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2017

Rodrigues, João F Matias; Schmidt, Thomas Sebastian Benedikt; Tackmann, Janko; von Mering, Christian (2017). MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics:Epub ahead of print.

Huerta-Cepas, Jaime; Forslund, Kristoffer; Coelho, Luis Pedro; Szklarczyk, Damian; Jensen, Lars Juhl; von Mering, Christian; Bork, Peer (2017). Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. Molecular Biology and Evolution, 34(8):2115-2122.

Rot, Gregor; Wang, Zhen; Huppertz, Ina; Modic, Miha; Lenče, Tina; Hallegger, Martina; Haberman, Nejc; Curk, Tomaž; von Mering, Christian; Ule, Jernej (2017). High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43. Cell Reports, 19(5):1056-1067.

Leuenberger, Pascal; Ganscha, Stefan; Kahraman, Abdullah; Cappelletti, Valentina; Boersema, Paul J; von Mering, Christian; Claassen, Manfred; Picotti, Paola (2017). Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability. Science, 355(6327):1-13.

Feigelman, Rounak; Kahlert, Christian R; Baty, Florent; Rassouli, Frank; Kleiner, Rebekka L; Kohler, Philipp; Brutsche, Martin H; von Mering, Christian (2017). Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. Microbiome, 5(1):20.

Junge, Alexander; Refsgaard, Jan C; Garde, Christian; Pan, Xiaoyong; Santos, Alberto; Alkan, Ferhat; Anthon, Christian; von Mering, Christian; Workman, Christopher T; Jensen, Lars Juhl; Gorodkin, Jan (2017). RAIN: RNA-protein Association and Interaction Networks. Database, 2017:1-9.

2016

Dolowschiak, Tamas; Mueller, Anna Angelika; Pisan, Lynn Joanna; Feigelman, Rounak; Felmy, Boas; Sellin, Mikael Erik; Namineni, Sukumar; Nguyen, Bidong Dinh; Wotzka, Sandra Yvonne; Heikenwalder, Mathias; von Mering, Christian; Mueller, Christoph; Hardt, Wolf-Dietrich (2016). IFN-γ Hinders Recovery from Mucosal Inflammation during Antibiotic Therapy for Salmonella Gut Infection. Cell Host & Microbe, 20(2):238-249.

Szklarczyk, Damian; Santos, Alberto; von Mering, Christian; Jensen, Lars Juhl; Bork, Peer; Kuhn, Michael (2016). STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Research, 44(D1):D380-D384.

Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer; Cook, Helen; Heller, Davide; Walter, Mathias C; Rattei, Thomas; Mende, Daniel R; Sunagawa, Shinichi; Kuhn, Michael; Jensen, Lars Juhl; von Mering, Christian; Bork, Peer (2016). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research, 44(D1):D286-D293.

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.

Franceschini, Andrea; Lin, Jianyi; von Mering, Christian; Jensen, Lars Juhl (2016). SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics, 32(7):1085-1087.

2015

Wang, Mingcong; Herrmann, Christina J; Simonovic, Milan; Szklarczyk, Damian; von Mering, Christian (2015). Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics, 15(18):3163-3168.

Takeuchi, Yayoi; Chaffron, Samuel; Salcher, Michaela M; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K (2015). Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. Systematic and Applied Microbiology, 38(5):330-339.

Stockenhuber, Reinhold; Zoller, Stefan; Shimizu-Inatsugi, Rie; Gugerli, Felix; Shimizu, Kentaro K; Widmer, Alex; Fischer, Martin C (2015). Efficient detection of novel nuclear markers for brassicaceae by transcriptome sequencing. PLoS ONE, 10(6):e0128181.

Schmich, Fabian; Szczurek, Ewa; Kreibich, Saskia; Dilling, Sabrina; Andritschke, Daniel; Casanova, Alain; Low, Shyan Huey; Eicher, Simone; Muntwiler, Simone; Emmenlauer, Mario; Rämö, Pauli; Conde-Alvarez, Raquel; von Mering, Christian; Hardt, Wolf-Dietrich; Dehio, Christoph; Beerenwinkel, Niko (2015). gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens. Genome Biology, 16:220.

