Publications of LP. Coelho

Publications of LP. Coelho

The individual publication lists here have to be considered only in the context of the Bork Group.
Authors in this color are/were of Bork Group. [Altmetric off].
The manuscripts available on our site are provided for your personal use only and may not be retransmitted or redistributed without written permissions from the paper's publisher and author. You may not upload any of this site's material to any public server, on-line service, network, or bulletin board without prior written permission from the publisher and author. You may not make copies for any commercial purpose. Please email us for any paper request!
2024 1 publication(s).
38.
Functional and evolutionary significance of unknown genes from uncultivated taxa.
Rodríguez Del Río Á, Giner-Lamia J, Cantalapiedra CP, Botas J, Deng Z, Hernández-Plaza A, Munar-Palmer M, Santamaría-Hernando S, Rodríguez-Herva JJ, Ruscheweyh HJ, Paoli L, Schmidt TSB, Sunagawa S, Bork P, López-Solanilla E, Coelho LP, Huerta-Cepas J
2024 Feb 18; 626(7998): 377-384. PubMed: 38109938.
Abstract + PDF
2023 2 publication(s).
37.
Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide.
Andrikopoulos P, Aron-Wisnewsky J, Chakaroun R, Myridakis A, Forslund SK, Nielsen T, Adriouch S, Holmes B, Chilloux J, Vieira-Silva S, Falony G, Salem JE, Andreelli F, Belda E, Kieswich J, Chechi K, Puig-Castellvi F, Chevalier M, Le Chatelier E, Olanipekun MT, Hoyles L, Alves R, Helft G, Isnard R, Køber L, Coelho LP, Rouault C, Gauguier D, Gøtze JP, Prifti E, Froguel P, MetaCardis Consortium , Zucker JD, Bäckhed F, Vestergaard H, Hansen T, Oppert JM, Blüher M, Nielsen J, Raes J, Bork P, Yaqoob MM, Stumvoll M, Pedersen O, Ehrlich SD, Clément K, Dumas ME
2023 Sep 20; 14(1): 5843. PubMed: 37730687.
Abstract + PDF
36.
Computational exploration of the global microbiome for antibiotic discovery.
Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, Chong H, Fullam A, Michael K, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP
2023 Sep 11; [Epub ahead of print] PubMed: 37693522.
Abstract
2022 5 publication(s).
35.
Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.
Belda E, Voland L, Tremaroli V, Falony G, Adriouch S, Assmann KE, Prifiti E, Aron-Wisnewsky J, Debédat J, Le Roy T, Nielsen T, Amouyal C, André S, Andreelli F, Blüher M, Chakaroun R, Chilloux J, Coelho LP, Dao MC, Das P, Fellahi S, Forslund S, Galleron N, Hansen TH, Holmes B, Ji B, Krogh Pedersen H, Le P, Le Chatelier E, Lewinter C, Mannerås-Holm L, Marquet F, Myridakis A, Pelloux V, Pons N, Quinquis B, Rouault C, Roume H, Salem JE, Sokolovska N, Søndertoft NB, Touch S, Vieira-Silva S, MetaCardis Consortium , Galan P, Holst J, Gøtze JP, Køber L, Vestergaard H, Hansen T, Hercberg S, Oppert JM, Nielsen J, Letunic I, Dumas ME, Stumvoll M, Pedersen OB, Bork P, Ehrlich SD, Zucker JD, Bäckhed F, Raes J, Clément K
Gut.
2022 Dec 11; 71(12): 2463-2480. PubMed: 35017197.
Abstract + PDF
34.
Towards the biogeography of prokaryotic genes.
Coelho LP, Alves RJ, Del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TSB, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S, Zhao XM, Nielsen HB, Huerta-Cepas J, Bork P
2022 Jan 15; 601(7892): 252-256. PubMed: 34912116.
Abstract + PDF
33.
Microbiome and metabolome features of the cardiometabolic disease spectrum.
Fromentin S, Forslund SK, Chechi K, Aron-Wisnewsky J, Chakaroun R, Nielsen T, Tremaroli V, Ji B, Prifti E, Myridakis A, Chilloux J, Andrikopoulos P, Fan Y, Olanipekun MT, Alves RJ, Adiouch S, Bar N, Talmor-Barkan Y, Belda E, Caesar R, Coelho LP, Falony G, Fellahi S, Galan P, Galleron N, Helft G, Hoyles L, Isnard R, Le Chatelier E, Julienne H, Olsson L, Pedersen HK, Pons N, Quinquis B, Rouault C, Roume H, Salem JE, Schmidt TSB, Vieira-Silva S, Li P, Zimmermann-Kogadeeva M, Lewinter C, Søndertoft NB, Hansen TH, Gauguier D, Gøtze JP, Køber L, Kornowski R, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Letunic I, Bäckhed F, Oppert JM, Nielsen J, Raes J, Bork P, Stumvoll M, Segal E, Clément K, Dumas ME, Ehrlich SD, Pedersen O
2022 Feb 17; 28(2): 303-314. PubMed: 35177860.
Abstract + PDF
32.
