Publications

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Selected Publications

Szklarczyk D, Morris J, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva N, Roth A, Bork P, Jensen LJ, von Mering C
"The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible."
Nucl Acids Res (2017), 45:D362-D368, doi: 10.1093/nar/gkw937. fulltext (PDF, 1538 KB)


Schmidt TSB, Matias Rodrigues JF, von Mering C
"A family of interaction-adjusted indices of community similarity."
ISME Journal (2016), doi: 10.1038/ismej.2016.139. fulltext (PDF, 5855 KB)


Franceschini A*, Meier R*, Casanova A*, Kreibich S*, Daga N, Andritschke D, Dilling S, Rämö P, Emmenlauer M, Kaufmann A, Conde-Alvarez R, Low SH, Pelkmans L, Helenius A*, Hardt WD, Dehio C, von Mering C*
"Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens."
PNAS (2014), 111(12):4548–4553. fulltext (PDF, 1478 KB)


Chaffron S, Rehrauer H, Pernthaler J, von Mering C
"A global network of coexisting microbes from environmental and whole-genome sequence data."
Genome Research (2010), 20(7): 947-959. fulltext (PDF, 2266 KB)


von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, and Bork P
"Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments."
Science (2007), 315(5815): 1126-1130. fulltext (PDF, 1221 KB)

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Citation Counts

For the latest citation counts, please refer to the public profile at Google Scholar Citations.

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Complete Bibliography

2017

Rot G, Wang Z, Huppertz I, Modic M, Lence T, Halleger M, Habermann N, Curk T, von Mering C, Ule J
"High-resolution RNA maps demonstrate common principles of splicing and polyadenylation regulation by TDP-43."
Cell Reports, in press.


Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P
"Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper."
Molecular Biology and Evolution, in press.


Feigelman R, Kahlert CR, Baty F, Rassouli F, Kleiner RL, Kohler P, Brutsche MH, von Mering C
"Sputum DNA sequencing in Cystic Fibrosis: non-invasive access to the lung microbiome and to pathogen details."
Microbiome, 5(1):20, doi: 10.1186/s40168-017-0234-1 fulltext (PDF, 1959 KB)


Junge A, Refsgaard JC, Garde C, Pan X, Santos A, Alkan F, Anthon C, von Mering C, Workman CT, Jensen LJ, Gorodkin J
"RAIN: RNA-protein Association and Interaction Networks."
Database (Oxford), 10;2017;baw167, doi: 10.1093/database/baw167 fulltext (PDF, 761 KB)


Szklarczyk D, Morris J, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva N, Roth A, Bork P, Jensen LJ, von Mering C
"The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible."
Nucl Acids Res, 45:D362-D368, doi: 10.1093/nar/gkw937 fulltext (PDF, 1538 KB)


Leuenberger P, Ganscha S, Kahraman A, Cappelletti V, Boersema PJ, von Mering C, Claassen M, Picotti P.
"Cell-wide analysis of protein thermal unfolding across species reveals the determinants of proteome thermostability"
Science, 24;355(6327), doi: 0.1126/science.aai7825 fulltext (PDF, 2591 KB)


2016

Schmidt TSB, Matias Rodrigues JF, von Mering C
"A family of interaction-adjusted indices of community similarity."
ISME Journal, doi: 10.1038/ismej.2016.139. fulltext (PDF, 5855 KB)


Dolowschiak T, Mueller AA, Pisan LJ, Feigelman R, Felmy B, Sellin ME, Namineni S, Nguyen BD, Wotzka SY, Heikenwalder M, von Mering C, Mueller C, Hardt WD.
"IFN-γ Hinders Recovery from Mucosal Inflammation during Antibiotic Therapy for Salmonella Gut Infection."
Cell Host Microbe, 20(2):238-49. doi: 10.1016/j.chom.2016.06.008. fulltext (PDF, 1975 KB)


Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C
"Standardized benchmarking in the quest for orthologs."
Nat Methods, 13(5):425-30. doi: 10.1038/nmeth.3830. fulltext (PDF, 673 KB)


