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Items: 1 to 50 of 112

1.

Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data.

Tackmann J, Matias Rodrigues JF, von Mering C.

Cell Syst. 2019 Sep 25;9(3):286-296.e8. doi: 10.1016/j.cels.2019.08.002. Epub 2019 Sep 18.

2.

Protein tyrosine phosphatase non-receptor type 22 modulates colitis in a microbiota-dependent manner.

Spalinger MR, Schmidt TS, Schwarzfischer M, Hering L, Atrott K, Lang S, Gottier C, Geirnaert A, Lacroix C, Dai X, Rawlings DJ, Chan AC, von Mering C, Rogler G, Scharl M.

J Clin Invest. 2019 May 20;129(6):2527-2541. doi: 10.1172/JCI123263. eCollection 2019 May 20.

3.

Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.

Lun XK, Szklarczyk D, Gábor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B.

Mol Cell. 2019 Jun 6;74(5):1086-1102.e5. doi: 10.1016/j.molcel.2019.04.021. Epub 2019 May 14.

4.

Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition.

Modic M, Grosch M, Rot G, Schirge S, Lepko T, Yamazaki T, Lee FCY, Rusha E, Shaposhnikov D, Palo M, Merl-Pham J, Cacchiarelli D, Rogelj B, Hauck SM, von Mering C, Meissner A, Lickert H, Hirose T, Ule J, Drukker M.

Mol Cell. 2019 Jun 6;74(5):951-965.e13. doi: 10.1016/j.molcel.2019.03.041. Epub 2019 Apr 29.

5.

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.

Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314. doi: 10.1093/nar/gky1085.

6.

Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites.

Tackmann J, Arora N, Schmidt TSB, Rodrigues JFM, von Mering C.

Microbiome. 2018 Oct 24;6(1):192. doi: 10.1186/s40168-018-0565-6.

7.

Viruses.STRING: A Virus-Host Protein-Protein Interaction Database.

Cook HV, Doncheva NT, Szklarczyk D, von Mering C, Jensen LJ.

Viruses. 2018 Sep 23;10(10). pii: E519. doi: 10.3390/v10100519.

8.

Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition.

Daga N, Eicher S, Kannan A, Casanova A, Low SH, Kreibich S, Andritschke D, Emmenlauer M, Jenkins JL, Hardt WD, Greber UF, Dehio C, von Mering C.

Nucleic Acids Res. 2018 Oct 12;46(18):9309-9320. doi: 10.1093/nar/gky798.

9.

Unexplored therapeutic opportunities in the human genome.

Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G.

Nat Rev Drug Discov. 2018 May;17(5):377. doi: 10.1038/nrd.2018.52. Epub 2018 Mar 23.

PMID:
29567993
10.

Unexplored therapeutic opportunities in the human genome.

Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G.

Nat Rev Drug Discov. 2018 May;17(5):317-332. doi: 10.1038/nrd.2018.14. Epub 2018 Mar 23. Review. Erratum in: Nat Rev Drug Discov. 2018 Mar 23;:.

11.

Preventive Trichuris suis ova (TSO) treatment protects immunocompetent rabbits from DSS colitis but may be detrimental under conditions of immunosuppression.

Leonardi I, Gerstgrasser A, Schmidt TSB, Nicholls F, Tewes B, Greinwald R, von Mering C, Rogler G, Frey-Wagner I.

Sci Rep. 2017 Nov 28;7(1):16500. doi: 10.1038/s41598-017-16287-4.

12.

MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis.

Matias Rodrigues JF, Schmidt TSB, Tackmann J, von Mering C.

Bioinformatics. 2017 Dec 1;33(23):3808-3810. doi: 10.1093/bioinformatics/btx517.

13.

Effects of oral antibiotics and isotretinoin on the murine gut microbiota.

Becker E, Schmidt TSB, Bengs S, Poveda L, Opitz L, Atrott K, Stanzel C, Biedermann L, Rehman A, Jonas D, von Mering C, Rogler G, Frey-Wagner I.

Int J Antimicrob Agents. 2017 Sep;50(3):342-351. doi: 10.1016/j.ijantimicag.2017.03.017. Epub 2017 Jul 6.

PMID:
28689869
14.

High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43.

Rot G, Wang Z, Huppertz I, Modic M, Lenče T, Hallegger M, Haberman N, Curk T, von Mering C, Ule J.

Cell Rep. 2017 May 2;19(5):1056-1067. doi: 10.1016/j.celrep.2017.04.028.

15.

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.

Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P.

