute phase after simian immunodeficiency virus infection. J Gen Virol, 97 (12): 3400-3412, 2017.

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M. Knobloch, G. A. Pilz, B. Ghesquiere, W. J. Kovacs, T. Wegleiter, D. L. Moore, M. Hruzova, N. Zamboni, P. Carmeliet and S. Jessberger, A Fatty Acid Oxidation-Dependent Metabolic Shift Regulates Adult Neural Stem Cell Activity. Cell Rep, 20 (9): 2144-2155, 2017.

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Lars Kuepfer, Olivia Clayton, Christoph Thiel, Henrik Cordes, Ramona Nudischer, Lars M. Blank, Vanessa Baier, Stephane Heymans, Florian Caiment, Adrian Roth, David A. Fluri, Jens M. Kelm, José Castell, Nathalie Selevsek, Ralph Schlapbach, Hector Keun, James Hynes, Ugis Sarkans, Hans Gmuender, Ralf Herwig, Steven Niederer, Johannes Schuchhardt, Matthew Segall and Jos Kleinjans, A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity. Archives of Toxicology, Berlin: Springer, 2017.

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S. C. Larsen, M. Leutert, V. Bilan, R. Martello, S. Jungmichel, C. Young, M. O. Hottiger and M. L. Nielsen, Proteome-Wide Identification of In Vivo ADP-Ribose Acceptor Sites by Liquid Chromatography-Tandem Mass Spectrometry. Methods Mol Biol, 1608: 149-162, 2017.

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M. Leutert, V. Bilan, P. Gehrig and M. O. Hottiger, Identification of ADP-Ribose Acceptor Sites on In Vitro Modified Proteins by Liquid Chromatography-Tandem Mass Spectrometry. Methods Mol Biol, 1608: 137-148, 2017.

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Y. Liu, M. Lardi, A. Pedrioli, L. Eberl and G. Pessi, NtrC-dependent control of exopolysaccharide synthesis and motility in Burkholderia cenocepacia H111. PLoS One, 12 (6): e0180362, 2017.

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M. E. Losfeld, E. Scibona, C. W. Lin, T. K. Villiger, R. Gauss, M. Morbidelli and M. Aebi, Influence of protein/glycan interaction on site-specific glycan heterogeneity. FASEB J, 31 (10): 4623-4635, 2017.

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P. Luciani, A. Estella-Hermoso de Mendoza, T. Casalini, S. Lang, K. Atrott, M. R. Spalinger, A. Pratsinis, J. Sobek, I. Frey-Wagner, J. Schumacher, J. C. Leroux and G. Rogler, Gastroresistant oral peptide for fluorescence imaging of colonic inflammation. J Control Release, 262: 118-126, 2017.

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L.Marquardt, M. Lacour, M. Hoernes, L. Opitz, R. Lecca, B. Volkmer, J. Reichenbach, D. Hohl, M. Ansari, H. Ozsahin, T. Gungor and J.Pachlopnik Schmid, Unusual dermatological presentation and immune phenotype in SCID due to an IL7R mutation: the value of whole-exome sequencing and the potential benefit of newborn screening. J Eur Acad Dermatol Venereol, 31 (3): e147-e148, 2017.

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R. Martello, M. Leutert, S. Jungmichel, V. Bilan, S. C. Larsen, C. Young, M. O. Hottiger and M. L. Nielsen, Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue. Nat Commun, 7: 12917, 2017.

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M. Mika, J. Maurer, I. Korten, A. Allemann, S. Aebi, S. D. Brugger, W. Qi, U. Frey, P. Latzin and M. Hilty, Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case-control study. Microbiome, 5 (1): 85, 2017.

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Begonia F. Olivencia, Andreas U. Müller, Bernd Roschitzki, Sibylle Burger, Eilika Weber-Ban and Frank Imkam, Mycobacterium smegmatis PafBC is involved in regulation of DNA damage response. Scientific Reports, 7 (1): 13987, London: Nature Publishing Group, 2017.

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Ulrich Omasits, Adithi R. Varadarajan, Michael Schmid, Sandra Goetze, Damianos Melidis, Marc Bourqui, Olga Nikolayeva, Maxime Québatte, Andrea Patrignani, Christoph Dehio, Juerg E. Frey, Mark D. Robinson, Bernd Wollscheid and Christian H. Ahrens, An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Research, 27 (12): 2095, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2017.

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K. Poljak, J. Breitling, R. Gauss, G. Rugarabamu, M. Pellanda and M. Aebi, Analysis of substrate specificity of Trypanosoma brucei oligosaccharyltransferases (OSTs) by functional expression of domain-swapped chimeras in yeast. J Biol Chem, 292 (49): 20342-20352, 2017.

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Kristina Poljak, Nathalie Selevsek, Elsy Ngwa, Jonas Grossmann, Marie Estelle Losfeld and Markus Aebi, Quantitative Profiling of N-linked Glycosylation Machinery in Yeast Saccharomyces cerevisiae. MOLECULAR & CELLULAR PROTEOMICS, mcp.RA117.000096, American Society for Biochemistry & Molecular Biology (ASBMB), 2017.

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Weihong Qi, Ralph Schlapbach and Hubert Rehrauer, RNA-Seq Data Analysis: From Raw Data Quality Control to Differential Expression Analysis. In Plant Germline Development, edited by Schmidt, Anja, 1669: 295-307, New York, NY: Humana Press, 2017.

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Bernd Roschitzki and Salomé LeibundGut-Landmann, Identification of Fungal T Cell Epitopes by Mass Spectrometry-Based Proteomics. In Vaccines for Invasive Fungal Infections: Methods and Protocols, edited by Kalkum, Markus, and Margarita Semis, 1625: 65-74, New York, NY: Humana Press, 2017.

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F. Sabino, O. Hermes and U. Auf dem Keller, Body Fluid Degradomics and Characterization of Basic N-Terminome. Methods Enzymol, 585: 177-199, 2017.

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H. M. Seth-Smith, S. Wanninger, N. Bachmann, H. Marti, W. Qi, M. Donati, A. di Francesco, A. Polkinghorne and N. Borel, The Chlamydia suis Genome Exhibits High Levels of Diversity, Plasticity, and Mobile Antibiotic Resistance: Comparative Genomics of a Recent Livestock Cohort Shows Influence of Treatment Regimes. Genome Biol Evol, 9 (3): 750-760, 2017.

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K. D. Singh, X. Zheng, S. Milstein, M. Keller, B. Roschitzki, J. Grossmann and M. O. Hengartner, Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C: elegans. PLoS One, 12 (7): e0182270, 2017.

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G. Sipos, A. N. Prasanna, M. C. Walter, E. O'Connor, B. Balint, K. Krizsan, B. Kiss, J. Hess, T. Varga, J. Slot, R. Riley, B. Boka, D. Rigling, K. Barry, J. Lee, S. Mihaltcheva, K. LaButti, A. Lipzen, R. Waldron, N. M. Moloney, C. Sperisen, L. Kredics, C. Vagvolgyi, A. Patrignani, D. Fitzpatrick, I. Nagy, S. Doyle, J. B. Anderson, I. V. Grigoriev, U. Guldener, M. Munsterkotter and L. G. Nagy, Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nat Ecol Evol, 1 (12): 1931-1941, 2017.

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K. Sugita, C. A. Steer, I. Martinez-Gonzalez, C. Altunbulakli, H. Morita, F. Castro-Giner, T. Kubo, P. Wawrzyniak, B. Ruckert, K. Sudo, S. Nakae, K. Matsumoto, L. O'Mahony, M. Akdis, F. Takei and C. A. Akdis, Type 2 innate lymphoid cells disrupt bronchial epithelial barrier integrity by targeting tight junctions through IL-13 in asthmatic patients. J Allergy Clin Immunol, 141 (1): 300-310 e11, 2017.

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A. Taylor-Brown, T. Pillonel, A. Bridle, W. Qi, N. L. Bachmann, T. L. Miller, G. Greub, B. Nowak, H. M. B. Seth-Smith, L. Vaughan and A. Polkinghorne, Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria. Environ Microbiol, 19 (5): 1899-1913, 2017.

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P. Vazquez-Gutierrez, M. J. Stevens, P. Gehrig, S. Barkow-Oesterreicher, C. Lacroix and C. Chassard, The extracellular proteome of two Bifidobacterium species reveals different adaptation strategies to low iron conditions. BMC Genomics, 18 (1): 41, 2017.

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Sophie Zatta, Hubert Rehrauer, Aykut Gram, Alois Boos and Mariusz P. Kowalewski, Transcriptome analysis reveals differences in mechanisms regulating cessation of luteal function in pregnant and non-pregnant dogs. BMC Genomics, 18 (1): 757, London: BioMed Central, 2017.

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Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria, Silvia Ardissone, Peter Redder, Giancarlo Russo, Antonio Frandi, Coralie Fumeaux, Andrea Patrignani, Ralph Schlapbach, Laurent Falquet and Patrick H. Viollier. PLoS Genetics, 12 (12): e1006499, San Francisco, CA: Public Library of Science, 2016.

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Prognostic value of cross-omics screening for kidney clear cell renal cancer survival, Slavica Dimitrieva, Ralph Schlapbach and Hubert Rehrauer. Biology Direct, 11: 68, London: BioMed Central, 2016.

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Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica, Timothy Paape, Masaomi Hatakeyama, Rie Shimizu-Inatsugi, Teo Cereghetti, Yoshihiko Onda, Tanaka Kenta, Jun Sese and Kentaro K. Shimizu. Molecular Biology and Evolution, 33 (11): 2781-2800, Oxford: Oxford University Press, 2016.

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Diurnal changes in the histone H3 signature H3K9ac|H3K27ac|H3S28p are associated with diurnal gene expression in Arabidopsis, Katja Baerenfaller, Huan Shu, Matthias Hirsch-Hoffmann, Johannes Fütterer, Lennart Opitz, Hubert Rehrauer, Lars Hennig and Wilhelm Gruissem. Plant Cell & Environment, 39 (11): 2557-2569, Oxford: Wiley-Blackwell, 2016.

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Brain interstitial fluid glutamine homeostasis is controlled by blood-brain barrier SLC7A5/LAT1 amino acid transporter, Elena Dolgodilina, Stefan Imobersteg, Endre Laczko, Tobias Welt, François Verrey and Victoria Makrides. Journal of Cerebral Blood Flow & Metabolism, 36 (11): 1929-1941, Thousand Oaks, CA: Sage, 2016.

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The H3 chaperone function of NASP is conserved in Arabidopsis, Vladimir Maksimov, Miyuki Nakamura, Thomas Wildhaber, Paolo Nanni, Margareta Ramström, Jonas Bergquist and Lars Hennig. The plant journal, 88 (3): 425-436, Oxford: Wiley-Blackwell, 2016.

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Structure, anti-Phytophthora and anti-tumor activities of a nortriterpenoid from the rhizome of Phlomis purpurea (Lamiaceae), Maria C. Mateus, Dina Neves, Bruno Dacunha, Endre Laczko, Cristiana Maia, Rúben Teixeira and Alfredo Cravador. Phytochemistry, 131: 158-164, Amsterdam: Elsevier, 2016.

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Host-Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts, Weihong Qi, Lloyd Vaughan, Pantelis Katharios, Ralph Schlapbach and Helena M.B. Seth-Smith. Genome biology and evolution, 8 (6): 1672-1689, Oxford: Oxford University Press, 2016.

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High-resolution community profiling of arbuscular mycorrhizal fungi, Klaus Schlaeppi, S. Franz Bender, Fabio Mascher, Giancarlo Russo, Andrea Patrignani, Tessa Camenzind, Stefan Hempel, Matthias C. Rillig and Marcel G.A. van der Heijden. New Phytologist, 212 (3): 780-791, Oxford: Wiley-Blackwell, 2016.

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Potential of Environmental Enrichment to Prevent Transgenerational Effects of Paternal Trauma, Katharina Gapp, Johannes Bohacek, Jonas Grossmann, Andrea M. Brunner, Francesca Manuella, Paolo Nanni and Isabelle M. Mansuy. Neuropsychopharmacology, 41 (11): 2749-2758, Basingstoke, Hampshire: Nature Publ. Group, 2016.

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Basement membrane protein ladinin-1 and the MIF-CD44-beta 1 integrin signaling axis are implicated in laryngeal cancer metastasis, Marko Klobučar, Mirela Sedić, Peter Gehrig, Jonas Grossmann, Mario Bilić, Lana Kovač-Bilić, Krešimir Pavelić and Sandra K. Pavelić. Biochimica et Biophysica Acta : BBA, 1862 (10): 1938-1954, Amsterdam: Elsevier, 2016.

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H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system, Maria Derkacheva, Shujing Liu, Duarte D. Figueiredo, Matthew Gentry, Iva Mozgova, Paolo Nanni, Min Tang, Mattias Mannervik, Claudia Köhler and Lars Hennig. Nature Plants, 2: 16126, London: Nature, 2016.

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The goat (Capra hircus) mammary gland secretory tissue proteome as influenced by weight loss: A study using label free proteomics, Lorenzo E. Hernández-Castellano, Ana M. Ferreira, Paolo Nanni, Jonas Grossmann, Anastasio Argüello, Juan Capote, Guohong Cai, John Lippolis, Noemí Castro and Andre M. de Almeida. Journal of Proteomics, 145: 60-69, Amsterdam: Elsevier, 2016.

