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Almeida, André M; Nanni, Paolo; Ferreira, Ana M; Fortes, Claudia; Grossmann, Jonas; Bessa, Rui J B; Costa, Paulo (2017). The longissimus thoracis muscle proteome in Alentejana bulls as affected by growth path. Journal of Proteomics, 152:206-215.

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

Neubauer, Jacqueline; Lecca, Maria Rita; Russo, Giancarlo; Bartsch, Christine; Medeiros-Domingo, Argelia; Berger, Wolfgang; Haas, Cordula (2017). Post-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.

Bilan, Vera; Leutert, Mario; Nanni, Paolo; Panse, Christian; Hottiger, Michael O (2017). Combining 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.

Briskine, Roman V; Shimizu, Kentaro K (2017). Positional bias in variant calls against draft reference assemblies. BMC Genomics, 18(1):263.

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

Marquardt, L; Lacour, M; Hoernes, M; Opitz, L; Lecca, R; Volkmer, B; Reichenbach, J; Hohl, D; Ansari, M; Ozsahin, H; Güngör, T; Pachlopnik Schmid, J (2017). 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. Journal of the European Academy of Dermatology and Venerology, 31(3):e147-e148.

Ardissone, Silvia; Redder, Peter; Russo, Giancarlo; Frandi, Antonio; Fumeaux, Coralie; Patrignani, Andrea; Schlapbach, Ralph; Falquet, Laurent; Viollier, Patrick H (2016). Cell cycle constraints and environmental control of local DNA hypomethylation in α-proteobacteria. PLoS Genetics, 12(12):e1006499.

Becker, Eugenia; Bengs, Susan; Aluri, Sirisha; Opitz, Lennart; Atrott, Kirstin; Stanzel, Claudia; Castro, Pedro A Ruiz; Rogler, Gerhard; Frey-Wagner, Isabelle (2016). Doxycycline, metronidazole and isotretinoin: Do they modify microRNA/mRNA expression profiles and function in murine T-cells? Scientific Reports, 6:37082.

Böhm, Maria; Wachtel, Marco; Marques, Joana G; Streiff, Natalie; Laubscher, Dominik; Nanni, Paolo; Mamchaoui, Kamel; Santoro, Raffaella; Schäfer, Beat W (2016). Helicase CHD4 is an epigenetic coregulator of PAX3-FOXO1 in alveolar rhabdomyosarcoma. Journal of Clinical Investigation, 126(11):4237-4249.

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

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

Maksimov, Vladimir; Nakamura, Miyuki; Wildhaber, Thomas; Nanni, Paolo; Ramström, Margareta; Bergquist, Jonas; Hennig, Lars (2016). The H3 chaperone function of NASP is conserved in Arabidopsis. The Plant Journal, 88(3):425-436.

Klobučar, Marko; Sedić, Mirela; Gehrig, Peter; Grossmann, Jonas; Bilić, Mario; Kovač-Bilić, Lana; Pavelić, Krešimir; Kraljević Pavelić, Sandra (2016). Basement membrane protein ladinin-1 and the MIF-CD44-β1 integrin signaling axis are implicated in laryngeal cancer metastasis. BBA - Biochimica et Biophysica Acta, 1862(10):1938-1954.

Gapp, Katharina; Bohacek, Johannes; Grossmann, Jonas; Brunner, Andrea M; Manuella, Francesca; Nanni, Paolo; Mansuy, Isabelle M (2016). Potential of environmental enrichment to prevent transgenerational effects of paternal trauma. Neuropsychopharmacology, 41(11):2749-2758.

Vogel, Christine; Bodenhausen, Natacha; Gruissem, Wilhelm; Vorholt, Julia A (2016). The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health. New Phytologist, 212(1):192-207.

Lin, Chia-Wei; Haeuptle, Micha A; Aebi, Markus (2016). Supercharging reagent for enhanced liquid chromatographic separation and charging of sialylated and high-molecular-weight glycopeptides for NanoHPLC-ESI-MS/MS analysis. Analytical Chemistry, 88(17):8484-8494.

Pfrunder, Stefanie; Grossmann, Jonas; Hunziker, Peter; Brunisholz, René; Gekenidis, Maria-Theresia; Drissner, David (2016). Bacillus cereus Group-Type Strain-Specific Diagnostic Peptides. Journal of Proteome Research, 15(9):3098-107.

Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver (2016). OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods, 13(9):741-748.

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

Malmersjö, Seth; Di Palma, Serena; Diao, Jiajie; Lai, Ying; Pfuetzner, Richard A; Wang, Austin L; McMahon, Moira A; Hayer, Arnold; Porteus, Matthew; Bodenmiller, Bernd; Brunger, Axel T; Meyer, Tobias (2016). Phosphorylation of residues inside the SNARE complex suppresses secretory vesicle fusion. EMBO Journal Online, 35(16):1810-1821.

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

Meder, Doris; Morales, Mònica; Pepperkok, Rainer; Schlapbach, Ralph; Tiran, Andreas; Van Minnebruggen, Geert (2016). 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. EMBO Reports, 17(8):1088-1093.

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

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

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

Kandiba, Lina; Lin, Chia-Wei; Aebi, Markus; Eichler, Jerry; Guerardel, Yann (2016). Structural characterization of the N-linked pentasaccharide decorating glycoproteins of the halophilic archaeon Haloferax volcanii. Glycobiology, 26(7):745-756.

Qi, Weihong; Vaughan, Lloyd; Katharios, Pantelis; Schlapbach, Ralph; Seth-Smith, Helena M B (2016). Host-associated genomic features of the novel uncultured intracellular pathogen ca. ichthyocystis revealed by direct sequencing of epitheliocysts. Genome Biology and Evolution, 8(6):1672-1689.

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

Williams, Evan G; Wu, Yibo; Jha, Pooja; Dubuis, Sébastien; Blattmann, Peter; Argmann, Carmen A; Houten, Sander M; Amariuta, Tiffany; Wolski, Witold; Zamboni, Nicola; Aebersold, Ruedi; Auwerx, Johan (2016). Systems proteomics of liver mitochondria function. Science, 352(6291):aad0189.

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

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

Fuentes, Alejandro; Carlos, Natacha; Ruiz, Yoslaine; Callard, Danay; Sánchez, Yadira; Ochagavía, María Elena; Seguin, Jonathan; Malpica-López, Nachelli; Hohn, Thomas; Lecca, Maria Rita; Pérez, Rosabel; Doreste, Vivian; Rehrauer, Hubert; Farinelli, Laurent; Pujol, Merardo; Pooggin, Mikhail M (2016). Field trial and molecular characterization of RNAi-transgenic tomato plants that exhibit resistance to tomato yellow leaf curl geminivirus. Molecular Plant-Microbe Interactions, 29(3):197-209.

Mahrez, Walid; Arellano, Minerva Susana Trejo; Moreno-Romero, Jordi; Nakamura, Miyuki; Shu, Huan; Nanni, Paolo; Köhler, Claudia; Gruissem, Wilhelm; Hennig, Lars (2016). H3K36ac is an evolutionary conserved plant histone modification that marks active genes. Plant Physiology, 170(3):1566-1577.

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

Paape, Timothy; Hatakeyama, Masaomi; Shimizu-Inatsugi, Rie; Cereghetti, Teo; Onda, Yoshihiko; Kenta, Tanaka; Sese, Jun; Shimizu, Kentaro K (2016). Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploidArabidopsis kamchatica. Molecular Biology and Evolution:1-44.

Freimoser, Florian Matthias; Hilber-Bodmer, Maja; Brunisholz, René; Drissner, David (2016). Direct identification of Monilinia brown rot fungi on infected fruits by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Chemical and Biological Technologies in Agriculture, 3:7.

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

Shimizu-Inatsugi, Rie; Terada, Aika; Hirose, Kyosuke; Kudoh, Hiroshi; Sese, Jun; Shimizu, Kentaro K (2016). Plant adaptive radiation mediated by polyploid plasticity in transcriptomes. Molecular Ecology:1-35.

