EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

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Publications

Total: 14 publication(s)

2016

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, Consortium M, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O. (2016)

Human gut microbes impact host serum metabolome and insulin sensitivity.

Nature (535):376-381. doi: 10.1038/nature18646
Europe PMC | doi

Saripella GV, Sonnhammer EL, Forslund K. (2016)

Benchmarking the next generation of homology inference tools.

Bioinformatics doi: 10.1093/bioinformatics/btw305
Europe PMC | doi

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. (2016)

Standardized benchmarking in the quest for orthologs.

Nat. Methods 13(5):425-430. doi: 10.1038/nmeth.3830
Europe PMC | doi

Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P. (2016)

MOCAT2: a metagenomic assembly, annotation and profiling framework.

Bioinformatics doi: 10.1093/bioinformatics/btw183
Europe PMC | doi

Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, de Vos WM. (2016)

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

Nat Commun 7 doi: 10.1038/ncomms10410
Europe PMC | doi

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. (2016)

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

Nucleic Acids Res 44(D1):D286-93. doi: 10.1093/nar/gkv1248
Europe PMC | doi


2015

Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Igor Costea P, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O. (2015)

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Nature 528(7581):262-266. doi: 10.1038/nature15766
Europe PMC | doi

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldon T. (2015)

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

Genome Biol. Evol. 7(7):1988-1999. doi: 10.1093/gbe/evv121
Europe PMC | doi


2014

Trachana K, Forslund K, Larsson T, Powell S, Doerks T, von Mering C, Bork P. (2014)

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.

PLoS ONE 9(11) doi: 10.1371/journal.pone.0111122
Europe PMC | doi

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerte-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. (2014)

STRING v10: protein-protein interaction networks, integrated over the tree of life.

Nucleic Acids Res. doi: 10.1093/nar/gku1003
Europe PMC | doi

Forslund K, Sunagawa S, Coelho LP, Bork P. (2014)

Metagenomic insights into the human gut resistome and the forces that shape it

Bioessays 36(3):316-329. doi: 10.1002/bies.201300143
Europe PMC | doi

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. (2014)

eggNOG v4.0: nested orthology inference across 3686 organisms

Nucleic Acids Res. 42(Database issue):D231-D239. doi: 10.1093/nar/gkt1253
Europe PMC | doi


2013

Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. (2013)

Country-specific antibiotic use practices impact the human gut resistome

Genome Res. 23(7):1163-1169. doi: 10.1101/gr.155465.113
Europe PMC | doi

Fuller JC, Khoueiry P, Dinkel H, Forslund K, Stamatakis A, Barry J, Budd A, Soldatos TG, Linssen K, Rajput AM, HUB Participants. (2013)

Biggest challenges in bioinformatics

EMBO Rep. 14(4):302-304. doi: 10.1038/embor.2013.34
Europe PMC | doi