2014

Schulz, Juliane Caroline; Zampieri, Mattia; Wanka, Stefanie; von Mering, Christian; Sauer, Uwe (2014). Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways. Science Signaling, 7(353):rs6.

Trachana, Kalliopi; Forslund, Kristoffer; Larsson, Tomas; Powell, Sean; Doerks, Tobias; von Mering, Christian; Bork, Peer (2014). A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PLoS ONE, 9(11):e111122.

Schmidt, Thomas S B; Matias Rodrigues, João F; von Mering, Christian (2014). Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale. PLoS Computational Biology, 10(4):e1003594.

Stockinger, Heinz; Altenhoff, Adrian M; Arnold, Konstantin; Bairoch, Amos; Bastian, Frederic; Bergmann, Sven; Bougueleret, Lydie; Bucher, Philipp; Delorenzi, Mauro; Lane, Lydie; Le Mercier, Philippe; Lisacek, Frédérique; Michielin, Olivier; Palagi, Patricia M; Rougemont, Jacques; Schwede, Torsten; von Mering, Christian; van Nimwegen, Erik; Walther, Daniel; Xenarios, Ioannis; Zavolan, Mihaela; Zdobnov, Evgeny M; Zoete, Vincent; Appel, Ron D (2014). Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Research, 42(Web Server):W436-W441.

Meier, Roger; Franceschini, Andrea; Horvath, Peter; Tetard, Marilou; Mancini, Roberta; von Mering, Christian; Helenius, Ari; Lozach, Pierre-Yves (2014). Genome-Wide Small Interfering RNA Screens Reveal VAMP3 as a Novel Host Factor Required for Uukuniemi Virus Late Penetration. Journal of Virology, 88(15):8565-8578.

Matias Rodrigues, João F; von Mering, Christian (2014). HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. Bioinformatics, 30(2):287-288.

Franceschini, Andrea; Meier, Roger; Casanova, Alain; Kreibich, Saskia; Daga, Neha; Andritschke, Daniel; Dilling, Sabrina; Rämö, Pauli; Emmenlauer, Mario; Kaufmann, Andreas; Conde-Álvarez, Raquel; Low, Shyan Huey; Pelkmans, Lucas; Helenius, Ari; Hardt, Wolf-Dietrich; Dehio, Christoph; von Mering, Christian (2014). Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proceedings of the National Academy of Sciences of the United States of America, 111(12):4548-4553.

Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Huerta-Cepas, Jaime; Gabaldón, Toni; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars J; von Mering, Christian; Bork, Peer (2014). eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research, 42(1):D231-D239.

2013

Ogura, Atsushi; Yoshida, Masa-aki; Moritaki, Takeya; Sese, Jun; Shimizu, Kentaro K; Sousounis, Konstantinos; Tsonis, Panagiotis A (2013). Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus. Scientific Reports, 3:1432.

Shimizu, Kentaro K (2013). Pollen, Pollen tube, Selfing, Pistil, Ovule, Endosperm, Embryo sac, Sporangium, Stamen. In: Iwasa, Yoh; Kuratani, Shigeru; Saitou, Naruya; Tsukaya, Hirokazu. Iwanami Biology Dictionary, 5th Edition. Tokyo: Iwanami, nn-nn.

Kobayashi, Masaki J; Shimizu, Kentaro K (2013). Challenges in studies on flowering time: interfaces between phenological research and the molecular network of flowering genes. Ecological Research, 28(2):161-172.

Tsuchimatsu, Takashi; Shimizu, Kentaro K (2013). Effects of pollen availability and the mutation bias on the fixation of mutations disabling the male specificity of self-incompatibility. Journal of Evolutionary Biology, 26(10):2221-2232.

Kobayashi, Masaki J; Takeuchi, Yayoi; Kenta, Tanaka; Kume, Tomonori; Diway, Bibian; Shimizu, Kentaro K (2013). Mass flowering of the tropical tree Shorea beccariana was preceded by expression changes in flowering and drought-responsive genes. Molecular Ecology, 22(18):4767-4782.