Javed, A; Leuchte, N; Salinas, G; Opitz, L; Stahl-Hennig, C; Sopper, S; Sauermann, U (2016). 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. Journal of General Virology, 97(12):3400-3412.

Sobek, Jens; Rehrauer, Hubert; Schauer, Stefan; Fischer, David; Patrignani, Andrea; Landgraf, Stephan; Korlach, Jonas; Schlapbach, Ralph (2016). Single-molecule DNA hybridisation studied by using a modified DNA sequencer: a comparison with surface plasmon resonance data. Methods and applications in fluorescence, 4(1):1-17.

Nuvolone, Mario; Hermann, Mario; Sorce, Silvia; Russo, Giancarlo; Tiberi, Cinzia; Schwarz, Petra; Minikel, Eric; Sanoudou, Despina; Pelczar, Pawel; Aguzzi, Adriano (2016). Strictly co-isogenic C57BL/6J-Prnp−/−mice: A rigorous resource for prion science. Journal of Experimental Medicine, 213(3):313-327.

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

Whittington, Camilla M; Griffith, Oliver W; Qi, Weihong; Thompson, Michael B; Wilson, Anthony B (2015). Seahorse Brood Pouch Transcriptome Reveals Common Genes Associated with Vertebrate Pregnancy. Molecular Biology and Evolution, 32(12):3114-3131.

de Vallière, Cheryl; Vidal, Solange; Clay, Ieuan; Jurisic, Giorgia; Tcymbarevich, Irina; Lang, Silvia; Ludwig, Marie-Gabrielle; Okoniewski, Michal; Eloranta, Jyrki J; Kullak-Ublick, Gerd A; Wagner, Carsten A; Rogler, Gerhard; Seuwen, Klaus (2015). The 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(6):475-490.

Rosenthal, Florian; Nanni, Paolo; Barkow-Oesterreicher, Simon; Hottiger, Michael O (2015). Optimization of LTQ-Orbitrap mass spectrometer parameters for the identification of ADP-ribosylation sites. Journal of Proteome Research, 14(9):4072-4079.

Kraljević Pavelić, Sandra; Klobučar, Marko; Sedić, Mirela; Micek, Vedran; Gehrig, Peter; Grossman, Jonas; Pavelić, Krešimir; Vojniković, Božidar (2015). UV-induced retinal proteome changes in the rat model of age-related macular degeneration. BBA - Biochimica et Biophysica Acta, 1852(9):1833-1845.

Mueller, Susanne; Wahlander, Asa; Selevsek, Nathalie; Otto, Claudia; Ngwa, Elsy Mankah; Poljak, Kristina; Frey, Alexander D; Aebi, Markus; Gauss, Robert (2015). Protein degradation corrects for imbalanced subunit stoichiometry in OST complex assembly. Molecular Biology of the Cell, 26(14):2596-608.

Meienberg, Janine; Zerjavic, Katja; Keller, Irene; Okoniewski, Michal; Patrignani, Andrea; Ludin, Katja; Xu, Zhenyu; Steinmann, Beat; Carrel, Thierry; Röthlisberger, Benno; Schlapbach, Ralph; Bruggmann, Rémy; Matyas, Gabor (2015). New insights into the performance of human whole-exome capture platforms. Nucleic Acids Research, 43(11):e76.

Gámez-Pozo, Angelo; Berges-Soria, Julia; Arevalillo, Jorge M; Nanni, Paolo; López-Vacas, Rocío; Navarro, Hilario; Grossmann, Jonas; Castaneda, Carlos A; Main, Paloma; Díaz-Almirón, Mariana; Espinosa, Enrique; Ciruelos, Eva; Fresno Vara, Juan Ángel (2015). Combined Label-Free Quantitative Proteomics and microRNA Expression Analysis of Breast Cancer Unravel Molecular Differences with Clinical Implications. Cancer Research, 75(11):2243-2253.

Lichtensteiger, Walter; Bassetti-Gaille, Catherine; Faass, Oliver; Axelstad, Marta; Boberg, Julie; Christiansen, Sofie; Rehrauer, Hubert; Georgijevic, Jelena Kühn; Hass, Ulla; Kortenkamp, Andreas; Schlumpf, Margret (2015). Differential 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(4):1477-1493.

Mika, Moana; Mack, Ines; Korten, Insa; Qi, Weihong; Aebi, Suzanne; Frey, Urs; Latzin, Philipp; Hilty, Markus (2015). Dynamics of the nasal microbiota in infancy: a prospective cohort study. Journal of Allergy and Clinical Immunology, 135(4):905-912.e11.

Hashemi Gheinani, Ali; Burkhard, Fiona C; Rehrauer, Hubert; Aquino Fournier, Catharine; Monastyrskaya, Katia (2015). MicroRNA MiR-199a-5p regulates smooth muscle cell proliferation and morphology by targeting WNT2 signaling pathway. Journal of Biological Chemistry, 290(11):7067-7086.

Selevsek, Nathalie; Chang, Ching-Yun; Gillet, Ludovic C; Navarro, Pedro; Bernhardt, Oliver M; Reiter, Lukas; Cheng, Lin-Yang; Vitek, Olga; Aebersold, Ruedi (2015). Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry. Molecular & Cellular Proteomics, 14(3):739-749.

Panse, Christian; Trachsel, Christian; Grossmann, Jonas; Schlapbach, Ralph (2015). specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. Bioinformatics, 31(13):2228-2231.

Walker, Robert A; Sharman, Philippa A; Miller, Catherine M; Lippuner, Christoph; Okoniewski, Michal; Eichenberger, Ramon M; Ramakrishnan, Chandra; Brossier, Fabien; Deplazes, Peter; Hehl, Adrian B; Smith, Nicholas C (2015). RNA Seq analysis of the Eimeria tenella gametocyte transcriptome reveals clues about the molecular basis for sexual reproduction and oocyst biogenesis. BMC Genomics, 16(1):94.

Gillespie, Stephen H; Ling, Clare L; Oravcova, Katarina; Pinheiro, Miguel; Wells, Louise; Bryant, Josephine M; McHugh, Timothy D; Bébéar, Cecile; Webster, David; Harris, Simon R; Seth-Smith, Helena M B; Thomson, Nicholas R (2015). Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen. Clinical Infectious Diseases, 60(3):381-388.

Eid, Wassim; Opitz, Lennart; Biason-Lauber, Anna (2015). Genome-wide identification of CBX2 targets: insights in the human sex development network. Molecular Endocrinology, 29(2):247-257.

Langridge, Gemma C; Fookes, Maria; Connor, Thomas R; Feltwell, Theresa; Feasey, Nicholas; Parsons, Bryony N; Seth-Smith, Helena M B; Barquist, Lars; Stedman, Anna; Humphrey, Tom; Wigley, Paul; Peters, Sarah E; Maskell, Duncan J; Corander, Jukka; Chabalgoity, Jose A; Barrow, Paul; Parkhill, Julian; Dougan, Gordon; Thomson, Nicholas R (2015). Patterns of genome evolution that have accompanied host adaptation in Salmonella. Proceedings of the National Academy of Sciences of the United States of America, 112(3):863-868.

Lu, Qingtao; Ding, Shunhua; Reiland, Sonja; Rödiger, Anja; Roschitzki, Bernd; Xue, Peng; Gruissem, Wilhelm; Lu, Congming; Baginsky, Sacha (2015). Identification and characterization of chloroplast casein kinase II from Oryza sativa (rice). Journal of Experimental Botany, 66(1):175-187.

Draganova, Kalina; Zemke, Martina; Zurkirchen, Luis; Valenta, Tomas; Cantù, Claudio; Okoniewski, Michal; Schmid, Marie-Theres; Hoffmans, Raymond; Götz, Magdalena; Basler, Konrad; Sommer, Lukas (2015). Wnt/β-catenin signaling regulates sequential fate decisions of murine cortical precursor cells. Stem Cells, 33(1):170-182.