Kamkina P, Snoek LB, Grossmann J, Volkers RJ, Sterken MG, Daube M, Roschitzki B, Fortes C, Schlapbach R, Roth A, von Mering C, Hengartner MO, Schrimpf SP, Kammenga JE
"Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans."
Mol Cell Proteomics, 15(5):1670-80. doi: 10.1074/mcp.M115.052548. fulltext (PDF, 2298 KB)


Franceschini A, Lin J, von Mering C, Jensen LJ
"SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles."
Bioinformatics, 32(7):1085-7. doi: 10.1093/bioinformatics/btv696.fulltext (PDF, 151 KB)


Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M
"STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data."
Nucleic Acids Res, 44(D1):D380-4. doi: 10.1093/nar/gkv1277.fulltext (PDF, 1412 KB)


Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C*, Bork P*
"eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences."
Nucleic Acids Res, 44(D1):D286-93.fulltext (PDF, 4626 KB)


2015

Schmich F, Szczurek E, Kreibich S, Dilling S, Andritschke D, Casanova A, Low SH, Eicher S, Muntwiler S, Emmenlauer M, Rämö P, Conde-Alvarez R, von Mering C, Hardt WD, Dehio C, Beerenwinkel N
"gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens."
Genome Biol, 16:220.fulltext (PDF, 1314 KB)


Wang MC, Herrmann CJ, Simonovic M, Szklarczyk D, von Mering C
"Version 4.0 of PaxDb: protein abundance data, integrated across model organisms, tissues and cell-lines."
Proteomics, 15(18):3163-8.fulltext (PDF, 451 KB)


Takeuchi Y, Chaffron S, Salcher MM, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, von Mering C, Pernthaler J, Shimizu KK
"Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes."
Syst Appl Microbiol, 38(5):330-9.fulltext (PDF, 2231 KB)


Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerte-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C
"STRING v10: protein-protein interaction networks, integrated over the tree of life."
Nucl Acids Res, 43:D447-52.fulltext (PDF, 2311 KB)


2014

Schulz J, Zampieri M, Wanka S, von Mering C, Sauer U
"Large-scale exploration of the functional role of phosphorylation in coordinating yeast metabolism."
Science Signaling 7(353):rs6.fulltext (PDF, 833 KB)


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 WD, Helenius A, Kasper C, Kaufmann A, Kreibich S, Kühbacher A, Kunszt P, Low SH, Mercer J, Mudrak D, Muntwiler S, Pelkmans L, Pizarro-Cerdá J, Podvinec M, Pujadas E, Rinn B, Rouilly V, Schmich F, Siebourg-Polster J, Snijder B, Stebler M, Studer G, Szczurek E, Truttmann M, von Mering C, Vonderheit A, Yakimovich A, Bühlmann P, Dehio C
"Simultaneous analysis of large-scale RNAi screens for pathogen entry."
BMC Genomics 15(1):1162.fulltext (PDF, 1941 KB)


Schmidt TSB, Matias Rodrigues JF, von Mering C
"Limits to Robustness and Reproducibility in the Demarcation of Operational Taxonomic Units."
Environmental Microbiology, doi:10.1111/1462-2920.12610.fulltext (PDF, 3290 KB)


Trachana K, Forslund K, Larsson T, Powell S, Doerks T, von Mering C, Bork P
"A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation."
PLOS One 9(11):e111122, doi:10.1371/journal.pone.0111122.fulltext (PDF, 2155 KB)


Soste M, Hrabakova R, Wanka S, Melnik A, Boersema P, Maiolica A, Wernas T, Tognetti M, von Mering C, Picotti P
"A sentinel protein assay for simultaneously quantifying cellular processes."
Nature Methods 11(10):1045-8. doi:10.1038/nmeth.3101.fulltext (PDF, 512 KB)


