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Items: 1 to 20 of 497

1.

Human gut microbes impact host serum metabolome and insulin sensitivity.

Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K; MetaHIT Consortium, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O.

Nature. 2016 Jul 21;535(7612):376-81.

PMID:
27409811
2.

CART-a chemical annotation retrieval toolkit.

Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P.

Bioinformatics. 2016 Jun 2. pii: btw233. [Epub ahead of print]

3.

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.

Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R.

PLoS One. 2016 May 12;11(5):e0155362. doi: 10.1371/journal.pone.0155362. eCollection 2016.

4.

MOCAT2: a metagenomic assembly, annotation and profiling framework.

Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P.

Bioinformatics. 2016 Apr 8. pii: btw183. [Epub ahead of print]

5.

A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.

Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin AC.

Nat Protoc. 2016 Jun;11(6):1021-38. doi: 10.1038/nprot.2016.059. Epub 2016 May 5.

PMID:
27149326
6.

Global genetic capacity for mixotrophy in marine picocyanobacteria.

Yelton AP, Acinas SG, Sunagawa S, Bork P, Pedrós-Alió C, Chisholm SW.

ISME J. 2016 May 3. doi: 10.1038/ismej.2016.64. [Epub ahead of print]

PMID:
27137127
7.

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.

Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M.

Cell Syst. 2015 Sep 23;1(3):224-37. doi: 10.1016/j.cels.2015.08.012. Epub 2015 Sep 17.

8.

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P.

Science. 2016 Apr 29;352(6285):586-9. doi: 10.1126/science.aad8852.

PMID:
27126044
9.

Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

Chen WH, Lu G, Bork P, Hu S, Lercher MJ.

Nat Commun. 2016 Apr 21;7:11334. doi: 10.1038/ncomms11334.

10.

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.

Letunic I, Bork P.

Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5. doi: 10.1093/nar/gkw290. Epub 2016 Apr 19.

11.

Gut Microbiota Linked to Sexual Preference and HIV Infection.

Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, Estany C, Herrero C, Saz J, Sirera G, Torrela A, Navarro J, Crespo M, Brander C, Negredo E, Blanco J, Guarner F, Calle ML, Bork P, Sönnerborg A, Clotet B, Paredes R.

EBioMedicine. 2016 Jan 28;5:135-46. doi: 10.1016/j.ebiom.2016.01.032. eCollection 2016 Mar.

12.

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.

13.

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

Cornejo-Castillo FM, Cabello AM, Salazar G, Sánchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG.

Nat Commun. 2016 Mar 22;7:11071. doi: 10.1038/ncomms11071.

14.

Spatiotemporal variation of mammalian protein complex stoichiometries.

Ori A, Iskar M, Buczak K, Kastritis P, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M.

Genome Biol. 2016 Mar 14;17:47. doi: 10.1186/s13059-016-0912-5.

15.

Bacterial antisense RNAs are mainly the product of transcriptional noise.

Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar M.

Sci Adv. 2016 Mar 4;2(3):e1501363. doi: 10.1126/sciadv.1501363. eCollection 2016 Mar.

16.

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.

Huerta-Cepas J, Serra F, Bork P.

Mol Biol Evol. 2016 Jun;33(6):1635-8. doi: 10.1093/molbev/msw046. Epub 2016 Feb 26.

17.

Plankton networks driving carbon export in the oligotrophic ocean.

Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum JR, Coelho LP, Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S; Tara Oceans Consortium Coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G.

Nature. 2016 Apr 28;532(7600):465-70. doi: 10.1038/nature16942. Epub 2016 Feb 10.

PMID:
26863193
18.

The exploration of network motifs as potential drug targets from post-translational regulatory networks.

Zhang XD, Song J, Bork P, Zhao XM.

Sci Rep. 2016 Feb 8;6:20558. doi: 10.1038/srep20558.

19.

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.

Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, de Vos WM.

Nat Commun. 2016 Jan 26;7:10410. doi: 10.1038/ncomms10410.

20.

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.

Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P.

Nucleic Acids Res. 2016 Feb 18;44(3):1192-202. doi: 10.1093/nar/gkw004. Epub 2016 Jan 14.

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