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Comprehensive Proteomic Analysis of Nitrogen-Starved Mycobacterium smegmatis Delta pup Reveals the Impact of Pupylation on Nitrogen Stress Response, Giuseppina Fascellaro, Agnese Petrera, Zon W. Lai, Paolo Nanni, Jonas Grossmann, Sibylle Burger, Martin L. Biniossek, Alejandro Gomez-Auli, Oliver Schilling and Frank Imkamp. Journal of Proteome Research, 15 (8): 2812-2825, Washington, DC: American Chemical Society, 2016.

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Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective, Tobias Kockmann, Christian Trachsel, Christian Panse, Asa Wahlander, Nathalie Selevsek, Jonas Grossmann, Witold E. Wolski and Ralph Schlapbach. Proteomics, 16 (15-16): 2183-2192, Weinheim: Wiley, 2016.

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Institutional core facilities: prerequisite for breakthroughs in the life sciences: Core facilities play an increasingly important role in biomedical research by providing scientists access to sophisticated technology and expertise, Doris Meder, Mònica Morales, Rainer Pepperkok, Ralph Schlapbach, Andreas Tiran and Geert van Minnebruggen. EMBO Reports, 17 (8): 1088-1093, Weinheim: Wiley, 2016.

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The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study, Moana Mika, Insa Korten, Weihong Qi, Nicolas Regamey, Urs Frey, Carmen Casaulta, Philipp Latzin, Markus Hilty and SCILD study group. The Lancet Respiratory Medicine, 4 (8): 627-635, Oxford: Elsevier, 2016.

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Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations, Ayako Izuno, Masaomi Hatakeyama, Tomoaki Nishiyama, Ichiro Tamaki, Rie Shimizu-Inatsugi, Ryuta Sasaki, Kentaro K. Shimizu and Yuji Isagi. Journal of plant research, 129 (4): 727-736, Tokyo: Botanical Society of Japan, 2016.

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IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation, Yavuz Oktay, Ege Ülgen, Özge Can, Cemaliye B. Akyerli, Şirin Yüksel, Yiğit Erdemgil, I. Melis Durasl, Octavian I. Henegariu, E. Paolo Nanni, Nathalie Selevsek, Jonas Grossmann, E. Zeynep Erson-Omay, Hanwen Bai, Manu Gupta, William Lee, Şevin Turcan, Aysel Özplnar, Jason T. Huse, M. Aydın Sav, Adrienne Flanagan, Murat Günel, O. Uğur Sezerman, M. Cengiz Yaklcler, M. Necmettin Pamir and Koray Özduman. Scientific Reports, 6: 27569, London: Nature Publishing Group, 2016.

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Haptoglobin Preserves Vascular Nitric Oxide Signaling during Hemolysis, Christian A. Schaer, Jeremy W. Deuel, Daniela Schildknecht, Leila Mahmoudi, Ines Garcia-Rubio, Catherine Owczarek, Stefan Schauer, Reinhard Kissner, Uddyalok Banerjee, Andre F. Palmer, Donat R. Spahn, David C. Irwin, Florence Vallelian, Paul W. Buehler and Dominik J. Schaer. American Journal of Respiratory and Critical Care Medicine, 193 (10): 1111-1122, New York, NY: American Thoracic Society, 2016.

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Oxidation of the N-Terminal Domain of the Wheat Metallothionein E-c-1 Leads to the Formation of Three Distinct Disulfide Bridges, Katsiaryna Tarasava, Serge Chesnov and Eva Freisinger. Biopolymers, 106 (3): 295-308, New York, NY: Wiley-Blackwell, 2016.

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Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen, Stephen H. Gillespie, Clare L. Ling, Katarina Oravcova, Miguel Pinheiro, Louise Wells, Josephine M. Bryant, Timothy D. McHugh, Cecile Bébéar, David Webster, Simon R. Harris, Helena M. Seth-Smith and Nicholas R. Thomson. Clinical Infectious Diseases, 60 (3): 381-388, Cary, NC: Oxford University Press, 2016.

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Long-term changes of bacterial and viral compositions in the intestine of a recovered Clostridium difficile patient after fecal microbiota transplantation, Felix Broecker, Jochen Klumpp, Markus Schuppler, Giancarlo Russo, Luc Biedermann, Michael Hombach, Gerhard Rogler and Karin Moelling. Cold Spring Harbor Molecular Case Studies, 2 (1): a000448, Cold Spring Harbor, NY: CSH Press, 2016.

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Hemoglobinuria-related acute kidney injury is driven by intrarenal oxidative reactions triggering a heme toxicity response, J. W. Deuel, C. A. Schaer, F. S. Boretti, L. Opitz, I. Garcia-Rubio, J. H. Baek, D. R. Spahn, P. W. Buehler and D. J. Schaer. Cell death & disease, 7: e2064, London, UK: Nature, 2016.

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Identification of Novel Death-Associated Protein Kinase 2 Interaction Partners by Proteomic Screening Coupled with Bimolecular Fluorescence Complementation, Barbara Geering, Zina Zokouri, Samuel Hürlemann, Bertran Gerrits, David Ausländer, Adrian Britschgi, Mario P. Tschan, Hans-Uwe Simon and Martin Fussenegger. Molecular and cellular biology, 36 (1): 132-143, Washington, DC: American Society for Microbiology, 2016.

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A follow-up of the multicenter collaborative study on HIV-1 drug resistance and tropism testing using 454 ultra deep pyrosequencing, E.P. St. John, B.B. Simen, G.S. Turenchalk, M.S. Braverman, I. Abbate, J. Aerssens, O. Bouchez, C. Gabriel, J. Izopet, K. Meixenberger, F. Di Giallonardo, R. Schlapbach, R. Paredes, J. Sakwa, G.G. Schmitz-Agheguian, A. Thielen, M. Victor, K.J. Metzner, M.P. Däumer, M. Danzer, S. Stabentheiner, J. Pröll, K. Hofer, J. Aerssens, W. Mostmans, K. Thys, H. Van Marck, J. Izopet, M. Dubois, F. Nicot, D. Milan, B. Thiele, C. Kuecherer, A. Nitsche, A. Radonic, P.W. Dabrowski, T. Lengauer, M.R. Capobianchi, A. Bruselles, E. Giombini, G. Rozera, B. Bartolini, F.M. Codoñer, C. Pou, H.F. Günthard, W.L. Yang, C. Aquino, R. Bruggmann, M. Künzli-Gontarczyk, D. Stephens, M. Makgamathe, G. Khan, M. Gordon and E. Moreno. PLoS ONE, 11 (1): e0146687, San Francisco, CA: Public Library of Science, 2016.

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Proteomic Analysis of the Rat Canalicular Membrane Reveals Expression of a Complex System of P4-ATPases in Liver, Pururawa M. Chaubey, Lia Hofstetter, Bernd Roschitzki and Bruno Stieger. PLoS ONE, 11 (6): e0158033, San Francisco, CA: Public Library of Science, 2016.

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SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis, Masaomi Hatakeyama, Lennart Opitz, Giancarlo Russo, Weihong Qi, Ralph Schlapbach and Hubert Rehrauer. BMC Bioinformatics, 17 (1): 228, London: BioMed Central, 2016.

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Natural genetic variation differentially affects the proteome and transcriptome in Caenorhabditis elegans, Polina Kamkina, L. Basten Snoek, Jonas Grossmann, Rita J.M. Volkers, Mark G. Sterken, Michael Daube, Bernd Roschitzki, Claudia Fortes, Ralph Schlapbach, Alexander Roth, Christian von Mering, Michael O. Hengartner, Sabine P. Schrimpf and Jan E. Kammenga. Molecular and Cellular Proteomics, 15 (5): 1670-1680, Bethesda, MD: American Society for Biochemistry and Molecular Biology, 2016.

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H3K36ac Is an Evolutionary Conserved Plant Histone Modification That Marks Active Genes, Walid Mahrez, Minerva S. Trejo Arellano, Jordi Moreno-Romero, Miyuki Nakamura, Huan Shu, Paolo Nanni, Claudia Köhler, Wilhelm Gruissem and Lars Hennig. Plant physiology, 170 (3): 1566-1577, Rockville, MD: American Society of Plant Physiologists, 2016.

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Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue, Rita Martello, Mario Leutert, Stephanie Jungmichel, Vera Bilan, Sara C. Larsen, Clifford Young, Michael O. Hottiger and Michael L. Nielsen. NATURE COMMUNICATIONS, 7: 12917, Springer Nature, 2016.

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IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation, Yavuz Oktay, Ege Ügen, Özge Can, Cemaliye B. Akyerli, Şirin Yüksel, Yiğit Erdemgil, I.M. Durasi, Octavian I. Henegariu, E.P. Nanni, Nathalie Selevsek, Jonas Grossmann, E.Z. Erson-Omay, Hanwen Bai, Manu Gupta, William Lee, Şevin Turcan, Aysel Özpinar, Jason T. Huse, M.A. Sav, Adrienne Flanagan, Murat Gunel, O.U. Sezerman, M.C. Yakicier, M.N. Pamir and Koray Özduman. Scientific Reports, 6: 27569, London: Nature Publishing Group, 2016.

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Bacillus cereus Group-Type Strain-Specific Diagnostic PeptidesStefanie Pfrunder, Jonas Grossmann, Peter Hunziker, René Brunisholz, Maria-Theresia Gekenidis and David Drissner. Journal of Proteome Research, 15 (9): 3098-3107, Washington, DC: American Chemical Society, 2016.

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Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular beta-proteobacteria, Helena M. Seth-Smith, Nancy Dourala, Alexander Fehr, Weihong Qi, Pantelis Katharios, Maja Ruetten, José M. Mateos, Lisbeth Nufer, Roseline Weilenmann, Urs Ziegler, Nicholas R. Thomson, Ralph Schlapbach and Lloyd Vaughan. The ISME journal : multisiciplinary journal of microbial ecology, 10 (7): 1791-1803, Basingstoke: Nature, 2016.

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Single-molecule DNA hybridisation studied by using a modified DNA sequencer: a comparison with surface plasmon resonance data, Jens Sobek, Hubert Rehrauer, Stefan Schauer, David Fischer, Andrea Patrignani, Stephan Landgraf, Jonas Korlach and Ralph Schlapbach. Methods and Applications in Fluorescence, 4 (1): 015002, Bristol: Institute of Physics, 2016.

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A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing, Elizabeth P. St John, Birgitte B. Simen, Gregory S. Turenchalk, Michael S. Braverman, Isabella Abbate, Jeroen Aerssens, Olivier Bouchez, Christian Gabriel, Jacques Izopet, Karolin Meixenberger, Francesca Di Giallonardo, Ralph Schlapbach, Roger Paredes, Roger Paredes, Gudrun G. Schmitz-Agheguian, Alexander Thielen, Martin Victor, Karin J. Metzner, Martin P. Daeumer and H. I. V. Alpha Study Grp. PLoS ONE, 11 (1): e0146687, San Francisco CA, USA: Public Library of Science, 2016.

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The Angiotensin Converting Enzyme Insertion/Deletion Polymorphism Modifies Exercise-Induced Muscle Metabolism, David Vaughan, Michael Brogioli, Thomas Maier, Andy White, Sarah Waldron, Jörn Rittweger, Marco Toigo, Jessica Wettstein, Endre Laczko and Martin Flück. PLoS ONE, 11 (3): e0149046, San Francisco, CA: Public Library of Science, 2016.

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Biner, O., Trachsel, C., Moser, A., Kopp, L., Langenegger, N., Kampfer, U., von Ballmoos, C., Nentwig, W., Schurch, S., Schaller, J., and Kuhn-Nentwig, L. (2015). external pageIsolation, N-glycosylations and Function of a Hyaluronidase-Like Enzyme from the Venom of the Spider Cupiennius salei. PloS one 10, e0143963.

Bostanci, N., Bao, K., Wahlander, A., Grossmann, J., Thurnheer, T., and Belibasakis, G. N. (2015). external pageSecretome of gingival epithelium in response to subgingival biofilms. Molecular oral microbiology 30, 323-335.

de Valliere, C., Vidal, S., Clay, I., Jurisic, G., Tcymbarevich, I., Lang, S., Ludwig, M. G., Okoniewski, M., Eloranta, J. J., Kullak-Ublick, G. A., et al. (2015). Texternal pagehe pH-sensing receptor OGR1 improves barrier function of epithelial cells and inhibits migration in an acidic environment. American journal of physiology Gastrointestinal and liver physiology 309, G475-490.

Deuel, J. W., Vallelian, F., Schaer, C. A., Puglia, M., Buehler, P. W., and Schaer, D. J. (2015). external pageDifferent target specificities of haptoglobin and hemopexin define a sequential protection system against vascular hemoglobin toxicity. Free radical biology & medicine 89, 931-943.

Dolgodilina, E., Imobersteg, S., Laczko, E., Welt, T., Verrey, F., and Makrides, V. (2015). external pageBrain interstitial fluid glutamine homeostasis is controlled by blood-brain barrier SLC7A5/LAT1 amino acid transporter. Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism.

Eid, W., Opitz, L., and Biason-Lauber, A. (2015). external pageGenome-wide identification of CBX2 targets: insights in the human sex development network. Molecular endocrinology 29, 247-257.