Meier R, Franceschini A, Horvath P, Tetard M, Mancini R, von Mering C, Helenius A, Lozach PY
"Genome-wide siRNA screens reveal VAMP3 as a novel host factor required for Uukuniemi virus late penetration."
J Virol 88(15):8565-78. doi:10.1128/JVI.00388-14.fulltext (PDF, 2990 KB)


Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Mercier PL, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD
"Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support."
Nucleic Acids Res 42:W436-41. doi:10.1093/nar/gku380.fulltext (PDF, 366 KB)


Schmidt TSB, Matias Rodrigues JF, von Mering C
"Ecological Consistency of SSU rRNA-based Operational Taxonomic Units at a Global Scale."
PLOS Computational Biology 10(4):e1003594. doi:10.1371/journal.pcbi.1003594.fulltext (PDF, 1926 KB)


Franceschini A*, Meier R*, Casanova A*, Kreibich S*, Daga N, Andritschke D, Dilling S, Rämö P, Emmenlauer M, Kaufmann A, Conde-Alvarez R, Low SH, Pelkmans L, Helenius A*, Hardt WD, Dehio C, von Mering C*
"Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens."
PNAS 111(12):4548–4553. doi:10.1073/pnas.1402353111.fulltext (PDF, 1478 KB)


Warinner C, Matias Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-García DC, Eppler E, Seiler R, Hansen L, Castruita JAS, Barkow-Oesterreicher S, Teoh KY, Kelstrup C, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis CM, Collins MJ, Gilbert TP, Rühli F, Cappellini E
"Pathogens and host immunity in the ancient human oral cavity."
Nature Genetics 46(4):336-44. doi:10.1038/ng.2906.fulltext (PDF, 1692 KB)


Matias Rodrigues JF, von Mering C
"HPC-CLUST: Distributed hierarchical clustering for very large sets of nucleotide sequences."
Bioinformatics 30(2):287-8. doi:10.1093/bioinformatics/btt657.fulltext (PDF, 231 KB)


Cai H, Kumar N, Bagheri HC, von Mering C, Robinson MD, Baudis M
"Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens."
BMC Genomics 15(1):82. doi:10.1186/1471-2164-15-82.fulltext (PDF, 1762 KB)


2013

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldon T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C*, Bork P*
"eggNOG v4.0: nested orthology inference across 3686 organisms."
Nucl Acids Res 42(1):D231-9. doi:10.1093/nar/gkt1253.fulltext (PDF, 6966 KB)


Maier L, Vyas R, Cordova CD, Lindsay H, Schmidt TSB, Brugiroux S, Periaswamy B, Bauer R, Sturm A, Schreiber F, von Mering C, Robinson MD, Stecher B, Hardt WD
"Microbiota-derived Hydrogen Fuels Salmonella Typhimurium Invasion of the Gut Ecosystem."
Cell Host Microbe 14(6):641-51. doi:10.1016/j.chom.2013.11.002.fulltext (PDF, 1862 KB)


Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher T, von Mering C, Jensen JL, Bork P
"STITCH 4: integration of protein-chemical interactions with user data."
Nucl Acids Res 42(1):D401-7. doi:10.1093/nar/gkt1207.fulltext (PDF, 8832 KB)


Franceschini A*, Szklarczyk D*, Frankild S*, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P*, von Mering C*, Jensen JL*
"STRING v9.1: protein-protein interaction networks, with increased coverage and integration."
Nucl Acids Res 40(1):D808-15. doi:10.1093/nar/gks1094.fulltext (PDF, 3483 KB)


2012

Kumar N, Haoyang C, von Mering C*, Baudis M*
"Specific genomic regions are differentially affected by copy number alterations across distinct cancer types, in aggregated cytogenetic data."
PLoS One 7(8):e43689.fulltext (PDF, 664 KB)


Wang M, Weiss M, Simonovic M, Haertinger G, Schrimpf SP, Hengartner MO, von Mering C
"PaxDb, a database of protein abundance averages across all three domains of life."
Mol Cell Proteomics 11(8):492-500.fulltext (PDF, 607 KB)


