Publications

ZORA Publication List

Publications

• 2016

  • Journal Article

    • Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., Jensen, L. J., von Mering, C., & Bork, P. (2016). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences Nucleic Acids Research, 44, D286–D293. https://doi.org/10.1093/nar/gkv1248
    • Szklarczyk, D., Santos, A., von Mering, C., Jensen, L. J., Bork, P., & Kuhn, M. (2016). STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data Nucleic Acids Research, 44, D380–D384. https://doi.org/10.1093/nar/gkv1277
    • Stockinger, H., Palagi, P. M., Durinx, C., Baudis, M., von Mering, C., Szövenyi, P., & et al. (2016). The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic Acids Research, 44, D27-37. https://doi.org/10.1093/nar/gkv1310
    • Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., Jensen, L. J., & von Mering, C. (2016). The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible Nucleic Acids Research, 45, D362–D368. https://doi.org/10.1093/nar/gkw937
    • Kamkina, P., Snoek, L. B., Grossmann, J., Volkers, R. J. M., Sterken, M. G., Daube, M., Roschitzki, B., Fortes, C., Schlapbach, R., Roth, A., von Mering, C., Hengartner, M. O., Schrimpf, S. P., & Kammenga, J. E. (2016). Natural genetic variation differentially affects the proteome and transcriptome in Caenorhabditis elegans Molecular & Cellular Proteomics, 15, 1670–1680. https://doi.org/10.1074/mcp.M115.052548
    • Franceschini, A., Lin, J., von Mering, C., & Jensen, L. J. (2016). SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles Bioinformatics, 32, 1085–1087. https://doi.org/10.1093/bioinformatics/btv696

• 2015

  • Journal Article

    • Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., Kuhn, M., Bork, P., Jensen, L. J., & von Mering, C. (2015). STRING v10: protein-protein interaction networks, integrated over the tree of life Nucleic Acids Research, 43, D447-52. https://doi.org/10.1093/nar/gku1003
    • Wang, M., Herrmann, C. J., Simonovic, M., Szklarczyk, D., & von Mering, C. (2015). Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines Proteomics, 15, 3163–3168. https://doi.org/10.1002/pmic.201400441
    • Takeuchi, Y., Chaffron, S., Salcher, M. M., Shimizu-Inatsugi, R., Kobayashi, M. J., Diway, B., von Mering, C., Pernthaler, J., & Shimizu, K. K. (2015). Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes Systematic and Applied Microbiology, 38, 330–339. https://doi.org/10.1016/j.syapm.2015.05.006
    • Schmidt, T. S. B., Matias Rodrigues, J. F., & von Mering, C. (2015). Limits to robustness and reproducibility in the demarcation of operational taxonomic units Environmental Microbiology, 17, 1689–1706. https://doi.org/10.1111/1462-2920.12610
    • Schmich, F., Szczurek, E., Kreibich, S., Dilling, S., Andritschke, D., Casanova, A., Low, S. H., Eicher, S., Muntwiler, S., Emmenlauer, M., Rämö, P., Conde-Alvarez, R., von Mering, C., Hardt, W.-D., Dehio, C., & Beerenwinkel, N. (2015). gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens Genome Biology, 16, 220. https://doi.org/10.1186/s13059-015-0783-1

• 2014

  • Journal Article

    • Rämö, P., Drewek, A., Arrieumerlou, C., Beerenwinkel, N., Ben-Tekaya, H., Cardel, B., Casanova, A., Conde-Alvarez, R., Cossart, P., Csúcs, G., Eicher, S., Emmenlauer, M., Greber, U., Hardt, W.-D., Helenius, A., Kasper, C., Kaufmann, A., Kreibich, S., Kühbacher, A., … Dehio, C. (2014). Simultaneous analysis of large-scale RNAi screens for pathogen entry BMC Genomics, 15, 1162. https://doi.org/10.1186/1471-2164-15-1162
    • Schulz, J. C., Zampieri, M., Wanka, S., von Mering, C., & Sauer, U. (2014). Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways Science Signaling, 7, rs6. https://doi.org/10.1126/scisignal.2005602
    • 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.
    • Soste, M., Hrabakova, R., Wanka, S., Melnik, A., Boersema, P., Maiolica, A., Wernas, T., Tognetti, M., von Mering, C., & Picotti, P. (2014). A sentinel protein assay for simultaneously quantifying cellular processes Nature Methods, 11, 1045–1048. https://doi.org/10.1038/nmeth.3101
    • Warinner, C., Rodrigues, J. F. M., Vyas, R., Trachsel, C., Shved, N., Grossmann, J., Radini, A., Hancock, Y., Tito, R. Y., Fiddyment, S., Speller, C., Hendy, J., Charlton, S., Luder, H. U., Salazar-García, D. C., Eppler, E., Seiler, R., Hansen, L. H., Castruita, J. A. S., … Cappellini, E. (2014). Pathogens and host immunity in the ancient human oral cavity Nature Genetics, 46, 336–344. https://doi.org/10.1038/ng.2906
    • Meier, R., Franceschini, A., Horvath, P., Tetard, M., Mancini, R., von Mering, C., Helenius, A., & Lozach, P.-Y. (2014). Genome-Wide Small Interfering RNA Screens Reveal VAMP3 as a Novel Host Factor Required for Uukuniemi Virus Late Penetration Journal of Virology, 88, 8565–8578. https://doi.org/10.1128/JVI.00388-14
    • Matias Rodrigues, J. F., & von Mering, C. (2014). HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences Bioinformatics, 30, 287–288. https://doi.org/10.1093/bioinformatics/btt657
    • Schmidt, T. S. B., Matias Rodrigues, J. F., & von Mering, C. (2014). Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale PLoS Computational Biology, 10, e1003594. https://doi.org/10.1371/journal.pcbi.1003594
    • Trachana, K., Forslund, K., Larsson, T., Powell, S., Doerks, T., von Mering, C., & Bork, P. (2014). A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation PLoS ONE, 9, e111122. https://doi.org/10.1371/journal.pone.0111122
    • Franceschini, A., Meier, R., Casanova, A., Kreibich, S., Daga, N., Andritschke, D., Dilling, S., Rämö, P., Emmenlauer, M., Kaufmann, A., Conde-Álvarez, R., Low, S. H., Pelkmans, L., Helenius, A., Hardt, W.-D., Dehio, C., & von Mering, C. (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, 4548–4553. https://doi.org/10.1073/pnas.1402353111
    • Stockinger, H., Altenhoff, A. M., Arnold, K., Bairoch, A., Bastian, F., Bergmann, S., Bougueleret, L., Bucher, P., Delorenzi, M., Lane, L., Le Mercier, P., Lisacek, F., Michielin, O., Palagi, P. M., Rougemont, J., Schwede, T., von Mering, C., van Nimwegen, E., Walther, D., … Appel, R. D. (2014). Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support Nucleic Acids Research, 42, W436–W441. https://doi.org/10.1093/nar/gku380
    • Cai, H., Kumar, N., Bagheri, H. C., von Mering, C., Robinson, M. D., & Baudis, M. (2014). Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens BMC Genomics, 15, 82. https://doi.org/10.1186/1471-2164-15-82
    • Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldón, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, L. J., von Mering, C., & Bork, P. (2014). eggNOG v4.0: nested orthology inference across 3686 organisms Nucleic Acids Research, 42, D231–D239. https://doi.org/10.1093/nar/gkt1253

