Header

UZH-Logo

Maintenance Infos

Items where Subject is "04 Faculty of Medicine > Functional Genomics Center Zurich"

Navigate back| Up a level
Export as
Number of items at this level: 479.

Huang, Sheng-Fu; Fischer, Sabrina; Koshkin, Alexey; Laczko, Endre; Fischer, David; Ogunshola, Omolara O (2020). Cell-specific metabolomic responses to injury: novel insights into blood-brain barrier modulation. Scientific Reports, 10(1):7760.

Boonpiyathad, Tadech; Capova, Gertruda; Duchna, Hans‐Werner; Croxford, Andrew L; Farine, Herve; Dreher, Anita; Clozel, Martine; Schreiber, Juliane; Kubena, Petr; Lunjani, Nonhlanhla; Mirer, David; Rückert, Beate; Satitsuksanoa, Pattraporn; Tan, Ge; Groenen, Peter M A; Bersuch, Eugen; Akdis, Mübeccel; Strasser, Daniel S; Renner, Ellen D; Akdis, Cezmi A (2020). Impact of high‐altitude therapy on type‐2 immune responses in asthma patients. Allergy, 75(1):84-94.

Pfefferlé, Marc; Ingoglia, Giada; Schaer, Christian A; Yalamanoglu, Ayla; Buzzi, Raphael M; Dubach, Irina L; Tan, Ge; López-​Cano, Emilio Y; Schulthess, Nadja; Hansen, Kerstin; Humar, Rok; Schaer, Dominik J; Vallelian, Florence (2020). Hemolysis transforms liver macrophages into anti-inflammatory erythrophagocytes. Journal of Clinical Investigation:Epub ahead of print.

Huang, Sheng-Fu; Othman, Alaa; Koshkin, Alexey; Fischer, Sabrina; Fischer, David; Zamboni, Nicola; Ono, Katsuhiko; Sawa, Tomohiro; Ogunshola, Omolara O (2020). Astrocyte glutathione maintains endothelial barrier stability. Redox Biology, 34:101576.

Kuo, Tony C Y; Hatakeyama, Masaomi; Tameshige, Toshiaki; Shimizu, Kentaro K; Sese, Jun (2020). Homeolog expression quantification methods for allopolyploids. Briefings in Bioinformatics, 21(2):395-407.

Woodhams, Douglas C; Rollins-Smith, Louise A; Reinert, Laura K; Lam, Briana A; Harris, Reid N; Briggs, Cheryl J; Vredenburg, Vance T; Patel, Bhumi T; Caprioli, Richard M; Chaurand, Pierre; Hunziker, Peter; Bigler, Laurent (2020). Probiotics Modulate a Novel Amphibian Skin Defense Peptide That Is Antifungal and Facilitates Growth of Antifungal Bacteria. Microbial Ecology, 79(1):192-202.

Kuon, Joel-E; Qi, Weihong; Schläpfer, Pascal; Hirsch-Hoffmann, Matthias; von Bieberstein, Philipp Rogalla; Patrignani, Andrea; Poveda, Lucy; Grob, Stefan; Keller, Miyako; Shimizu-Inatsugi, Rie; Grossniklaus, Ueli; Vanderschuren, Hervé; Gruissem, Wilhelm (2019). Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars. BMC Biology, 17(1):75.

Kuzmanov, Aleksandar; Qi, Weihong; Stenz, Nadja; Bochud, Pierre-Yves; Kutalik, Zoltan; Wojtowicz, Agnieszka; Hofbauer, Günther (2019). rs34567942 a Novel Susceptibility Single Nucleotide Polymorphism for Cutaneous Squamous Cell Carcinoma in Organ Transplant Recipients. Acta Dermato-Venereologica, 99(13):1303-1304.

Taylor, Scott; Pieri, Kyriaki; Nanni, Paolo; Tica, Jure; Barratt, Jonathan; Didangelos, Athanasios (2019). Phosphatidylethanolamine binding protein-4 (PEBP4) is increased in IgA nephropathy and is associated with IgA-positive B-cells in affected kidneys. Journal of autoimmunity, 105:102309.

Rao, Tata Nageswara; Hansen, Nils; Hilfiker, Julian; Rai, Shivam; Majewska, Julia-Magdalena; Leković, Danijela; Gezer, Deniz; Andina, Nicola; Galli, Serena; Cassel, Teresa; Geier, Florian; Delezie, Julien; Nienhold, Ronny; Hao-Shen, Hui; Beisel, Christian; Di Palma, Serena; Dimeloe, Sarah; Trebicka, Jonel; Wolf, Dominik; Gassmann, Max; Fan, Teresa W-M; Lane, Andrew N; Handschin, Christoph; Dirnhofer, Stefan; Kröger, Nicolaus; Hess, Christoph; Radimerski, Thomas; Koschmieder, Steffen; Čokić, Vladan P; Skoda, Radek C (2019). JAK2-mutant hematopoietic cells display metabolic alterations that can be targeted to treat myeloproliferative neoplasms. Blood, 134(21):1832-1846.

Mehta, Devang; Hirsch-Hoffmann, Matthias; Were, Mariam; Patrignani, Andrea; Zaidi, Syed Shan-E-Ali; Were, Hassan; Gruissem, Wilhelm; Vanderschuren, Hervé (2019). A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field. Nucleic Acids Research, 47(2):e9-e9.

Noya, Sara B; Colameo, David; Brüning, Franziska; Spinnler, Andrea; Mircsof, Dennis; Opitz, Lennart; Mann, Matthias; Tyagarajan, Shiva K; Robles, Maria S; Brown, Steven A (2019). The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep. Science, 366(6462):eaav2642.

Nowak, Marta; Rehrauer, Hubert; Ay, Serhan S; Findik, Murat; Boos, Alois; Kautz, Ewa; Kowalewski, Mariusz P (2019). Gene expression profiling of the canine placenta during normal and antigestagen-induced luteolysis. General and Comparative Endocrinology, 282:113194.

Trilla-Fuertes, Lucía; Gámez-Pozo, Angelo; Díaz-Almirón, Mariana; Prado-Vázquez, Guillermo; Zapater-Moros, Andrea; López-Vacas, Rocío; Nanni, Paolo; Zamora, Pilar; Espinosa, Enrique; Fresno Vara, Juan Ángel (2019). Computational metabolism modeling predicts risk of distant relapse-free survival in breast cancer patients. Future Oncology (London, England), 15(30):3483-3490.

Geber, Jonny; Tromp, Monica; Scott, Ashley; Bouwman, Abigail; Nanni, Paolo; Grossmann, Jonas; Hendy, Jessica; Warinner, Christina (2019). Relief food subsistence revealed by microparticle and proteomic analyses of dental calculus from victims of the Great Irish Famine. Proceedings of the National Academy of Sciences of the United States of America, 116(39):19380-19385.

Pickel, Christina; Günter, Julia; Ruiz-Serrano, Amalia; Spielmann, Patrick; Fabrizio, Jacqueline-Alba; Wolski, Witold; Peet, Daniel J; Wenger, Roland H; Scholz, Carsten C (2019). Oxygen-dependent bond formation with FIH regulates the activity of the client protein OTUB1. Redox Biology, 26:101265.

Junier, Thomas; Huber, Michael; Schmutz, Stefan; Kufner, Verena; Zagordi, Osvaldo; Neuenschwander, Stefan; Ramette, Alban; Kubacki, Jakub; Bachofen, Claudia; Qi, Weihong; Laubscher, Florian; Cordey, Samuel; Kaiser, Laurent; Beuret, Christian; Barbié, Valérie; Fellay, Jacques; Lebrand, Aitana (2019). Viral metagenomics in the clinical realm: lessons learned from a Swiss-wide ring trial. Genes, 10(9):E655.

Miller, Blake A; Brewer, Amy; Nanni, Paolo; Lim, Joseph J; Callanan, John J; Grossmann, Jonas; Kunz, Laura; de Almeida, André M; Meade, Kieran G; Chapwanya, Aspinas (2019). Characterization of circulating plasma proteins in dairy cows with cytological endometritis. Journal of Proteomics, 205:103421.

Volkmer, Benjamin; Planas, Raquel; Gossweiler, Emanuel; Lünemann, Anna; Opitz, Lennart; Mauracher, Andrea; Nüesch, Ursina; Gayden, Tenzin; Kaiser, Daniela; Drexel, Barbara; Dumrese, Claudia; Jabado, Nada; Vavassori, Stefano; Pachlopnik Schmid, Jana (2019). Recurrent inflammatory disease caused by a heterozygous mutation in CD48. Journal of Allergy and Clinical Immunology, 144(5):1441-1445.e17.

Schori, Christian; Trachsel, Christian; Grossmann, Jonas; Barben, Maya; Klee, Katrin; Storti, Federica; Samardzija, Marijana; Grimm, Christian (2019). A chronic hypoxic response in photoreceptors alters the vitreous proteome in mice. Experimental Eye Research, 185:107690.