Mol Biol Evol. 2017 Aug 1;34(8):2115-2122. doi: 10.1093/molbev/msx148.

16.

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability.

Leuenberger P, Ganscha S, Kahraman A, Cappelletti V, Boersema PJ, von Mering C, Claassen M, Picotti P.

Science. 2017 Feb 24;355(6327). pii: eaai7825. doi: 10.1126/science.aai7825.

PMID:
28232526
17.

Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details.

Feigelman R, Kahlert CR, Baty F, Rassouli F, Kleiner RL, Kohler P, Brutsche MH, von Mering C.

Microbiome. 2017 Feb 10;5(1):20. doi: 10.1186/s40168-017-0234-1.

18.

RAIN: RNA-protein Association and Interaction Networks.

Junge A, Refsgaard JC, Garde C, Pan X, Santos A, Alkan F, Anthon C, von Mering C, Workman CT, Jensen LJ, Gorodkin J.

Database (Oxford). 2017 Jan 10;2017. doi: 10.1093/database/baw167. Print 2017. Erratum in: Database (Oxford). 2017 Jan 1;2017(1):.

19.

A family of interaction-adjusted indices of community similarity.

Schmidt TS, Matias Rodrigues JF, von Mering C.

ISME J. 2017 Mar;11(3):791-807. doi: 10.1038/ismej.2016.139. Epub 2016 Dec 9.

20.

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C.

Nucleic Acids Res. 2017 Jan 4;45(D1):D362-D368. doi: 10.1093/nar/gkw937. Epub 2016 Oct 18.

21.

IFN-γ Hinders Recovery from Mucosal Inflammation during Antibiotic Therapy for Salmonella Gut Infection.

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.

Cell Host Microbe. 2016 Aug 10;20(2):238-49. doi: 10.1016/j.chom.2016.06.008. Epub 2016 Jul 21.

22.

Standardized benchmarking in the quest for orthologs.

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; Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.

Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4.

23.

Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans.

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.

Mol Cell Proteomics. 2016 May;15(5):1670-80. doi: 10.1074/mcp.M115.052548. Epub 2016 Mar 4.

24.

SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.

Franceschini A, Lin J, von Mering C, Jensen LJ.

Bioinformatics. 2016 Apr 1;32(7):1085-7. doi: 10.1093/bioinformatics/btv696. Epub 2015 Nov 26.

25.

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.

Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M.

Nucleic Acids Res. 2016 Jan 4;44(D1):D380-4. doi: 10.1093/nar/gkv1277. Epub 2015 Nov 20.

26.

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

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.

Nucleic Acids Res. 2016 Jan 4;44(D1):D286-93. doi: 10.1093/nar/gkv1248. Epub 2015 Nov 17.

27.

Erratum to: gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens.

Schmich F, Szczurek E, Kreibich S, Dilling S, Andritschke D, Casanova A, Low SH, Eicher S, Muntwiler S, Emmenlauer M, Rämo P, Conde-Alvarez R, von Mering C, Hardt WD, Dehio C, Beerenwinkel N.

Genome Biol. 2015 Oct 21;16:233. doi: 10.1186/s13059-015-0807-x. No abstract available.

28.

gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens.

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.

Genome Biol. 2015 Oct 7;16:220. doi: 10.1186/s13059-015-0783-1. Erratum in: Genome Biol. 2015;16:233.

29.

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes.

Takeuchi Y, Chaffron S, Salcher MM, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, von Mering C, Pernthaler J, Shimizu KK.

Syst Appl Microbiol. 2015 Jul;38(5):330-9. doi: 10.1016/j.syapm.2015.05.006. Epub 2015 Jun 16.

30.

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

Wang M, Herrmann CJ, Simonovic M, Szklarczyk D, von Mering C.

Proteomics. 2015 Sep;15(18):3163-8. doi: 10.1002/pmic.201400441. Epub 2015 Mar 12.

31.

Simultaneous analysis of large-scale RNAi screens for pathogen entry.

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.

BMC Genomics. 2014 Dec 22;15:1162. doi: 10.1186/1471-2164-15-1162.

32.

Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways.

Schulz JC, Zampieri M, Wanka S, von Mering C, Sauer U.

Sci Signal. 2014 Nov 25;7(353):rs6. doi: 10.1126/scisignal.2005602.

PMID:
25429078
33.

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.

Trachana K, Forslund K, Larsson T, Powell S, Doerks T, von Mering C, Bork P.

PLoS One. 2014 Nov 4;9(11):e111122. doi: 10.1371/journal.pone.0111122. eCollection 2014.

34.

STRING v10: protein-protein interaction networks, integrated over the tree of life.