Junttila, Sanna; Saarela, Ulla; Halt, Kimmo; Manninen, Aki; Pärssinen, Heikki; Lecca, M Rita; Brändli, André W; Sims-Lucas, Sunder; Skovorodkin, Ilya; Vainio, Seppo J (2015). Functional Genetic Targeting of Embryonic Kidney Progenitor Cells Ex Vivo. Journal of the American Society of Nephrology (JASN), 26(5):1126-1137.

Russo, Giancarlo; Patrignani, Andrea; Poveda, Lucy; Hoehn, Frederic; Scholtka, Bettina; Schlapbach, Ralph; Garvin, Alex M (2015). Highly sensitive, non-invasive detection of colorectal cancer mutations using single molecule, third generation sequencing. Applied and Translational Genomics, 7:32-39.

Müller-Edenborn, Kamila; Léger, Karolin; Glaus Garzon, Jesus F; Oertli, Carole; Mirsaidi, Ali; Richards, Peter J; Rehrauer, Hubert; Spielmann, Patrick; Hoogewijs, David; Borsig, Lubor; Hottiger, Michael O; Wenger, Roland H (2015). Hypoxia attenuates the proinflammatory response in colon cancer cells by regulating IκB. OncoTarget, 6(24):20288-20301.

Säle, Verena; Aguilera, Paula; Laczko, Endre; Mäder, Paul; Berner, Alfred; Zihlmann, Urs; van der Heijden, Marcel G A; Oehl, Fritz (2015). Impact of conservation tillage and organic farming on the diversity of arbuscular mycorrhizal fungi. Soil Biology and Biochemistry, 84:38-52.

Urner, M; Schläpfer, M; Herrmann, I K; Hasler, M; Schimmer, R R; Booy, C; Roth Z'graggen, B; Rehrauer, H; Aigner, F; Minshall, R D; Stark, W J; Beck-Schimmer, B (2015). Insight into the beneficial immunomodulatory mechanism of the sevoflurane metabolite hexafluoro-2-propanol in a rat model of endotoxaemia. Clinical and Experimental Immunology, 181(3):468-479.

Biner, Olivier; Trachsel, Christian; Moser, Aline; Kopp, Lukas; Langenegger, Nicolas; Kämpfer, Urs; von Ballmoos, Christoph; Nentwig, Wolfgang; Schürch, Stefan; Schaller, Johann; Kuhn-Nentwig, Lucia (2015). Isolation, N-glycosylations and function of a hyaluronidase-like enzyme from the venom of the spider cupiennius salei. PLoS ONE, 10(12):e0143963.

Broecker, Felix; Klumpp, Jochen; Schuppler, Markus; Russo, Giancarlo; Biedermann, Luc; Hombach, Michael; Rogler, Gerhard; Moelling, Karin (2015). Long-term changes of bacterial and viral compositions in the intestine of a recoveredClostridium difficilepatient after fecal microbiota transplantation. Molecular Case Studies:448.

Vallelian, F; Deuel, J W; Opitz, L; Schaer, C A; Puglia, M; Lönn, M; Engelsberger, W; Schauer, S; Karnaukhova, E; Spahn, D R; Stocker, R; Buehler, P W; Schaer, D J (2015). Proteasome inhibition and oxidative reactions disrupt cellular homeostasis during heme stress. Cell Death and Differentiation, 22(4):597-611.

Portevin, Damien; Pflüger, Valentin; Otieno, Patricia; Brunisholz, René; Vogel, Guido; Daubenberger, Claudia (2015). Quantitative whole-cell MALDI-TOF MS fingerprints distinguishes human monocyte sub-populations activated by distinct microbial ligands. BMC Biotechnology, 15(24):online.

Krismer, Jasmin; Sobek, Jens; Steinhoff, Robert F; Fagerer, Stephan R; Pabst, Martin; Zenobi, Renato (2015). Screening of Chlamydomonas reinhardtii Populations with Single-Cell Resolution by Using a High-Throughput Microscale Sample Preparation for Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. Applied and Environmental Microbiology, 81(16):5546-5551.

Bastida, F; Selevsek, N; Torres, I F; Hernández, T; García, C (2015). Soil restoration with organic amendments: linking cellular functionality and ecosystem processes. Scientific Reports, 5:15550.

Norling, Martin; Bishop, Richard P; Pelle, Roger; Qi, Weihong; Henson, Sonal; Drábek, Elliott F; Tretina, Kyle; Odongo, David; Mwaura, Stephen; Njoroge, Thomas; Bongcam-Rudloff, Erik; Daubenberger, Claudia A; Silva, Joana C (2015). The 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):online.

Salm, Fabiana; Dimitrova, Valeriya; von Bueren, André O; Ćwiek, Paulina; Rehrauer, Hubert; Djonov, Valentin; Anderle, Pascale; Arcaro, Alexandre (2015). The phosphoinositide 3-kinase p110α isoform regulates leukemia inhibitory factor receptor expression via c-Myc and miR-125b to promote cell proliferation in medulloblastoma. PLoS ONE, 10(4):e0123958.

Trachsel, Christian; Panse, Christian; Grossmann, Jonas (2014). specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics. Bioconductor R Package v1.1.13 Bioc 3.0, University of Zurich.

Fischer, David; Panse, Christian; Laczko, Endre (2014). cosmiq - COmbining Single Masses Into Quantities. Bioconductor R Package v1.1.0 BioC 3.0, University of Zurich.

Schneider, Christoph; Nobs, Samuel P; Kurrer, Michael; Rehrauer, Hubert; Thiele, Christoph; Kopf, Manfred (2014). Induction of the nuclear receptor PPAR-γ by the cytokine GM-CSF is critical for the differentiation of fetal monocytes into alveolar macrophages. Nature Immunology, 15(11):1026-1037.

Schreiner, Dietmar; Nguyen, Thi-Minh; Russo, Giancarlo; Heber, Steffen; Patrignani, Andrea; Ahrné, Erik; Scheiffele, Peter (2014). Targeted combinatorial alternative splicing generates brain region-specific repertoires of neurexins. Neuron, 84(2):386-398.

Wachtel, Marco; Rakic, Jelena; Okoniewski, Michal; Bode, Peter; Niggli, Felix; Schäfer, Beat W (2014). FGFR4 signaling couples to Bim and not Bmf to discriminate subsets of alveolar rhabdomyosarcoma cells. International Journal of Cancer, 135(7):1543-1552.

Wiewiórka, Marek S; Messina, Antonio; Pacholewska, Alicja; Maffioletti, Sergio; Gawrysiak, Piotr; Okoniewski, Michał J (2014). SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision. Bioinformatics, 30(18):2652-2653.

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Felder, Kathrin M; Carranza, Paula M; Gehrig, Peter M; Roschitzki, Bernd; Barkow-Oesterreicher, Simon; Hoelzle, Katharina; Riedel, Katharina; Kube, Michael; Hoelzle, Ludwig E (2012). Insights into the gene expression profile of uncultivable hemotrophic Mycoplasma suis during acute infection, obtained using proteome analysis. Journal of Bacteriology, 194(6):1505-1514.

Testoni, Stefania; Bartolone, Elena; Rossi, Marco; Patrignani, Andrea; Bruggmann, Rémy; Lichtner, Peter; Tetens, Jens; Gentile, Arcangelo; Drögemüller, Cord (2012). KDM2B is implicated in bovine lethal multi-organic developmental dysplasia. PLoS ONE, 7(9):e45634.

Maglietta, Rosalia; Liuzzi, Vania Cosma; Cattaneo, Elisa; Laczko, Endre; Piepoli, Ada; Panza, Anna; Carella, Massimo; Palumbo, Orazio; Staiano, Teresa; Buffoli, Federico; Andriulli, Angelo; Marra, Giancarlo; Ancona, Nicola (2012). Molecular pathways undergoing dramatic transcriptomic changes during tumor development in the human colon. BMC Cancer, 12:608.