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.
Khedkar S, Smyshlyaev G, Letunic I, Maistrenko OM, Coelho LP, Orakov A, Forslund SK, Hildebrand F, Luetge M, Schmidt TSB, Barabas O, Bork P
2022 Apr 8; 50(6): 3155-3168. PubMed: 35323968.
Abstract + PDF
31.
Drivers and determinants of strain dynamics following fecal microbiota transplantation.
Schmidt TSB, Li SS, Maistrenko OM, Akanni W, Coelho LP, Dolai S, Fullam A, Glazek AM, Hercog R, Herrema H, Jung F, Kandels S, Orakov A, Thielemann R, von Stetten M, Van Rossum T, Benes V, Borody TJ, de Vos WM, Ponsioen CY, Nieuwdorp M, Bork P
2022 Sep 15; 28(9): 1902-1912. PubMed: 36109636.
Abstract + PDF
2021 3 publication(s).
30.
Metagenomic assessment of the global diversity and distribution of bacteria and fungi.
Bahram M, Netherway T, Frioux C, Ferretti P, Coelho LP, Geisen S, Bork P, Hildebrand F
2021 Jan; 23(1): 316-326. PubMed: 33185929.
Abstract + PDF
29.
Combinatorial, additive and dose-dependent drug-microbiome associations.
Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, Markó L, Aron-Wisnewsky J, Nielsen T, Moitinho-Silva L, Schmidt TSB, Falony G, Vieira-Silva S, Adriouch S, Alves RJ, Assmann K, Bastard JP, Birkner T, Caesar R, Chilloux J, Coelho LP, Fezeu L, Galleron N, Helft G, Isnard R, Ji B, Kuhn M, Le Chatelier E, Myridakis A, Olsson L, Pons N, Prifti E, Quinquis B, Roume H, Salem JE, Sokolovska N, Tremaroli V, Valles-Colomer M, Lewinter C, Søndertoft NB, Pedersen HK, Hansen TH, MetaCardis Consortium , Gøtze JP, Køber L, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Oppert JM, Letunic I, Nielsen J, Bäckhed F, Ehrlich SD, Dumas ME, Raes J, Pedersen O, Clément K, Stumvoll M, Bork P
2021 Dec 8; 600(7889): 500-505. PubMed: 34880489.
Abstract + PDF
28.
GUNC: detection of chimerism and contamination in prokaryotic genomes.
2021 Jun 13; 22(1): 178. PubMed: 34120611.
Abstract + PDF
2020 3 publication(s).
27.
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
2020 May 11; 14(5): 1247-1259. PubMed: 32047279.
Abstract + PDF
26.
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernández-Plaza A, Orakov AN, Forslund SK, Sunagawa S, Zeller G, Huerta-Cepas J, Coelho LP, Bork P
2020 Jan 8; 48: D621-D625. PubMed: 31647096.
Abstract + PDF
25.
Statin therapy is associated with lower prevalence of gut microbiota dysbiosis.
Vieira-Silva S, Falony G, Belda E, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, Nguyen TTD, Proost S, Prifti E, Tremaroli V, Pons N, Le Chatelier E, Andreelli F, Bastard JP, Coelho LP, Galleron N, Hansen TH, Hulot JS, Lewinter C, Pedersen HK, Quinquis B, Rouault C, Roume H, Salem JE, Søndertoft NB, Touch S, MetaCardis Consortium: , Dumas E-M , Ehrlich SD, Galan P, Gøtze JP, Hansen T, Holst JJ, Køber L, Letunic I, Nielsen J, Oppert J-M , Stumvoll M, Vestergaard H, Zucker J-D , Bork P, Pedersen O, Bäckhed F, Clément K, Raes J
2020 May; 581(7808): 310-315. PubMed: 32433607.
Abstract + PDF
2019 6 publication(s).
24.
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Coelho LP, Alves RJ, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P
2019 Jun 3; 7(1): 84. PubMed: 31159881.
Abstract + PDF
23.
Global Trends in Marine Plankton Diversity across Kingdoms of Life.
Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Tara Oceans coordinators , Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, De Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L, Collaborators , Acinas SG, Babin M, Bork P, Boss E, Bowler C, Cochrane G, De Vargas C, Follows M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Iudicone D, Jaillon O, Kandels S, Karp-Boss L, Karsenti E, Not F, Ogata H, Pesant S, Poulton N, Raes J, Sardet C, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Wincker P.