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52. doi: 10.1093/nar/gku1003. Epub 2014 Oct 28.

35.

A sentinel protein assay for simultaneously quantifying cellular processes.

Soste M, Hrabakova R, Wanka S, Melnik A, Boersema P, Maiolica A, Wernas T, Tognetti M, von Mering C, Picotti P.

Nat Methods. 2014 Oct;11(10):1045-8. doi: 10.1038/nmeth.3101. Epub 2014 Sep 7.

PMID:
25194849
36.

Limits to robustness and reproducibility in the demarcation of operational taxonomic units.

Schmidt TS, Matias Rodrigues JF, von Mering C.

Environ Microbiol. 2015 May;17(5):1689-706. doi: 10.1111/1462-2920.12610. Epub 2014 Sep 29.

PMID:
25156547
37.

Genome-wide small interfering RNA screens reveal VAMP3 as a novel host factor required for Uukuniemi virus late penetration.

Meier R, Franceschini A, Horvath P, Tetard M, Mancini R, von Mering C, Helenius A, Lozach PY.

J Virol. 2014 Aug;88(15):8565-78. doi: 10.1128/JVI.00388-14. Epub 2014 May 21.

38.

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, 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.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub 2014 May 3.

39.

Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale.

Schmidt TS, Matias Rodrigues JF, von Mering C.

PLoS Comput Biol. 2014 Apr 24;10(4):e1003594. doi: 10.1371/journal.pcbi.1003594. eCollection 2014 Apr.

40.

Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens.

Franceschini A, Meier R, Casanova A, Kreibich S, Daga N, Andritschke D, Dilling S, Rämö P, Emmenlauer M, Kaufmann A, Conde-Álvarez R, Low SH, Pelkmans L, Helenius A, Hardt WD, Dehio C, von Mering C.

Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4548-53. doi: 10.1073/pnas.1402353111. Epub 2014 Mar 10.

41.

Pathogens and host immunity in the ancient human oral cavity.

Warinner C, 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 LH, Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup CD, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis CM Jr, Collins MJ, Gilbert MT, Rühli F, Cappellini E.

Nat Genet. 2014 Apr;46(4):336-44. doi: 10.1038/ng.2906. Epub 2014 Feb 23.

42.

Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens.

Cai H, Kumar N, Bagheri HC, von Mering C, Robinson MD, Baudis M.

BMC Genomics. 2014 Jan 29;15:82. doi: 10.1186/1471-2164-15-82.

43.

Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem.

Maier L, Vyas R, Cordova CD, Lindsay H, Schmidt TS, Brugiroux S, Periaswamy B, Bauer R, Sturm A, Schreiber F, von Mering C, Robinson MD, Stecher B, Hardt WD.

Cell Host Microbe. 2013 Dec 11;14(6):641-51. doi: 10.1016/j.chom.2013.11.002.

44.

eggNOG v4.0: nested orthology inference across 3686 organisms.

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9. doi: 10.1093/nar/gkt1253. Epub 2013 Dec 1.

45.

STITCH 4: integration of protein-chemical interactions with user data.

Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7. doi: 10.1093/nar/gkt1207. Epub 2013 Nov 28.

46.

HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences.

Matias Rodrigues JF, von Mering C.

Bioinformatics. 2014 Jan 15;30(2):287-8. doi: 10.1093/bioinformatics/btt657. Epub 2013 Nov 9.

47.

STRING v9.1: protein-protein interaction networks, with increased coverage and integration.

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ.

Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15. doi: 10.1093/nar/gks1094. Epub 2012 Nov 29.

48.

Specific genomic regions are differentially affected by copy number alterations across distinct cancer types, in aggregated cytogenetic data.

Kumar N, Cai H, von Mering C, Baudis M.

PLoS One. 2012;7(8):e43689. doi: 10.1371/journal.pone.0043689. Epub 2012 Aug 24.

49.

High confidence prediction of essential genes in Burkholderia cenocepacia.

Juhas M, Stark M, von Mering C, Lumjiaktase P, Crook DW, Valvano MA, Eberl L.

PLoS One. 2012;7(6):e40064. doi: 10.1371/journal.pone.0040064. Epub 2012 Jun 29.

50.

PaxDb, a database of protein abundance averages across all three domains of life.

Wang M, Weiss M, Simonovic M, Haertinger G, Schrimpf SP, Hengartner MO, von Mering C.

Mol Cell Proteomics. 2012 Aug;11(8):492-500. doi: 10.1074/mcp.O111.014704. Epub 2012 Apr 24.

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