Gamez-Pozo, A., Berges-Soria, J., Arevalillo, J. M., Nanni, P., Lopez-Vacas, R., Navarro, H., Grossmann, J., Castaneda, C. A., Main, P., Diaz-Almiron, M., et al. (2015). external pageCombined Label-Free Quantitative Proteomics and microRNA Expression Analysis of Breast Cancer Unravel Molecular Differences with Clinical Implications. Cancer research 75, 2243-2253.

Gelderman, M. P., Baek, J. H., Yalamanoglu, A., Puglia, M., Vallelian, F., Burla, B., Vostal, J., Schaer, D. J., and Buehler, P. W. (2015). external pageReversal of hemochromatosis by apotransferrin in non-transfused and transfused Hbbth3/+ (heterozygous B1/B2 globin gene deletion) mice. Haematologica 100, 611-622.

Gillespie, S. H., Ling, C. L., Oravcova, K., Pinheiro, M., Wells, L., Bryant, J. M., McHugh, T. D., Bebear, C., Webster, D., Harris, S. R., et al. (2015). external pageGenomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 60, 381-388.

Hartung, M. L., Gruber, D. C., Koch, K. N., Gruter, L., Rehrauer, H., Tegtmeyer, N., Backert, S., and Muller, A. (2015). H. pylori-Induced DNA Strand Breaks Are Introduced by Nucleotide Excision Repair Endonucleases and Promote NF-kappaB Target Gene Expression. Cell reports 13, 70-79.

Hashemi Gheinani, A., Burkhard, F. C., Rehrauer, H., Aquino Fournier, C., and Monastyrskaya, K. (2015). external pageMicroRNA MiR-199a-5p regulates smooth muscle cell proliferation and morphology by targeting WNT2 signaling pathway. The Journal of biological chemistry 290, 7067-7086.

Hegedus, T., Chaubey, P. M., Varady, G., Szabo, E., Saranko, H., Hofstetter, L., Roschitzki, B., Stieger, B., and Sarkadi, B. (2015). external pageInconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications. Database : the journal of biological databases and curation 2015, bav056.

Hehl, A. B., Basso, W. U., Lippuner, C., Ramakrishnan, C., Okoniewski, M., Walker, R. A., Grigg, M. E., Smith, N. C., and Deplazes, P. (2015). external pageAsexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes. BMC genomics 16, 66.

Hofmann, A., Thiesler, T., Gerrits, B., Behnke, S., Sobotzki, N., Omasits, U., Bausch-Fluck, D., Bock, T., Aebersold, R., Moch, H., et al. (2015). external pageSurfaceome of classical Hodgkin and non-Hodgkin lymphoma. Proteomics Clinical applications 9, 661-670.

Katharios, P., Seth-Smith, H. M., Fehr, A., Mateos, J. M., Qi, W., Richter, D., Nufer, L., Ruetten, M., Guevara Soto, M., Ziegler, U., et al. (2015). external pageEnvironmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp. Scientific reports 5, 17609.

Kraljevic Pavelic, S., Klobucar, M., Sedic, M., Micek, V., Gehrig, P., Grossman, J., Pavelic, K., and Vojnikovic, B. (2015). external pageUV-induced retinal proteome changes in the rat model of age-related macular degeneration. Biochimica et biophysica acta 1852, 1833-1845.

Langridge, G. C., Fookes, M., Connor, T. R., Feltwell, T., Feasey, N., Parsons, B. N., Seth-Smith, H. M., Barquist, L., Stedman, A., Humphrey, T., et al. (2015). external pagePatterns of genome evolution that have accompanied host adaptation in Salmonella. Proceedings of the National Academy of Sciences of the United States of America 112, 863-868.

Lichtensteiger, W., Bassetti-Gaille, C., Faass, O., Axelstad, M., Boberg, J., Christiansen, S., Rehrauer, H., Georgijevic, J. K., Hass, U., Kortenkamp, A., and Schlumpf, M. (2015). external pageDifferential gene expression patterns in developing sexually dimorphic rat brain regions exposed to antiandrogenic, estrogenic, or complex endocrine disruptor mixtures: glutamatergic synapses as target. Endocrinology 156, 1477-1493.

Lu, Q., Ding, S., Reiland, S., Rodiger, A., Roschitzki, B., Xue, P., Gruissem, W., Lu, C., and Baginsky, S. (2015). external pageIdentification and characterization of chloroplast casein kinase II from Oryza sativa (rice). Journal of experimental botany 66, 175-187.

Meienberg, J., Zerjavic, K., Keller, I., Okoniewski, M., Patrignani, A., Ludin, K., Xu, Z., Steinmann, B., Carrel, T., Rothlisberger, B., et al. (2015). external pageNew insights into the performance of human whole-exome capture platforms. Nucleic acids research 43, e76.

Mika, M., Mack, I., Korten, I., Qi, W., Aebi, S., Frey, U., Latzin, P., and Hilty, M. (2015). external pageDynamics of the nasal microbiota in infancy: a prospective cohort study. The Journal of allergy and clinical immunology 135, 905-912 e911.

Mueller, S., Wahlander, A., Selevsek, N., Otto, C., Ngwa, E. M., Poljak, K., Frey, A. D., Aebi, M., and Gauss, R. (2015). external pageProtein degradation corrects for imbalanced subunit stoichiometry in OST complex assembly. Molecular biology of the cell 26, 2596-2608.

Muller-Edenborn, K., Leger, K., Glaus Garzon, J. F., Oertli, C., Mirsaidi, A., Richards, P. J., Rehrauer, H., Spielmann, P., Hoogewijs, D., Borsig, L., et al. (2015). external pageHypoxia attenuates the proinflammatory response in colon cancer cells by regulating IkappaB. Oncotarget.

Norling, M., Bishop, R. P., Pelle, R., Qi, W., Henson, S., Drabek, E. F., Tretina, K., Odongo, D., Mwaura, S., Njoroge, T., et al. (2015). external pageThe genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence. BMC genomics 16, 729.

Nowak, M. D., Russo, G., Schlapbach, R., Huu, C. N., Lenhard, M., and Conti, E. (2015). external pageThe draft genome of Primula veris yields insights into the molecular basis of heterostyly. Genome biology 16, 12.

Oishi, N., Duscha, S., Boukari, H., Meyer, M., Xie, J., Wei, G., Schrepfer, T., Roschitzki, B., Boettger, E. C., and Schacht, J. (2015). external pageXBP1 mitigates aminoglycoside-induced endoplasmic reticulum stress and neuronal cell death. Cell death & disease 6, e1763.

Panse, C., Trachsel, C., Grossmann, J., and Schlapbach, R. (2015). external pagespecL-an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. Bioinformatics 31, 2228-2231.

Portevin, D., Pfluger, V., Otieno, P., Brunisholz, R., Vogel, G., and Daubenberger, C. (2015). external pageQuantitative whole-cell MALDI-TOF MS fingerprints distinguishes human monocyte sub-populations activated by distinct microbial ligands. BMC biotechnology 15, 24.

Rosenthal, F., Nanni, P., Barkow-Oesterreicher, S., and Hottiger, M. O. (2015). external pageOptimization of LTQ-Orbitrap Mass Spectrometer Parameters for the Identification of ADP-Ribosylation Sites. Journal of proteome research.

Salm, F., Dimitrova, V., von Bueren, A. O., Cwiek, P., Rehrauer, H., Djonov, V., Anderle, P., and Arcaro, A. (2015). external pageThe Phosphoinositide 3-Kinase p110alpha Isoform Regulates Leukemia Inhibitory Factor Receptor Expression via c-Myc and miR-125b to Promote Cell Proliferation in Medulloblastoma. PloS one 10, e0123958.

Selevsek, N., Chang, C. Y., Gillet, L. C., Navarro, P., Bernhardt, O. M., Reiter, L., Cheng, L. Y., Vitek, O., and Aebersold, R. (2015). external pageReproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry. Molecular & cellular proteomics : MCP 14, 739-749.

Surace, L., Lysenko, V., Fontana, A. O., Cecconi, V., Janssen, H., Bicvic, A., Okoniewski, M., Pruschy, M., Dummer, R., Neefjes, J., et al. (2015). external pageComplement is a central mediator of radiotherapy-induced tumor-specific immunity and clinical response. Immunity 42, 767-777.

Urner, M., Schlapfer, M., Herrmann, I. K., Hasler, M., Schimmer, R. R., Booy, C., Roth Z'graggen, B., Rehrauer, H., Aigner, F., Minshall, R. D., et al. (2015). external pageInsight into the beneficial immunomodulatory mechanism of the sevoflurane metabolite hexafluoro-2-propanol in a rat model of endotoxaemia. Clinical and experimental immunology 181, 468-479.

Vallelian, F., Garcia-Rubio, I., Puglia, M., Kahraman, A., Deuel, J. W., Engelsberger, W. R., Mason, R. P., Buehler, P. W., and Schaer, D. J. (2015). external pageSpin trapping combined with quantitative mass spectrometry defines free radical redistribution within the oxidized hemoglobin:haptoglobin complex. Free radical biology & medicine 85, 259-268.

Vallelian, F., Gelderman-Fuhrmann, M. P., Schaer, C. A., Puglia, M., Opitz, L., Baek, J. H., Vostal, J., Buehler, P. W., and Schaer, D. J. (2015). external pageIntegrative proteome and transcriptome analysis of extramedullary erythropoiesis and its reversal by transferrin treatment in a mouse model of beta-thalassemia. Journal of proteome research 14, 1089-1100.

Walker, R. A., Sharman, P. A., Miller, C. M., Lippuner, C., Okoniewski, M., Eichenberger, R. M., Ramakrishnan, C., Brossier, F., Deplazes, P., Hehl, A. B., and Smith, N. C. (2015). external pageRNA Seq analysis of the Eimeria tenella gametocyte transcriptome reveals clues about the molecular basis for sexual reproduction and oocyst biogenesis. BMC genomics 16, 94.

Whittington, C. M., Griffith, O. W., Qi, W., Thompson, M. B., and Wilson, A. B. (2015). external pageSeahorse Brood Pouch Transcriptome Reveals Common Genes Associated with Vertebrate Pregnancy. Molecular biology and evolution 32, 3114-3131.

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Urosevic-Maiwald, M., Barysch, M. J., Cheng, P. F., Karpova, M. B., Steinert, H., Okoniewski, M. J., and Dummer, R. (2015). external pageIn vivo profiling reveals immunomodulatory effects of sorafenib and dacarbazine on melanoma. Oncoimmunology 4, e988458.

Allie, F., E. J. Pierce, M. J. Okoniewski and C. Rey (2014)
"external pageTranscriptional analysis of South African cassava mosaic virus-infected susceptible and tolerant landraces of cassava highlights differences in resistance, basal defense and cell wall associated genes during infection".
BMC Genomics 15: 1006.

Aregger, F., D. E. Uehlinger, J. Witowski, R. A. Brunisholz, P. Hunziker, F. J. Frey and A. Jorres (2014)
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Kidney Int 85(4): 909-919.

Azzi, A., R. Dallmann, A. Casserly, H. Rehrauer, A. Patrignani, B. Maier, A. Kramer and S. A. Brown (2014)
"external pageCircadian behavior is light-reprogrammed by plastic DNA methylation".
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Brunner, A. M., P. Nanni and I. M. Mansuy (2014)
"external pageEpigenetic marking of sperm by post-translational modification of histones and protamines".
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Draganova, K., M. Zemke, L. Zurkirchen, T. Valenta, C. Cantu, M. J. Okoniewski, M. T. Schmid, R. Hoffmans, M. Götz, K. Basler and L. Sommer (2014)
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Stem Cells 33(1): 170-182. DOI 10.1002/stem.1820

Drissner, D., M. T. Gekenidis, R. Schlapbach and R. Brunisholz (2014)
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Giallonardo, F. D., A. Topfer, M. Rey, S. Prabhakaran, Y. Duport, C. Leemann, S. Schmutz, N. K. Campbell, B. Joos, M. R. Lecca, A. Patrignani, M. Daumer, C. Beisel, P. Rusert, A. Trkola, H. F. Gunthard, V. Roth, N. Beerenwinkel and K. J. Metzner (2014)
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Greminger, M. P., K. N. Stolting, A. Nater, B. Goossens, N. Arora, R. Bruggmann, A. Patrignani, B. Nussberger, R. Sharma, R. H. Kraus, L. N. Ambu, I. Singleton, L. Chikhi, C. P. van Schaik and M. Krutzen (2014)
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Kentner, D., G. Martano, M. Callon, P. Chiquet, M. Brodmann, O. Burton, A. Wahlander, P. Nanni, N. Delmotte, J. Grossmann, J. Limenitakis, R. Schlapbach, P. Kiefer, J. A. Vorholt, S. Hiller and D. Bumann (2014)
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Proteomics 14(6): 725-737.

Myburgh, R., O. Cherpin, E. Schlaepfer, H. Rehrauer, R. F. Speck, K. H. Krause and P. Salmon (2014)
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Abplanalp, J., E. Laczko, N. J. Philp, J. Neidhardt, J. Zuercher, P. Braun, D. F. Schorderet, F. L. Munier, F. Verrey, W. Berger, S. M. Camargo and B. Kloeckener-Gruissem (2013)
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Aregger, F., D. E. Uehlinger, J. Witowski, R. A. Brunisholz, P. Hunziker, F. J. Frey and A. Jorres (2013)
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"PGC-1alpha determines light damage susceptibility of the murine retina".
PLoS One 7(2): e31272.