2019 Nov 14; 179(5): 1084-1097.e21. PubMed: 31730851.
Abstract + PDF
22.
Microbial abundance, activity and population genomic profiling with mOTUs2.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves RJ, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S
2019 Mar 4; 10(1): 1014. PubMed: 30833550.
Abstract + PDF
21.
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.
Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Tara Oceans Consortium Coordinators , Acinas SG, Babin M, Bork P, Bowler C, De Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S
2019 Nov 14; 179(5): 1068-1083.e21. PubMed: 31730850.
Abstract + PDF
20.
Extensive transmission of microbes along the gastrointestinal tract.
Schmidt TSB, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, Wilmes P, Bork P
2019 Feb 12; 8: . PubMed: 30747106.
Abstract + PDF
19.
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G
2019 Apr 1; 25(4): 679-689. PubMed: 30936547.
Abstract + PDF
2018 4 publication(s).
18.
Structure and function of the global topsoil microbiome.
Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P
2018 Aug 1; 560(7717): 233-237. PubMed: 30069051.
Abstract + PDF
17.
Similarity of the dog and human gut microbiomes in gene content and response to diet.
Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR, Li Q, Bork P
2018 Apr 19; 6(1): 72. PubMed: 29669589.
Abstract + PDF
16.
Selective maternal seeding and environment shape the human gut microbiome.
Korpela K, Costea PI, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P
2018 Apr 1; 28(4): 561-568. PubMed: 29496731.
Abstract + PDF
15.
Recovery of gut microbiota of healthy adults following antibiotic exposure.
Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen MF, Nielsen HB, Bork P, Wang J, Vilsbøll T, Hansen T, Knop FK, Arumugam M, Pedersen O
2018 Nov 22; 3(11): 1255-1265. PubMed: 30349083.
Abstract + PDF
2017 7 publication(s).
14.
Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.
Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U
2017 Jun 29; 9(1): 61. PubMed: 28662719.
PDF
13.
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.
Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U
2017 Apr 28; 9(1): 39. PubMed: 28449715.
Abstract + PDF
12.
Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.
Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, De Vargas C
2017 Oct 31; 6: . PubMed: 29087936.
Abstract + PDF
11.
Subspecies in the global human gut microbiome.
Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P
2017 Dec 14; 13(12): 960. PubMed: 29242367.
Abstract + PDF
10.
metaSNV: A tool for metagenomic strain level analysis.
Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P
2017; 12(7): e0182392. PubMed: 28753663.
Abstract + PDF
9.
Towards standards for human fecal sample processing in metagenomic studies.
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 Nov 2; 35(11): 1069-1076. PubMed: 28967887.
Abstract + PDF
8.
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
2017 Aug 1; 34(8): 2115-2122. PubMed: 28460117.
Abstract + PDF
2016 2 publication(s).
7.
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 J, Coelho LP, Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, 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 Apr 28; 532(7600): 465-470. Epub 2016 Feb 10; PubMed: 26863193.
Abstract + PDF
6.
MOCAT2: a metagenomic assembly, annotation and profiling framework.
2016 Aug 15; 32(16): 2520-3. Epub 2016 Apr 8; PubMed: 27153620.
Abstract + PDF
2015 2 publication(s).
5.
Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images.
Coelho LP, Pato C, Friães A, Neumann A, von Köckritz-Blickwede M, Ramirez M, Carriço JA
2015 Jul 15; 31(14): 2364-70. PubMed: 25792554.
Abstract
4.
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, 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 May 22; 348(6237): 1261359. PubMed: 25999513.
Abstract + PDF
2014 2 publication(s).
3.
Metagenomic insights into the human gut resistome and the forces that shape it.
2014 Mar 29; 36(3): 316-29. Epub 2014 Jan 29; PubMed: 24474281.
Abstract + PDF
2.
Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection.
Liehl P, Zuzarte-Luís V, Chan J, Zillinger T, Baptista F, Carapau D, Konert M, Hanson KK, Carret C, Lassnig C, Müller M, Kalinke U, Saeed M, Chora AF, Golenbock DT, Strobl B, Prudêncio M, Coelho LP, Kappe SH, Superti-Furga G, Pichlmair A, Vigário AM, Rice CM, Fitzgerald KA, Barchet W, Mota MM
2014 Jan; 20(1): 47-53. PubMed: 24362933.
Abstract
2013 1 publication(s).
1.
Metagenomic species profiling using universal phylogenetic marker genes.
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 Dec 20; 10(12): 1196-9. Epub 2013 Oct 20; PubMed: 24141494.
Abstract + PDF