Trachsel, Christian; Siegemund, Doreen; Kämpfer, Urs; Kopp, Lukas S; Bühr, Claudia; Grossmann, Jonas; Lüthi, Christoph; Cunningham, Monica; Nentwig, Wolfgang; Kuhn-Nentwig, Lucia; Schürch, Stefan; Schaller, Johann (2012). Multicomponent venom of the spider Cupiennius salei: a bioanalytical investigation applying different strategies. FEBS Journal, 279(15):2683-2694.

Hilty, Markus; Qi, Weihong; Brugger, Silvio D; Frei, Laurence; Agyeman, Philipp; Frey, Pascal M; Aebi, Suzanne; Mühlemann, Kathrin (2012). Nasopharyngeal microbiota in infants with acute otitis media. Journal of Infectious Diseases, 205(7):1048-1055.

Egger, Anna; Samardzija, Marijana; Sothilingam, Vithiyanjali; Tanimoto, Naoyuki; Lange, Christina; Salatino, Silvia; Fang, Lei; Garcia-Garrido, Marina; Beck, Susanne; Okoniewski, Michal J; Neutzner, Albert; Seeliger, Mathias W; Grimm, Christian; Handschin, Christoph (2012). PGC-1α determines light damage susceptibility of the murine retina. PLoS ONE, 7(2):e31272.

Bauer, Chris; Kleinjung, Frank; Rutishauser, Dorothea; Panse, Christian; Chadt, Alexandra; Dreja, Tanja; Al-Hasani, Hadi; Reinert, Knut; Schlapbach, Ralph; Schuchhardt, Johannes (2012). PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios. BMC Bioinformatics, 13:34.

Rampitsch, Christof; Tinker, Nicholas A; Subramaniam, Rajagopal; Barkow-Oesterreicher, Simon; Laczko, Endre (2012). Phosphoproteome profile of Fusarium graminearum grown in vitro under nonlimiting conditions. Proteomics, 12(7):1002-1005.

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

Bischof, Sylvain; Grossmann, Jonas; Gruissem, Wilhelm (2012). Proteomics and its application in plant biotechnology. In: Altman, Arie; Hasegawa, Paul Michael. Plant Biotechnology and Agriculture. Prospects for the 21st Century. San Diego: Academic Press, 55-65.

Jovanovic, Marko; Reiter, Lukas; Clark, Alejandra; Weiss, Manuel; Picotti, Paola; Rehrauer, Hubert; Frei, Andreas; Neukomm, Lukas; Kaufman, Ethan; Wollscheid, Bernd; Simard, Martin J; Miska, Eric; Aebersold, Ruedi; Gerber, Andre P; Hengartner, Michael O (2012). RIPchipSRM, a new combinatorial large scale approach identifies a set of translationally regulated bantam/miR58 targets in C. elegans. Genome Research, 22(7):1360-1371.

Henrichs, Sina; Wang, Bangjun; Fukao, Yoichiro; Zhu, Jinsheng; Charrier, Laurence; Bailly, Aurélien; Oehring, Sophie C; Linnert, Miriam; Weiwad, Matthias; Endler, Anne; Nanni, Paolo; Pollmann, Stephan; Mancuso, Stefano; Schulz, Alexander; Geisler, Markus (2012). Regulation of ABCB1/PGP1-catalysed auxin transport by linker phosphorylation. EMBO Journal Online, 31(13):2965-2980.

Jang, Jae-Hwi; Rickenbacher, Andreas; Humar, Bostjan; Weber, Achim; Raptis, Dimitri Aristotle; Lehmann, Kuno; Stieger, Bruno; Moritz, Wolfgang; Soll, Christopher; Georgiev, Panco; Fischer, David; Laczko, Endre; Graf, Rolf; Clavien, Pierre-Alain (2012). Serotonin protects mouse liver from cholestatic injury by decreasing bile salt pool after bile duct ligation. Hepatology, 56(1):209-218.

Keiblinger, Katharina M; Wilhartitz, Inés C; Schneider, Thomas; Roschitzki, Bernd; Schmid, Emanuel; Eberl, Leo; Riedel, Kathrin; Zechmeister-Boltenstern, Sophie (2012). Soil metaproteomics – Comparative evaluation of protein extraction protocols. Soil Biology and Biochemistry, 54(15-10):14-24.

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

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Piepoli, Ada; Palmieri, Orazio; Maglietta, Rosalia; Panza, Anna; Cattaneo, Elisa; Latiano, Anna; Laczko, Endre; Gentile, Annamaria; Carella, Massimo; Mazzoccoli, Gianluigi; Ancona, Nicola; Marra, Giancarlo; Andriulli, Angelo (2012). The expression of leucine-rich repeat gene family members in colorectal cancer. Experimental Biology and Medicine, 237(10):1123-1128.

Seeger, Markus A; Mittal, Anshumali; Velamakanni, Saroj; Hohl, Michael; Schauer, Stefan; Salaa, Ihsene; Grütter, Markus G; van Veen, Hendrik W (2012). Tuning the drug efflux activity of an ABC transporter in vivo by in vitro selected DARPin binders. PLoS ONE, 7(6):e37845.

Schneider, Thomas; Keiblinger, Katharina M; Schmid, Emanuel; Sterflinger-Gleixner, Katja; Ellersdorfer, Günther; Roschitzki, Bernd; Richter, Andreas; Eberl, Leo; Zechmeister-Boltenstern, Sophie; Riedel, Kathrin (2012). Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions. The ISME journal, 6(9):1749-1762.

Pellegrino, M W; Farooqui, S; Fröhli, E; Rehrauer, H; Kaeser-Pebernard, S; Müller, F; Gasser, R B; Hajnal, A (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.

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

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

Filippini, M; Svercel, M; Laczko, E; Kaech, A; Ziegler, U; Bagheri, Homayoun C (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. International Journal of Systematic and Evolutionary Microbiology, 61(Pt 1):184-189.

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

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

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

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

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

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

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

Veljkovic, E; Jiricny, J; Menigatti, M; Rehrauer, H; Han, W (2011). Chronic exposure to cigarette smoke condensate in vitro induces epithelial to mesenchymal transition-like changes in human bronchial epithelial cells, BEAS-2B. Toxicology in Vitro, 25(2):446-453.

Reiland, S; Finazzi, G; Endler, A; Willig, A; Baerenfaller, K; Grossmann, J; Gerrits, B; Rutishauser, D; Gruissem, W; Rochaix, J D; Baginsky, S (2011). Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF). Proceedings of the National Academy of Sciences of the United States of America (PNAS), 108(31):12955-12960.

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

Müller, W; Türker, C (2011). Data management in life sciences. it - Information Technology, 53(5):215-216.

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

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

Rosenthal, F; Messner, S; Roschitzki, B; Gehrig, P; Nanni, P; Hottiger, M O (2011). Identification of distinct amino acids as ADP-ribose acceptor sites by mass spectrometry. Methods in Molecular Biology, 780(Part 1):57-66.

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

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

Hu, J; Stiehl, D P; Setzer, C; Wichmann, D; Shinde, D A; Rehrauer, H; Hradecky, P; Gassmann, M; Gorr, T A (2011). Interaction of HIF and USF signaling pathways at human genes flanked by hypoxia-response elements and E-box palindromes. Molecular Cancer Research, 9(11):1520-1536.

Türker, C; Akal, F; Schlapbach, R (2011). Life sciences data and application integration with B-fabric. Journal of Integrative Bioinformatics, 8(2):159.

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

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

Bischof, S; Baerenfaller, K; Wildhaber, T; Troesch, R; Vidi, P A; Roschitzki, B; Hirsch-Hoffmann, M; Hennig, L; Kessler, F; Gruissem, W; Baginsky, S (2011). Plastid proteome assembly without Toc159: photosynthetic protein import and accumulation of N-acetylated plastid precursor proteins. Plant Cell, 23(11):3911-3928.

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

Bratuś, A; Neuenschwander, S; Piestrzyńska-Kajtoch, A; Świtoński, M; Klukowska-Rötzler, J; Słota, E (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.