Juhas M, Stark M, von Mering C, Lumjiaktase P, Crook DW, Valvano MA, Eberl L
"High Confidence Prediction of Essential Genes in Burkholderia Cenocepacia."
PLoS One 7(6):e40064.fulltext (PDF, 553 KB)


Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ*, von Mering C*, Bork P*
"eggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges."
Nucl Acids Res 40:D284-D289.fulltext (PDF, 5223 KB)


Atamna-Ismaeel N, Finkel O, Glaser F, von Mering C, Vorholt JA, Koblizek M, Belkin S, Beja O
"Bacterial anoxygenic photosynthesis on plant leaf surfaces."
Env Microbiol Rep 4(2):1-8. doi:10.1111/j.1758-2229.2011.00323.x.fulltext (PDF, 489 KB)


Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P
"STITCH 3: Zooming in on protein-chemical interactions."
Nucl Acids Res 40:D876-80.fulltext (PDF, 3347 KB)


Schrimpf SP, von Mering C, Bendixen E, Heazlewood JL, Bumann D, Omenn G, Hengartner MO
"The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland."
Proteomics 12(3):346-50. doi:10.1002/pmic.201290015.fulltext (PDF, 161 KB)


Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, van Wijk K, von Mering C, Weiss M, Zheng X
"The HUPO initiative on Model Organism Proteomes, iMOP."
Proteomics 12(3):340-5. doi:10.1002/pmic.201290014.fulltext (PDF, 430 KB)


2011

Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, von Mering C, Vorholt JA
"Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice."
ISME J 6(7):1378-90. doi:10.1038/ismej.2011.192.fulltext (PDF, 677 KB)


Takeuchi Y, Salcher MM, Ushio M, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, von Mering C, Pernthaler J, Shimizu KK
"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.fulltext (PDF, 317 KB)


Atamna-Ismaeel N, Finkel OM, Glaser F, Sharon I, Schneider R, Post AF, Spudich JL, von Mering C, Vorholt JA, Iluz D, Beja O, Belkin S
"Microbial rhodopsins on leaf surfaces of terrestial plants."
Environ Microbiol 14(1):140-6, doi:10.1111/j.1462-2920.2011.02554.x.fulltext (PDF, 539 KB)


Schilling S, Willecke M, Aegerter-Wilmsen T, Cirpka OA, Basler K, von Mering C
"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.fulltext (PDF, 1067 KB)


Misselwitz B*, Dilling S*, Vonaesch P*, Sacher R, Snijder B, Schlumberger M, Rout S, Stark M, von Mering C, Pelkmans L, Hardt WD
"RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42."
Mol Syst Biol 7:474.fulltext (PDF, 2592 KB)


Szklarczyk D*, Franceschini A*, Kuhn M*, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P*, Jensen LJ*, von Mering C*
"The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored."
Nucl Acids Res 39:D561-8.fulltext (PDF, 8676 KB)


2010

Bodenmiller B*, Wanka S*, Kraft C, Urban J, Campbell D, Pedrioli P, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat K, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R
"Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast."
Science Signalling 21;3(153):rs4.fulltext (PDF, 901 KB)


Stark M, Berger SA, Stamatakis A, von Mering C
"MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies."
BMC Genomics 11:461.fulltext (PDF, 3746 KB)


Endt K, Stecher B, Chaffron S, Slack E, Tchitchek N, Benecke A, Van Maele L, Sirard JC, Mueller AJ, Heikenwalder M, Macpherson AJ, Strugnell R, von Mering C, Hardt WD
"The Microbiota Mediates Pathogen Clearance from the Gut Lumen after Non-Typhoidal Salmonella Diarrhea."
PLoS Pathogens 6(9): pii e1001097.fulltext (PDF, 5580 KB)


Wuest SE, Vijverberg K, Schmidt A, Weiss M, Gheyselinck J, Lohr M, Wellmer F, Rahnenführer J, von Mering C, Grossniklaus U
"Arabidopsis Female Gametophyte Gene Expression Map Reveals Similarities between Plant and Animal Gametes."
Current Biology 20(6):506-512.fulltext (PDF, 1509 KB)