Eisele, P. S., S. Salatino, J. Sobek, M. O. Hottiger and C. Handschin (2012)
"The PGC-1 coactivators repress the transcriptional activity of NF-kappaB in skeletal muscle cells".
J Biol Chem.

Felder, K. M., P. M. Carranza, P. M. Gehrig, B. Roschitzki, S. Barkow-Oesterreicher, K. Hoelzle, K. Riedel, M. Kube and L. E. Hoelzle (2012)
"Insights into the gene expression profile of uncultivable hemotrophic Mycoplasma suis during acute infection, obtained using proteome analysis".
J Bacteriol 194(6): 1505-1514.

Filippini, M., W. Qi, J. Blom, A. Goesmann, T. H. Smits and H. C. Bagheri (2012)
"Genome sequence of Fibrella aestuarina BUZ 2(T), a filamentous marine bacterium".
J Bacteriol 194(13): 3555.

Henrichs, S., B. Wang, Y. Fukao, J. Zhu, L. Charrier, A. Bailly, S. C. Oehring, M. Linnert, M. Weiwad, A. Endler, P. Nanni, S. Pollmann, S. Mancuso, A. Schulz and M. Geisler (2012)
"Regulation of ABCB1/PGP1-catalysed auxin transport by linker phosphorylation".
EMBO J 31(13): 2965-2980.

Henson, S., R. P. Bishop, S. Morzaria, P. R. Spooner, R. Pelle, L. Poveda, M. Ebeling, E. Kung, U. Certa, C. A. Daubenberger and W. Qi (2012)
"High-resolution genotyping and mapping of recombination and gene conversion in the protozoan Theileria parva using whole genome sequencing".
BMC Genomics 13(1): 503.

Hilty, M., W. Qi, S. D. Brugger, L. Frei, P. Agyeman, P. M. Frey, S. Aebi and K. Muhlemann (2012)
"Nasopharyngeal microbiota in infants with acute otitis media".
J Infect Dis 205(7): 1048-1055.

Huwiler, S. G., C. Beyer, J. Frohlich, H. Hennecke, T. Egli, D. Schurmann, H. Rehrauer and H. M. Fischer (2012)
"Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields".
Bioelectromagnetics 33(6): 488-496.

Jang, J. H., A. Rickenbacher, B. Humar, A. Weber, D. A. Raptis, K. Lehmann, B. Stieger, W. Moritz, C. Soll, P. Georgiev, D. Fischer, E. Laczko, R. Graf and P. A. Clavien (2012)
"Serotonin protects mouse liver from cholestatic injury by decreasing bile salt pool after bile duct ligation".
Hepatology 56(1): 209-218.

Jovanovic, M., L. Reiter, A. Clark, M. Weiss, P. Picotti, H. Rehrauer, A. Frei, L. J. Neukomm, E. Kaufman, B. Wollscheid, M. J. Simard, E. A. Miska, R. Aebersold, A. P. Gerber and M. O. Hengartner (2012)
"RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans".
Genome research 22(7): 1360-1371.

Keiblinger, K. M., T. Schneider, B. Roschitzki, E. Schmid, L. Eberl, I. HÃ¤mmerle, A. Leitner, A. Richter, W. Wanek, K. Riedel and S. Zechmeister-Boltenstern (2012)
"Effects of stoichiometry and temperature perturbations on beech leaf litter decompostion, enzyme activities and protein expression.".
Biogeosciences.

Keiblinger, K. M., I. C. Wilhartitz, T. Schneider, B. Roschitzki, E. Schmid, L. Eberl, K. Riedel and S. Zechmeister-Boltenstern (2012)
"Soil metaproteomics - Comparative evaluation of protein extraction protocols".
Soil Biol Biochem 54(15-10): 14-24.

Klaus, A., C. Polge, S. Zorman, Y. Auchli, R. Brunisholz and U. Schlattner (2012)
"A two-dimensional screen for AMPK substrates identifies tumor suppressor fumarate hydratase as a preferential AMPKalpha2 substrate".
J Proteomics 75(11): 3304-3313.

Leitner, S., W. Wanek, B. Wild, I. Haemmerle, L. Kohl, K. M. Keiblinger, S. Zechmeister-Boltenstern and A. Richter (2012)
"Influence of litter chemistry and stoichiometry on glucan depolymerization during decomposition of beech (Fagus sylvatica L.) litter".
Soil Biol Biochem 50(6): 174-187.

Maglietta, R., V. C. Liuzzi, E. Cattaneo, E. Laczko, A. Piepoli, A. Panza, M. Carella, O. Palumbo, T. Staiano, F. Buffoli, A. Andriulli, G. Marra and N. Ancona (2012)
"Molecular pathways undergoing dramatic transcriptomic changes during tumor development in the human colon".
BMC cancer 12: 608.

Mayank, P., J. Grossman, S. Wuest, A. Boisson-Dernier, B. Roschitzki, P. Nanni, T. Nuhse and U. Grossniklaus (2012)
"Characterization of the phosphoproteome of mature Arabidopsis pollen".
Plant J 72(1): 89-101.

Moretti, M., D. Minerdi, P. Gehrig, A. Garibaldi, M. L. Gullino and K. Riedel (2012)
"A bacterial-fungal metaproteomic analysis enlightens an intriguing multicomponent interaction in the rhizosphere of Lactuca sativa".
J Proteome Res 11(4): 2061-2077.

Mugasa, J., W. Qi, S. Rusch, M. Rottmann and H. P. Beck (2012)
"Genetic diversity of expressed Plasmodium falciparum var genes from Tanzanian children with severe malaria".
Malar J 11: 230.

Muller, M., A. Patrignani, H. Rehrauer, W. Gruissem and L. Hennig (2012)
"Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays".
Plant methods 8(1): 18.

Okoniewski, M. J., A. Lesniewska, A. Szabelska, J. Zyprych-Walczak, M. Ryan, M. Wachtel, T. Morzy, B. Schafer and R. Schlapbach (2012)
"Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage".
Nucleic acids research 40(9): e63.

Ortea, I., B. Roschitzki, J. G. Ovalles, J. L. Longo, I. de la Torre, I. Gonzalez, J. J. Gomez-Reino and A. Gonzalez (2012)
"Discovery of serum proteomic biomarkers for prediction of response to infliximab (a monoclonal anti-TNF antibody) treatment in rheumatoid arthritis: an exploratory analysis".
J Proteomics 77: 372-382.

Piepoli, A., O. Palmieri, R. Maglietta, A. Panza, E. Cattaneo, A. Latiano, E. Laczko, A. Gentile, M. Carella, G. Mazzoccoli, N. Ancona, G. Marra and A. Andriulli (2012)
"The expression of leucine-rich repeat gene family members in colorectal cancer".
Exp Biol Med (Maywood) 237(10): 1123-1128.

Rampitsch, C., N. A. Tinker, R. Subramaniam, S. Barkow-Oesterreicher and E. Laczko (2012)
"Phosphoproteome profile of Fusarium graminearum grown in vitro under nonlimiting conditions".
Proteomics 12(7): 1002-1005.

Schneider, T., D. P. Persson, S. Husted, M. Schellenberg, P. Gehrig, Y. Lee, E. Martinoia, J. K. Schjoerring and S. Meyer (2012)
"A proteomics approach to investigate the process of Zn hyperaccumulation in Noccaea caerulescens (J & C. Presl) F.K. Meyer".
Plant J.

Schneider, T., K. M. Keiblinger, E. Schmid, K. Sterflinger-Gleixner, G. Ellersdorfer, B. Roschitzki, A. Richter, L. Eberl, S. Zechmeister-Boltenstern and K. Riedel (2012)
"Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions".
ISME J 6(9): 1749-1762.

Seeger, M. A., A. Mittal, S. Velamakanni, M. Hohl, S. Schauer, I. Salaa, M. G. Grutter and H. W. van Veen (2012)
"Tuning the Drug Efflux Activity of an ABC Transporter invivo by in vitro Selected DARPin Binders".
PLoS One 7(6): e37845.

Shakhova, O., D. Zingg, S. M. Schaefer, L. Hari, G. Civenni, J. Blunschi, S. Claudinot, M. Okoniewski, F. Beermann, D. Mihic-Probst, H. Moch, M. Wegner, R. Dummer, Y. Barrandon, P. Cinelli and L. Sommer (2012)
"Sox10 promotes the formation and maintenance of giant congenital naevi and melanoma".
Nat Cell Biol 14(8): 882-890.

Shi, Y., U. Moura, I. Opitz, A. Soltermann, H. Rehrauer, S. Thies, W. Weder, R. A. Stahel and E. Felley-Bosco (2012)
"Role of hedgehog signaling in malignant pleural mesothelioma".
Clinical cancer research : an official journal of the American Association for Cancer Research 18(17): 4646-4656.

Testoni, S., E. Bartolone, M. Rossi, A. Patrignani, R. Bruggmann, P. Lichtner, J. Tetens, A. Gentile and C. Drogemuller (2012)
"KDM2B is implicated in bovine lethal multi-organic developmental dysplasia".
PLoS One 7(9): e45634.

Trachsel, C., D. Siegemund, U. Kampfer, L. S. Kopp, C. Buhr, J. Grossmann, C. Luthi, M. Cunningham, W. Nentwig, L. Kuhn-Nentwig, S. Schurch and J. Schaller (2012)
"Multicomponent venom of the spider Cupiennius salei: a bioanalytical investigation applying different strategies".
FEBS J 279(15): 2683-2694.

Trinh, H. V., G. Lesage, V. Chennamparampil, B. Vollenweider, C. J. Burckhardt, S. Schauer, M. Havenga, U. F. Greber and S. Hemmi (2012)
"Avidity binding of human adenovirus serotypes 3 and 7 to the membrane cofactor CD46 triggers infection".
J Virol 86(3): 1623-1637.

Toyofuku, M., B. Roschitzki, K. Riedel and L. Eberl (2012)
"Identification of proteins associated with the Pseudomonas aeruginosa biofilm extracellular matrix".
J Proteome Res 11(10): 4906-4915.

Tweedie-Cullen, R. Y., A. M. Brunner, J. Grossmann, S. Mohanna, D. Sichau, P. Nanni, C. Panse and I. M. Mansuy (2012)
"Identification of combinatorial patterns of post-translational modifications on individual histones in the mouse brain".
PLoS One 7(5): e36980.

Wollenick, K., J. Hu, G. Kristiansen, P. Schraml, H. Rehrauer, U. Berchner-Pfannschmidt, J. Fandrey, R. H. Wenger and D. P. Stiehl (2012)
"Synthetic transactivation screening reveals ETV4 as broad coactivator of hypoxia-inducible factor signaling".
Nucleic acids research 40(5): 1928-1943.

Abu-Ali, G. S., A. C. Springman, L. M. Ouellette, W. Qi, S. K. Vanaja, T. M. Bergholz, D. W. Lacher, J. Tietjen, J. T. Riordan and S. D. Manning (2011)
"Molecular Evolution of Enterhemorrhagic E. coli and Application to Epidemiology".
In: Population Genetics of Bacteria: a Tribute to Thomas S. Whittam. S. T. Walk and P. C. Feng, Washington DC, ASM Press, pages.

Asp, T., S. Byrne, H. Gundlach, R. Bruggmann, K. F. Mayer, J. R. Andersen, M. Xu, M. Greve, I. Lenk and T. Lubberstedt (2011)
"Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice".
Molecular genetics and genomics : MGG 286(5-6): 433-447.

Bischof, S., K. Baerenfaller, T. Wildhaber, R. Troesch, P. A. Vidi, B. Roschitzki, M. Hirsch-Hoffmann, L. Hennig, F. Kessler, W. Gruissem and S. Baginsky (2011)
"Plastid Proteome Assembly without Toc159: Photosynthetic Protein Import and Accumulation of N-Acetylated Plastid Precursor Proteins".
The Plant cell 23(11): 3911-3928.

Bratus, A., S. Neuenschwander, A. Piestrzynska-Kajtoch, M. Switonski, J. Klukowska-Rotzler and E. Slota (2011)
"Polymorphisms in Dmrt1 Coding and Promoter Regions Are Probably Not Causative for Swine Sex Reversal (Xx, Sry-Negative) Syndrome".
Annals of Animal Science 11(1): 17-26.

Calvino, M., R. Bruggmann and J. Messing (2011)
"Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems".
BMC Genomics 12: 356.

Cattaneo, E., E. Laczko, F. Buffoli, F. Zorzi, M. A. Bianco, M. Menigatti, Z. Bartosova, R. Haider, B. Helmchen, J. Sabates-Bellver, A. Tiwari, J. Jiricny and G. Marra (2011)
"Preinvasive colorectal lesion transcriptomes correlate with endoscopic morphology (polypoid vs. nonpolypoid)".
EMBO molecular medicine 3(6): 334-347.