Fischer, Martin C; Rellstab, Christian; Tedder, Andrew; Zoller, Stefan; Gugerli, Felix; Shimizu, Kentaro K; Holderegger, Rolf; Widmer, Alex (2013). Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps. Molecular Ecology, 22(22):5594-5607.

Franceschini, Andrea; Szklarczyk, Damian; Frankild, Sune; Kuhn, Michael; Simonovic, Milan; Roth, Alexander; Lin, Jianyi; Minguez, Pablo; Bork, Peer; von Mering, Christian; Jensen, Lars J (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research, 41(D 1):D808-D815.

Wicker, Thomas; Oberhaensli, Simone; Parlange, Francis; Buchmann, Jan P; Shatalina, Margarita; Roffler, Stefan; Ben-David, Roi; Doležel, Jaroslav; Šimkova, Hana; Schulze-Lefert, Paul; Spanu, Pietro D; Bruggmann, Rémy; Amselem, Joelle; Quesneville, Hadi; van Themaat, Emiel Ver Loren; Paape, Timothy; Shimizu, Kentaro K; Keller, Beat (2013). The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nature Genetics, 45(9):1092-1096.

2012

Atamna-Ismaeel, Nof; Finkel, Omri; Glaser, Fabian; von Mering, Christian; Vorholt, Julia A; Koblížek, Michal; Belkin, Shimshon; Béjà, Oded (2012). Bacterial anoxygenic photosynthesis on plant leaf surfaces. Environmental Microbiology Reports, 4(2):209-216.

Juhas, Mario; Stark, Manuel; von Mering, Christian; Lumjiaktase, Puthapoom; Crook, Derrick W; Valvano, Miguel A; Eberl, Leo (2012). High confidence prediction of essential genes in burkholderia cenocepacia. PLoS ONE, 7(6):e40064.

Knief, C; Delmotte, N; Chaffron, S; Stark, M; Innerebner, G; Wassmann, R; von Mering, C; Vorholt, J A (2012). Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME Journal, 6(7):1378-1390.

Tsuchimatsu, Takashi; Kaiser, Pascal; Yew, Chow-Lih; Bachelier, Julien B; Shimizu, Kentaro K (2012). Recent loss of self-incompatibility by degradation of the male component in allotetraploid Arabidopsis kamchatica. PLoS Genetics, 8(7):e1002838.

Jones, A M E; Aebersold, R; Ahrens, C H; Apweiler, R; Baerenfaller, K; Baker, M; Bendixen, E; Briggs, S; Brownridge, P; Brunner, E; Daube, M; Deutsch, E W; Grossniklaus, U; Heazlewood, J L; Hengartner, M O; Hermjakob, H; Jovanovic, M; Lawless, C; Lochnit, G; Martens, L; Ravnsborg, C; Schrimpf, S P; Shim, Y H; Subasic, D; Tholey, A; van Wijk, K; von Mering, C; Weiss, M; Zheng, X (2012). The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics, 12(3):340-345.

Schrimpf, S P; von Mering, C; Bendixen, E; Heazlewood, J L; Bumann, D; Omenn, G; Hengartner, M O (2012). The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland. Proteomics, 12(3):346-350.

de la Chaux, Nicole; Tsuchimatsu, Takashi; Shimizu, Kentaro K; Wagner, Andreas (2012). The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata. Mobile DNA, 3:2.

Powell, S; Szklarczyk, D; Trachana, K; Roth, A; Kuhn, M; Muller, J; Arnold, R; Rattei, T; Letunic, I; Doerks, T; Jensen, L J; von Mering, C; Bork, P (2012). eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research, 40(D1):D284-D289.

2011

Yoshida, Masa-aki; Ishikura, Yukiko; Moritaki, Takeya; Shoguchi, Eiichi; Shimizu, Kentaro K; Sese, Jun; Ogura, Atsushi (2011). Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation. Gene, 483(1-2):63-71.

Shimizu, Kentaro K; Kudoh, Hiroshi; Kobayashi, Masaki J (2011). Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology. Annals of Botany, 108(4):777-787.

Kawagoe, Tetsuhiro; Shimizu, Kentaro K; Kakutani, Tetsuji; Kudoh, Hiroshi (2011). Coexistence of trichome variation in a natural plant population: A combined study using ecological and candidate gene approaches. PLoS ONE, 6(7):e22184.

