Publications

ZORA Publication List

Publications

• 2014

  • Journal Article

    • Soste, Martin; Hrabakova, Rita; Wanka, Stefanie; Melnik, Andre; Boersema, Paul; Maiolica, Alessio; Wernas, Timon; Tognetti, Marco; von Mering, Christian; Picotti, Paola (2014). A sentinel protein assay for simultaneously quantifying cellular processes. Nature Methods, 11(10):1045-1048.
    • 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; Cappellini, Enrico (2014). Pathogens and host immunity in the ancient human oral cavity. Nature Genetics, 46(4):336-344.
    • Kuhn, Michael; Szklarczyk, Damian; Pletscher-Frankild, Sune; Blicher, Thomas H; von Mering, Christian; Jensen, Lars J; Bork, Peer (2014). STITCH 4: integration of protein–chemical interactions with user data. Nucleic Acids Research, 42(D1):D401-D407.
    • 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.
    • 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.
    • 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.
    • Cai, Haoyang; Kumar, Nitin; Bagheri, Homayoun C; von Mering, Christian; Robinson, Mark D; Baudis, Michael (2014). Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genomics, 15:82.
    • 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.
    • 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.
    • 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.
    • Matias Rodrigues, João F; von Mering, Christian (2014). HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. Bioinformatics, 30(2):287-288.

• 2013

  • Journal Article

    • Maier, Lisa; Vyas, Rounak; Cordova, Carmen Dolores; Lindsay, Helen; Schmidt, Thomas Sebastian Benedikt; Brugiroux, Sandrine; Periaswamy, Balamurugan; Bauer, Rebekka; Sturm, Alexander; Schreiber, Frank; von Mering, Christian; Robinson, Mark D; Stecher, Bärbel; Hardt, Wolf-Dietrich (2013). Microbiota-derived hydrogen fuels salmonella typhimurium invasion of the gut ecosystem. Cell Host & Microbe, 14(6):641-651.
    • 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.

• 2012

  • Journal Article

    • Kumar, Nitin; Cai, Haoyang; von Mering, Christian; Baudis, Michael (2012). Specific Genomic Regions Are Differentially Affected by Copy Number Alterations across Distinct Cancer Types, in Aggregated Cytogenetic Data. PLoS ONE, 7(8):e43689.
    • Wang, Mingcong; Weiss, Manuel; Simonovic, Milan; Haertinger, Gabriele; Schrimpf, Sabine P; Hengartner, Michael O; von Mering, Christian (2012). PaxDb, a database of protein abundance averages across all three domains of life. Molecular & Cellular Proteomics, 11(8):492-500.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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

  • Journal Article

    • 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.
    • 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.
    • Atamna-Ismaeel, N; Finkel, O M; Glaser, F; Sharon, I; Schneider, R; Post, A F; Spudich, J L; von Mering, C; Vorholt, J A; Iluz, D; Béjà, O; Belkin, S (2011). Microbial rhodopsins on leaf surfaces of terrestrial plants. Environmental Microbiology, 14(1):140-146.
    • 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.
    • Misselwitz, B; Dilling, S; Vonaesch, P; Sacher, R; Snijder, B; Schlumberger, M; Rout, S; Stark, M; von Mering, C; Pelkmans, L; Hardt, W D (2011). RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42. Molecular Systems Biology, 7:474.
    • 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.

• 2010

  • Journal Article

    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.

• 2009

  • Journal Article

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

• 2008

  • Journal Article

    • 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.
    • 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.
    • 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.

• 2007

  • Journal Article

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

• 1998

  • Journal Article

    • Shmerling, D; Hegyi, I; Fischer, Marek; Blättler, T; Brandner, S; Götz, J; Rülicke, T; Flechsig, E; Cozzio, A; von Mering, C; Hangartner, C; Aguzzi, Adriano; Weissmann, C (1998). Expression of amino-terminally truncated PrP in the mouse leading to ataxia and specific cerebellar lesions.. Cell, 93(2):203-214.

Pagination