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Items: 1 to 20 of 106

1.

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.

2.

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.

PMID:
30215772
3.

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
4.

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;:.

PMID:
29472638
5.

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.

6.

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.

7.

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
8.

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.

9.

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.

10.

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
11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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