• 2013

  • Journal Article

    • Maier, L., Vyas, R., Cordova, C. D., Lindsay, H., Schmidt, T. S. B., Brugiroux, S., Periaswamy, B., Bauer, R., Sturm, A., Schreiber, F., von Mering, C., Robinson, M. D., Stecher, B., & Hardt, W.-D. (2013). Microbiota-derived hydrogen fuels salmonella typhimurium invasion of the gut ecosystem Cell Host & Microbe, 14, 641–651. https://doi.org/10.1016/j.chom.2013.11.002
    • Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., & Jensen, L. J. (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration Nucleic Acids Research, 41, D808–D815. https://doi.org/10.1093/nar/gks1094

• 2012

  • Journal Article

    • Kumar, N., Cai, H., von Mering, C., & Baudis, M. (2012). Specific Genomic Regions Are Differentially Affected by Copy Number Alterations across Distinct Cancer Types, in Aggregated Cytogenetic Data PLoS ONE, 7, e43689. https://doi.org/10.1371/journal.pone.0043689
    • Wang, M., Weiss, M., Simonovic, M., Haertinger, G., Schrimpf, S. P., Hengartner, M. O., & von Mering, C. (2012). PaxDb, a database of protein abundance averages across all three domains of life Molecular & Cellular Proteomics, 11, 492–500. https://doi.org/10.1074/mcp.O111.014704
    • 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 The ISME Journal, 6, 1378–1390. https://doi.org/10.1038/ismej.2011.192
    • Atamna-Ismaeel, N., Finkel, O., Glaser, F., von Mering, C., Vorholt, J. A., Koblížek, M., Belkin, S., & Béjà, O. (2012). Bacterial anoxygenic photosynthesis on plant leaf surfaces Environmental Microbiology Reports, 4, 209–216. https://doi.org/10.1111/j.1758-2229.2011.00323.x
    • Juhas, M., Stark, M., von Mering, C., Lumjiaktase, P., Crook, D. W., Valvano, M. A., & Eberl, L. (2012). High confidence prediction of essential genes in burkholderia cenocepacia PLoS ONE, 7, e40064. https://doi.org/10.1371/journal.pone.0040064
    • 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., … Zheng, X. (2012). The HUPO initiative on Model Organism Proteomes, iMOP Proteomics, 12, 340–345. https://doi.org/10.1002/pmic.201290014
    • 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, D284–D289. https://doi.org/10.1093/nar/gkr1060
    • 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, 346–350. https://doi.org/10.1002/pmic.201290015

• 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. https://doi.org/10.1093/nar/gkr1011
    • 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, D561–D568. https://doi.org/10.1093/nar/gkq973
    • Takeuchi, Y., Salcher, M. M., Ushio, M., Shimizu-Inatsugi, R., Kobayashi, M. J., Diway, B., von Mering, C., Pernthaler, J., & Shimizu, K. 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, e25144. https://doi.org/10.1371/journal.pone.0025144
    • 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, 140–146. https://doi.org/10.1111/j.1462-2920.2011.02554.x
    • 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. https://doi.org/10.1038/msb.2011.7
    • 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, e1002025. https://doi.org/10.1371/journal.pcbi.1002025

• 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. https://doi.org/10.1186/1471-2164-11-461
    • 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, 1297–1306. https://doi.org/10.1002/pmic.200900414
    • 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, 506–512. https://doi.org/10.1016/j.cub.2010.01.051
    • 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, 947–959. https://doi.org/10.1101/gr.104521.109
    • 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, e1001097. https://doi.org/10.1371/journal.ppat.1001097
    • 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, e1000711. https://doi.org/10.1371/journal.ppat.1000711
    • 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., … Aebersold, R. (2010). Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast Science Signaling, 3, rs4. https://doi.org/10.1126/scisignal.2001182
    • 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. https://doi.org/10.1093/nar/gkp951
    • 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. https://doi.org/10.1093/nar/gkp937

• 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, 106, 16428–16433. https://doi.org/10.1073/pnas.0905240106

Pagination