Craig, V. J., S. B. Cogliatti, J. Imig, C. Renner, S. Neuenschwander, H. Rehrauer, R. Schlapbach, S. Dirnhofer, A. Tzankov and A. Muller (2011)
"Myc-mediated repression of microRNA-34a promotes high-grade transformation of B-cell lymphoma by dysregulation of FoxP1".
Blood 117(23): 6227-6236.

Craig, V. J., S. B. Cogliatti, H. Rehrauer, T. Wundisch and A. Muller (2011)
"Epigenetic silencing of microRNA-203 dysregulates ABL1 expression and drives Helicobacter-associated gastric lymphomagenesis".
Cancer Res 71(10): 3616-3624.

Duc, L., S. Neuenschwander, H. Rehrauer and J. Zeyer (2011)
"Application of a nifH microarray to assess the impact of environmental factors on free-living diazotrophs in a glacier forefield".
Can J Microbiol 57(2): 105-114.

El-Badry, A. M., J. H. Jang, A. Elsherbiny, C. Contaldo, Y. Tian, D. A. Raptis, E. Laczko, W. Moritz, R. Graf and P. A. Clavien (2011)
"Chemical composition of hepatic lipids mediates reperfusion injury of the macrosteatotic mouse liver through thromboxane A(2)".
Journal of hepatology 55(6): 1291-1299.

Filippini, M., M. Svercel, E. Laczko, A. Kaech, U. Ziegler and H. C. Bagheri (2011)
"Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family Cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008".
Int J Syst Evol Microbiol 61(Pt 1): 184-189.

Frei, C., I. Opitz, A. Soltermann, B. Fischer, U. Moura, H. Rehrauer, W. Weder, R. Stahel and E. Felley-Bosco (2011)
"Pleural mesothelioma side populations have a precursor phenotype".
Carcinogenesis 32(9): 1324-1332.

Hu, J., D. P. Stiehl, C. Setzer, D. Wichmann, D. A. Shinde, H. Rehrauer, P. Hradecky, M. Gassmann and T. A. Gorr (2011)
"Interaction of HIF and USF Signaling Pathways in Human Genes Flanked by Hypoxia-Response Elements and E-box Palindromes".
Mol Cancer Res 9(11): 1520-1536.

Imig, J., N. Motsch, J. Y. Zhu, S. Barth, M. Okoniewski, T. Reineke, M. Tinguely, A. Faggioni, P. Trivedi, G. Meister, C. Renner and F. A. Grasser (2011)
"microRNA profiling in Epstein-Barr virus-associated B-cell lymphoma".
Nucleic Acids Res 39(5): 1880-1893.

Jacobsen, M., S. Cirera, D. Joller, G. Esteso, S. S. Kracht, I. Edfors, C. Bendixen, A. L. Archibald, P. Vogeli, S. Neuenschwander, H. U. Bertschinger, A. Rampoldi, L. Andersson, M. Fredholm and C. B. Jorgensen (2011)
"Characterisation of five candidate genes within the ETEC F4ab/ac candidate region in pigs".
BMC research notes 4: 225.

Kaempfer, T., E. Duerst, P. Gehrig, B. Roschitzki, D. Rutishauser, J. Grossmann, G. Schoedon, F. Vallelian and D. J. Schaer (2011)
"Extracellular hemoglobin polarizes the macrophage proteome toward Hb-clearance, enhanced antioxidant capacity and suppressed HLA class 2 expression".
J Proteome Res 10(5): 2397-2408.

Kariminejad, A., R. Kariminejad, A. Moshtagh, M. Zanganeh, M. H. Kariminejad, S. Neuenschwander, M. Okoniewski, E. Wey, A. Schinzel and A. Baumer (2011)
"Pericentric inversion of chromosome 18 in parents leading to a phenotypically normal child with segmental uniparental disomy 18".
European journal of human genetics : EJHG 19(5): 555-560.

Kaufmann, S., J. Sobek, M. Textor and E. Reimhult (2011)
"Supported lipid bilayer microarrays created by non-contact printing".
Lab on a chip 11(14): 2403-2410.

Kovac, M., E. Laczko, R. Haider, J. Jiricny, H. Mueller, K. Heinimann and G. Marra (2011)
"Familial colorectal cancer: eleven years of data from a registry program in Switzerland".
Familial cancer 10(3): 605-616.

Kumar, N., H. Rehrauer, H. Cai and M. Baudis (2011)
"CDCOCA: a statistical method to define complexity dependence of co-occuring chromosomal aberrations".
BMC Med Genomics 4: 21.

Lesniewska, A. and M. J. Okoniewski (2011)
"rnaSeqMap: a Bioconductor package for RNA sequencing data exploration".
BMC Bioinformatics 12: 200.

McElroy, K., L. Mouton, L. Du Pasquier, W. Qi and D. Ebert (2011)
"Characterisation of a large family of polymorphic collagen-like proteins in the endospore-forming bacterium Pasteuria ramosa".
Res Microbiol 162(7): 701-714.

MÃ¼ller, W. and C. TÃ¼rker (2011)
"Data Management in Life Sciences".
Information Technology 53: 215-216.

Okoniewski, M. J., A. Lesniewska, A. Szabelska, J. Zyprych-Walczak, M. Ryan, M. Wachtel, T. Morzy, B. Schaffer and R. Schlapbach (2011)
"Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage".
Nucleic acids research.

Owiti, J., J. Grossmann, P. Gehrig, C. Dessimoz, C. Laloi, M. B. Hansen, W. Gruissem and H. Vanderschuren (2011)
"iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration".
Plant J 67(1): 145-156.

Pellegrino, M. W., S. Farooqui, E. Frohli, H. Rehrauer, S. Kaeser-Pebernard, F. Muller, R. B. Gasser and A. Hajnal (2011)
"LIN-39 and the EGFR/RAS/MAPK pathway regulate C. elegans vulval morphogenesis via the VAB-23 zinc finger protein".
Development 138(21): 4649-4660.

Rampoldi, A., M. J. Jacobsen, H. U. Bertschinger, D. Joller, E. Burgi, P. Vogeli, L. Andersson, A. L. Archibald, M. Fredholm, C. B. Jorgensen and S. Neuenschwander (2011)
"The receptor locus for Escherichia coli F4ab/F4ac in the pig maps distal to the MUC4-LMLN region".
Mammalian genome : official journal of the International Mammalian Genome Society 22(1-2): 122-129.

Reiland, S., G. Finazzi, A. Endler, A. Willig, K. Baerenfaller, J. Grossmann, B. Gerrits, D. Rutishauser, W. Gruissem, J. D. Rochaix and S. Baginsky (2011)
"Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF)".
Proc Natl Acad Sci U S A 108(31): 12955-12960.

Reiland, S., J. Grossmann, K. Baerenfaller, P. Gehrig, A. Nunes-Nesi, A. R. Fernie, W. Gruissem and S. Baginsky (2011)
"Integrated proteome and metabolite analysis of the de-etiolation process in plastids from rice (Oryza sativa L.)".
Proteomics 11(9): 1751-1763.

Roschitzki, B., S. Schauer and P. R. Mittl (2011)
"Recognition of host proteins by Helicobacter cysteine-rich protein C".
Curr Microbiol 63(3): 239-249.

Rosenthal, F., S. Messner, B. Roschitzki, P. Gehrig, P. Nanni and M. O. Hottiger (2011)
"Identification of distinct amino acids as adp-ribose acceptor sites by mass spectrometry".
Methods Mol Biol 780: 57-66.

Sidi, R., G. Pasello, I. Opitz, A. Soltermann, M. Tutic, H. Rehrauer, W. Weder, R. A. Stahel and E. Felley-Bosco (2011)
"Induction of senescence markers after neo-adjuvant chemotherapy of malignant pleural mesothelioma and association with clinical outcome: An exploratory analysis".
Eur J Cancer 47(2): 326-332.

TÃ¼rker, C. (2011)
"Managing Life Sciences Projects and Data with B-Fabrics.".
Information Technology: 40-41.

Turker, C., F. Akal and R. Schlapbach (2011)
"Life sciences data and application integration with B-fabric".
J Integr Bioinform 8(2): 159.

Tyagarajan, S. K., H. Ghosh, G. E. Yevenes, I. Nikonenko, C. Ebeling, C. Schwerdel, C. Sidler, H. U. Zeilhofer, B. Gerrits, D. Muller and J. M. Fritschy (2011)
"Regulation of GABAergic synapse formation and plasticity by GSK3beta-dependent phosphorylation of gephyrin".
Proc Natl Acad Sci U S A 108(1): 379-384.

Vettermann, C., D. Castor, A. Mekker, B. Gerrits, M. Karas and H. M. Jack (2011)
"Proteome profiling suggests a pro-inflammatory role for plasma cells through release of high-mobility group box 1 protein".
Proteomics 11(7): 1228-1237.

Walter, D., S. Satheesha, P. Albrecht, B. C. Bornhauser, V. D'Alessandro, S. M. Oesch, H. Rehrauer, I. Leuschner, E. Koscielniak, C. Gengler, H. Moch, M. Bernasconi, F. K. Niggli and B. W. Schafer (2011)
"CD133 positive embryonal rhabdomyosarcoma stem-like cell population is enriched in rhabdospheres".
PLoS One 6(5): e19506.

Wiedl, T., S. Arni, B. Roschitzki, J. Grossmann, S. Collaud, A. Soltermann, S. Hillinger, R. Aebersold and W. Weder (2011)
"Activity-based proteomics: identification of ABHD11 and ESD activities as potential biomarkers for human lung adenocarcinoma".
J Proteomics 74(10): 1884-1894.

Wohlschlager, T., A. Butschi, K. Zurfluh, S. C. Vonesch, U. Auf dem Keller, P. Gehrig, S. Bleuler-Martinez, M. O. Hengartner, M. Aebi and M. Kunzler (2011)
"Nematotoxicity of Marasmius oreades Agglutinin (MOA) Depends on Glycolipid Binding and Cysteine Protease Activity".
J Biol Chem 286(35): 30337-30343.

Wollenick, K., J. Hu, G. Kristiansen, P. Schraml, H. Rehrauer, U. Berchner-Pfannschmidt, J. Fandrey, R. H. Wenger and D. P. Stiehl (2011)
"Synthetic transactivation screening reveals ETV4 as broad coactivator of hypoxia-inducible factor signaling".
Nucleic Acids Res.

Yepiskoposyan, H., F. Aeschimann, D. Nilsson, M. Okoniewski and O. Muhlemann (2011)
"Autoregulation of the nonsense-mediated mRNA decay pathway in human cells".
RNA 17(12): 2108-2118.

Agne, B., C. Andres, C. Montandon, B. Christ, A. Ertan, F. Jung, S. Infanger, S. Bischof, S. Baginsky and F. Kessler (2010)
"The acidic A-domain of Arabidopsis TOC159 occurs as a hyperphosphorylated protein".
Plant Physiol 153(3): 1016-1030.

Albinger-Hegyi, A., S. J. Stoeckli, S. Schmid, M. Storz, G. Iotzova, N. M. Probst-Hensch, H. Rehrauer, M. Tinguely, H. Moch and I. Hegyi (2010)
"Lysyl oxidase expression is an independent marker of prognosis and a predictor of lymph node metastasis in oral and oropharyngeal squamous cell carcinoma (OSCC)".
Int J Cancer 126(11): 2653-2662.

Altmeyer, M., M. Barthel, M. Eberhard, H. Rehrauer, W. D. Hardt and M. O. Hottiger (2010)
"Absence of PARP1 delays the onset of Salmonella-induced gut inflammation".
Infect Immun 78(8): 3420-3431.

Alzamora, R., R. F. Thali, F. Gong, C. Smolak, H. Li, C. J. Baty, C. A. Bertrand, Y. Auchli, R. A. Brunisholz, D. Neumann, K. R. Hallows and N. M. Pastor-Soler (2010)
"PKA regulates vacuolar H+-ATPase localization and activity via direct phosphorylation of the A subunit in kidney cells".
J Biol Chem 285(32): 24676-24685.

Aregger, F., C. Pilop, D. E. Uehlinger, R. Brunisholz, T. P. Carrel, F. J. Frey and B. M. Frey (2010)
"Urinary proteomics before and after extracorporeal circulation in patients with and without acute kidney injury".
J Thorac Cardiovasc Surg 139(3): 692-700.

Babik, W., M. Stuglik, W. Qi, M. Kuenzli, K. Kuduk, P. Koteja and J. Radwan (2010)
"Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate".
BMC Genomics 11(1): 390.

Banu, L. D., G. Conrads, H. Rehrauer, H. Hussain, E. Allan and J. R. van der Ploeg (2010)
"The Streptococcus mutans serine/threonine kinase, PknB, regulates competence development, bacteriocin production, and cell wall metabolism".
Infect Immun 78(5): 2209-2220.

Bettermann, K., M. Vucur, J. Haybaeck, C. Koppe, J. Janssen, F. Heymann, A. Weber, R. Weiskirchen, C. Liedtke, N. Gassler, M. Muller, R. de Vos, M. J. Wolf, Y. Boege, G. M. Seleznik, N. Zeller, D. Erny, T. Fuchs, S. Zoller, S. Cairo, M. A. Buendia, M. Prinz, S. Akira, F. Tacke, M. Heikenwalder, C. Trautwein and T. Luedde (2010)
"TAK1 suppresses a NEMO-dependent but NF-kappaB-independent pathway to liver cancer".
Cancer Cell 17(5): 481-496.