Schilling, S; Willecke, M; Aegerter-Wilmsen, T; Cirpka, O A; Basler, K; von Mering, C (2011). Cell-sorting at the a/p boundary in the Drosophila wing primordium: a computational model to consolidate observed non-local effects of hh signaling. PLoS Computational Biology, 7(4):e1002025.

Saito, Hideyuki; Sese, Jun; Shimizu-Inatsugi, Rie; Kamimura, Shoko; Yamada, Tadayasu; Shimizu, Kentaro K (2011). Development of DNA microarray for Fagus crenata. Forest Tree Breeding of Hokkaido, 54(2):11-14.

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.

Tsuchimatsu, Takashi; Shimizu, Kentaro K (2011). How the model species Arabidopsis thaliana became self-fertilizing: evolution of breeding systems revealed by DNA sequence information. Kagaku To Seibutsu, 49(6):364-366.

Takeuchi, Yayoi; Salcher, Michaela M; Ushio, Masayuki; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K (2011). In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus nepenthes. PLoS ONE, 6(9):e25144.

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.

Takeuchi, Yayoi; Shimizu, Kentaro K (2011). Potential application of pollen genotyping for evolutionary genetic and genomic studies: linkage/recombination analysis and haplotype sequencing, in Ecological Research Monographs ‘Single-Pollen Genotyping’. In: Isagi, Y; Suyama, Y. Single-Pollen Genotyping. Tokyo [etc.]: Springer, 111-123.

Kuhn, M; Szklarczyk, D; Franceschini, A; von Mering, C; Jensen, L J; Bork, P (2011). STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Research:Online.

Begemann, M; Spengler, S; Kanber, D; Haake, A; Baudis, M; Leisten, I; Binder, G; Markus, S; Rupprecht, T; Segerer, H; Fricke-Otto, S; Mühlenberg, R; Siebert, R; Buiting, K; Eggermann, T (2011). Silver-Russell patients showing a broad range of ICR1 and ICR2 hypomethylation in different tissues. Clinical Genetics, 80(1):83-88.

Szklarczyk, D; Franceschini, A; Kuhn, M; Simonovic, M; Roth, A; Minguez, P; Doerks, T; Stark, M; Muller, J; Bork, P; Jensen, L J; von Mering, C (2011). The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research, 39(Sup 1):D561-D568.

Takeuchi, Yayoi; Shimizu, Kentaro K (2011). The study of microbial diversity and function using metagenomics. Shuseibutsugaku kenkyū, 34:123-138.

Zust, Tobias; Joseph, Bindu; Shimizu, Kentaro K; Kliebenstein, Daniel J; Turnbull, Lindsay A (2011). Using knockout mutants to reveal the growth costs of defensive traits. Proceedings of the Royal Society B: Biological Sciences, 278(1718):2598-2603.

2010

Craig, V J; Arnold, I; Gerke, C; Huynh, M Q; Wundisch, T; Neubauer, A; Renner, C; Falkow, S; Mueller, A (2010). Gastric MALT lymphoma B cells express polyreactive, somatically mutated immunoglobulins. Blood, 115(3):581-591.

Tsuchimatsu, Takashi; Shimizu, Kentaro K (2010). From outcrossing to selfing: the evolutionary transition of reproductive systems in Arabidopsis. Iden:7-12.

Stark, M; Berger, S A; Stamatakis, A; von Mering, C (2010). MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics, 11:461.

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.

Tsuchimatsu, Takashi; Shimizu, Kentaro K (2010). The genetic basis for the evolution of self-compatibility in Arabidopsis. BSJ Review:90-95.

Aikawa, Shinichiro; Kobayashi, Masaki J; Satake, Akiko; Shimizu, Kentaro K; Kudoh, Hiroshi (2010). Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 107(25):11632-11637.

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.

Eggermann, T; Spengler, S; Bachmann, N; Baudis, M; Mau-Holzmann, U A; Singer, S; Rossier, E (2010). Chromosome 11p15 duplication in Silver-Russell syndrome due to a maternally inherited translocation t(11;15). American Journal of Medical Genetics. Part A, 152A(6):1484-1487.

