Korpela K, Costea PI, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P. (2018)

Selective maternal seeding and environment shape the human gut microbiome.

Genome Res. doi: 10.1101/gr.233940.117
Europe PMC | doi

Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P. (2017)

Subspecies in the global human gut microbiome.

Mol. Syst. Biol. 13(12) doi: 10.15252/msb.20177589
Europe PMC | doi

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. (2017)

Towards standards for human fecal sample processing in metagenomic studies.

Nat Biotechnol. 35(11) doi: 10.1038/nbt.3960
Europe PMC | doi

Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C. (2017)

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.

Elife 6 doi: 10.7554/eLife.26066
Europe PMC | doi

Huerta-Cepas J, Forslund K, Pedro Coelho L, Szklarczyk D, Juhl Jensen L, von Mering C, Bork P. (2017)

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.

Mol Biol Evol 34(8):2115-2122. doi: 10.1093/molbev/msx148
Europe PMC | doi

Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P. (2017)

metaSNV: A tool for metagenomic strain level analysis.

PLoS One 12(7) doi: 10.1371/journal.pone.0182392
Europe PMC | doi

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. (2017)

Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Genome Med 9(1):61. doi: 10.1186/s13073-017-0451-z
Europe PMC | doi

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. (2017)

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Genome Med 9(1):1-13. doi: 10.1186/s13073-017-0428-y
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 32(16):2520-2523. doi: 10.1093/bioinformatics/btw183
Europe PMC | doi

Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, 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. (2016)

Plankton networks driving carbon export in the oligotrophic ocean.

Nature doi: 10.1038/nature16942
Europe PMC | doi

Coelho LP, Pato C, Friaes A, Neumann A, von Kockritz-Blickwede M, Ramirez M, Carrico JA. (2015)

Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images

Bioinformatics 31(14):2364-2370. doi: 10.1093/bioinformatics/btv156
Europe PMC | doi

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. (2015)

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

Science 348(6237) doi: 10.1126/science.1261359
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

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P. (2013)

Metagenomic species profiling using universal phylogenetic marker genes

Nat. Methods 10(12):1196-1199. doi: 10.1038/nmeth.2693
Europe PMC | doi