Bodenmiller, B., S. Wanka, C. Kraft, J. Urban, D. Campbell, P. G. Pedrioli, B. Gerrits, P. Picotti, H. Lam, O. Vitek, M. Y. Brusniak, B. Roschitzki, C. Zhang, K. M. Shokat, R. Schlapbach, A. Colman-Lerner, G. P. Nolan, A. I. Nesvizhskii, M. Peter, R. Loewith, C. von Mering and R. Aebersold (2010)
"Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast".
Sci Signal 3(153): rs4.

Bremer, J., T. O'Connor, C. Tiberi, H. Rehrauer, J. Weis and A. Aguzzi (2010)
"Ablation of Dicer from murine Schwann cells increases their proliferation while blocking myelination".
PLoS One 5(8): e12450.

Brulle, J. K., T. Grau, A. Tschumi, Y. Auchli, R. Burri, S. Polsfuss, P. M. Keller, P. Hunziker and P. Sander (2010)
"Cloning, expression and characterization of Mycobacterium tuberculosis lipoprotein LprF".
Biochem Biophys Res Commun 391(1): 679-684.

Carranza, P., A. Grunau, T. Schneider, I. Hartmann, A. Lehner, R. Stephan, P. Gehrig, J. Grossmann, K. Groebel, L. E. Hoelzle, L. Eberl and K. Riedel (2010)
"A gel-free quantitative proteomics approach to investigate temperature adaptation of the food-borne pathogen Cronobacter turicensis 3032".
Proteomics 10(18): 3248-3261.

Casutt, M. S., T. Huber, R. Brunisholz, M. Tao, G. Fritz and J. Steuber (2010)
"Localization and function of the membrane-bound riboflavin in the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae".
J Biol Chem 285(35): 27088-27099.

Chaffron, S., H. Rehrauer, J. Pernthaler and C. von Mering (2010)
"A global network of coexisting microbes from environmental and whole-genome sequence data".
Genome Res 20(7): 947-959.

Charrier, C., P. Machado, R. Y. Tweedie-Cullen, D. Rutishauser, I. M. Mansuy and A. Triller (2010)
"A crosstalk between beta1 and beta3 integrins controls glycine receptor and gephyrin trafficking at synapses".
Nat Neurosci 13(11): 1388-1395.

Djouder, N., R. D. Tuerk, M. Suter, P. Salvioni, R. F. Thali, R. Scholz, K. Vaahtomeri, Y. Auchli, H. Rechsteiner, R. A. Brunisholz, B. Viollet, T. P. Makela, T. Wallimann, D. Neumann and W. Krek (2010)
"PKA phosphorylates and inactivates AMPKalpha to promote efficient lipolysis".
EMBO J 29(2): 469-481.

Ebert, D. and W. Qi (2010)
"An Evolutionary Ecology Perspective on Comparative Metagenomics ".
Metagenomics and Its Application in Agriculture, Biomedicine and Environmental Studies 211-236.

Feng, J., E. Lucchinetti, G. Enkavi, Y. Wang, P. Gehrig, B. Roschitzki, M. C. Schaub, E. Tajkhorshid, K. Zaugg and M. Zaugg (2010)
"Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria".
Am J Physiol Cell Physiol 298(3): C740-748.

Gerrits, B. and B. Bodenmiller (2010)
"Mapping of phosphorylation sites by LC-MS/MS".
Methods Mol Biol 658: 127-136.

Grisel, N., S. Zoller, M. Kunzli-Gontarczyk, T. Lampart, M. Munsterkotter, I. Brunner, L. Bovet, J. P. Metraux and C. Sperisen (2010)
"Transcriptome responses to aluminum stress in roots of aspen (Populus tremula)".
BMC Plant Biol 10(1): 185.

Grossmann, J., B. Roschitzki, C. Panse, C. Fortes, S. Barkow-Oesterreicher, D. Rutishauser and R. Schlapbach (2010)
"Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods".
J Proteomics 73(9): 1740-1746.

Hofmann, A., B. Gerrits, A. Schmidt, T. Bock, D. Bausch-Fluck, R. Aebersold and B. Wollscheid (2010)
"Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells".
Blood 116(13): e26-34.

Horlacher, T., M. A. Oberli, D. B. Werz, L. Krock, S. Bufali, R. Mishra, J. Sobek, K. Simons, M. Hirashima, T. Niki and P. H. Seeberger (2010)
"Determination of carbohydrate-binding preferences of human galectins with carbohydrate microarrays".
Chembiochem 11(11): 1563-1573.

Imig, J., N. Motsch, J. Y. Zhu, S. Barth, M. Okoniewski, T. Reineke, M. Tinguely, A. Faggioni, P. Trivedi, G. Meister, C. Renner and F. A. Grasser (2010)
"microRNA profiling in Epstein-Barr virus-associated B-cell lymphoma".
Nucleic Acids Res.

Jeger, S., K. Zimmermann, A. Blanc, J. Grunberg, M. Honer, P. Hunziker, H. Struthers and R. Schibli (2010)
"Site-specific and stoichiometric modification of antibodies by bacterial transglutaminase".
Angew Chem Int Ed Engl 49(51): 9995-9997.

Koch, M., N. Delmotte, H. Rehrauer, J. A. Vorholt, G. Pessi and H. Hennecke (2010)
"Rhizobial adaptation to hosts, a new facet in the legume root-nodule symbiosis".
Mol Plant Microbe Interact 23(6): 784-790.

Lecca, M. R., C. Maag, E. G. Berger and T. Hennet (2010)
"Fibrotic response in fibroblasts from congenital disorders of glycosylation".
J Cell Mol Med.

List, C., W. Qi, E. Maag, B. Gottstein, N. Muller and I. Felger (2010)
"Serodiagnosis of Echinococcus spp. infection: explorative selection of diagnostic antigens by peptide microarray".
PLoS Negl Trop Dis 4(8): e771.

Meienberg, J., M. Rohrbach, S. Neuenschwander, K. Spanaus, C. Giunta, S. Alonso, E. Arnold, C. Henggeler, S. Regenass, A. Patrignani, S. Azzarello-Burri, B. Steiner, A. O. Nygren, T. Carrel, B. Steinmann and G. Matyas (2010)
"Hemizygous deletion of COL3A1, COL5A2, and MSTN causes a complex phenotype with aortic dissection: a lesson for and from true haploinsufficiency".
Eur J Hum Genet 18(12): 1315-1321.

Messner, S., M. Altmeyer, H. Zhao, A. Pozivil, B. Roschitzki, P. Gehrig, D. Rutishauser, D. Huang, A. Caflisch and M. O. Hottiger (2010)
"PARP1 ADP-ribosylates lysine residues of the core histone tails".
Nucleic Acids Res 38(19): 6350-6362.

Minder, E. I., X. Schneider-Yin, R. Mamet, L. Horev, S. Neuenschwander, A. Baumer, F. Austerlitz, H. Puy and N. Schoenfeld (2010)
"A homoallelic FECH mutation in a patient with both erythropoietic protoporphyria and palmar keratoderma".
J Eur Acad Dermatol Venereol 24(11): 1349-1353.

Moretti, M., A. Grunau, D. Minerdi, P. Gehrig, B. Roschitzki, L. Eberl, A. Garibaldi, M. L. Gullino and K. Riedel (2010)
"A proteomics approach to study synergistic and antagonistic interactions of the fungal-bacterial consortium Fusarium oxysporum wild-type MSA 35".
Proteomics 10(18): 3292-3320.

Morf, L., C. Spycher, H. Rehrauer, C. A. Fournier, H. G. Morrison and A. B. Hehl (2010)
"The transcriptional response to encystation stimuli in Giardia lamblia is restricted to a small set of genes".
Eukaryot Cell 9(10): 1566-1576.

Nikolaev, Y., C. Deillon, S. R. Hoffmann, L. Bigler, S. Friess, R. Zenobi, K. Pervushin, P. Hunziker and B. Gutte (2010)
"The leucine zipper domains of the transcription factors GCN4 and c-Jun have ribonuclease activity".
PLoS One 5(5): e10765.

Passannante, M., C. O. Marti, C. Pfefferli, P. S. Moroni, S. Kaeser-Pebernard, A. Puoti, P. Hunziker, C. Wicky and F. Muller (2010)
"Different Mi-2 complexes for various developmental functions in Caenorhabditis elegans".
PLoS One 5(10): e13681.

Pimenova, T., C. Pereira, P. Gehrig, P. Buehler, D. Schaer and R. Zenobi (2010)
"Quantitative mass spectrometry defines an oxidative hotspot in hemoglobin that is specifically protected by haptoglobin".
J Proteome Res 9(8): 4061-4070.

Rampoldi, A., M. J. Jacobsen, H. U. Bertschinger, D. Joller, E. Burgi, P. Vogeli, L. Andersson, A. L. Archibald, M. Fredholm, C. B. Jorgensen and S. Neuenschwander (2010)
"The receptor locus for Escherichia coli F4ab/F4ac in the pig maps distal to the MUC4-LMLN region".
Mamm Genome.

Rehrauer, H., C. Aquino, W. Gruissem, S. R. Henz, P. Hilson, S. Laubinger, N. Naouar, A. Patrignani, S. Rombauts, H. Shu, Y. Van de Peer, M. Vuylsteke, D. Weigel, G. Zeller and L. Hennig (2010)
"AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling".
Plant Physiol 152(2): 487-499.

Roltgen, K., W. Qi, M. T. Ruf, E. Mensah-Quainoo, S. J. Pidot, T. Seemann, T. P. Stinear, M. Kaser, D. Yeboah-Manu and G. Pluschke (2010)
"Single nucleotide polymorphism typing of Mycobacterium ulcerans reveals focal transmission of buruli ulcer in a highly endemic region of Ghana".
PLoS Negl Trop Dis 4(7): e751.

Schneider, T., B. Gerrits, R. Gassmann, E. Schmid, M. O. Gessner, A. Richter, T. Battin, L. Eberl and K. Riedel (2010)
"Proteome analysis of fungal and bacterial involvement in leaf litter decomposition".
Proteomics 10(9): 1819-1830.

Sonda, S., L. Morf, I. Bottova, H. Baetschmann, H. Rehrauer, A. Caflisch, M. A. Hakimi and A. B. Hehl (2010)
"Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia".
Mol Microbiol 76(1): 48-67.

Srinivas, N., P. Jetter, B. J. Ueberbacher, M. Werneburg, K. Zerbe, J. Steinmann, B. Van der Meijden, F. Bernardini, A. Lederer, R. L. Dias, P. E. Misson, H. Henze, J. Zumbrunn, F. O. Gombert, D. Obrecht, P. Hunziker, S. Schauer, U. Ziegler, A. Kach, L. Eberl, K. Riedel, S. J. DeMarco and J. A. Robinson (2010)
"Peptidomimetic antibiotics target outer-membrane biogenesis in Pseudomonas aeruginosa".
Science 327(5968): 1010-1013.

Steuble, M., B. Gerrits, A. Ludwig, J. M. Mateos, T. M. Diep, M. Tagaya, A. Stephan, P. Schatzle, B. Kunz, P. Streit and P. Sonderegger (2010)
"Molecular characterization of a trafficking organelle: dissecting the axonal paths of calsyntenin-1 transport vesicles".
Proteomics 10(21): 3775-3788.

Thali, R. F., R. D. Tuerk, R. Scholz, Y. Yoho-Auchli, R. A. Brunisholz and D. Neumann (2010)
"Novel candidate substrates of AMP-activated protein kinase identified in red blood cell lysates".
Biochem Biophys Res Commun 398(2): 296-301.

Trollmann, R., H. Rehrauer, C. Schneider, G. Krischke, N. Huemmler, S. Keller, W. Rascher and M. Gassmann (2010)
"Late-gestational systemic hypoxia leads to a similar early gene response in mouse placenta and developing brain".
Am J Physiol Regul Integr Comp Physiol 299(6): R1489-1499.

TÃ¼rker, C., F. Akal, D. Joho, C. Panse, S. Barkow-Oesterreicher, H. Rehrauer and R. Schlapbach (2010)
"On-the fly integration of Life Sciences Applications (Demonstration)". 7th Iinternational Conference on Data Integration in th eLife Sciences (DILS 2010), Gothenbourg, Sweden.

TÃ¼rker, C., F. Akal, D. Joho, C. Panse, S. Barkow-Oesterreicher, H. Rehrauer and R. Schlapbach (2010)
"B-Fabric: The Swiss Army Knife for Life Sciences". EDBT 2010, Lausanne, Switzerland, ACM.

Tyagarajan, S. K., H. Ghosh, G. E. Yevenes, I. Nikonenko, C. Ebeling, C. Schwerdel, C. Sidler, H. U. Zeilhofer, B. Gerrits, D. Muller and J. M. Fritschy (2010)
"Regulation of GABAergic synapse formation and plasticity by GSK3{beta}-dependent phosphorylation of gephyrin".
Proc Natl Acad Sci U S A 108(1): 379-384.

Urban, P. L., A. Amantonico, S. R. Fagerer, P. Gehrig and R. Zenobi (2010)
"Mass spectrometric method incorporating enzymatic amplification for attomole-level analysis of target metabolites in biological samples".
Chem Commun (Camb) 46(13): 2212-2214.