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.

Tsuchimatsu, Takashi; Suwabe, Keita; Shimizu-Inatsugi, Rie; Isokawa, Sachiyo; Pavlidis, Pavlos; Städler, Thomas; Suzuki, Go; Takayama, Seiji; Watanabe, Masao; Shimizu, Kentaro K (2010). Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene. Nature, 464(7293):1342-1346.

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.

Ahrens, C H; Brunner, E; Basler, K (2010). Quantitative proteomics: a central technology for systems biology. Journal of Proteomics, 73(4):820-827.

Eggermann, T; Schönherr, N; Spengler, S; Jäger, S; Denecke, B; Binder, G; Baudis, M (2010). Identification of a 21q22 duplication in a Silver-Russell syndrome patient further narrows down the Down syndrome critical region. American Journal of Medical Genetics. Part A, 152A(2):356-359.

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.

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.

Wuest, S E; Vijverberg, K; Schmidt, A; Weiss, M; Gheyselinck, J; Lohr, M; Wellmer, F; Rahnenführer, J; von Mering, C; Grossniklaus, U (2010). Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes. Current Biology, 20(6):506-512.

Seeholzer, Sabine; Tsuchimatsu, Takashi; Jordan, Tina; Bieri, Stéphane; Pajonk, Simone; Yang, Wenxiang; Jahoor, Ahmed; Shimizu, Kentaro K; Keller, Beat; Schulze-Lefert, Paul (2010). Diversity at the Mla powdery mildew resistance locus from cultivated barley reveals sites of positive selection. Molecular Plant-Microbe Interactions, 23(4):497-509.

Aegerter-Wilmsen, T; Smith, A C; Christen, A J; Aegerter, C M; Hafen, E; Basler, K (2010). Exploring the effects of mechanical feedback on epithelial topology. Development, 137(3):499-506.

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.

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.

Peralta, R; Baudis, M; Vazquez, G; Juárez, S; Ortiz, R; Decanini, H; Hernandez, D; Gallegos, F; Valdivia, A; Piña, P; Salcedo, M (2010). Increased expression of cellular retinol-binding protein 1 in laryngeal squamous cell carcinoma. Journal of Cancer Research and Clinical Oncology, 136(6):931-938.

Stecher, B; Chaffron, S; Käppeli, R; Hapfelmeier, S; Freedrich, S; Weber, T C; Kirundi, J; Suar, M; McCoy, K D; von Mering, C; Macpherson, A J; Hardt, W D (2010). Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathogens, 6(1):e1000711.

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.

Lacunza, E; Baudis, M; Colussi, A G; Segal-Eiras, A; Croce, M V; Abba, M C (2010). MUC1 oncogene amplification correlates with protein overexpression in invasive breast carcinoma cells. Cancer Genetics and Cytogenetics, 201(2):102-110.

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.

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.

Toller, I M; Hitzler, I; Sayi, A; Mueller, A (2010). Prostaglandin E2 prevents Helicobacter-induced gastric preneoplasia and facilitates persistent infection in a mouse model. Gastroenterology, 138(4):1455-1467.e4 .

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.

Kuhn, M; Szklarczyk, D; Franceschini, A; Campillos, M; von Mering, C; Jensen, L J; Beyer, A; Bork, P (2010). STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Research, 38 (Da:D552-D556.

Weiss, M; Schrimpf, S; Hengartner, M O; Lercher, M J; von Mering, C (2010). Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome. Proteomics, 10(6):1297-1306.

Kelemen, J Z; Ratna, P; Scherrer, S; Becskei, A (2010). Spatial epigenetic control of mono- and bistable gene expression. PLoS Biology, 8(3):e1000332.

Spengler, S; Schönherr, N; Binder, G; Wollmann, H; Fricke-Otto, S; Mühlenberg, R; Denecke, B; Baudis, M; Eggermann, T (2010). Submicroscopic chromosomal imbalances in idiopathic Silver-Russell syndrome (SRS): the SRS phenotype overlaps with the 12q14 microdeletion syndrome. Journal of Medical Genetics, 47(5):356-360.