Chaffron S, Rehrauer H, Pernthaler J, von Mering C
"A global network of coexisting microbes from environmental and whole-genome sequence data."
Genome Res. 20(7): 947-959.fulltext (PDF, 2266 KB)


Weiss M, Schrimpf S, Hengartner M, Lercher M and von Mering C
"Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome."
Proteomics 10(6):1297-1306.fulltext (PDF, 458 KB)


Stecher B*, Chaffron S*, Käppeli R, Hapfelmeier S, Freedrich S, Weber TC, Kirundi J, Suar M, McCoy K, von Mering C, Macpherson AJ and Hardt WD
"Like will to like: Abundances of closely related species as predictive values for the susceptibility to intestinal colonization by pathogenic and commensal bacteria."
PLoS Pathogens 6(1):e1000711.fulltext (PDF, 2528 KB)


Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ and Bork P
"eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced Non-supervised Orthologous Groups, species and functional annotations."
Nucleic Acids Res. 38(1): D190-5.fulltext (PDF, 1607 KB)


Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A and Bork P
"STITCH2: an interaction network database for small molecules and proteins."
Nucleic Acids Res. 38(1): D552-6.fulltext (PDF, 4260 KB)


2009

Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C and Vorholt JA
"Community proteogenomics reveals new insights into the physiology of phyllosphere bacteria."
Proc Natl Acad Sci U S A 106(38):16428-33.fulltext (PDF, 863 KB)


Hausmann G, von Mering C* and Basler K*
"The hedgehog signaling pathway: where did it come from?"
PLoS Biology 7(6):e1000146.fulltext (PDF, 527 KB)


Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmstrom J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE, Aebersold R, von Mering C* and Hengartner MO*
"Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes."
PLoS Biology 7(3):e48.fulltext (PDF, 648 KB)


Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P and von Mering C
"STRING 8 - a global view on proteins and their functional interactions in 630 organisms."
Nucleic Acids Res. 37(1): D412-6.fulltext (PDF, 3673 KB)


2008

Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P and Hugenholtz P
"Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat."
Mol Syst Biol. 4: 198.fulltext (PDF, 341 KB)


Kuhn M, von Mering C, Campillos M, Jensen LJ and Bork P
"STITCH: interaction networks of chemicals and proteins."
Nucleic Acids Res. 36(1): D684-8.fulltext (PDF, 1173 KB)


Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P
"eggNOG: automated construction and annotation of orthologous groups of genes."
Nucleic Acids Res. 36(1): D250-4.fulltext (PDF, 2640 KB)


von Mering C
"Protein-Protein Interaction Networks: Assembly and Analysis."
IN: Bioinformatics - A Swiss Perspective (Editors: Ron Appel and Ernest Feytmans, Swiss Institute of Bioinformatics, Lausanne). Amazon


2007

Chaffron S, von Mering C
"Termites in the woodwork."
Genome Biol. 8(11): 229.fulltext (PDF, 182 KB)


Stecher B, Robbiani R, Walker AW, Westendorf AM, Barthel M, Kremer M, Chaffron S, Macpherson AJ, Buer J, Parkhill J, Dougan G, von Mering C, Hardt WD
"Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota."
PLoS Biol. 5(10): e244.fulltext (PDF, 1310 KB)


Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P
"Quantitative assessment of protein function prediction from metagenomics shotgun sequences."
Proc Natl Acad Sci U S A. 104(35): 13913-8.fulltext (PDF, 352 KB)


Boettner M, Steffens C, von Mering C, Bork P, Stahl U, Lang C
"Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia postoris - a comparative view on 79 human genes."
J Biotechnol. 130(1): 1-10.fulltext (PDF, 386 KB)