Lim, Pei Jin; Lindert, Uschi; Opitz, Lennart; Hausser, Ingrid; Rohrbach, Marianne; Giunta, Cecilia (2019). Transcriptome Profiling of Primary Skin Fibroblasts Reveal Distinct Molecular Features Between PLOD1- and FKBP14-Kyphoscoliotic Ehlers–Danlos Syndrome. Genes, 10(7):517.

Thoms, Franziska; Jennings, Gary T; Maudrich, Melanie; Vogel, Monique; Haas, Stefanie; Zeltins, Andris; Hofmann-Lehmann, Regina; Riond, Barbara; Grossmann, Jonas; Hunziker, Peter; Fettelschoss-Gabriel, Antonia; Senti, Gabriela; Kündig, Thomas M; Bachmann, Martin F (2019). Immunization of cats to induce neutralizing antibodies against Fel d 1, the major feline allergen in human subjects. Journal of Allergy and Clinical Immunology, 144(1):193-203.

Amon, Sabine; Meier-Abt, Fabienne; Gillet, Ludovic C; Dimitrieva, Slavica; Theocharides, Alexandre P A; Manz, Markus G; Aebersold, Ruedi (2019). Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry. Molecular & Cellular Proteomics, 18(7):1454-1467.

Brugger, Silvio D; Kraemer, Julia G; Qi, Weihong; Bomar, Lindsey; Oppliger, Anne; Hilty, Markus (2019). Age-Dependent Dissimilarity of the Nasopharyngeal and Middle Ear Microbiota in Children With Acute Otitis Media. Frontiers in Genetics, 10:555.

Li, Shuo; Morita, Hideaki; Sokolowska, Milena; Tan, Ge; Boonpiyathad, Tadech; Opitz, Lennart; Orimo, Keisuke; Archer, Stuart K; Jansen, Kirstin; Tang, Mimi L K; Purcell, Damian; Plebanski, Magdalena; Akdis, Cezmi A (2019). Gene expression signatures of circulating human type 1, 2, and 3 innate lymphoid cells. Journal of Allergy and Clinical Immunology, 143(6):2321-2325.

Morita, H; Kubo, Terufumi; Ruckert, B; Ravindran, Avinash; Soyka, M B; Rinaldi, A O; Sugita, Kazunari; Wawrzyniak, Marcin; Wawrzyniak, P; Motomura, Kenichiro; Tamari, M; Orimo, K; Okada, N; Arae, Ken; Saito, Kazuki; Altunbulakli, Can; Castro-Giner, Francesc; Tan, Ge; Neumann, A; Sudo, Katsuko; O'Mahony, L; Honda, K; Nakae, Susumu; Saito, H; Mjösberg, J; Nilsson, Gunnar; Matsumoto, Kenji; Akdis, Mübeccel; Akdis, Cezmi A (2019). Induction of human regulatory innate lymphoid cells from group 2 innate lymphoid cells by retinoic acid. Journal of Allergy and Clinical Immunology, 143(6):2190-2201.e9.

Komuczki, Juliana; Tuzlak, Selma; Friebel, Ekaterina; Hartwig, Tom; Spath, Sabine; Rosenstiel, Philip; Waisman, Ari; Opitz, Lennart; Oukka, Mohammed; Schreiner, Bettina; Pelczar, Pawel; Becher, Burkhard (2019). Fate-Mapping of GM-CSF Expression Identifies a Discrete Subset of Inflammation-Driving T Helper Cells Regulated by Cytokines IL-23 and IL-1β. Immunity, 50(5):1289-1304.e6.

Sarker, Gitalee; Sun, Wenfei; Rosenkranz, David; Pelczar, Pawel; Opitz, Lennart; Efthymiou, Vissarion; Wolfrum, Christian; Peleg-Raibstein, Daria (2019). Maternal overnutrition programs hedonic and metabolic phenotypes across generations through sperm tsRNAs. Proceedings of the National Academy of Sciences of the United States of America, 116(21):10547-10556.

Wang, Ming; Tan, Ge; Eljaszewicz, Andrzej; Meng, Yifan; Wawrzyniak, Paulina; Acharya, Swati; Altunbulakli, Can; Westermann, Patrick; Dreher, Anita; Yan, Liying; Wang, Chengshuo; Akdis, Mubeccel; Zhang, Luo; Nadeau, Kari C; Akdis, Cezmi A (2019). Laundry detergents and detergent residue after rinse directly disrupt tight junction barrier integrity in human bronchial epithelial cells. Journal of Allergy and Clinical Immunology, 143(5):1892-1903.

Egloff, Pascal; Zimmermann, Iwan; Arnold, Fabian M; Hutter, Cedric A J; Morger, Damien; Opitz, Lennart; Poveda, Lucy; Keserue, Hans-Anton; Panse, Christian; Roschitzki, Bernd; Seeger, Markus A (2019). Engineered peptide barcodes for in-depth analyses of binding protein libraries. Nature Methods, 16(5):421-428.

Balaz, Miroslav; Becker, Anton S; Balazova, Lucia; Straub, Leon; Müller, Julian; Gashi, Gani; Maushart, Claudia Irene; Sun, Wenfei; Dong, Hua; Moser, Caroline; Horvath, Carla; Efthymiou, Vissarion; Rachamin, Yael; Modica, Salvatore; Zellweger, Caroline; Bacanovic, Sara; Stefanicka, Patrik; Varga, Lukas; Ukropcova, Barbara; Profant, Milan; Opitz, Lennart; Amri, Ez-Zoubir; Akula, Murali K; Bergo, Martin; Ukropec, Jozef; Falk, Christian; Zamboni, Nicola; Betz, Matthias Johannes; Burger, Irene A; Wolfrum, Christian (2019). Inhibition of Mevalonate Pathway Prevents Adipocyte Browning in Mice and Men by Affecting Protein Prenylation. Cell Metabolism, 29(4):901-916.e8.

Verheijen, M; Lienhard, M; Schrooders, Y; Clayton, O; Nudischer, R; Boerno, S; Timmermann, B; Selevsek, N; Schlapbach, R; Gmuender, H; Gotta, S; Geraedts, J; Herwig, R; Kleinjans, J; Caiment, F (2019). DMSO induces drastic changes in human cellular processes and epigenetic landscape in vitro. Scientific Reports, 9:4641.

Kombrink, Anja; Tayyrov, Annageldi; Essig, Andreas; Stöckli, Martina; Micheller, Sebastian; Hintze, John; van Heuvel, Yasemin; Dürig, Natalia; Lin, Chia-Wei; Kallio, Pauli T; Aebi, Markus; Künzler, Markus (2019). Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria. The ISME journal, 13(3):588-602.

Boonpiyathad, Tadech; van de Veen, Willem; Wirz, Oliver; Sokolowska, Milena; Rückert, Beate; Tan, Ge; Sangasapaviliya, Atik; Pradubpongsa, Panitan; Fuengthong, Rattanaporn; Thantiworasit, Pattarawat; Sirivichayakul, Sunee; Ruxrungtham, Kiat; Akdis, Cezmi A; Akdis, Mübeccel (2019). Role of Der p 1-specific B cells in immune tolerance during 2 years of house dust mite-specific immunotherapy. Journal of Allergy and Clinical Immunology, 143(3):1077-1086.e10.

Rollins, Katherine A; Opitz, Lennart; Arnold, Myrtha; Simon, Eric; Neubauer, Heike; Wolfrum, Susanne (2019). The L cell transcriptome is unaffected by vertical sleeve gastrectomy but highly dependent upon position within the gastrointestinal tract. Peptides, 113:22-34.

Tan, Ge; Opitz, Lennart; Schlapbach, Ralph; Rehrauer, Hubert (2019). Long fragments achieve lower base quality in Illumina paired-end sequencing. Scientific Reports, 9:2856.

Imeri, Faik; Nolan, Karen A; Bapst, Andreas M; Santambrogio, Sara; Abreu-Rodríguez, Irene; Spielmann, Patrick; Pfundstein, Svende; Libertini, Silvana; Crowther, Lisa; Orlando, Ilaria M C; Dahl, Sophie L; Keodara, Anna; Kuo, Willy; Kurtcuoglu, Vartan; Scholz, Carsten C; Qi, Weihong; Hummler, Edith; Hoogewijs, David; Wenger, Roland H (2019). Generation of renal Epo-producing cell lines by conditional gene tagging reveals rapid HIF-2 driven Epo kinetics, cell autonomous feedback regulation, and a telocyte phenotype. Kidney International, 95(2):375-387.

Ramakrishnan, Chandra; Maier, Simone; Walker, Robert A; Rehrauer, Hubert; Joekel, Deborah E; Winiger, Rahel R; Basso, Walter U; Grigg, Michael E; Hehl, Adrian B; Deplazes, Peter; Smith, Nicholas C (2019). An experimental genetically attenuated live vaccine to prevent transmission of Toxoplasma gondii by cats. Scientific Reports, 9(1):1474.