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.

Endt, K; Stecher, B; Chaffron, S; Slack, E; Tchitchek, N; Benecke, A; Van Maele, L; Sirard, J-C; Mueller, A J; Heikenwalder, M; Macpherson, A J; Strugnell, R; von Mering, C; Hardt, W-D (2010). The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathogens, 6(9):e1001097.

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.

Muller, J; Szklarczyk, D; Julien, P; Letunic, I; Roth, A; Kuhn, M; Powell, S; von Mering, C; Doerks, T; Jensen, L J; Bork, P (2010). eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Research, 38 (Da:D190-D195.

2009

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.

Reiter, L; Claassen, M; Schrimpf, S P; Jovanovic, M; Schmidt, A; Buhmann, J M; Hengartner, M O; Aebersold, R (2009). Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Molecular & Cellular Proteomics, 8(11):2405-2417.

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.

Köhler, K; Brunner, E; Guan, X L; Boucke, K; Greber, U F; Mohanty, S; Barth, J M; Wenk, M R; Hafen, E (2009). A combined proteomic and genetic analysis identifies a role for the lipid desaturase Desat1 in starvation-induced autophagy in Drosophila. Autophagy, 5(7):980-990.

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.

Delmotte, N; Knief, C; Chaffron, S; Innerebner, G; Roschitzki, B; Schlapbach, R; von Mering, C; Vorholt, J A (2009). Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 106(38):16428-16433.

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

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

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

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

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

Tan, C S H; Bodenmiller, B; Pasculescu, A; Jovanovic, M; Hengartner, M O; Jørgensen, C; Bader, G D; Aebersold, R; Pawson, T; Linding, R (2009). Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Science Signaling, 2(81):ra39.

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.

Hausmann, G; von Mering, C; Basler, K (2009). The hedgehog signaling pathway: where did it come from? PLoS Biology, 7(6):e1000146.

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.

Ratna, P; Scherrer, S; Fleischli, C; Becskei, A (2009). Synergy of repression and silencing gradients along the chromosome. Journal of Molecular Biology, 387(4):826-839.

Becskei, A (2009). Linearization through distortion: a new facet of negative feedback in signalling. Molecular Systems Biology, 5:255.

Boerma, E G; Siebert, R; Kluin, P M; Baudis, M (2009). Translocations involving 8q24 in Burkitt lymphoma and other malignant lymphomas: a historical review of cytogenetics in the light of todays knowledge. Leukemia, 23(2):225-234.

Jensen, L J; Kuhn, M; Stark, M; Chaffron, S; Creevey, C; Muller, J; Doerks, T; Julien, P; Roth, A; Simonovic, M; Bork, P; von Mering, C (2009). STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research, 37(Databa):D412-D416.

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.

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.

Buetti-Dinh, A; Ungricht, R; Kelemen, J Z; Shetty, C; Ratna, P; Becskei, A (2009). Control and signal processing by transcriptional interference. Molecular Systems Biology, 5:300.

Nienhaus, U; Aegerter-Wilmsen, T; Aegerter, C M (2009). Determination of mechanical stress distribution in Drosophila wing discs using photoelasticity. Mechanisms of Development, 126(11-12):942-949.

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.

Boisson-Dernier, A; Roy, S; Kritsas, K; Grobei, M A; Jaciubek, M; Schroeder, J I; Grossniklaus, U (2009). Disruption of the pollen-expressed FERONIA homologs ANXUR1 and ANXUR2 triggers pollen tube discharge. Development, 136(19):3279-3288.

Shimizu, Kentaro K; Takeuchi, Yayoi (2009). Ecological genomics – a novel approach toward community ecology. In: Ohgushi, T; Kondo, M; Yoshida, T. New challenges in community ecology. Kyoto, JP: Kyoto University Press, 223-241.

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.

Shimizu, Kentaro K (2009). Pollen tubes and hairs. In: Ishii, R. Plant Encyclopedia. Tokyo, Japan: s.n. , 207-208.

Mueller, A; Sayi, A; Hitzler, I (2009). Protective and pathogenic functions of T-cells are inseparable during the Helicobacter-host interaction. Discovery medicine, 8(41):68-73.