Vettermann, C; Castor, D; Mekker, A; Gerrits, B; Karas, M; Jäck, H M (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.

Roschitzki, B; Schauer, S; Mittl, P R E (2011). Recognition of host proteins by Helicobacter cysteine-rich protein C. Current Microbiology, 63(3):239-249.

Tyagarajan, S K; Ghosh, H; Yévenes, G E; Nikonenko, I; Ebeling, C; Schwerdel, C; Sidler, C; Zeilhofer, H U; Gerrits, B; Müller, D; Fritschy, J M (2011). Regulation of GABAergic synapse formation and plasticity by GSK3beta-dependent phosphorylation of gephyrin. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 108(1):379-384.

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

Rampoldi, A; Jacobsen, M J; Bertschinger, H U; Joller, D; Bürgi, E; Vögeli, P; Andersson, L; Archibald, A L; Fredholm, M; Jørgensen, C B; Neuenschwander, S (2011). The receptor locus for Escherichia coli F4ab/F4ac in the pig maps distal to the MUC4-LMLN region. Mammalian Genome, 22(1-2):122-129.

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

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

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

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

Altmeyer, M; Barthel, M; Eberhard, M; Rehrauer, H; Hardt, W D; Hottiger, M O (2010). Absence of poly(ADP-ribose) polymerase 1 delays the onset of Salmonella enterica serovar Typhimurium-induced gut inflammation. Infection and Immunity, 78(8):3420-3431.

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

Albinger-Hegyi, A; Stoeckli, S J; Schmid, S; Storz, M; Iotzova, G; Probst-Hensch, N M; Rehrauer, H; Tinguely, M; Moch, H; Hegyi, I (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). International Journal of Cancer, 126(11):2653 -2662.

Zeisberger, S M; Zoller, S; Riegel, M; Chen, S; Krenning, G; Harmsen, M C; Sachinidis, A; Zisch, A H (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 to Cells, 15(7):671-687.

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

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

Türker, C; Akal, F; Joho, D; Panse, C; Barkow-Oesterreicher, S; Rehrauer, H; Schlapbach, R (2010). B-Fabric: the Swiss Army Knife for life sciences. In: Proceedings of the 13th International Conference on Extending Database Technology, Lausanne, Switzerland, 22 March 2010 - 26 March 2010, 717-720.

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

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

Brülle, J K; Grau, T; Tschumi, A; Auchli, Y; Burri, R; Polsfuss, S; Keller, P M; Hunziker, P; Sander, P (2010). Cloning, expression and characterization of Mycobacterium tuberculosis lipoprotein LprF. Biochemical and Biophysical Research Communications (BBRC), 391(1):679-684.

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

Minder, E I; Schneider-Yin, X; Mamet, R; Horev, L; Neuenschwander, S; Baumer, A; Austerlitz, F; Puy, H; Schoenfeld, N (2010). A homoallelic FECH mutation in a patient with both erythropoietic protoporphyria and palmar keratoderma. Journal of the European Academy of Dermatology and Venereology, 24(11):1349-1353.

Moretti, M; Grunau, A; Minerdi, D; Gehrig, P; Roschitzki, B; Eberl, L; Garibaldi, A; Gullino, M L; Riedel, K (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.

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

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

Ebert, D; Qi, W (2010). An evolutionary ecology perspective on comparative metagenomics. In: Li, R W. Metagenomics and Its Application in Agriculture, Biomedicine and Environmental Studies. NY: Haippauge, Nova Science Publishers, 211-236.

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

Wilson, D L; Rathinam, V A K; Qi, W; Wick, L M; Landgraf, Jeff; Bell, J A; Plovanich-Jones, A; Parrish, J; Finley, R L; Mansfield, L S; Linz, J E (2010). Genetic diversity in Campylobacter jejuni is associated with differential colonization of broiler chickens and C57BL/6J IL10-deficient mice. Microbiology, 156(7):2046-2057.

International Brachypodium Initiative; Vogel, J P; Wicker, T; Buchmann, J P; et al (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463(7282):763-768.

Vallelian, F; Schaer, C A; Kaempfer, T; Gehrig, P; Duerst, E; Schoedon, G; Schaer, D J (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.

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

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

Trollmann, R; Rehrauer, H; Schneider, C; Krischke, G; Huemmler, N; Keller, S; Rascher, W; Gassmann, M (2010). Late-gestational systemic hypoxia leads to a similar early gene response in mouse placenta and developing brain. American Journal of Physiology. Regulatory, Integrative and Comparative Physiology, 299(6):1489-1499.

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

Gerrits, Bertran; Bodenmiller, Bernd (2010). Mapping of phosphorylation sites by LC-MS/MS. Methods in Molecular Biology, 658:127-136.

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

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

Thali, R F; Tuerk, R D; Scholz, R; Yoho-Auchli, Y; Brunisholz, R A; Neumann, D (2010). Novel candidate substrates of AMP-activated protein kinase identified in red blood cell lysates. Biochemical and Biophysical Research Communications (BBRC), 398(2):296-301.

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

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

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

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

Koch, M; Delmotte, N; Rehrauer, H; Vorholt, J A; Pessi, G; Hennecke, H (2010). Rhizobial adaptation to hosts, a new facet in the legume root-nodule symbiosis. Molecular Plant - Microbe Interactions, 23(6):784-90.

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Jeger, S; Zimmermann, K; Blanc, A; Grünberg, J; Honer, M; Hunziker, P; Struthers, H; Schibli, R (2010). Site-specific and stoichiometric modification of antibodies by bacterial transglutaminase. Angewandte Chemie Internationale Edition, 49(51):9995-9997.

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

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

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

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

Feng, J; Lucchinetti, E; Enkavi, G; Wang, Y; Gehrig, P; Roschitzki, B; Schaub, M C; Tajkhorshid, E; Zaugg, K; Zaugg, M (2010). Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria. American Journal of Physiology: Cell Physiology, 298(3):C740-C748.

Aregger, F; Pilop, C; Uehlinger, D E; Brunisholz, R; Carrel, T P; Frey, F J; Frey, Brigitte M (2010). Urinary proteomics before and after extracorporeal circulation in patients with and without acute kidney injury. The Journal of Thoracic and Cardiovascular Surgery, 139(3):692-700.

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

Tschumi, A; Nai, C; Auchli, Y; Hunziker, P; Gehrig, P; Keller, P; Grau, T; Sander, P (2009). Identification of apolipoprotein n-acyltransferase (LNT) in mycobacteria. Journal of Biological Chemistry, 284(40):27146-27156.

Pahlich, S; Quero, L; Roschitzki, B; Leemann-Zakaryan, R P; Gehring, H (2009). Analysis of Ewing Sarcoma (EWS)-Binding Proteins: Interaction with hnRNP M, U, and RNA-Helicases p68/72 within Protein-RNA Complexes. Journal of Proteome Research, 8(10):4455-4465.

Pilop, C; Aregger, F; Gromann, R C; Brunisholz, R; Gerrits, B; Schaffner, T; Gromann, J H; Mátyás, G; Carrel, T; Frey, Brigitte M (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.

Liu, J; Bandyopadhyay, N; Ranka, S; Baudis, M; Kahveci, T (2009). Inferring Progression Models for CGH data. Bioinformatics, 25(17):2208-2215.

Schönmann, S; Loy, A; Wimmersberger, C; Sobek, J; Aquino, C; Vandamme, P; Frey, Beat; Rehrauer, H; Eberl, L (2009). 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia. Environmental Microbiology, 11(4):779-800.

Thoma, R S; Smith, J S; Sandoval, W; Leone, J W; Hunziker, P; Hampton, B; Linse, K D; Denslow, N D (2009). The ABRF Edman Sequencing Research Group 2008 Study: investigation into homopolymeric amino acid N-terminal sequence tags and their effects on automated Edman degradation. Journal of Biomolecular Techniques, 20(4):216-225.