Miller, Blake; Selevsek, Nathalie; Grossmann, Jonas; Kilminster, Tanya; Scanlon, Tim; Daniels, Matthew; Nanni, Paolo; Milton, John; Oldham, Chris; Greeff, Johan; Chapwanya, Aspinas; Bergfelt, Don; de Almeida, André M (2019). Ovine liver proteome: Assessing mechanisms of seasonal weight loss tolerance between Merino and Damara sheep. Journal of Proteomics, 191:180-190.

Nüesch, Ursina; Mauracher, Andrea A; Opitz, Lennart; Volkmer, Benjamin; Michalak-Mićka, Katarzyna; Kamarashev, Jivko; Hartwig, Tom; Reichmann, Ernst; Becher, Burkhard; Vavassori, Stefano; Pachlopnik Schmid, Jana (2019). Epithelial proliferation in inflammatory skin disease is regulated by tetratricopeptide repeat domain 7 (Ttc7) in fibroblasts and lymphocytes. Journal of Allergy and Clinical Immunology, 143(1):292-304.e8.

Zhou, Xuan; Stevens, Marc J A; Neuenschwander, Stefan; Schwarm, Angela; Kreuzer, Michael; Bratus-Neuenschwander, Anna; Zeitz, Johanna O (2018). The transcriptome response of the ruminal methanogen Methanobrevibacter ruminantium strain M1 to the inhibitor lauric acid. BMC Research Notes, 11(1):135.

Gökbuget, Deniz; Pereira, Jorge A; Opitz, Lennart; Christe, Dominik; Kessler, Tobias; Marchais, Antonin; Suter, Ueli (2018). The miRNA biogenesis pathway prevents inappropriate expression of injury response genes in developing and adult Schwann cells. Glia, 66(12):2632-2644.

Roth, Ronelle; Chiapello, Marco; Montero, Héctor; Gehrig, Peter; Grossmann, Jonas; O'Holleran, Kevin; Hartken, Denise; Walters, Fergus; Yang, Shu-Yi; Hillmer, Stefan; Schumacher, Karin; Bowden, Sarah; Craze, Melanie; Wallington, Emma J; Miyao, Akio; Sawers, Ruairidh; Martinoia, Enrico; Paszkowski, Uta (2018). A rice Serine/Threonine receptor-like kinase regulates arbuscular mycorrhizal symbiosis at the peri-arbuscular membrane. Nature Communications, 9:4677.

Perdikari, Aliki; Leparc, Germán Gastón; Balaz, Miroslav; Pires, Nuno D; Lidell, Martin E; Sun, Wenfei; Fernandez-Albert, Francesc; Müller, Sebastian; Akchiche, Nassila; Dong, Hua; Balazova, Lucia; Opitz, Lennart; Röder, Eva; et al; Wolfrum, Christian (2018). BATLAS: Deconvoluting Brown Adipose Tissue. Cell Reports, 25(3):784-797.e4.

Schmid, Michael; Frei, Daniel; Patrignani, Andrea; Schlapbach, Ralph; Frey, Jürg E; Remus-Emsermann, Mitja N P; Ahrens, Christian H (2018). Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats. Nucleic Acids Research, 46(17):8953-8965.

Yángüez, Emilio; Hunziker, Annika; Dobay, Maria Pamela; Yildiz, Soner; Schading, Simon; Elshina, Elizaveta; Karakus, Umut; Gehrig, Peter; Grossmann, Jonas; Dijkman, Ronald; Schmolke, Mirco; Stertz, Silke (2018). Phosphoproteomic-based kinase profiling early in influenza virus infection identifies GRK2 as antiviral drug target. Nature Communications, 9:3679.

Sabino, Fabio; Egli, Fabian E; Savickas, Simonas; Holstein, Jörg; Kaspar, Daniela; Rollmann, Mika; Kizhakkedathu, Jayachandran N; Pohlemann, Tim; Smola, Hans; Auf dem Keller, Ulrich (2018). Comparative Degradomics of Porcine and Human Wound Exudates Unravels Biomarker Candidates for Assessment of Wound Healing Progression in Trauma Patients. Journal of Investigative Dermatology, 138(2):413-422.

Bostanci, Nagihan; Bao, Kai; Li, Xiaofei; Maekawa, Tomoki; Grossmann, Jonas; Panse, Christian; Briones, Ruel A; Resuello, Ranillo R G; Tuplano, Joel V; Garcia, Cristina A G; Reis, Edimara S; Lambris, John D; Hajishengallis, George (2018). Gingival Exudatome Dynamics Implicate Inhibition of the Alternative Complement Pathway in the Protective Action of the C3 Inhibitor Cp40 in Nonhuman Primate Periodontitis. Journal of Proteome Research, 17(9):3153-3175.

Williams, Evan G; Wu, Yibo; Wolski, Witold; Yong Kim, Jun; Lan, Jiayi; Hasan, Moaraj; Halter, Christian; Jha, Pooja; Ryu, Dongryeol; Auwerx, Johan; Aebersold, Ruedi (2018). Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population. Molecular & Cellular Proteomics, 17(9):1766-1777.

Ho, Pei-Yin; Li, Hui; Pavlov, Tengis S; Tuerk, Roland D; Tabares, Diego; Brunisholz, René; Neumann, Dietbert; Staruschenko, Alexander; Hallows, Kenneth R (2018). β1Pix exchange factor stabilizes the ubiquitin ligase Nedd4-2 and plays a critical role in ENaC regulation by AMPK in kidney epithelial cells. Journal of Biological Chemistry, 293(29):11612-11624.

Mika, Moana; Nita, Izabela; Morf, Laura; Qi, Weihong; Beyeler, Seraina; Bernasconi, Eric; Marsland, Benjamin J; Ott, Sebastian R; von Garnier, Christophe; Hilty, Markus (2018). Microbial and host immune factors as drivers of COPD. ERJ Open Research, 4(3):00015-2018.

Qi, Weihong; Cascarano, Maria Chiara; Schlapbach, Ralph; Katharios, Pantelis; Vaughan, Lloyd; Seth-Smith, Helena M B (2018). Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity. Genome Biology and Evolution, 10(6):1363-1374.

Anjanappa, Ravi B; Mehta, Devang; Okoniewski, Michal J; Szabelska-Berȩsewicz, Alicja; Gruissem, Wilhelm; Vanderschuren, Hervé (2018). Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response. Molecular Plant Pathology, 19(2):476-489.

Seltmann, Kristin; Meyer, Michael; Sulcova, Jitka; Kockmann, Tobias; Wehkamp, Ulrike; Weidinger, Stephan; auf dem Keller, Ulrich; Werner, Sabine (2018). Humidity-regulated CLCA2 protects the epidermis from hyperosmotic stress. Science Translational Medicine, 10(440):eaao4650.

Felley-Bosco, Emanuela; Rehrauer, Hubert (2018). Non-Coding Transcript Heterogeneity in Mesothelioma: Insights from Asbestos-Exposed Mice. International Journal of Molecular Sciences, 19(4):1163.

von Ziegler, Lukas M; Selevsek, Nathalie; Tweedie-Cullen, Ry Y; Kremer, Eloïse; Mansuy, Isabelle M (2018). Subregion-Specific Proteomic Signature in the Hippocampus for Recognition Processes in Adult Mice. Cell Reports, 22(12):3362-3374.

Schori, Christian; Trachsel, Christian; Grossmann, Jonas; Zygoula, Ioanna; Barthelmes, Daniel; Grimm, Christian (2018). The Proteomic Landscape in the Vitreous of Patients With Age-Related and Diabetic Retinal Disease. Investigative Ophthalmology & Visual Science [IOVS], 59(4):AMD31-AMD40.

Sipos, György; Prasanna, Arun N; Walter, Mathias C; et al; Rigling, Daniel; Patrignani, Andrea (2018). Author Correction: Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nature Ecology and Evolution, 2(3):577.

Trilla-Fuertes, Lucía; Gámez-Pozo, Angelo; Arevalillo, Jorge M; Díaz-Almirón, Mariana; Prado-Vázquez, Guillermo; Zapater-Moros, Andrea; Navarro, Hilario; Aras-López, Rosa; Dapía, Irene; López-Vacas, Rocío; Nanni, Paolo; Llorente-Armijo, Sara; Arias, Pedro; Borobia, Alberto M; Maín, Paloma; Feliú, Jaime; Espinosa, Enrique; Fresno Vara, Juan Ángel (2018). Molecular characterization of breast cancer cell response to metabolic drugs. OncoTarget, 9(11):9645-9660.

Baiwir, Dominique; Nanni, Paolo; Müller, Susanne; Smargiasso, Nicolas; Morsa, Denis; De Pauw, Edwin; Mazzucchelli, Gabriel (2018). Gel-Free Proteomics. In: Martinho de Almeida, Andre. Proteomics in Domestic Animals: from Farm to Systems Biology. Cham, 55-101.

