Luis Pedro Coelho - Publications

European Molecular Biology Laborator (EMBL), Heidelberg, Baden-Württemberg, Germany 
Computational Biology

35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Dmitrijeva M, Tackmann J, Matias Rodrigues JF, Huerta-Cepas J, Coelho LP, von Mering C. A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer. Nature Ecology & Evolution. PMID 38443606 DOI: 10.1038/s41559-024-02357-0  0.614
2023 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, et al. Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature. PMID 38109938 DOI: 10.1038/s41586-023-06955-z  0.473
2023 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, ... ... Coelho LP, et al. Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide. Nature Communications. 14: 5843. PMID 37730687 DOI: 10.1038/s41467-023-39824-4  0.701
2023 Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquín-Díaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, et al. Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? Environment International. 178: 108089. PMID 37441817 DOI: 10.1016/j.envint.2023.108089  0.595
2022 Lai S, Pan S, Sun C, Coelho LP, Chen WH, Zhao XM. metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies. Genome Biology. 23: 242. PMID 36376928 DOI: 10.1186/s13059-022-02810-y  0.516
2022 Chong H, Zha Y, Yu Q, Cheng M, Xiong G, Wang N, Huang X, Huang S, Sun C, Wu S, Chen WH, Coelho LP, Ning K. EXPERT: transfer learning-enabled context-aware microbial community classification. Briefings in Bioinformatics. PMID 36124759 DOI: 10.1093/bib/bbac396  0.546
2022 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, et al. Drivers and determinants of strain dynamics following fecal microbiota transplantation. Nature Medicine. 28: 1902-1912. PMID 36109636 DOI: 10.1038/s41591-022-01913-0  0.411
2022 Pan S, Zhu C, Zhao XM, Coelho LP. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments. Nature Communications. 13: 2326. PMID 35484115 DOI: 10.1038/s41467-022-29843-y  0.317
2022 Khedkar S, Smyshlyaev G, Letunic I, Maistrenko OM, Coelho LP, Orakov A, Forslund SK, Hildebrand F, Luetge M, Schmidt TSB, Barabas O, Bork P. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. Nucleic Acids Research. PMID 35323968 DOI: 10.1093/nar/gkac163  0.763
2022 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 R, ... ... Coelho LP, et al. Microbiome and metabolome features of the cardiometabolic disease spectrum. Nature Medicine. PMID 35177860 DOI: 10.1038/s41591-022-01688-4  0.749
2022 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, ... ... Coelho LP, et al. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism. Gut. PMID 35017197 DOI: 10.1136/gutjnl-2021-325753  0.747
2021 Coelho LP, Alves R, Del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, et al. Towards the biogeography of prokaryotic genes. Nature. PMID 34912116 DOI: 10.1038/s41586-021-04233-4  0.753
2021 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, ... ... Coelho LP, et al. Combinatorial, additive and dose-dependent drug-microbiome associations. Nature. 600: 500-505. PMID 34880489 DOI: 10.1038/s41586-021-04177-9  0.743
2021 Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D, Mende DR, Schmidt TSB, Bork P. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biology. 22: 178. PMID 34120611 DOI: 10.1186/s13059-021-02393-0  0.681
2020 Bahram M, Netherway T, Frioux C, Ferretti P, Coelho LP, Geisen S, Bork P, Hildebrand F. Metagenomic assessment of the global distribution of bacteria and fungi. Environmental Microbiology. PMID 33185929 DOI: 10.1111/1462-2920.15314  0.484
2020 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, ... ... Coelho LP, et al. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature. 581: 310-315. PMID 32433607 DOI: 10.1038/S41586-020-2269-X  0.748
2019 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, et al. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell. 179: 1068-1083.e21. PMID 31730850 DOI: 10.1016/J.Cell.2019.10.014  0.618
2019 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. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. Nucleic Acids Research. PMID 31647096 DOI: 10.1093/Nar/Gkz1002  0.749
2019 Coelho LP, Alves R, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P. NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. Microbiome. 7: 84. PMID 31159881 DOI: 10.1186/S40168-019-0684-8  0.457
2019 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, et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature Medicine. PMID 30936547 DOI: 10.1038/S41591-019-0406-6  0.726
2019 Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, et al. Microbial abundance, activity and population genomic profiling with mOTUs2. Nature Communications. 10: 1014. PMID 30833550 DOI: 10.1038/S41467-019-08844-4  0.765
2019 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, et al. Extensive transmission of microbes along the gastrointestinal tract. Elife. 8. PMID 30747106 DOI: 10.7554/Elife.42693  0.598
2018 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, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology. PMID 30349083 DOI: 10.1038/S41564-018-0257-9  0.72
2018 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, et al. Structure and function of the global topsoil microbiome. Nature. PMID 30069051 DOI: 10.1038/S41586-018-0386-6  0.679
2018 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. Similarity of the dog and human gut microbiomes in gene content and response to diet. Microbiome. 6: 72. PMID 29669589 DOI: 10.1186/S40168-018-0450-3  0.664
2018 Korpela K, Costea PI, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P. Selective maternal seeding and environment shape the human gut microbiome. Genome Research. PMID 29496731 DOI: 10.1101/Gr.233940.117  0.338
2017 Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P. Subspecies in the global human gut microbiome. Molecular Systems Biology. 13: 960. PMID 29242367 DOI: 10.15252/Msb.20177589  0.679
2017 Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C. Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes. Elife. 6. PMID 29087936 DOI: 10.7554/Elife.26066  0.405
2017 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, et al. Towards standards for human fecal sample processing in metagenomic studies. Nature Biotechnology. PMID 28967887 DOI: 10.1038/Nbt.3960  0.585
2017 Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P. metaSNV: A tool for metagenomic strain level analysis. Plos One. 12: e0182392. PMID 28753663 DOI: 10.1371/Journal.Pone.0182392  0.454
2016 Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P. MOCAT2: a metagenomic assembly, annotation and profiling framework. Bioinformatics (Oxford, England). PMID 27153620 DOI: 10.1093/Bioinformatics/Btw183  0.616
2016 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, et al. Plankton networks driving carbon export in the oligotrophic ocean. Nature. PMID 26863193 DOI: 10.1038/Nature16942  0.551
2015 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, et al. Ocean plankton. Structure and function of the global ocean microbiome. Science (New York, N.Y.). 348: 1261359. PMID 25999513 DOI: 10.1126/Science.1261359  0.771
2014 Forslund K, Sunagawa S, Coelho LP, Bork P. Metagenomic insights into the human gut resistome and the forces that shape it. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 36: 316-29. PMID 24474281 DOI: 10.1002/Bies.201300143  0.416
2013 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, et al. Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods. 10: 1196-9. PMID 24141494 DOI: 10.1038/Nmeth.2693  0.755
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