Vallelian, F., C. A. Schaer, T. Kaempfer, P. Gehrig, E. Duerst, G. Schoedon and D. J. Schaer (2010)
"Glucocorticoid treatment skews human monocyte differentiation into a hemoglobin-clearance phenotype with enhanced heme-iron recycling and antioxidant capacity".
Blood 116(24): 5347-5356.

Veljkovic, E., J. Jiricny, M. Menigatti, H. Rehrauer and W. Han (2010)
"Chronic exposure to cigarette smoke condensate in vitro induces epithelial to mesenchymal transition-like changes in human bronchial epithelial cells, BEAS-2B".
Toxicol In Vitro.

Vogel, J. P. e. a. (2010)
"Genome sequencing and analysis of the model grass Brachypodium distachyon".
Nature 463(7282): 763-768.

Weber, A., R. Boger, B. Vick, T. Urbanik, J. Haybaeck, S. Zoller, A. Teufel, P. H. Krammer, J. T. Opferman, P. R. Galle, M. Schuchmann, M. Heikenwalder and H. Schulze-Bergkamen (2010)
"Hepatocyte-specific deletion of the antiapoptotic protein myeloid cell leukemia-1 triggers proliferation and hepatocarcinogenesis in mice".
Hepatology 51(4): 1226-1236.

Widmer, C. C., C. P. Pereira, P. Gehrig, F. Vallelian, G. Schoedon, P. W. Buehler and D. J. Schaer (2010)
"Hemoglobin can attenuate hydrogen peroxide-induced oxidative stress by acting as an antioxidative peroxidase".
Antioxid Redox Signal 12(2): 185-198.

Wilson, D. L., V. K. Rathinam, W. Qi, L. M. Wick, J. Landgraf, J. A. Bell, A. Plovanich-Jones, J. Parrish, R. L. Finley, L. S. Mansfield and J. E. Linz (2010)
"Genetic Diversity in Campylobacter jejuni is Associated with Differential Colonization of Broiler Chickens and C57BL/6J IL10 Deficient Mice".
Microbiology 156(Pt 7): 2046-2057.

Worthington, J., M. Bertani, H. L. Chan, B. Gerrits and J. F. Timms (2010)
"Transcriptional profiling of ErbB signalling in mammary luminal epithelial cells--interplay of ErbB and IGF1 signalling through IGFBP3 regulation".
BMC Cancer 10: 490.

Zeisberger, S. M., S. Zoller, M. Riegel, S. Chen, G. Krenning, M. C. Harmsen, A. Sachinidis and A. H. Zisch (2010)
"Optimization of the culturing conditions of human umbilical cord blood-derived endothelial colony-forming cells under xeno-free conditions applying a transcriptomic approach".
Genes Cells 15(7): 671-687.

Abu-Ali, G. S., D. W. Lacher, L. M. Wick, W. Qi and T. S. Whittam (2009)
"Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex".
BMC Genomics 10: 296.

Albinger-Hegyi, A., S. J. Stoeckli, S. Schmid, M. Storz, G. Iotzova, N. M. Probst-Hensch, H. Rehrauer, M. Tinguely, H. Moch and I. Hegyi (2009)
"Lysyl oxidase expression is an independent marker of prognosis and a predictor of lymph node metastasis in oral and oropharyngeal squamous cell carcinoma (OSCC)".
Int J Cancer 123(11): 2653-2662.

Baumgartel, K., R. Y. Tweedie-Cullen, J. Grossmann, P. Gehrig, M. Livingstone-Zatchej and I. M. Mansuy (2009)
"Changes in the Proteome after Neuronal Zif268 Overexpression".
J Proteome Res 8(7): 3298-3316.

Berthier, C. C., C. Pally, G. Weckbecker, F. Raulf, H. Rehrauer, U. Wagner, M. Le Hir and H. P. Marti (2009)
"Experimental heart transplantation: effect of cyclosporine on expression and activity of metzincins".
Swiss Med Wkly 139(15-16): 233-240.

Carranza, P., I. Hartmann, A. Lehner, R. Stephan, P. Gehrig, J. Grossmann, S. Barkow-Oesterreicher, B. Roschitzki, L. Eberl and K. Riedel (2009)
"Proteomic profiling of Cronobacter turicensis 3032, a food-borne opportunistic pathogen".
Proteomics 9(13): 3564-3579.

Delmotte, N., C. Knief, S. Chaffron, G. Innerebner, B. Roschitzki, R. Schlapbach, C. von Mering and J. A. Vorholt (2009)
"Community proteogenomics reveals insights into the physiology of phyllosphere bacteria".
Proc Natl Acad Sci U S A 106(38): 16428-16433.

Djouder, N., R. D. Tuerk, M. Suter, P. Salvioni, R. F. Thali, R. Scholz, K. Vaahtomeri, Y. Auchli, H. Rechsteiner, R. A. Brunisholz, B. Viollet, T. P. Makela, T. Wallimann, D. Neumann and W. Krek (2009)
"PKA phosphorylates and inactivates AMPKalpha to promote efficient lipolysis".
Embo J 29(3): 469-481.

Drissner, D., P. Gehrig, R. Marti, E. Hildbrand and F. Hesford (2009)
"Identification of a Red Wine Marker in Residues from a 13th Century Cellar".
Chimia 63(3): 169-169.

Duc, L., S. Neuenschwander, H. Rehrauer, U. Wagner, J. Sobek, R. Schlapbach and J. Zeyer (2009)
"Development and experimental validation of a nifH oligonucleotide microarray to study diazotrophic communities in a glacier forefield".
Environ Microbiol 11(8): 2179-2189.

Endler, A., S. Reiland, B. Gerrits, U. G. Schmidt, S. Baginsky and E. Martinoia (2009)
"In vivo phosphorylation sites of barley tonoplast proteins identified by a phosphoproteomic approach".
Proteomics 9(2): 310-321.

Falk, N., M. Kaestli, W. Qi, M. Ott, K. Baea, A. Cortes and H. P. Beck (2009)
"Analysis of Plasmodium falciparum var genes expressed in children from Papua New Guinea".
J Infect Dis 200(3): 347-356.

Feng, J., E. Lucchinetti, G. Enkavi, Y. Wang, P. Gehrig, B. Roschitzki, M. C. Schaub, E. Tajkhorshid, K. Zaugg and M. Zaugg (2009)
"Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria".
Am J Physiol Cell Physiol 298(3): C740-748.

Gamper, M., V. Viereck, V. Geissbuhler, J. Eberhard, J. Binder, C. Moll, H. Rehrauer and R. Moser (2009)
"Gene expression profile of bladder tissue of patients with ulcerative interstitial cystitis".
BMC Genomics 10: 199.

Gehrig, P. M., B. Roschitzki, D. Rutishauser, S. Reiland and R. Schlapbach (2009)
"Phosphorylated serine and threonine residues promote site-specific fragmentation of singly charged, arginine-containing peptide ions".
Rapid Commun Mass Spectrom 23(10): 1435-1445.

Goetze, S., E. Qeli, C. Mosimann, A. Staes, B. Gerrits, B. Roschitzki, S. Mohanty, E. M. Niederer, E. Laczko, E. Timmerman, V. Lange, E. Hafen, R. Aebersold, J. Vandekerckhove, K. Basler, C. H. Ahrens, K. Gevaert and E. Brunner (2009)
"Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster".
PLoS Biol 7(11): e1000236.

Grobei, M. A., E. Qeli, E. Brunner, H. Rehrauer, R. Zhang, B. Roschitzki, K. Basler, C. H. Ahrens and U. Grossniklaus (2009)
"Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function".
Genome Res 19(10): 1786-1800.

Haybaeck, J., N. Zeller, M. J. Wolf, A. Weber, U. Wagner, M. O. Kurrer, J. Bremer, G. Iezzi, R. Graf, P. A. Clavien, R. Thimme, H. Blum, S. A. Nedospasov, K. Zatloukal, M. Ramzan, S. Ciesek, T. Pietschmann, P. N. Marche, M. Karin, M. Kopf, J. L. Browning, A. Aguzzi and M. Heikenwalder (2009)
"A lymphotoxin-driven pathway to hepatocellular carcinoma".
Cancer Cell 16(4): 295-308.

Hecht, M. L., B. Rosental, T. Horlacher, O. Hershkovitz, J. L. De Paz, C. Noti, S. Schauer, A. Porgador and P. H. Seeberger (2009)
"Natural cytotoxicity receptors NKp30, NKp44 and NKp46 bind to different heparan sulfate/heparin sequences".
J Proteome Res 8(2): 712-720.

Hodel, E. M., S. D. Ley, W. Qi, F. Ariey, B. Genton and H. P. Beck (2009)
"A microarray-based system for the simultaneous analysis of single nucleotide polymorphisms in human genes involved in the metabolism of anti-malarial drugs".
Malar J 8: 285.

Huber, A., B. Bodenmiller, A. Uotila, M. Stahl, S. Wanka, B. Gerrits, R. Aebersold and R. Loewith (2009)
"Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis".
Genes Dev 23(16): 1929-1943.

Jecklin, M. C., S. Schauer, C. E. Dumelin and R. Zenobi (2009)
"Label-free determination of protein-ligand binding constants using mass spectrometry and validation using surface plasmon resonance and isothermal titration calorimetry".
J Mol Recognit 22(4): 319-329.

Kraljevic Pavelic, S., M. Sedic, K. Hock, S. Vucinic, D. Jurisic, P. Gehrig, M. Scott, R. Schlapbach, T. Cacev, S. Kapitanovic and K. Pavelic (2009)
"An integrated proteomics approach for studying the molecular pathogenesis of Dupuytren's disease".
J Pathol 217(4): 524-533.

Meier-Trummer, C. S., H. Rehrauer, M. Franchini, A. Patrignani, U. Wagner and M. Ackermann (2009)
"Malignant catarrhal fever of cattle is associated with low abundance of IL-2 transcript and a predominantly latent profile of ovine herpesvirus 2 gene expression".
PLoS One 4(7): e6265.

Montani, L., B. Gerrits, P. Gehrig, A. Kempf, L. Dimou, B. Wollscheid and M. E. Schwab (2009)
"Neuronal Nogo-A modulates growth cone motility via Rho-GTP/LIMK1/cofilin in the unlesioned adult nervous system".
J Biol Chem 284(16): 10793-10807.

Mugasa, J. P., M. Rottman, W. Qi, H. Mshinda and H. P. Beck (2009)
"Analysis of Plasmodium falciparum var Gene Repertoire Expressed in Childrenwith Severe Malaria from Tanzania".
Infection Genetics and Evolution 9(3): 378-378.

Pahlich, S., L. Quero, B. Roschitzki, R. P. Leemann-Zakaryan and H. Gehring (2009)
"Analysis of Ewing sarcoma (EWS)-binding proteins: interaction with hnRNP M, U, and RNA-helicases p68/72 within protein-RNA complexes".
J Proteome Res 8(10): 4455-4465.

Pilop, C., F. Aregger, R. C. Gorman, R. Brunisholz, B. Gerrits, T. Schaffner, J. H. Gorman, 3rd, G. Matyas, T. Carrel and B. M. Frey (2009)
"Proteomic analysis in aortic media of patients with Marfan syndrome reveals increased activity of calpain 2 in aortic aneurysms".
Circulation 120(11): 983-991.

Pimenova, T., L. Meier, B. Roschitzki, G. Paraschiv, M. Przybylski and R. Zenobi (2009)
"Polystyrene beads as an alternative support material for epitope identification of a prion-antibody interaction using proteolytic excision-mass spectrometry".
Anal Bioanal Chem 395(5): 1395-1401.

Qi, W., M. Kaser, K. Roltgen, D. Yeboah-Manu and G. Pluschke (2009)
"Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing".
PLoS Pathog 5(9): e1000580.

Qi, W., G. Nong, J. F. Preston, F. Ben-Ami and D. Ebert (2009)
"Comparative metagenomics of Daphnia symbionts".
BMC Genomics 10: 172.

Raschle, T., D. Speziga, W. Kress, C. Moccand, P. Gehrig, N. Amrhein, E. Weber-Ban and T. B. Fitzpatrick (2009)
"Intersubunit cross-talk in pyridoxal 5'-phosphate synthase, coordinated by the C terminus of the synthase subunit".
J Biol Chem 284(12): 7706-7718.

Reding, T., U. Wagner, A. B. Silva, L. K. Sun, M. Bain, S. Y. Kim, D. Bimmler and R. Graf (2009)
"Inflammation-dependent expression of SPARC during development of chronic pancreatitis in WBN/Kob rats and a microarray gene expression analysis".
Physiol Genomics 38(2): 196-204.

Rehrauer, H., C. Aquino, W. Gruissem, S. Henz, P. Hilson, S. Laubinger, N. Naouar, A. Patrignani, S. Rombauts, H. Shu, Y. Van de Peer, M. Vuylsteke, D. Weigel, G. Zeller and L. Hennig (2009)
"AGRONOMICS1 - A new resource for Arabidopsis transcriptome profiling".
Plant Physiol 152(2): 487-499.

Reiland, S., G. Messerli, K. Baerenfaller, B. Gerrits, A. Endler, J. Grossmann, W. Gruissem and S. Baginsky (2009)
"Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks".
Plant Physiol 150(2): 889-903.