Raes J, Korbel JO, Lercher MJ, von Mering C and Bork P
"Prediction of effective genome size in metagenomic samples."
Genome Biol. 8(1): R10.fulltext (PDF, 622 KB)


von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N and Bork P
"Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments."
Science 315(5815): 1126-1130.fulltext (PDF, 1221 KB)


von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B and Bork P
"STRING 7 -- recent developments in the integration and prediction of protein interactions."
Nucleic Acids Res. 35(1): D358-62.fulltext (PDF, 2465 KB)


von Mering C
"Inferring protein function from genomic context"
IN: Bioinformatics - From Genomes to Therapies (Editor: Thomas Lengauer, MPI for Informatics, Saarbruecken). Amazon


2006

Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM
"Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle."
PLoS Genet. 2(10): 1-13.fulltext (PDF, 1398 KB)


Foerstner KU, von Mering C and Bork P
"Comparative analysis of environmental sequences: potential and challenges."
Philos Trans R Soc Lond B Biol Sci 361(1467): 519-523.fulltext (PDF, 212 KB)


Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B and Bork P
"Toward automatic reconstruction of a highly resolved tree of life."
Science 311(5765): 1283-1287.fulltext (PDF, 470 KB)


Campillos M, von Mering C, Jensen LJ and Bork P
"Identification and analysis of evolutionarily cohesive functional modules in protein networks."
Genome Res 16(3): 374-382.fulltext (PDF, 761 KB)


2005

Zdobnov EM, von Mering C, Letunic I and Bork P
"Consistency of genome-based methods in measuring Metazoan evolution."
FEBS Lett 579(15): 3355-3361.fulltext (PDF, 300 KB)


von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA and Bork P
"STRING: known and predicted protein-protein associations, integrated and transferred across organisms."
Nucleic Acids Res 33: D433-437.fulltext (PDF, 489 KB)


Tringe SG*, von Mering C*, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P and Rubin EM
"Comparative metagenomics of microbial communities."
Science 308(5721): 554-557.fulltext (PDF, 345 KB)


Foerstner KU, von Mering C, Hooper SD and Bork P
"Environments shape the nucleotide composition of genomes."
EMBO Rep 6(12): 1208-1213.fulltext (PDF, 187 KB)


Ciccarelli FD, von Mering C, Suyama M, Harrington ED, Izaurralde E and Bork P
"Complex genomic rearrangements lead to novel primate gene function."
Genome Res 15(3): 343-351.fulltext (PDF, 439 KB)


2004

Krause R, von Mering C, Bork P and Dandekar T
"Shared components of protein complexes--versatile building blocks or biochemical artefacts?"
Bioessays 26(12): 1333-1343.fulltext (PDF, 293 KB)


Korbel JO, Jensen LJ, von Mering C and Bork P
"Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs."
Nat Biotechnol 22(7): 911-917.fulltext (PDF, 1429 KB)


Jensen LJ, Lagarde J, von Mering C and Bork P
"ArrayProspector: a web resource of functional associations inferred from microarray expression data."
Nucleic Acids Res 32(Web Server issue): W445-448.fulltext (PDF, 344 KB)


Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MA, Delany ME, Dodgson JB, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang SP, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RP, Aerts J, van der Poel JJ, Ellegren H, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MD, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WR, Rogers J, Buerstedde JM, Wilson SA, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Wong GK, Wang J, Liu B, Wang J, Yu J, Yang H, Nefedov M, Koriabine M, Dejong PJ, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He J, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SM, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao Z, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandstrom M, Axelsson E, Backstrom N, Berlin S, Webster MT, Pourquie O, Reymond A, Ucla C, Antonarakis SE, Long M, Emerson JJ, Betran E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, Kent WJ, Haussler D, Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, Fulton LA, Mardis ER and Wilson RK
"Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution."
Nature 432(7018): 695-716.fulltext (PDF, 1406 KB)


Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C and Apweiler R
"The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data."
Nat Biotechnol 22(2): 177-183.fulltext (PDF, 1517 KB)


Doerks T, von Mering C and Bork P
"Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes."
Nucleic Acids Res 32(21): 6321-6326.fulltext (PDF, 396 KB)


