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Items: 1 to 20 of 37

1.

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.

Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR.

Nat Microbiol. 2018 Apr;3(4):514-522. doi: 10.1038/s41564-018-0123-9. Epub 2018 Mar 19.

PMID:
29556107
2.

Extensive impact of non-antibiotic drugs on human gut bacteria.

Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A.

Nature. 2018 Mar 29;555(7698):623-628. doi: 10.1038/nature25979. Epub 2018 Mar 19.

PMID:
29555994
3.

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.

4.

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.

5.

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.

6.

The SIDER database of drugs and side effects.

Kuhn M, Letunic I, Jensen LJ, Bork P.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1075-9. doi: 10.1093/nar/gkv1075. Epub 2015 Oct 19.

7.

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.

8.

Coiled-coil proteins facilitated the functional expansion of the centrosome.

Kuhn M, Hyman AA, Beyer A.

PLoS Comput Biol. 2014 Jun 5;10(6):e1003657. doi: 10.1371/journal.pcbi.1003657. eCollection 2014 Jun.

9.

Development of a Kinetic Assay for Late Endosome Movement.

Esner M, Meyenhofer F, Kuhn M, Thomas M, Kalaidzidis Y, Bickle M.

J Biomol Screen. 2014 Aug;19(7):1070-8. doi: 10.1177/1087057114524278. Epub 2014 Feb 20.

PMID:
24556389
10.

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.

11.

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.

12.

Systematic identification of proteins that elicit drug side effects.

Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P.

Mol Syst Biol. 2013;9:663. doi: 10.1038/msb.2013.10.

13.

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.

Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P.

Mol Syst Biol. 2013;9:662. doi: 10.1038/msb.2013.20.

14.

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.

15.

Prediction of drug combinations by integrating molecular and pharmacological data.

Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P.

PLoS Comput Biol. 2011 Dec;7(12):e1002323. doi: 10.1371/journal.pcbi.1002323. Epub 2011 Dec 29.

16.

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.

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.

Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. doi: 10.1093/nar/gkr1060. Epub 2011 Nov 16.

17.

STITCH 3: zooming in on protein-chemical interactions.

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

Nucleic Acids Res. 2012 Jan;40(Database issue):D876-80. doi: 10.1093/nar/gkr1011. Epub 2011 Nov 9.

18.

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.

Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, Kaksonen M, Russell RB, Gavin AC.

Mol Syst Biol. 2010 Nov 30;6:430. doi: 10.1038/msb.2010.87.

19.

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.

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.

Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8. doi: 10.1093/nar/gkq973. Epub 2010 Nov 2.

20.

Drug-induced regulation of target expression.

Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P.

PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000925. doi: 10.1371/journal.pcbi.1000925.

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