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

Gerstung, M; Baudis, M; Moch, H; Beerenwinkel, N (2009). Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics, 25(21):2809-2815.

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

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

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

Shimizu-Inatsugi, Rie; Lihova, Judita; Iwanaga, Hiroko; Kudoh, Hiroshi; Savolainen, Outi; Watanabe, Kuniaki; Yakubov, Valentin V; Shimizu, Kentaro K (2009). The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri. Molecular Ecology, 18(19):4024-4048.

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.

2008

Shimizu, Kentaro K; Ito, Toshiro; Ishiguro, Sumie; Okada, Kiyotaka (2008). MAA3 (MAGATAMA3) helicase gene is required for female gametophyte development and pollen tube guidance in Arabidopsis thaliana. Plant & Cell Physiology, 49(10):1478-1483.

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.

Roos, A; Elbracht, M; Baudis, M; Senderek, J; Schönherr, N; Eggermann, T; Schüler, H M (2008). A 10.7 Mb interstitial deletion of 13q21 without phenotypic effect defines a further non-pathogenic euchromatic variant. American Journal of Medical Genetics. Part A, 146A(18):2417-2420.

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.

Hoischen, A; Ehrler, M; Fassunke, J; Simon, M; Baudis, M; Landwehr, C; Radlwimmer, B; Lichter, P; Schramm, J; Becker, A J; Weber, R G (2008). Comprehensive characterization of genomic aberrations in gangliogliomas by CGH, array-based CGH and interphase FISH. Brain Pathology, 18(3):326-337.

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.

Fujimoto, Ryo; Kinoshita, Yuki; Kawabe, Akira; Kinoshita, Tetsu; Takashima, Kazuya; Nordborg, Magnus; Nasrallah, Mikhail E; Shimizu, Kentaro K; Kudoh, Hiroshi; Kakutani, Tetsuji (2008). Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genetics, 4(4)::e1000048..

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.

Shimizu, Kentaro K; Shimizu-Inatsugi, Rie; Tsuchimatsu, Takashi; Purugganan, Michael D (2008). Independent origins of self-compatibility in Arabidopsis thaliana. Molecular Ecology, 17(2):704-714.

Jensen, L J; Julien, P; Kuhn, M; von Mering, C; Muller, J; Doerks, T; Bork, P (2008). eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Research, 36(Databa):D250-D254.

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.

Bauer, V L; Braselmann, H; Henke, M; Mattern, D; Walch, A; Unger, K; Baudis, M; Lassmann, S; Huber, R; Wienberg, J; Werner, M; Zitzelsberger, H F (2008). Chromosomal changes characterize head and neck cancer with poor prognosis. Journal of Molecular Medicine, 86(12):1353-1365.

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.

Shimizu, Kentaro K (2008). Letter from laboratories in foreign countries 9. International research environment grown in Switzerland: Institute of Plant Biology, University of Zurich. Society of Evolutionary Studies, Japan News, 9:10-16.

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.

Kunin, V; Raes, J; Harris, J K; Spear, J R; Walker, J J; Ivanova, N; von Mering, C; Bebout, B M; Pace, N R; Bork, P; Hugenholtz, P (2008). Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Molecular Systems Biology, 4:198.

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.

Nieländer, I; Martín-Subero, J I; Wagner, F; Baudis, M; Gesk, S; Harder, L; Hasenclever, D; Klapper, W; Kreuzer, M; Pott, C; Martinez-Climent, J A; Dreyling, M; Arnold, N; Siebert, R (2008). Recurrent loss of the Y chromosome and homozygous deletions within the pseudoautosomal region 1: association with male predominance in mantle cell lymphoma. Haematologica, 93(6):949-950.

Kuhn, M; von Mering, C; Campillos, M; Jensen, L J; Bork, P (2008). STITCH: interaction networks of chemicals and proteins. Nucleic Acids Research, 36(Databa):D684-D688.

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.

2007

Baudis, Michael (2007). Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer, 7:226.

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.