Falk, N; Kaestli, M; Qi, W; Ott, M; Baea, K; Cortés, A; Beck, H P (2009). Analysis of Plasmodium falciparum var genes expressed in children from Papua New Guinea. Journal of Infectious Diseases, 200(3):347-56.

Baumgärtel, K; Tweedie-Cullen, R Y; Grossmann, J; Gehrig, P; Livingstone-Zatchej, M; Mansuy, I M (2009). Changes in the proteome after neuronal Zif268 overexpression. Journal of Proteome Research, 8(7):3298-3316.

Zheng, L; Kanagaraj, R; Mihaljevic, B; Schwendener, S; Sartori, A A; Gerrits, B; Shevelev, I; Janscak, P (2009). MRE11 complex links RECQ5 helicase to sites of DNA damage. Nucleic Acids Research, 37(8):2645-2657.

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

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Tennant, S M; Tauschek, M; Azzopardi, K; Bigham, A; Bennett-Wood, V; Hartland, E L; Qi, W; Whittam, T S; Robins-Browne, R M (2009). Characterisation of atypical enteropathogenic E. coli strains of clinical origin. BMC Microbiology, 9:117.

Schrimpf, S P; Weiss, M; Reiter, L; Ahrens, C H; Jovanovic, M; Malmström, J; Brunner, E; Mohanty, S; Lercher, M J; Hunziker, P E; Aebersold, R; von Mering, C; Hengartner, M O (2009). Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biology, 7(3):e48.

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

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

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

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

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

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

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

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

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

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

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

Meier-Trummer, C S; Rehrauer, H; Franchini, M; Patrignani, A; Wagner, U; Ackermann, A (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):1-12.

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

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

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

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

Schneider, T; Schellenberg, M; Meyer, S; Keller, F; Gehrig, P; Riedel, K; Lee, Y; Eberl, L; Martinoia, E (2009). Quantitative detection of changes in the leaf-mesophyll tonoplast proteome in dependency of a cadmium exposure of barley (Hordeum vulgare L.) plants. Proteomics, 9(10):2668-77.

Bug, S; Dürig, J; Oyen, F; Klein-Hitpass, L; Martin-Subero, J I; Harder, L; Baudis, M; Arnold, N; Kordes, U; Dührsen, U; Schneppenheim, R; Siebert, R (2009). Recurrent loss, but lack of mutations, of the SMARCB1 tumor suppressor gene in T-cell prolymphocytic leukemia with TCL1A-TCRAD juxtaposition. Cancer Genetics and Cytogenetics, 192(1):44-47.

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

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

Tuerk, R D; Auchli, Y; Thali, R F; Scholz, R; Wallimann, T; Brunisholz, R A; Neumann, D (2009). Tracking and quantification of 32P-labeled phosphopeptides in liquid chromatography matrix-assisted laser desorption/ionization mass spectrometry. Analytical Biochemistry, 390(2):141-148.

Sims, A H; Smethurst, G J; Hey, Y; Okoniewski, M J; Pepper, S D; Howell, A; Miller, C J; Clarke, R B (2008). The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis. BMC Medical Genomics, 1:42.

Rehrauer, H; Schönmann, S; Eberl, L; Schlapbach, R (2008). PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays. Bioinformatics, 24(16):i83-i89.

Amantonico, A; Oh, J Y; Sobek, J; Heinemann, M; Zenobi, R (2008). Mass spectrometric method for analyzing metabolites in yeast with single cell sensitivity. Angewandte Chemie Internationale Edition, 47(29):5382-5385.

Foerg, C; Weller, K M; Rechsteiner, H; Nielsen, H M; Fernández-Carneado, J; Brunisholz, R; Giralt, E; Merkle, H P (2008). Metabolic cleavage and translocation efficiency of selected cell penetrating peptides: a comparative study with epithelial cell cultures. The AAPS Journal, 10(2):349-359.

Pierce, A; Unwin, R D; Evans, C A; Griffiths, S; Carney, L; Zhang, L; Jaworska, E; Lee, C F; Blinco, D; Okoniewski, M J; Miller, C J; Bitton, D A; Spooncer, E; Whetton, A D (2008). Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases. Molecular & Cellular Proteomics, 7(5):853-63.

Buerki, C; Rothgiesser, K M; Valovka, T; Owen, H R; Rehrauer, H; Fey, M; Lane, W S; Hottiger, M O (2008). Functional relevance of novel p300-mediated lysine 314 and 315 acetylation of RelA/p65. Nucleic Acids Research, 36(5):1665-1680.

Rohde, B; Hans, J; Martens, S; Baumert, A; Hunziker, P; Matern, U (2008). Anthranilate N-methyltransferase, a branch-point enzyme of acridone biosynthesis. The Plant Journal, 53(3):541-553.

Payeli, S K; Latini, R; Gebhard, K; Patrignani, A; Wagner, U; Lüscher, T F; Tanner, F C (2008). Prothrombotic gene expression profile in vascular smooth muscle cells of human saphenous vein, but not internal mammary artery. Arteriosclerosis, Thrombosis and Vascular Biology, 28(4):705-710.

Eng, J K; Fischer, B; Grossmann, J; Maccoss, M J (2008). A fast SEQUEST cross correlation algorithm. Journal of Proteome Research, 7(10):4598-4602.

Kraljevic Pavelic, S; Sedic, M; Hock, K; Vucinic, S; Jurisic, D; Gehrig, P; Scott, M; Schlapbach, R; Cacev, T; Kapitanovic, S; Pavelic, K (2008). An integrated proteomics approach for studying the molecular pathogenesis of Dupuytren's disease. Journal of Pathology, 217(4):524-533.

Bich, C; Scott, M; Panagiotidis, A; Wenzel, R J; Nazabal, A; Zenobi, R (2008). Characterization of antibody-antigen interactions: comparison between surface plasmon resonance measurements and high-mass matrix-assisted laser desorption/ionization mass spectrometry. Analytical Biochemistry, 375(1):35-45.

Wimmer, U; Ferrari, E; Hunziker, P; Hübscher, U (2008). Control of DNA polymerase lambda stability by phosphorylation and ubiquitination during the cell cycle. EMBO Reports, 9(10):1027-1033.

Scheuermann, J; Dumelin, C E; Melkko, S; Zhang, Y; Mannocci, L; Jaggi, M; Sobek, J; Neri, D (2008). DNA-encoded chemical libraries for the discovery of MMP-3 inhibitors. Bioconjugate Chemistry, 19(3):778-785.

Sedic, M; Poznic, M; Gehrig, P; Scott, M; Schlapbach, R; Hranjec, M; Karminski-Zamola, G; Pavelic, K; Kraljevic Pavelic, S (2008). Differential antiproliferative mechanisms of novel derivative of benzimidazo[1,2-alpha]quinoline in colon cancer cells depending on their p53 status. Molecular Cancer Therapeutics, 7(7):2121-2132.

Pimenova, T; Nazabal, A; Roschitzki, B; Seebacher, J; Rinner, O; Zenobi, R (2008). Epitope mapping on bovine prion protein using chemical cross-linking and mass spectrometry. Journal of Mass Spectrometry, 43(2):185-195.

Baerenfaller, K; Grossmann, J; Grobei, M A; Hull, R; Hirsch-Hoffmann, M; Yalovsky, S; Zimmermann, P; Grossniklaus, U; Gruissem, W; Baginsky, S (2008). Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science, 320(5878):938-941.

Kleinert, P; Schmidt, M W I; Zurbriggen, K; Speer, O; Schmugge, M; Roschitzki, B; Durka, S S; Leopold, U; Kuster, T; Heizmann, C W; Frischknecht, H; Troxler, H (2008). Mass spectrometry: a tool for enhanced detection of hemoglobin variants. Clinical Chemistry, 54(1):69-76.

Bodenmiller, B; Campbell, D; Gerrits, B; Lam, H; Jovanovic, M; Picotti, P; Schlapbach, R; Aebersold, R (2008). PhosphoPep--a database of protein phosphorylation sites in model organisms. Nature Biotechnology, 26(12):1339-1340.