Lasar, David; Rosenwald, Matthias; Kiehlmann, Elke; Balaz, Miroslav; Tall, Bettina; Opitz, Lennart; Lidell, Martin E; Zamboni, Nicola; Krznar, Petra; Sun, Wenfei; Varga, Lukas; Stefanicka, Patrik; Ukropec, Jozef; Nuutila, Pirjo; Virtanen, Kirsi; Amri, Ez-Zoubir; Enerbäck, Sven; Wahli, Walter; Wolfrum, Christian (2018). Peroxisome Proliferator Activated Receptor Gamma Controls Mature Brown Adipocyte Inducibility through Glycerol Kinase. Cell Reports, 22(3):760-773.

Shao, Wenguang; Pedrioli, Patrick G A; Wolski, Witold; Scurtescu, Cristian; Schmid, Emanuel; Vizcaíno, Juan A; Courcelles, Mathieu; Schuster, Heiko; Kowalewski, Daniel; Marino, Fabio; Arlehamn, Cecilia S L; Vaughan, Kerrie; Peters, Bjoern; Sette, Alessandro; Ottenhoff, Tom H M; Meijgaarden, Krista E; Nieuwenhuizen, Natalie; Kaufmann, Stefan H E; Schlapbach, Ralph; Castle, John C; Nesvizhskii, Alexey I; Nielsen, Morten; Deutsch, Eric W; Campbell, David S; Moritz, Robert L; Zubarev, Roman A; Ytterberg, Anders Jimmy; Purcell, Anthony W; Marcilla, Miguel; Paradela, Alberto; et al (2018). The SysteMHC Atlas project. Nucleic Acids Research, 46(D1):D1237-D1247.

Habjanič, Jelena; Zerbe, Oliver; Freisinger, Eva (2018). A histidine-rich Pseudomonas metallothionein with a disordered tail displays higher binding capacity for cadmium than zinc. Metallomics, 10(10):1415-1429.

Sugita, Kazunari; Steer, Catherine A; Martinez-Gonzalez, Itziar; Altunbulakli, Can; Morita, Hideaki; Castro-Giner, Francesc; Kubo, Terufumi; Wawrzyniak, Paulina; Rückert, Beate; Sudo, Katsuko; Nakae, Susumu; Matsumoto, Kenji; O'Mahony, Liam; Akdis, Mübeccel; Takei, Fumio; Akdis, Cezmi A (2018). Type 2 innate lymphoid cells disrupt bronchial epithelial barrier integrity by targeting tight junctions through IL-13 in asthmatic patients. Journal of Allergy and Clinical Immunology, 141(1):300-310.e11.

Gekenidis, Maria-Theresia; Qi, Weihong; Hummerjohann, Jörg; Zbinden, Reinhard; Walsh, Fiona; Drissner, David (2018). Antibiotic-resistant indicator bacteria in irrigation water: High prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. PLoS ONE, 13(11):e0207857.

Neubauer, Jacqueline; Lecca, Maria Rita; Russo, Giancarlo; Bartsch, Christine; Medeiros-Domingo, Argelia; Berger, Wolfgang; Haas, Cordula (2018). Exome analysis in 34 sudden unexplained death (SUD) victims mainly identified variants in channelopathy-associated genes. International journal of legal medicine, 132(4):1057-1065.

Kuo, Tony; Hatakeyama, Masaomi; Tameshige, Toshiaki; Shimizu, Kentaro K; Sese, Jun (2018). Homeolog expression quantification methods for allopolyploids. bioRxiv 426437, University of Zurich.

Hatakeyama, Masaomi; Aluri, Sirisha; Balachadran, Mathi Thumilan; Sivarajan, Sajeevan Radha; Patrignani, Andrea; Grüter, Simon; Poveda, Lucy; Shimizu-Inatsugi, Rie; Baeten, John; Francoijs, Kees-Jan; Nataraja, Karaba N; Reddy, Yellodu A Nanja; Phadnis, Shamprasad; Ravikumar, Ramapura L; Schlapbach, Ralph; Sreeman, Sheshshayee M; Shimizu, Kentaro K (2018). Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. DNA Research, 25(1):39-47.

Schaer, Christian A; Owczarek, Catherine; Deuel, Jeremy W; Schauer, Stefan; Baek, Jin Hyen; Yalamanoglu, Ayla; Hardy, Matthew P; Scotney, Pierre D; Schmidt, Peter M; Pelzing, Matthias; Soupourmas, Peter; Buehler, Paul W; Schaer, Dominik J (2018). Phenotype-specific recombinant haptoglobin polymers co-expressed with C1r-like protein as optimized hemoglobin-binding therapeutics. BMC Biotechnology:18:15.

Leutert, Mario; Menzel, Stephan; Braren, Rickmer; Rissiek, Björn; Hopp, Ann-Katrin; Nowak, Kathrin; Bisceglie, Lavinia; Gehrig, Peter; Li, Hui; Zolkiewska, Anna; Koch-Nolte, Friedrich; Hottiger, Michael O (2018). Proteomic Characterization of the Heart and Skeletal Muscle Reveals Widespread Arginine ADP-Ribosylation by the ARTC1 Ectoenzyme. Cell Reports, 24(7):1916-1929.e5.

Trachsel, Christian; Panse, Christian; Kockmann, Tobias; Wolski, Witold Eryk; Grossmann, Jonas; Schlapbach, Ralph (2018). rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics. bioRxiv 304485, University of Zurich.

Poljak, Kristina; Breitling, Jörg; Gauss, Robert; Rugarabamu, George; Pellanda, Mauro; Aebi, Markus (2017). Analysis of substrate specificity of Trypanosoma brucei oligosaccharyltransferases (OSTs) by functional expression of domain-swapped chimeras in yeast. Journal of Biological Chemistry, 292(49):20342-20352.

Sipos, György; Prasanna, Arun N; Walter, Mathias C; O'Connor, Eoin; Bálint, Balázs; Krizsán, Krisztina; Kiss, Brigitta; Hess, Jaqueline; Varga, Torda; Slot, Jason; Riley, Robert; Bóka, Bettina; Rigling, Daniel; Barry, Kerrie; Lee, Juna; Mihaltcheva, Sirma; LaButti, Kurt; Lipzen, Anna; Waldron, Rose; Moloney, Nicola M; Sperisen, Christoph; Kredics, László; Vágvölgyi, Csaba; Patrignani, Andrea; Fitzpatrick, David; Nagy, István; Doyle, Sean; Anderson, James B; Grigoriev, Igor V; Güldener, Ulrich; et al (2017). Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nature Ecology and Evolution, 1(12):1931-1941.

Leonardi, Irina; Gerstgrasser, Alexandra; Schmidt, Thomas S B; Nicholls, Flora; Tewes, Bernhard; Greinwald, Roland; von Mering, Christian; Rogler, Gerhard; Frey-Wagner, Isabelle (2017). Preventive Trichuris suis ova (TSO) treatment protects immunocompetent rabbits from DSS colitis but may be detrimental under conditions of immunosuppression. Scientific Reports, 7(1):16500.

Fudrini Olivencia, Begonia; Müller, Andreas U; Roschitzki, Bernd; Burger, Sibylle; Weber-Ban, Eilika; Imkamp, Frank (2017). Mycobacterium smegmatis PafBC is involved in regulation of DNA damage response. Scientific Reports, 7(1):13987.

Losfeld, Marie-Estelle; Scibona, Ernesto; Lin, Chia-Wei; Villiger, Thomas K; Gauss, Robert; Morbidelli, Massimo; Aebi, Markus (2017). Influence of protein/glycan interaction on site-specific glycan heterogeneity. FASEB Journal, 31(10):4623-4635.

Luciani, Paola; Estella-Hermoso de Mendoza, Ander; Casalini, Tommaso; Lang, Silvia; Atrott, Kirstin; Spalinger, Marianne R; Pratsinis, Anna; Sobek, Jens; Frey-Wagner, Isabelle; Schumacher, Jens; Leroux, Jean-Christophe; Rogler, Gerhard (2017). Gastroresistant oral peptide for fluorescence imaging of colonic inflammation. Journal of Controlled Release, 262:118-126.

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

Item, Flurin; Wueest, Stephan; Lemos, Vera; Stein, Sokrates; Lucchini, Fabrizio C; Denzler, Rémy; Fisser, Muriel C; Challa, Tenagne D; Pirinen, Eija; Kim, Youngsoo; Hemmi, Silvio; Gulbins, Erich; Gross, Atan; O'Reilly, Lorraine A; Stoffel, Markus; Auwerx, Johan; Konrad, Daniel (2017). Fas cell surface death receptor controls hepatic lipid metabolism by regulating mitochondrial function. Nature Communications, 8:480.

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

Becker, Eugenia; Schmidt, Thomas S B; Bengs, Susan; Poveda, Lucy; Opitz, Lennart; Atrott, Kirstin; Stanzel, Claudia; Biedermann, Luc; Rehman, Ateequr; Jonas, Daniel; von Mering, Christian; Rogler, Gerhard; Frey-Wagner, Isabelle (2017). Effects of oral antibiotics and isotretinoin on the murine gut microbiota. International Journal of Antimicrobial Agents, 50(3):342-351.

