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Results: 1 to 20 of 467

1.

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains.

Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC.

Cell Rep. 2015 Sep 1;12(9):1519-30. doi: 10.1016/j.celrep.2015.07.054. Epub 2015 Aug 20.

2.

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T; Quest for Orthologs Species Tree Working Group.

Genome Biol Evol. 2015 Jul 1;7(7):1988-99. doi: 10.1093/gbe/evv121.

3.

Ocean plankton. Determinants of community structure in the global plankton interactome.

Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J.

Science. 2015 May 22;348(6237):1262073. doi: 10.1126/science.1262073.

PMID:
25999517
4.

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean.

de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horák A, Jaillon O, Lima-Mendez G, Lukeš J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans Coordinators, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E.

Science. 2015 May 22;348(6237):1261605. doi: 10.1126/science.1261605.

PMID:
25999516
5.

Ocean plankton. Patterns and ecological drivers of ocean viral communities.

Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB.

Science. 2015 May 22;348(6237):1261498. doi: 10.1126/science.1261498.

PMID:
25999515
6.

Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport.

Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans Coordinators, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D.

Science. 2015 May 22;348(6237):1261447. doi: 10.1126/science.1261447.

PMID:
25999514
7.

Ocean plankton. Structure and function of the global ocean microbiome.

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P.

Science. 2015 May 22;348(6237):1261359. doi: 10.1126/science.1261359.

PMID:
25999513
8.

Tara Oceans. Tara Oceans studies plankton at planetary scale. Introduction.

Bork P, Bowler C, de Vargas C, Gorsky G, Karsenti E, Wincker P.

Science. 2015 May 22;348(6237):873. doi: 10.1126/science.aac5605. Epub 2015 May 21. No abstract available.

PMID:
25999501
9.

Computational eco-systems biology in Tara Oceans: translating data into knowledge.

Sunagawa S, Karsenti E, Bowler C, Bork P.

Mol Syst Biol. 2015 May 21;11(5):809. doi: 10.15252/msb.20156272. No abstract available.

10.

Metabolic dependencies drive species co-occurrence in diverse microbial communities.

Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR.

Proc Natl Acad Sci U S A. 2015 May 19;112(20):6449-54. doi: 10.1073/pnas.1421834112. Epub 2015 May 4.

11.

Inter-individual differences in the gene content of human gut bacterial species.

Zhu A, Sunagawa S, Mende DR, Bork P.

Genome Biol. 2015 Apr 21;16:82. doi: 10.1186/s13059-015-0646-9.

12.

Temporal and technical variability of human gut metagenomes.

Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P.

Genome Biol. 2015 Apr 8;16:73. doi: 10.1186/s13059-015-0639-8.

13.

Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs).

Mackmull MT, Iskar M, Parca L, Singer S, Bork P, Ori A, Beck M.

Mol Cell Proteomics. 2015 May;14(5):1350-60. doi: 10.1074/mcp.M114.042499. Epub 2015 Mar 9.

14.

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.

Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, Gavin AC, Bork P, Serrano L.

Mol Syst Biol. 2015 Jan 21;11(1):780. doi: 10.15252/msb.20145558.

15.

Potential of fecal microbiota for early-stage detection of colorectal cancer.

Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P.

Mol Syst Biol. 2014 Nov 28;10:766. doi: 10.15252/msb.20145645.

16.

The InterPro protein families database: the classification resource after 15 years.

Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D213-21. doi: 10.1093/nar/gku1243. Epub 2014 Nov 26.

17.

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P.

Nucleic Acids Res. 2014 Dec 16;42(22):13525-33. doi: 10.1093/nar/gku1147. Epub 2014 Nov 14.

18.

Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.

Betts MJ, Lu Q, Jiang Y, Drusko A, Wichmann O, Utz M, Valtierra-Gutiérrez IA, Schlesner M, Jaeger N, Jones DT, Pfister S, Lichter P, Eils R, Siebert R, Bork P, Apic G, Gavin AC, Russell RB.

Nucleic Acids Res. 2015 Jan;43(2):e10. doi: 10.1093/nar/gku1094. Epub 2014 Nov 11.

19.

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.

20.

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P.

Nucleic Acids Res. 2015 Jan;43(Database issue):D494-502. doi: 10.1093/nar/gku1081. Epub 2014 Oct 31.

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