Feng, J; Zhu, M; Schaub, M C; Gehrig, P; Roschitzki, B; Lucchinetti, E; Zaugg, M (2008). Phosphoproteome analysis of isoflurane-protected heart mitochondria: phosphorylation of adenine nucleotide translocator-1 on Tyr194 regulates mitochondrial function. Cardiovascular Research, 80(1):20-29.

Pani, E; Menigatti, M; Schubert, S; Hess, D; Gerrits, B; Klempnauer, K H; Ferrari, S (2008). Pin1 interacts with c-Myb in a phosphorylation-dependent manner and regulates its transactivation activity. Biochimica et Biophysica Acta, 1783(6):1121-1128.

Pflieger, D; Jünger, M A; Müller, M; Rinner, O; Lee, H; Gehrig, P M; Gstaiger, M; Aebersold, R (2008). Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation. Molecular and Cellular Proteomics, 7(2):326-346.

Berthier, C C; Wahl, P R; Le Hir, M; Wagner, U; Rehrauer, H; Wüthrich, R P; Serra, A L (2008). Sirolimus ameliorates the enhanced expression of metalloproteinases in a rat model of autosomal dominant polycystic kidney disease. Nephrology, Dialysis, Transplantation, 23(3):880-889.

Polymenidou, M; Moos, R; Scott, M; Sigurdson, C; Shi, Y Z; Yajima, B; Hafner-Bratkovic, I; Jerala, R; Hornemann, S; Wuthrich, K; Bellon, A; Vey, M; Garen, G; James, M N G; Kav, N; Aguzzi, A (2008). The POM monoclonals: a comprehensive set of antibodies to non-overlapping prion protein epitopes. PLoS ONE, 3(12):e3872.

Baginsky, S; Grossmann, J; Gruissem, W (2007). Proteome analysis of chloroplast mRNA processing and degradation. Journal of Proteome Research, 6(2):809-820.

Pessi, G; Ahrens, C H; Rehrauer, H; Lindemann, A; Hauser, F; Fischer, H M; Hennecke, H (2007). Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules. Molecular Plant-Microbe Interactions, 20(11):1353-1363.

Drissner, D; Kunze, G; Callewaert, N; Gehrig, P; Tamasloukht, M; Boller, T; Felix, G; Amrhein, N; Bucher, M (2007). Lyso-phosphatidylcholine is a signal in the arbuscular mycorrhizal symbiosis. Science, 318(5848):265-268.

Bergmüller, E; Gehrig, P M; Gruissem, W (2007). Characterization of post-translational modifications of histone H2B-variants isolated from Arabidopsis thaliana. Journal of Proteome Research, 6(9):3655-3668.

Knipp, M; Karotki, A V; Chesnov, S; Natile, G; Sadler, P J; Brabec, V; Vasák, M (2007). Reaction of Zn7metallothionein with cis- and trans-[Pt(N-donor)2Cl2] anticancer complexes: trans-Pt(II) complexes retain their N-donor ligands. Journal of Medicinal Chemistry, 50(17):4075-4086.

Mátyás, G; Alonso, S; Patrignani, A; Marti, M; Arnold, E; Magyar, I; Henggeler, C; Carrel, T; Steinmann, B; Berger, W (2007). Large genomic fibrillin-1 (FBN1) gene deletions provide evidence for true haploinsufficiency in Marfan syndrome. Human Genetics, 122(1):23-32.

Tuerk, R D; Thali, R F; Auchli, Y; Rechsteiner, H; Brunisholz, R A; Schlattner, U; Wallimann, T; Neumann, D (2007). New candidate targets of AMP-activated protein kinase in murine brain revealed by a novel multidimensional substrate-screen for protein kinases. Journal of Proteome Research, 6(8):3266-3277.

Braun, O; Knipp, M; Chesnov, S; Vasák, M (2007). Specific reactions of S-nitrosothiols with cysteine hydrolases: A comparative study between dimethylargininase-1 and CTP synthetase. Protein Science, 16(8):1522-1534.

Pogoryelov, D; Reichen, C; Klyszejko, A L; Brunisholz, R; Muller, D J; Dimroth, P; Meier, T (2007). The oligomeric state of c rings from cyanobacterial F-ATP synthases varies from 13 to 15. Journal of Bacteriology, 189(16):5895-902.

Potthast, F; Gerrits, B; Häkkinen, J; Rutishauser, D; Ahrens, C H; Roschitzki, B; Baerenfaller, K; Munton, R P; Walther, P; Gehrig, P; Seif, P; Seeberger, P H; Schlapbach, R (2007). The Mass Distance Fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry. Journal of Chromatography B, 854(1-2):173-182.

Rehrauer, H; Zoller, S; Schlapbach, R (2007). MAGMA: analysis of two-channel microarrays made easy. Nucleic Acids Research, 35(Web Se):W86-90.

Reinhardt, A; Emmenegger, C; Gerrits, B; Panse, C; Dommen, J; Baltensperger, U; Zenobi, R; Kalberer, M (2007). Ultrahigh mass resolution and accurate mass measurements as a tool to characterize oligomers in secondary organic aerosols. Analytical Chemistry, 79(11):4074-4082.

Bovet, C; Wortmann, A; Eiler, S; Granger, F; Ruff, M; Gerrits, B; Moras, D; Zenobi, R (2007). Estrogen receptor-ligand complexes measured by chip-based nanoelectrospray mass spectrometry: an approach for the screening of endocrine disruptors. Protein Science, 16(5):938-946.

Fakitsas, P; Adam, G; Daidié, D; van Bemmelen, M X; Fouladkou, F; Patrignani, A; Wagner, U; Warth, R; Camargo, S M R; Staub, O; Verrey, F (2007). Early aldosterone-induced gene product regulates the epithelial sodium channel by deubiquitylation. Journal of the American Society of Nephrology (JASN), 18(4):1084-1092.

Maillet, I; Berndt, P; Malo, C; Rodriguez, S; Brunisholz, R A; Pragai, Z; Arnold, S; Langen, H; Wyss, M (2007). From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach. Proteomics, 7(7):1097-1106.

Raschle, T; Arigoni, D; Brunisholz, R; Rechsteiner, H; Amrhein, N; Fitzpatrick, T B (2007). Reaction mechanism of pyridoxal 5'-phosphate synthase: detection of an enzyme-bound chromophoric intermediate. Journal of Biological Chemistry, 282(9):6098-6105.

Mayer, D; Molawi, K; Martínez-Sobrido, L; Ghanem, A; Thomas, S; Baginsky, S; Grossmann, J; García-Sastre, A; Schwemmle, M (2007). Identification of cellular interaction partners of the influenza virus ribonucleoprotein complex and polymerase complex using proteomic-based approaches. Journal of Proteome Research, 6(2):672-682.

Kleffmann, T; von Zychlinski, A; Russenberger, D; Hirsch-Hoffmann, M; Gehrig, P; Gruissem, W; Baginsky, S (2007). Proteome dynamics during plastid differentiation in rice. Plant Physiology, 143(2):912-923.

Munton, R P; Tweedie-Cullen, R; Livingstone-Zatchej, M; Weinandy, F; Waidelich, M; Longo, D; Gehrig, P; Potthast, F; Rutishauser, D; Gerrits, B; Panse, C; Schlapbach, R; Mansuy, I M (2007). Qualitative and quantitative analyses of protein phosphorylation in naive and stimulated mouse synaptosomal preparations. Molecular & Cellular Proteomics, 6(2):283-293.

El-Andaloussi, N; Valovka, T; Toueille, M; Hassa, P O; Gehrig, P; Covic, M; Hübscher, U; Hottiger, M O (2007). Methylation of DNA polymerase beta by protein arginine methyltransferase 1 regulates its binding to proliferating cell nuclear antigen. FASEB Journal, 21(1):26-34.