Knobloch, Marlen; Pilz, Gregor-Alexander; Ghesquière, Bart; Kovacs, Werner J; Wegleiter, Thomas; Moore, Darcie L; Hruzova, Martina; Zamboni, Nicola; Carmeliet, Peter; Jessberger, Sebastian (2017). A Fatty Acid Oxidation-Dependent Metabolic Shift Regulates Adult Neural Stem Cell Activity. Cell Reports, 20(9):2144-2155.

Mika, Moana; Maurer, Josua; Korten, Insa; Allemann, Aurélie; Aebi, Suzanne; Brugger, Silvio D; Qi, Weihong; Frey, Urs; Latzin, Philipp; Hilty, Markus (2017). 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:5:85.

Seth-Smith, Helena M B; Katharios, Pantelis; Dourala, Nancy; Mateos, José M; Fehr, Alexander G J; Nufer, Lisbeth; Ruetten, Maja; Guevara Soto, Maricruz; Vaughan, Lloyd (2017). Ca. Similichlamydia in epitheliocystis co-infection of gilthead seabream gills: unique morphological features of a deep branching chlamydial family. Frontiers in Microbiology, 8:508.

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

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.

Vazquez-Gutierrez, Pamela; Stevens, Marc J A; Gehrig, Peter; Barkow-Oesterreicher, Simon; Lacroix, Christophe; Chassard, Christophe (2017). The extracellular proteome of two Bifidobacterium species reveals different adaptation strategies to low iron conditions. BMC Genomics, 18(1):41.

Drissner, David; Brunisholz, René (2017). Biotyping Meets Proteomics. In: Colgrave, Michelle L.. Proteomics in Food Science: From Farm to Fork. Elsevier: Elsevier, 433-447.

Bisceglie, Lavinia; Bartolomei, Giody; Hottiger, Michael O (2017). ADP-ribose-specific chromatin-affinity purification for investigating genome-wide or locus-specific chromatin ADP-ribosylation. Nature Protocols, 12(9):1951-1961.

Amini, Parisa; Ettlin, Julia; Opitz, Lennart; Clementi, Elena; Malbon, Alexandra; Markkanen, Enni (2017). An 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.

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

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.

Becker, Katja; Haldimann, Klara; Selchow, Petra; Reinau, Lukas M; Dal Molin, Michael; Sander, Peter (2017). Lipoprotein Glycosylation by Protein-O-Mannosyltransferase (MAB_1122c) Contributes to Low Cell Envelope Permeability and Antibiotic Resistance of Mycobacterium abscessus. Frontiers in Microbiology, 8:2123.

Liu, Yilei; Lardi, Martina; Pedrioli, Alessandro; Eberl, Leo; Pessi, Gabriella (2017). NtrC-dependent control of exopolysaccharide synthesis and motility in Burkholderia cenocepacia H111. PLoS ONE, 12(6):e0180362.

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

Qi, Weihong; Schlapbach, Ralph; Rehrauer, Hubert (2017). RNA-Seq Data Analysis: From Raw Data Quality Control to Differential Expression Analysis. Methods in Molecular Biology, 1669:295-307.

Rosenwald, Matthias; Efthymiou, Vissarion; Opitz, Lennart; Wolfrum, Christian (2017). SRF and MKL1 Independently Inhibit Brown Adipogenesis. PLoS ONE, 12(1):e0170643.

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, Jana (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.

Dimitrieva, Slavica; Schlapbach, Ralph; Rehrauer, Hubert (2016). Prognostic value of cross-omics screening for kidney clear cell renal cancer survival. Biology Direct, 11(1):68.

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.

Ramírez Ríos, Sacnicte; Lamarche, Frédéric; Cottet-Rousselle, Cécile; Klaus, Anna; Tuerk, Roland; Thali, Ramon; Auchli, Yolanda; Brunisholz, René; Neumann, Dietbert; Barret, Luc; Tokarska-Schlattner, Malgorzata; Schlattner, Uwe (2014). Regulation of brain-type creatine kinase by AMP-activated protein kinase: interaction, phosphorylation and ER localization. BBA - Biochimica et Biophysica Acta, 1837(8):1271-1283.

Kentner, David; Martano, Giuseppe; Callon, Morgane; Chiquet, Petra; Brodmann, Maj; Burton, Olga; Wahlander, Asa; Nanni, Paolo; Delmotte, Nathanaël; Grossmann, Jonas; Limenitakis, Julien; Schlapbach, Ralph; Kiefer, Patrick; Vorholt, Julia A; Hiller, Sebastian; Bumann, Dirk (2014). Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth. Proceedings of the National Academy of Sciences of the United States of America, 111(27):9929-9934.

Gekenidis, Maria-Theresia; Studer, Patrick; Wüthrich, Simone; Brunisholz, René; Drissner, David (2014). Beyond the matrix-assisted laser desorption ionization (MALDI) biotyping workflow: in search of microorganism-specific tryptic peptides enabling discrimination of subspecies. Applied and Environmental Microbiology, 80(14):4234-4241.

Simona, Benjamin R; Brunisholz, René A; Morhard, Robert; Hunziker, Peter; Vörös, János (2014). Coagulation at the blood-electrode interface: the role of electrochemical desorption and degradation of fibrinogen. Langmuir, 30(24):7227-7234.

Vanderschuren, Hervé; Nyaboga, Evans; Poon, Jacquelyne S; Baerenfaller, Katja; Grossmann, Jonas; Hirsch-Hoffmann, Matthias; Kirchgessner, Norbert; Nanni, Paolo; Gruissem, Wilhelm (2014). Large-Scale Proteomics of the Cassava Storage Root and Identification of a Target Gene to Reduce Postharvest Deterioration. Plant Cell, 26(5):1913-1924.

Schmidt, Anja; Schmid, Marc W; Klostermeier, Ulrich C; Qi, Weihong; Guthörl, Daniela; Sailer, Christian; Waller, Manuel; Rosenstiel, Philip; Grossniklaus, Ueli (2014). Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation. PLoS Genetics, 10(7):e1004476.

Azzi, Abdelhalim; Dallmann, Robert; Casserly, Alison; Rehrauer, Hubert; Patrignani, Andrea; Maier, Bert; Kramer, Achim; Brown, Steven A (2014). Circadian behavior is light-reprogrammed by plastic DNA methylation. Nature Neuroscience, 17(3):377-382.

Müller, Jonas E N; Litsanov, Boris; Bortfeld-Miller, Miriam; Trachsel, Christian; Grossmann, Jonas; Brautaset, Trygve; Vorholt, Julia A (2014). Proteomic analysis of the thermophilic methylotroph Bacillus methanolicus MGA3. Proteomics, 14(6):725-37.

Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y; Tito, Raul Y; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-García, Domingo C; Eppler, Elisabeth; Seiler, Roger; Hansen, Lars H; Castruita, José Alfredo Samaniego; Barkow-Oesterreicher, Simon; Teoh, Kai Yik; Kelstrup, Christian D; Olsen, Jesper V; Nanni, Paolo; Kawai, Toshihisa; Willerslev, Eske; von Mering, Christian; Lewis, Cecil M; Collins, Matthew J; Gilbert, M Thomas P; Rühli, Frank J; Cappellini, Enrico (2014). Pathogens and host immunity in the ancient human oral cavity. Nature Genetics, 46(4):336-344.

Vonlanthen, Janine; Okoniewski, Michal J; Menigatti, Mirco; Cattaneo, Elisa; Pellegrini-Ochsner, Daniela; Haider, Ritva; Jiricny, Josef; Staiano, Teresa; Buffoli, Federico; Marra, Giancarlo (2014). A comprehensive look at transcription factor gene expression changes in colorectal adenomas. BMC Cancer, 14:46.

Adamsen, Dea; Ramaekers, Vincent; Ho, Horace T B; Britschgi, Corinne; Rüfenacht, Véronique; Meili, David; Bobrowski, Elise; Philippe, Paule; Nava, Caroline; Van Maldergem, Lionel; Bruggmann, Rémy; Walitza, Susanne; Wang, Joanne; Grünblatt, Edna; Thöny, Beat (2014). Autism spectrum disorder associated with low serotonin in CSF and mutations in the SLC29A4 plasma membrane monoamine transporter (PMAT) gene. Molecular Autism, 5:43.

Bratus, Anna; Aeschlimann, Andre; Russo, Giancarlo; Sprott, Haiko (2014). Candidate gene approach in genetic epidemiological studies of osteoarthritis-related pain. Pain, 155(2):217-221.

Youhanna, Sonia; Weber, Julien; Beaujean, Viviane; Glaudemans, Bob; Sobek, Jens; Devuyst, Olivier (2014). Determination of uromodulin in human urine: influence of storage and processing. Nephrology, Dialysis, Transplantation, 29(1):136-145.