Doerks T, Andrade MA, Lathe W, 3rd, von Mering C and Bork P
"Global analysis of bacterial transcription factors to predict cellular target processes."
Trends Genet 20(3): 126-131.fulltext (PDF, 107 KB)


Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling C, Ernst P, Gailus-Durner V, Glatting KH, Gohla R, Gossling F, Grote K, Heidtke K, Herrmann A, O'Keeffe S, Kiesslich O, Kolibal S, Korbel JO, Lengauer T, Liebich I, van der Linden M, Luz H, Meissner K, von Mering C, Mevissen HT, Mewes HW, Michael H, Mokrejs M, Muller T, Pospisil H, Rarey M, Reich JG, Schneider R, Schomburg D, Schulze-Kremer S, Schwarzer K, Sommer I, Springstubbe S, Suhai S, Thoppae G, Vingron M, Warfsmann J, Werner T, Wetzler D, Wingender E and Zimmer R
"The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources."
Bioinformatics 20(2): 268-270.fulltext (PDF, 45 KB)


Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I and Marcotte EM
"Protein interaction networks from yeast to human."
Curr Opin Struct Biol 14(3): 292-299.fulltext (PDF, 154 KB)


2003

von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA and Bork P
"Genome evolution reveals biochemical networks and functional modules."
Proc Natl Acad Sci U S A 100(26): 15428-15433.fulltext (PDF, 580 KB)


von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P and Snel B
"STRING: a database of predicted functional associations between proteins."
Nucleic Acids Res 31(1): 258-261.fulltext (PDF, 555 KB)


Krause R, von Mering C and Bork P
"A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens."
Bioinformatics 19(15): 1901-1908.fulltext (PDF, 265 KB)


Huynen MA, Snel B, von Mering C and Bork P
"Function prediction and protein networks."
Curr Opin Cell Biol 15(2): 191-198.fulltext (PDF, 157 KB)


2002

Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC and Bork P
"Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster."
Science 298(5591): 149-159.fulltext (PDF, 387 KB)


von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S and Bork P
"Comparative assessment of large-scale data sets of protein-protein interactions."
Nature 417(6887): 399-403.fulltext (PDF, 163 KB)


von Mering C and Bork P
"Teamed up for transcription."
Nature 417(6891): 797-798.fulltext (PDF, 149 KB)


Christophides GK, Zdobnov E, Barillas-Mury C, Birney E, Blandin S, Blass C, Brey PT, Collins FH, Danielli A, Dimopoulos G, Hetru C, Hoa NT, Hoffmann JA, Kanzok SM, Letunic I, Levashina EA, Loukeris TG, Lycett G, Meister S, Michel K, Moita LF, Muller HM, Osta MA, Paskewitz SM, Reichhart JM, Rzhetsky A, Troxler L, Vernick KD, Vlachou D, Volz J, von Mering C, Xu J, Zheng L, Bork P and Kafatos FC
"Immunity-related genes and gene families in Anopheles gambiae."
Science 298(5591): 159-165.fulltext (PDF, 475 KB)


2001 and earlier

Flechsig E, Shmerling D, Hegyi I, Raeber AJ, Fischer M, Cozzio A, von Mering C, Aguzzi A and Weissmann C
"Prion protein devoid of the octapeptide repeat region restores susceptibility to scrapie in PrP knockout mice."
Neuron 27(2): 399-408.fulltext (PDF, 617 KB)


von Mering C and Basler K
"Distinct and regulated activities of human Gli proteins in Drosophila."
Curr Biol 9(22): 1319-1322.fulltext (PDF, 117 KB)


Shmerling D, Hegyi I, Fischer M, Blattler T, Brandner S, Gotz J, Rulicke T, Flechsig E, Cozzio A, von Mering C, Hangartner C, Aguzzi A and Weissmann C
"Expression of amino-terminally truncated PrP in the mouse leading to ataxia and specific cerebellar lesions."
Cell 93(2): 203-214.fulltext (PDF, 934 KB)