Brunner, E; Ahrens, C H; Mohanty, S; Baetschmann, H; Loevenich, S; Potthast, F; Deutsch, E W; Panse, C; de Lichtenberg, U; Rinner, O; Lee, H; Pedrioli, P G A; Malmstrom, J; Koehler, K; Schrimpf, S; Krijgsveld, J; Kregenow, F; Heck, A J R; Hafen, E; Schlapbach, R; Aebersold, R (2007). A high-quality catalog of the Drosophila melanogaster proteome. Nature Biotechnology, 25(5):576-583.

Schlosser, E; Otero, C; Wuensch, C; Kessler, B; Edelmann, M; Brunisholz, R; Drexler, I; Legler, D F; Groettrup, M (2007). A novel cytosolic class I antigen-processing pathway for endoplasmic-reticulum-targeted proteins. EMBO Reports, 8(10):945-51.

Grossmann, J; Fischer, B; Baerenfaller, K; Owiti, J; Buhmann, J M; Gruissem, W; Baginsky, S (2007). A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments. Proteomics, 7(23):4245-4254.

Cannavo, E; Gerrits, B; Marra, G; Schlapbach, R; Jiricny, J (2007). Characterization of the interactome of the human MutL homologues MLH1, PMS1, and PMS. Journal of Biological Chemistry, 282(5):2976-86.

Mathur, S; Badertscher, M; Scott, M; Zenobi, R (2007). Critical evaluation of mass spectrometric measurement of dissociation constants: accuracy and cross-validation against surface plasmon resonance and circular dichroism for the calmodulin-melittin system. Physical Chemistry Chemical Physics (PCCP), 9(47):6187-6198.

Nowik, M; Lecca, M R; Velic, A; Rehrauer, H; Brändli, A W; Wagner, C A (2007). Genome-wide gene expression profiling reveals renal genes regulated during metabolic acidosis. Physiological Genomics, 32(3):322-334.

Eckhardt, K; Troger, J; Reissmann, J; Katschinski, D M; Wagner, K F; Stengel, P J; Paasch, U; Hunziker, P; Borter, E; Barth, S; Schlafli, P; Spielmann, P; Stiehl, D P; Camenisch, G; Wenger, R H (2007). Male germ cell expression of the PAS domain kinase PASKIN and its novel target eukaryotic translation elongation factor eEF1A1. Cellular Physiology and Biochemistry, 20(1-4):227-240.

Roos, F F; Jacob, R; Grossmann, J; Fischer, B; Buhmann, J M; Gruissem, W; Baginsky, S; Widmayer, P (2007). PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra. Bioinformatics, 23(22):3016-3023.

Bodenmiller, B; Malmstrom, J; Gerrits, B; Campbell, D; Lam, H; Schmidt, A; Rinner, O; Mueller, L N; Shannon, P T; Pedrioli, P G; Panse, C; Lee, H K; Schlapbach, R; Aebersold, R (2007). PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Molecular Systems Biology, 3:139.

Sabates-Bellver, J; Van der Flier, L G; de Palo, M; Cattaneo, E; Maake, C; Rehrauer, H; Laczko, E; Kurowski, M A; Bujnicki, J M; Menigatti, M; Luz, J; Ranalli, T V; Gomes, V; Pastorelli, A; Faggiani, R; Anti, M; Jiricny, J; Clevers, H; Marra, G (2007). Transcriptome profile of human colorectal adenomas. Molecular Cancer Research, 5(12):1263-1275.

David, D C; Ittner, L M; Gehrig, P; Nergenau, D; Shepherd, C; Halliday, G; Götz, J (2006). Beta-amyloid treatment of two complementary P301L tau-expressing Alzheimer's disease models reveals similar deregulated cellular processes. Proteomics, 6(24):6566-6577.

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

Cai, H; Gehrig, P; Scott, T M; Zimmermann, R; Schlapbach, R; Zisch, A H (2006). MnSOD marks cord blood late outgrowth endothelial cells and accompanies robust resistance to oxidative stress. Biochemical and Biophysical Research Communications (BBRC), 350(2):364-369.

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

Fischer, B; Grossmann, J; Roth, V; Gruissem, W; Baginsky, S; Buhmann, J M (2006). Semi-supervised LC/MS alignment for differential proteomics. Bioinformatics, 22(14):e132-40.

Diet, A; Link, B; Seifert, G J; Schellenberg, B; Wagner, U; Pauly, M; Reiter, W D; Ringli, C (2006). The Arabidopsis root hair cell wall formation mutant lrx1 is suppressed by mutations in the RHM1 gene encoding a UDP-L-rhamnose synthase. Plant Cell, 18(7):1630-1641.

Bernasconi, M; Berger, C; Sigrist, J A; Bonanomi, A; Sobek, J; Niggli, F K; Nadal, D (2006). Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray. Virology Journal, 43(3):1-15.

Sobek, J; Bartscherer, K; Jacob, A; Hoheisel, J D; Angenendt, P (2006). Microarray technology as a universal tool for high-throughput analysis of biological systems. Combinatorial chemistry & high throughput screening, 9(5):365-380.

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

Liu, J; Mohammed, J; Carter, J; Ranka, S; Kahveci, T; Baudis, M (2006). Distance-based clustering of CGH data. Bioinformatics, 22(16):1971-1978.

Nesvizhskii, A I; Roos, F F; Grossmann, J; Vogelzang, M; Eddes, J S; Gruissem, W; Baginsky, S; Aebersold, R (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. Molecular and Cellular Proteomics, 5(4):652-670.

Hoerstrup, S P; Cummings Mrcs, I; Lachat, M; Schoen, F J; Jenni, R; Leschka, S; Neuenschwander, S; Schmidt, D; Mol, A; Günter, C; Gössi, M; Genoni, M; Zund, G (2006). Functional growth in tissue-engineered living, vascular grafts: follow-up at 100 weeks in a large animal model. Circulation, 114(1 Supp):I 159-I 166.

Schmidt, D; Mol, A; Breymann, C; Achermann, J; Odermatt, B; Gössi, M; Neuenschwander, S; Prêtre, René; Genoni, M; Zund, G; Hoerstrup, S P (2006). Living autologous heart valves engineered from human prenatally harvested progenitors. Circulation Research, 114(1 Suppl):I125-I131.

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

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

Lourdel, S; Loffing, J; Favre, G; Paulais, M; Nissant, A; Fakitsas, P; Créminon, C; Féraille, E; Verrey, F; Teulon, J; Doucet, A; Deschênes, G (2005). Hyperaldosteronemia and activation of the epithelial sodium channel are not required for sodium retention in puromycin-induced nephrosis. Journal of the American Society of Nephrology (JASN), 16(12):3642-3650.

Grossmann, J; Roos, F F; Cieliebak, M; Lipták, Z; Mathis, L K; Müller, M; Gruissem, W; Baginsky, S (2005). AUDENS: a tool for automated peptide de novo sequencing. Journal of Proteome Research, 4(5):1768-1774.

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

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

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

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

Vandesompele, J; Baudis, M; De Preter, K; Van Roy, N; Ambros, P; Bown, N; Brinkschmidt, C; Christiansen, H; Combaret, V; Lastowska, M; Nicholson, J; O'Meara, A; Plantaz, D; Stallings, R; Brichard, B; Van den Broecke, C; De Bie, S; De Paepe, A; Laureys, G; Speleman, F (2005). Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma. Journal of Clinical Oncology, 23(10):2280-2299.

Benke, D; Fakitsas, P; Roggenmoser, C; Michel, C; Rudolph, U; Mohler, H (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. Journal of Biological Chemistry, 279(42):43654-43660.

Gehrig, P M; Hunziker, P E; Zahariev, S; Pongor, S (2004). Fragmentation pathways of N(G)-methylated and unmodified arginine residues in peptides studied by ESI-MS/MS and MALDI-MS. Journal of the American Society for Mass Spectrometry, 15(2):142-149.

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

Angenendt, P; Glökler, J; Sobek, J; Lehrach, H; Cahill, D J (2003). Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications. Journal of chromatography. A, 1009(1-2):97-104.

This list was generated on Wed Jul 26 22:14:43 2017 CEST.