Warinner, C; Hendy, J; Speller, C; Cappellini, E; Fischer, R; Trachsel, C; Arneborg, J; Lynnerup, N; Craig, O E; Swallow, D M; Fotakis, A; Christensen, R J; Olsen, J V; Liebert, A; Montalva, N; Fiddyment, S; Charlton, S; Mackie, M; Canci, A; Bouwman, Abigail S; Rühli, Frank J; Gilbert, M T P; Collins, M J (2014). Direct evidence of milk consumption from ancient human dental calculus. Scientific Reports, 4:7104.

Brunner, Andrea M; Nanni, Paolo; Mansuy, Isabelle M (2014). Epigenetic marking of sperm by post-translational modification of histones and protamines. Epigenetics & Chromatin, 7:2.

Di Giallonardo, Francesca; Töpfer, Armin; Rey, Melanie; Prabhakaran, Sandhya; Duport, Yannick; Leemann, Christine; Schmutz, Stefan; Campbell, Nottania K; Joos, Beda; Lecca, Maria Rita; Patrignani, Andrea; Däumer, Martin; Beisel, Christian; Rusert, Peter; Trkola, Alexandra; Günthard, Huldrych F; Roth, Volker; Beerenwinkel, Niko; Metzner, Karin J (2014). Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Research, 42(14):e115.

Greminger, Maja P; Stölting, Kai N; Nater, Alexander; Goossens, Benoit; Arora, Natasha; Bruggmann, Rémy; Patrignani, Andrea; Nussberger, Beatrice; Sharma, Reeta; Kraus, Robert H S; Ambu, Laurentius N; Singleton, Ian; Chikhi, Lounes; van Schaik, Carel P; Krützen, Michael (2014). Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms. BMC Genomics, 15:16.

Aregger, Fabienne; Uehlinger, Dominik E; Witowski, Janusz; Brunisholz, René A; Hunziker, Peter; Frey, Felix J; Jörres, Achim (2014). Identification of IGFBP-7 by urinary proteomics as a novel prognostic marker in early acute kidney injury. Kidney International, 85(4):909-919.

Rampoldi, A; Bertschinger, H U; Bürgi, E; Dolf, G; Sidler, X; Bratus, A; Vögeli, P; Neuenschwander, S (2014). Inheritance of porcine receptors for enterotoxigenic Escherichia coli with 1 fimbriae F4ad and their relation to other F4 receptors 2. Animal, 8(6):859-866.

Myburgh, Renier; Cherpin, Ophélie; Schlaepfer, Erika; Rehrauer, Hubert; Speck, Roberto F; Krause, Karl-Heinz; Salmon, Patrick (2014). Optimization of critical hairpin features allows miRNA-based gene knockdown upon single-copy transduction. Molecular Therapy - Nucleic Acids, 3:e207.

Wampfler, Petra B; Tosevski, Vinko; Nanni, Paolo; Spycher, Cornelia; Hehl, Adrian B (2014). Proteomics of Secretory and Endocytic Organelles in Giardia lamblia. PLoS ONE, 9(4):e94089.

Uzozie, Anuli; Nanni, Paolo; Staiano, Teresa; Grossmann, Jonas; Barkow-Oesterreicher, Simon; Shay, Jerry W; Tiwari, Amit; Buffoli, Federico; Laczko, Endre; Marra, Giancarlo (2014). Sorbitol dehydrogenase overexpression and other aspects of dysregulated protein expression in human precancerous colorectal neoplasms: a quantitative proteomics study. Molecular & Cellular Proteomics, 13(5):1198-1218.

Schlage, Pascal; Egli, Fabian E; Nanni, Paolo; Wang, Lauren W; Kizhakkedathu, Jayachandran N; Apte, Suneel S; Auf dem Keller, Ulrich (2014). Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome. Molecular & Cellular Proteomics, 13(2):580-593.

Allie, Farhahna; Pierce, Erica J; Okoniewski, Michal J; Rey, Chrissie (2014). Transcriptional 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.

Motamedi, Fariba Jian; Badro, Danielle A; Clarkson, Michael; Lecca, M Rita; Bradford, Stephen T; Buske, Fabian A; Saar, Kathrin; Hübner, Norbert; Brändli, André W; Schedl, Andreas (2014). WT1 controls antagonistic FGF and BMP-pSMAD pathways in early renal progenitors. Nature Communications, 5:4444.

Drissner, David; Gekenidis, Maria-Theresia; Schlapbach, Ralph; Brunisholz, René (2014). When Time-to-Result Matters: Identification of Microbes Based on MALDI-TOF Protein and Peptide Profiling. CHIMIA International Journal for Chemistry, 68(6):453.

Kempf, Anissa; Montani, Laura; Petrinovic, Marija M; Schroeter, Aileen; Weinmann, Oliver; Patrignani, Andrea; Schwab, Martin E (2013). Upregulation of axon guidance molecules in the adult central nervous system of Nogo-A knockout mice restricts neuronal growth and regeneration. European Journal of Neuroscience, 38(11):3567-3579.

Craveiro, Luis M; Weinmann, Oliver; Roschitzki, Bernd; Gonzenbach, Roman R; Zörner, Björn; Montani, Laura; Yee, Benjamin K; Feldon, Joram; Willi, Roman; Schwab, Martin E (2013). Infusion of anti-Nogo-A antibodies in adult rats increases growth and synapse related proteins in the absence of behavioral alterations. Experimental Neurology, 250:52-68.

Park, C Sehwan; Rehrauer, Hubert; Mansuy, Isabelle M (2013). Genome-wide analysis of H4K5 acetylation associated with fear memory in mice. BMC Genomics, 14:539.

Aleksiev, Tyanko; Barkow-Oesterreicher, Simon; Kunszt, Peter; Maffioletti, Sergio; Murri, Riccardo; Panse, Christian (2013). VM-MAD: A cloud/cluster software for service-oriented academic environments. In: Supercomputing - 28th International Supercomputing Conference, ISC 2013, Leipzig, 16 June 2013 - 20 June 2013, 447-461.

Anders, Simon; McCarthy, Davis J; Chen, Yunshun; Okoniewski, Michal; Smyth, Gordon K; Huber, Wolfgang; Robinson, Mark D (2013). Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nature Protocols, 8(9):1765-1786.

Tyagarajan, Shiva K; Ghosh, Himanish; Yévenes, Gonzalo E; Imanishi, Susumu Y; Zeilhofer, Hanns Ulrich; Gerrits, Bertran; Fritschy, Jean-Marc (2013). Extracellular signal-regulated kinase and glycogen synthase kinase 3β regulate gephyrin postsynaptic aggregation and GABAergic synaptic function in a calpain-dependent mechanism. Journal of Biological Chemistry, 288(14):9634-9647.

Trinh, Hung V; Grossmann, Jonas; Gehrig, Peter; Roschitzki, Bernd; Schlapbach, Ralph; Greber, Urs F; Hemmi, Silvio (2013). iTRAQ-based and label-free proteomics approaches for studies of human adenovirus infections. International Journal of Proteomics, 2013:581862.

Biason-Lauber, Anna; Böni-Schnetzler, Marianne; Hubbard, Basil P; Bouzakri, Karim; Brunner, Andrea; Cavelti-Weder, Claudia; Keller, Cornelia; Meyer-Böni, Monika; Meier, Daniel T; Brorsson, Caroline; Timper, Katharina; Leibowitz, Gil; Patrignani, Andrea; Bruggmann, Remy; Boily, Gino; Zulewski, Henryk; Geier, Andreas; Cermak, Jennifer M; Elliott, Peter; Ellis, James L; Westphal, Christoph; Knobel, Urs; Eloranta, Jyrki J; Kerr-Conte, Julie; Pattou, François; Konrad, Daniel; Matter, Christian M; Fontana, Adriano; Rogler, Gerhard; Schlapbach, Ralph; Regairaz, Camille; Carballido, José M; Glaser, Benjamin; McBurney, Michael W; Pociot, Flemming; Sinclair, David A; Donath, Marc Y (2013). Identification of a SIRT1 mutation in a family with type 1 Diabetes. Cell Metabolism, 17(3):448-455.

Sobek, Jens; Schauer, Stefan; Rehrauer, Hubert; Fischer, David; Patrignani, Andrea; Landgraf, Stephan; Schlapbach, Ralph (2013). Single molecule interactions studied by using a modified DNA sequencer: a comparison with surface plasmon resonance. In: SPIE, San Francisco, 2 February 2013 - 2 February 2013, 85960Y.

Alzamora, Rodrigo; Al-Bataineh, Mohammad M; Liu, Wen; Gong, Fan; Li, Hui; Thali, Ramon F; Joho-Auchli, Yolanda; Brunisholz, René A; Satlin, Lisa M; Neumann, Dietbert; Hallows, Kenneth R; Pastor-Soler, Núria M (2013). AMP-activated protein kinase regulates the vacuolar H+-ATPase via direct phosphorylation of the A subunit (ATP6V1A) in the kidney. American Journal of Physiology. Renal, Fluid and Electrolyte Physiology, 305(7):F943-F956.