Rutishauser, D., K. D. Mertz, R. Moos, E. Brunner, T. Rulicke, A. M. Calella and A. Aguzzi (2009)
"The comprehensive native interactome of a fully functional tagged prion protein".
PLoS One 4(2): e4446.

Sayi, A., E. Kohler, I. Hitzler, I. Arnold, R. Schwendener, H. Rehrauer and A. Muller (2009)
"The CD4+ T cell-mediated IFN-gamma response to Helicobacter infection is essential for clearance and determines gastric cancer risk".
J Immunol 182(11): 7085-7101.

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Ahrens, C. H., U. Wagner, H. K. Rehrauer, C. TÃ¼rker and R. Schlapbach (2007)
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Berthier, C. C., P. R. Wahl, M. Le Hir, H. P. Marti, U. Wagner, H. Rehrauer, R. P. Wuthrich and A. L. Serra (2007)
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Drissner, D., G. Kunze, N. Callewaert, P. Gehrig, M. Tamasloukht, T. Boller, G. Felix, N. Amrhein and M. Bucher (2007)
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Kleffmann, T., A. von Zychlinski, D. Russenberger, M. Hirsch-Hoffmann, P. Gehrig, W. Gruissem and S. Baginsky (2007)
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Knipp, M., A. V. Karotki, S. Chesnov, G. Natile, P. J. Sadler, V. Brabec and M. Vasak (2007)
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Mayer, D., K. Molawi, L. Martinez-Sobrido, A. Ghanem, S. Thomas, S. Baginsky, J. Grossmann, A. Garcia-Sastre and M. Schwemmle (2007)
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Munton, R. P., R. Tweedie-Cullen, M. Livingstone-Zatchej, F. Weinandy, M. Waidelich, D. Longo, P. Gehrig, F. Potthast, D. Rutishauser, B. Gerrits, C. Panse, R. Schlapbach and I. M. Mansuy (2007)
"Qualitative and Quantitative Analyses of Protein Phosphorylation in Naive and Stimulated Mouse Synaptosomal Preparations".
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Pessi, G., C. H. Ahrens, H. Rehrauer, A. Lindemann, F. Hauser, H. M. Fischer and H. Hennecke (2007)
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Pogoryelov, D., C. Reichen, A. L. Klyszejko, R. Brunisholz, D. J. Muller, P. Dimroth and T. Meier (2007)
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Potthast, F., B. Gerrits, J. Hakkinen, D. Rutishauser, C. H. Ahrens, B. Roschitzki, K. Baerenfaller, R. P. Munton, P. Walther, P. Gehrig, P. Seif, P. H. Seeberger and R. Schlapbach (2007)
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Rehrauer, H., S. Zoller and R. Schlapbach (2007)
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Cannavo, E., B. Gerrits, G. Marra, R. Schlapbach and J. Jiricny (2006)
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David, D. C., L. M. Ittner, P. Gehrig, D. Nergenau, C. Shepherd, G. Halliday and J. Gotz (2006)
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"Gene expression profiles of different breast cancer cells compared with their responsiveness to fermented mistletoe (Viscum album L.) extracts Iscador from oak (Quercus), pine (Pinus), white fir (Abies) and apple tree (Malus) in vitro".
Arzneimittelforschung 56(6A): 483-496.

El-Andaloussi, N., T. Valovka, M. Toueille, R. Steinacher, F. Focke, P. Gehrig, M. Covic, P. O. Hassa, P. Schar, U. Hubscher and M. O. Hottiger (2006)
"Arginine methylation regulates DNA polymerase beta".
Mol Cell 22(1): 51-62.

Fischer, B., J. Grossmann, V. Roth, W. Gruissem, S. Baginsky and J. M. Buhmann (2006)
"Semi-supervised LC/MS alignment for differential proteomics".
Bioinformatics 22(14): e132-140.

Gyenesei, A., R. Schlapbach, E. Stolte and U. Wagner (2006)
"Frequent pattern discovery without binarization: Mining attribute profiles".
Knowledge Discovery in Databases: Pkdd 2006, Proceedings 4213: 528-535.

Hauser, F., A. Lindemann, S. Vuilleumier, A. Patrignani, R. Schlapbach, H. M. Fischer and H. Hennecke (2006)
"Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region".
Mol Genet Genomics 275(1): 55-67.

Hoerstrup, S. P., I. Cummings Mrcs, M. Lachat, F. J. Schoen, R. Jenni, S. Leschka, S. Neuenschwander, D. Schmidt, A. Mol, C. Gunter, M. Gossi, M. Genoni and G. Zund (2006)
"Functional growth in tissue-engineered living, vascular grafts: follow-up at 100 weeks in a large animal model".
Circulation 114(1 Suppl): I159-166.

Kraljevic, S., M. Sedic, M. Scott, P. Gehrig, R. Schlapbach and K. Pavelic (2006)
"Casting light on molecular events underlying anti-cancer drug treatment: What can be seen from the proteomics point of view?".
Cancer Treat Rev 32(8): 619-629.

Laczko, E. (2006)
"Method for predicting biological, biochemical, biophysical, or pharmacological characteristics of a substance". In, 23912 EP, F. Hoffmann-La Roche Ltd., Basel, Switzerland, pages.

Murtaza, I., G. Marra, R. Schlapbach, A. Patrignani, M. Kunzli, U. Wagner, J. Sabates and A. Dutt (2006)
"A preliminary investigation demonstrating the effect of quercetin on the expression of genes related to cell-cycle arrest, apoptosis and xenobiotic metabolism in human CO115 colon-adenocarcinoma cells using DNA microarray".
Biotechnol Appl Biochem 45(Pt 1): 29-36.

Nesvizhskii, A. I., F. F. Roos, J. Grossmann, M. Vogelzang, J. S. Eddes, W. Gruissem, S. Baginsky and R. Aebersold (2006)
"Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides".
Mol Cell Proteomics 5(4): 652-670.

Ramadan, T., S. M. Camargo, V. Summa, P. Hunziker, S. Chesnov, K. M. Pos and F. Verrey (2006)
"Basolateral aromatic amino acid transporter TAT1 (Slc16a10) functions as an efflux pathway".
Journal of Cellular Physiology 206(3): 771-779.

Riedel, K., P. Carranza, P. Gehrig, F. Potthast and L. Eberl (2006)
"Towards the proteome of Burkholderia cenocepacia H111: setting up a 2-DE reference map".
Proteomics 6(1): 207-216.

Schmidt, D., A. Mol, C. Breymann, J. Achermann, B. Odermatt, M. Gossi, S. Neuenschwander, R. Pretre, M. Genoni, G. Zund and S. P. Hoerstrup (2006)
"Living autologous heart valves engineered from human prenatally harvested progenitors".
Circulation 114(1 Suppl): I125-131.

Schmidt, D., A. Mol, B. Odermatt, S. Neuenschwander, C. Breymann, M. Gossi, M. Genoni, G. Zund and S. P. Hoerstrup (2006)
"Engineering of biologically active living heart valve leaflets using human umbilical cord-derived progenitor cells".
Tissue Eng 12(11): 3223-3232.

Siddique, M. A., J. Grossmann, W. Gruissem and S. Baginsky (2006)
"Proteome analysis of bell pepper (Capsicum annuum L.) chromoplasts".
Plant Cell Physiol 47(12): 1663-1673.

Sobek, J., K. Bartscherer, A. Jacob, J. D. Hoheisel and P. Angenendt (2006)
"Microarray technology as a universal tool for high-throughput analysis of biological systems".
Comb Chem High Throughput Screen 9(5): 365-380.

Zimmermann, P., B. Schildknecht, D. Craigon, M. Garcia-Hernandez, W. Gruissem, S. May, G. Mukherjee, H. Parkinson, S. Rhee, U. Wagner and L. Hennig (2006)
"MIAME/Plant - adding value to plant microarrray experiments".
Plant Methods 2: 1.

Dallinger, R., M. Chabicovsky, E. Hodl, C. Prem, P. Hunziker and C. Manzl (2005)
"Copper in Helix pomatia (Gastropoda) is regulated by one single cell type: differently responsive metal pools in rhogocytes".
American Journal of Physiology - Regulatory Integrative & Comparative Physiology 289(4): R1185-1195.

Fischer, B., V. Roth, F. Roos, J. Grossmann, S. Baginsky, P. Widmayer, W. Gruissem and J. M. Buhmann (2005)
"NovoHMM: a hidden Markov model for de novo peptide sequencing".
Anal Chem 77(22): 7265-7273.

Gressmann, H., B. Linz, R. Ghai, K. P. Pleissner, R. Schlapbach, Y. Yamaoka, C. Kraft, S. Suerbaum, T. F. Meyer and M. Achtman (2005)
"Gain and loss of multiple genes during the evolution of Helicobacter pylori".
PLoS Genet 1(4): e43.

Grossmann, J., F. F. Roos, M. Cieliebak, Z. Liptak, L. K. Mathis, M. Muller, W. Gruissem and S. Baginsky (2005)
"AUDENS: a tool for automated peptide de novo sequencing".
J Proteome Res 4(5): 1768-1774.

Lecca, M. R., U. Wagner, A. Patrignani, E. G. Berger and T. Hennet (2005)
"Genome-wide analysis of the unfolded protein response in fibroblasts from congenital disorders of glycosylation type-I patients".
Faseb J 19(2): 240-242.

Lourdel, S., J. Loffing, G. Favre, M. Paulais, A. Nissant, P. Fakitsas, C. Creminon, E. Feraille, F. Verrey, J. Teulon, A. Doucet and G. Deschenes (2005)
"Hyperaldosteronemia and activation of the epithelial sodium channel are not required for sodium retention in puromycin-induced nephrosis".
J Am Soc Nephrol 16(12): 3642-3650.

Melkko, S., J. Sobek, G. Guarda, J. Scheuermann, C. E. Dumelin and D. Neri (2005)
"Encoded self-assembling chemical libraries".
Chimia 59(11): 798-802.

Mittag, D., S. Vieths, L. Vogel, D. Wagner-Loew, A. Starke, P. Hunziker, W. M. Becker and B. K. Ballmer-Weber (2005)
"Birch pollen-related food allergy to legumes: identification and characterization of the Bet v 1 homologue in mungbean (Vigna radiata), Vig r 1".
Clinical & Experimental Allergy 35(8): 1049-1055.

Potthast, F., J. Ocenasek, D. Rutishauser, M. Pelikan and R. Schlapbach (2005)
"Database independent detection of isotopically labeled MS/MS spectrum peptide pairs".
J Chromatogr B Analyt Technol Biomed Life Sci 817(2): 225-230.

Scheurer, S. B., J. N. Rybak, C. Roesli, R. A. Brunisholz, F. Potthast, R. Schlapbach, D. Neri and G. Elia (2005)
"Identification and relative quantification of membrane proteins by surface biotinylation and two-dimensional peptide mapping".
Proteomics 5(11): 2718-2728.

Schrimpf, S. P., V. Meskenaite, E. Brunner, D. Rutishauser, P. Walther, J. Eng, R. Aebersold and P. Sonderegger (2005)
"Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry".
Proteomics 5(10): 2531-2541.

Benke, D., P. Fakitsas, C. Roggenmoser, C. Michel, U. Rudolph and H. Mohler (2004)
"Analysis of the presence and abundance of GABAA receptors containing two different types of alpha subunits in murine brain using point-mutated alpha subunits".
J Biol Chem 279(42): 43654-43660.

Gehrig, P. M., P. E. Hunziker, S. Zahariev and S. Pongor (2004)
"Fragmentation pathways of N(G)-methylated and unmodified arginine residues in peptides studied by ESI-MS/MS and MALDI-MS".
J Am Soc Mass Spectrom 15(2): 142-149.

Niehus, E., H. Gressmann, F. Ye, R. Schlapbach, M. Dehio, C. Dehio, A. Stack, T. F. Meyer, S. Suerbaum and C. Josenhans (2004)
"Genome-wide analysis of transcriptional hierarchy and feedback regulation in the flagellar system of Helicobacter pylori".
Mol Microbiol 52(4): 947-961.

Pellegrini, A., A. J. Hulsmeier, P. Hunziker and U. Thomas (2004)
"Proteolytic fragments of ovalbumin display antimicrobial activity".
Biochimica Et Biophysica Acta-General Subjects 1672(2): 76-85.

Rozhkova, A., C. U. Stirnimann, P. Frei, U. Grauschopf, R. Brunisholz, M. G. Grutter, G. Capitani and R. Glockshuber (2004)
"Structural basis and kinetics of inter- and intramolecular disulfide exchange in the redox catalyst DsbD".
Embo J 23(8): 1709-1719.

Sartori, A. A., G. M. Lingaraju, P. Hunziker, F. K. Winkler and J. Jiricny (2004)
"Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases".
Nucleic Acids Research 32(22): 6531-6539.

Angenendt, P., J. Glokler, J. Sobek, H. Lehrach and D. J. Cahill (2003)

"Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications". J Chromatogr A 1009(1-2): 97-104.

Paglinawan, R., U. Malipiero, R. Schlapbach, K. Frei, W. Reith and A. Fontana (2003)

"TGFbeta directs gene expression of activated microglia to an anti-inflammatory phenotype strongly focusing on chemokine genes and cell migratory genes".
Glia 44(3): 219-231.