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Results: 1 to 20 of 82

1.

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(1):1162. [Epub ahead of print]

PMID:
25534632
[PubMed - as supplied by publisher]
Free Article
2.

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
[PubMed - in process]
3.

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.

PMID:
25369365
[PubMed - in process]
Free PMC Article
4.

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

PMID:
25352553
[PubMed - in process]
Free Article
5.

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
[PubMed - indexed for MEDLINE]
6.

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

Schmidt TS, Matias Rodrigues JF, von Mering C.

Environ Microbiol. 2014 Aug 26. doi: 10.1111/1462-2920.12610. [Epub ahead of print]

PMID:
25156547
[PubMed - as supplied by publisher]
7.

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.

PMID:
24850728
[PubMed - indexed for MEDLINE]
Free Article
8.

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.

PMID:
24792157
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
24763141
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
24616511
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
24562188
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
24476156
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
24331462
[PubMed - indexed for MEDLINE]
Free Article
14.

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.

PMID:
24297252
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
24293645
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
24215029
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
23203871
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
22937079
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
22768221
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
22535208
[PubMed - indexed for MEDLINE]
Free PMC Article

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