Riwanto, Meliana; Rohrer, Lucia; Roschitzki, Bernd; Besler, Christian; Landmesser, Ulf; et al (2013). Altered activation of endothelial anti- and proapoptotic pathways by high-density lipoprotein from patients with coronary artery disease: role of high-density lipoprotein-proteome remodeling. Circulation, 127(8):891-904.

Spycher, Cornelia; Herman, Emily K; Morf, Laura; Qi, Weihong; Rehrauer, Hubert; Aquino Fournier, Catharine; Dacks, Joel B; Hehl, Adrian B (2013). An ER-directed transcriptional response to unfolded protein stress in the absence of conserved sensor-transducer proteins in Giardia lamblia. Molecular Microbiology, 88(4):754-771.

Weisser, Hendrik; Nahnsen, Sven; Grossmann, Jonas; Nilse, Lars; Quandt, Andreas; Brauer, Hendrik; Sturm, Marc; Kenar, Erhan; Kohlbacher, Oliver; Aebersold, Ruedi; Malmström, Lars (2013). An automated pipeline for high-throughput label-free quantitative proteomics. Journal of Proteome Research, 12(4):1628-1644.

Derkacheva, Maria; Steinbach, Yvonne; Wildhaber, Thomas; Mozgová, Iva; Mahrez, Walid; Nanni, Paolo; Bischof, Sylvain; Gruissem, Wilhelm; Hennig, Lars (2013). Arabidopsis MSI1 connects LHP1 to PRC2 complexes. EMBO Journal Online, 32(14):2073-2085.

Rehrauer, Hubert; Opitz, Lennart; Tan, Ge; Sieverling, Lina; Schlapbach, Ralph (2013). Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching. BMC Bioinformatics, 14:370.

Bischof, Sylvain; Umhang, Martin; Eicke, Simona; Streb, Sebastian; Qi, Weihong; Zeeman, Samuel C (2013). Cecropia peltata accumulates starch or soluble glycogen by differentially regulating starch biosynthetic genes. Plant Cell, 25(4):1400-1415.

Schaefer, S; Hassa, P O; Sieber-Ruckstuhl, N S; Piechotta, M; Reusch, C E; Roschitzki, B; Boretti, F S (2013). Characterization of recombinant human and bovine thyroid-stimulating hormone preparations by mass spectrometry and determination of their endotoxin content. BMC Veterinary Research, 9:141.

Schaer, Christian A; Laczko, Endre; Schoedon, Gabriele; Schaer, Dominik J; Vallelian, Florence (2013). Chloroquine interference with hemoglobin endocytic trafficking suppresses adaptive heme and iron homeostasis in macrophages: the paradox of an antimalarial agent. Oxidative Medicine and Cellular Longevity, 2013:870472.

Omasits, Ulrich; Quebatte, Maxime; Stekhoven, Daniel J; Fortes, Claudia; Roschitzki, Bernd; Robinson, Mark D; Dehio, Christoph; Ahrens, Christian H (2013). Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome. Genome Research, 23(11):1916-1927.

Sobek, Jens; Aquino, Catharine; Weigel, Wilfried; Schlapbach, Ralph (2013). Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays. BMC Biophysics, 6:8.

Tiwari, Amit; Schneider, Mirjam; Fiorino, Antonio; Haider, Ritva; Okoniewski, Michal J; Roschitzki, Bernd; Uzozie, Anuli; Menigatti, Mirco; Jiricny, Josef; Marra, Giancarlo (2013). Early insights into the function of KIAA1199, a markedly overexpressed protein in human colorectal tumors. PLoS ONE, 8(7):e69473.

Barkow-Oesterreicher, Simon; Tuerker, Can; Panse, Christian (2013). FCC – An automated rule-based processing tool for life science data. Source Code for Biology and Medicine, 8:3.

Seth-Smith, H M B; Harris, S R; Scott, P; Parmar, S; Marsh, P; Unemo, M; Clarke, I N; Parkhill, J; Thomson, N R (2013). Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA. Nature Protocols, 8(12):2404-2412.

Mohme, M; Hotz, C; Stevanovic, S; Binder, T; Lee, J H; Okoniewski, M; Sospedra, M; Eiermann, T; Rammensee, H G; Martin, R (2013). HLA-DR15-derived self-peptides are involved in increased autologous T cell proliferation in multiple sclerosis. Brain, 136(Pt 6):1783-1798.

Bostanci, Nagihan; Ramberg, Per; Wahlander, Åsa; Grossman, Jonas; Jönsson, Daniel; Barnes, Virginia Monsul; Papapanou, Panos N (2013). Label-free quantitative proteomics reveals differentially regulated proteins in experimental gingivitis. Journal of Proteome Research, 12(2):657-678.

Garzoni, Christian; Brugger, Silvio D; Qi, Weihong; Wasmer, Sarah; Cusini, Alexia; Dumont, Philippe; Gorgievski-Hrisoho, Meri; Mühlemann, Kathrin; von Garnier, Christophe; Hilty, Markus (2013). Microbial communities in the respiratory tract of patients with interstitial lung disease. Thorax, 68(12):1150-1156.

Bluwstein, A; Kumar, N; Léger, K; Traenkle, J; van Oostrum, J; Rehrauer, H; Baudis, Michael; Hottiger, M O (2013). PKC signaling prevents irradiation-induced apoptosis of primary human fibroblasts. Cell Death and Disease, 4:e498.

Nanni, Paolo; Panse, Christian; Gehrig, Peter; Mueller, Susanne; Grossmann, Jonas; Schlapbach, Ralph (2013). PTM MarkerFinder, a software tool to detect and validate spectra from peptides carrying post-translational modifications. Proteomics, 13(15):2251-2255.

Okoniewski, Michal J; Meienberg, Janine; Patrignani, Andrea; Szabelska, Alicja; Matyas, Gabor; Schlapbach, Ralph (2013). Precise breakpoint localization of large genomic deletions using PacBio and Illumina next-generation sequencers. BioTechniques, 54(2):98-100.

Sharma, Anu; Bode, Beata; Moch, Holger; Okoniewski, Michal; Knuth, Alexander; von Boehmer, Lotta; van den Broek, Maries (2013). Radiotherapy of human sarcoma promotes an intratumoral immune effector signature. Clinical Cancer Research, 19(17):4843-4853.

Nuvolone, Mario; Kana, Veronika; Hutter, Gregor; Sakata, Daiji; Mortin-Toth, Steven M; Russo, Giancarlo; Danska, Jayne S; Aguzzi, Adriano (2013). SIRPα polymorphisms, but not the prion protein, control phagocytosis of apoptotic cells. Journal of Experimental Medicine, 210(12):2539-2552.

Quiblier, Chantal; Seidl, Kati; Roschitzki, Bernd; Zinkernagel, Annelies S; Berger-Bächi, Brigitte; Senn, Maria M (2013). Secretome analysis defines the major role of SecDF in Staphylococcus aureus virulence. PLoS ONE, 8(5):e63513.

Wojtalla, Anna; Fischer, Barbara; Kotelevets, Nataliya; Mauri, Francesco A; Sobek, Jens; Rehrauer, Hubert; Wotzkow, Carlos; Tschan, Mario P; Seckl, Michael J; Zangemeister-Wittke, Uwe; Arcaro, Alexandre (2013). Targeting the phosphoinositide 3-kinase p110-α isoform impairs cell proliferation, survival, and tumor growth in small cell lung cancer. Clinical Cancer Research, 19(1):96-105.

Abplanalp, Jeanette; Laczko, Endre; Philip, Nancy J; Neidhardt, John; Zuercher, Jurian; Braun, Philipp; Schorderet, Daniel F; Munier, Francis L; Verrey, François; Berger, Wolfgang; Camargo, Simone M R; Kloeckener-Gruissem, Barbara (2013). The cataract and Glucosuria associated monocarboxylate transporter MCT12 is a new creatine transporter. Human Molecular Genetics, 22(16):3218-3226.

Eisele, Petra S; Salatino, Silvia; Sobek, Jens; Hottiger, Michael O; Handschin, Christoph (2013). The peroxisome proliferator-activated receptor γ coactivator 1α/β (PGC-1) coactivators repress the transcriptional activity of NF-κB in skeletal muscle cells. Journal of Biological Chemistry, 288(4):2246-2260.

Schicht, Sabine; Qi, Weihong; Poveda, Lucy; Strube, Christina (2013). The predicted secretome and transmembranome of the poultry red mite Dermanyssus gallinae. Parasites & Vectors, 6:259.

Sedeek, Khalid E M; Qi, Weihong; Schauer, Monica A; Gupta, Alok K; Poveda, Lucy; Xu, Shuqing; Liu, Zhong-Jian; Grossniklaus, Ueli; Schiestl, Florian P; Schlüter, Philipp M (2013). Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive Orchids. PLoS ONE, 8(5):e64621.

Schicht, Sabine; Qi, Weihong; Poveda, Lucy; Strube, Christina (2013). Whole transcriptome analysis of the poultry red mite Dermanyssus gallinae (De Geer, 1778). Parasitology, 18:1-11.