Dürig, J; Bug, S; Klein-Hitpass, L; Boes, T; Jöns, T; Martin-Subero, J I; Harder, L; Baudis, M; Dührsen, U; Siebert, R (2007). Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocytic leukemia with inv(14)(q11q32). Leukemia, 21(10):2153-2163.

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.

Shimizu, Kentaro K (2007). Basic principles of evolutionary genomics - 10 introductions for molecular biologists. In: Shimizu, Kentaro K; Hasebe, Mitsuyasu. Plant Evolution. Tokyo: Shujunsha, 48-57.

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.

Becskei, A; Grusby, M J (2007). Contribution of IL-12R mediated feedback loop to Th1 cell differentiation. FEBS Letters, 581(27):5199-5206.

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.

Shimizu, Kentaro K (2007). Ecologist@world, No. 8. From postdoc in the USA to the lab start up in Switzerland. Japanese Journal of Ecology, 57(3):432-437.

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.

Raes, J; Korbel, J O; Lercher, M J; von Mering, C; Bork, P (2007). Prediction of effective genome size in metagenomic samples. Genome Biology, 8:R10.

Harrington, E D; Singh, A H; Doerks, T; Letunic, I; von Mering, C; Jensen, L J; Raes, J; Bork, P (2007). Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 104(35):13913-13918.

von Mering, C; Hugenholtz, P; Raes, J; Tringe, S G; Doerks, T; Jensen, L J; Ward, N; Bork, P (2007). Quantitative phylogenetic assessment of microbial communities in diverse environments. Science, 315(5815):1126-1130.

von Mering, C; Jensen, L J; Kuhn, M; Chaffron, S; Doerks, T; Krüger, B; Snel, B; Bork, P (2007). STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Research, 35(Databa):D358-D362.

Stecher, B; Robbiani, R; Walker, A W; Westendorf, A M; Barthel, M; Kremer, M; Chaffron, S; Macpherson, A J; Buer, J; Parkhill, J; Dougan, G; von Mering, C; Hardt, W-D (2007). Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biology, 5(10):2177-2189.

Shimizu-Inatsugi, Rie; Shimizu, Kentaro K (2007). Speciation and evolution of reproductive systems. In: Shimizu, Kentaro K; Hasebe, Mitsuyasu. Plant Evolution. Tokyo: Shujunsha, 83-91.

Chaffron, S; von Mering, C (2007). Termites in the woodwork. Genome Biology, 8:229.

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.

Shimizu, Kentaro K (2007). Wild Arabidopsis and its relatives. In: Shimizu, Kentaro K; Hasebe, Mitsuyasu. Plant Evolution. Tokyo: Shujunsha, 16-17.

2006

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.

Shimizu, Kentaro K; Purugganan, Michael D (2006). Arabidopsis as a model organism in evolutionary genetics. In: Fox, Charles W; Wolf, Jason B. Evolutionary Genetics: Concepts And Case Studies. New York: Oxford Univ Press, 453-455.

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

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

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

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

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

Baudis, Michael (2006). Online database and bioinformatics toolbox to support data mining in cancer cytogenetics. BioTechniques, 40(3):269-272.

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.

2005

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

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

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

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

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

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

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

2004

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.

2003

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.

2002

Shimizu, Kentaro K (2002). A dream beyond scientific fields: in the special issue "how is the life as a scientist?". Science Journal Kagaku, 72(4):470-471.

2001

Bentz, M; Barth, T F; Brüderlein, S; Bock, D; Schwerer, M J; Baudis, M; Joos, S; Viardot, A; Feller, A C; Müller-Hermelink, H K; Lichter, P; Döhner, H; Möller, P (2001). Gain of chromosome arm 9p is characteristic of primary mediastinal B-cell lymphoma (MBL): comprehensive molecular cytogenetic analysis and presentation of a novel MBL cell line. Genes, Chromosomes & Cancer, 30(4):393-401.

1997

Werner, C A; Döhner, H; Joos, S; Trümper, L H; Baudis, M; Barth, T F; Ott, G; Möller, P; Lichter, P; Bentz, M (1997). High-level DNA amplifications are common genetic aberrations in B-cell neoplasms. American Journal of Pathology, 151(2):335-342.

This list was generated on Mon Oct 23 01:36:19 2017 CEST.