Shi, Yandong; Moura, Ubiratan; Opitz, Isabelle; Soltzermann, Alex; Rehrauer, Hubert; Thies, Svenja; Weder, Walter; Stahel, Rolf A; Felley-Bosco, Emanuela (2012). Role of hedgehog signaling in malignant pleural mesothelioma. Clinical Cancer Research, 18(17):4646-4656.

Moretti, Marino; Minerdi, Daniela; Gehrig, Peter; Garibaldi, Angelo; Gullino, Maria Lodovica; Riedel, Katharina (2012). A bacterial-fungal metaproteomic analysis enlightens an intriguing multicomponent interaction in the rhizosphere of Lactuca sativa. Journal of Proteome Research, 11(4):2061-2077.

Bär, Eva; Gladiator, André; Bastidas, Sonia; Roschitzki, Bernd; Acha-Orbea, Hans; Oxenius, Annette; LeibundGut-Landmann, Salomé (2012). A novel Th cell epitope of Candida albicans mediates protection from fungal infection. Journal of Immunology, 188(11):5636-5643.

Schneider, Thomas; Persson, Daniel Pergament; Husted, Søren; Schellenberg, Maja; Gehrig, Peter; Lee, Youngsook; Martinoia, Enrico; Schjoerring, Jan K; Meyer, Stefan (2012). A proteomics approach to investigate the process of Zn hyperaccumulation in Noccaea caerulescens (J & C. Presl) F.K. Meyer. The Plant Journal, 73(1):131-142.

Klaus, Anna; Polge, Cécile; Zorman, Sarah; Auchli, Yolanda; Brunisholz, René; Schlattner, Uwe (2012). A two-dimensional screen for AMPK substrates identifies tumor suppressor fumarate hydratase as a preferential AMPKα2 substrate. Journal of Proteomics, 75(11):3304-3313.

Cooksley-Decasper, Seraina; Reiser, Hans; Thommen, Daniela S; Biedermann, Barbara; Neidhart, Michel; Gawinecka, Joanna; Cathomas, Gieri; Franzeck, Fabian C; Wyss, Christophe; Klingenberg, Roland; Nanni, Paolo; Roschitzki, Bernd; Matter, Christian; Wolint, Petra; Emmert, Maximilian Y; Husmann, Marc; Amann-Vesti, Beatrice; Maier, Wilibald; Gay, Steffen; Lüscher, Thomas F; von Eckardstein, Arnold; Hof, Danielle (2012). Antibody phage display assisted identification of junction plakoglobin as a potential biomarker for atherosclerosis. PLoS ONE, 7(10):e47985.

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

Mayank, Pururawa; Grossman, Jonas; Wuest, Samuel; Boisson-Dernier, Aurélien; Roschitzki, Bernd; Nanni, Paolo; Nühse, Thomas; Grossniklaus, Ueli (2012). Characterization of the phosphoproteome of mature Arabidopsis pollen. The Plant Journal, 72(1):89-101.

Casanova, Elisa A; Okoniewski, Michal J; Cinelli, Paolo (2012). Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos. PLoS ONE, 7(10):e47107.

Bratus, Anna (2012). DM Domain Genes: Sexual and somatic development during vertebrate embryogenesis. In: Ken-ichi, Sato. Embryogenesis. Rijeka: InTech, 39-66.

Ortea, Ignacio; Roschitzki, Bernd; Ovalles, Juan Gabriel; Longo, Javier López; de la Torre, Inmaculada; González, Isidoro; Gómez-Reino, Juan J; González, Antonio (2012). Discovery of serum proteomic biomarkers for prediction of response to infliximab (a monoclonal anti-TNF antibody) treatment in rheumatoid arthritis: an exploratory analysis. Journal of Proteomics, 77:372-382.

Keiblinger, K M; Schneider, T; Roschitzki, B; Schmid, E; Eberl, L; Hämmerle, I; Leitner, S; Richter, A; Wanek, W; Riedel, K; Zechmeister-Boltenstern, S (2012). Effects of stoichiometry and temperature perturbations on beech leaf litter decomposition, enzyme activities and protein expression. Biogeosciences, 9(11):4537-4551.

Müller, Marlen; Patrignani, Andrea; Rehrauer, Hubert; Gruissem, Wilhelm; Hennig, Lars (2012). Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays. Plant Methods, 8:18.

Mugasa, Joseph; Qi, Weihong; Rusch, Sebastian; Rottmann, Matthias; Beck, Hans-Peter (2012). Genetic diversity of expressed Plasmodium falciparum var genes from Tanzanian children with severe malaria. Malaria Journal, 11:230.

Filippini, Manuela; Qi, Weihong; Blom, Jochen; Goesmann, Alexander; Smits, Theo H M; Bagheri, Homayoun C (2012). Genome sequence of Fibrella aestuarina BUZ 2(T), a filamentous marine bacterium. Journal of Bacteriology, 194(13):3555.

Huwiler, Simona G; Beyer, Christian; Fröhlich, Jürg; Hennecke, Hauke; Egli, Thomas; Schürmann, David; Rehrauer, Hubert; Fischer, Hans-Martin (2012). Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields. Bioelectromagnetics, 33(6):488-496.

Henson, Sonal; Bishop, Richard P; Morzaria, Subhash; Spooner, Paul R; Pelle, Roger; Poveda, Lucy; Ebeling, Martin; Küng, Erich; Certa, Ulrich; Daubenberger, Claudia A; Qi, Weihong (2012). High-resolution genotyping and mapping of recombination and gene conversion in the protozoan Theileria parva using whole genome sequencing. BMC Genomics, 13:503.

Tweedie-Cullen, Ry Y; Brunner, Andrea M; Grossmann, Jonas; Mohanna, Safa; Sichau, David; Nanni, Paolo; Panse, Christian; Mansuy, Isabelle M (2012). Identification of combinatorial patterns of post-translational modifications on individual histones in the mouse brain. PLoS ONE, 7(5):e36980.

Toyofuku, Masanori; Roschitzki, Bernd; Riedel, Katharina; Eberl, Leo (2012). Identification of proteins associated with the Pseudomonas aeruginosa biofilm extracellular matrix. Journal of Proteome Research, 11(10):4906-4915.

Leitner, Sonja; Wanek, Wolfgang; Wild, Birgit; Haemmerle, Ieda; Kohl, Lukas; Keiblinger, Katharina M; Zechmeister-Boltenstern, Sophie; Richter, Andreas (2012). Influence of litter chemistry and stoichiometry on glucan depolymerization during decomposition of beech (Fagus sylvatica L.) litter. Soil Biology and Biochemistry, 50(6):174-187.

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.

Shakhova, Olga; Zingg, Daniel; Schaefer, Simon M; Hari, Lisette; Civenni, Gianluca; Blunschi, Jacqueline; Claudinot, Stéphanie; Okoniewski, Michal; Beermann, Friedrich; Mihic-Probst, Daniela; Moch, Holger; Wegner, Michael; Dummer, Reinhard; Barrandon, Yann; Cinelli, Paolo; Sommer, Lukas (2012). Sox10 promotes the formation and maintenance of giant congenital naevi and melanoma. Nature Cell Biology, 14(8):882-890.

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.

Baerenfaller, Katja; Massonnet, Catherine; Walsh, Sean; Baginsky, Sacha; Bühlmann, Peter; Hennig, Lars; Hirsch-Hoffmann, Matthias; Howell, Katharine A; Kahlau, Sabine; Radziejwoski, Amandine; Russenberger, Doris; Rutishauser, Dorothea; Small, Ian; Stekhoven, Daniel; Sulpice, Ronan; Svozil, Julia; Wuyts, Nathalie; Stitt, Mark; Hilson, Pierre; Granier, Christine; Gruissem, Wilhelm (2012). Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit. Molecular Systems Biology, 8:606.

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, Michael (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.

Abu-Ali, G S; Springman, A C; Ouellette, L M; Qi, W; Vanaja, S K; Bergholz, T M; Lacher, D W; Tietjen, J A; Riordan, J T; Manning, S D (2011). Molecular evolution of enterhemorrhagic Escherichia coli and application to epidemiology. In: Walk, S T; Feng, P C H. Population genetics of bacteria : a tribute to Thomas S. Whittam. Washington, DC, US: ASM Press, 287-302.

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, Angelika; Stephan, Roger; 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.

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

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.

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

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

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

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.

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

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.

List, C; Qi, W; Maag, E; Gottstein, B; Müller, N; Felger, I (2010). Serodiagnosis of Echinococcus spp. infection: explorative selection of diagnostic antigens by peptide microarray. PLoS Neglected Tropical Diseases, 4(8):e771.

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.

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

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, Michael; 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.

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

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

Türker, C; Akal, F; Joho, D; Schlapbach, R (2009). B-fabric: An open source life sciences data management system. Lecture Notes in Computer Science, 5566:185-190.

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, Roger; 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, Michael; 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, 3:43.

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, Michael (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, Mario; 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.

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, Michael; 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 Fri Aug 7 00:47:32 2020 CEST.