Luis Pedro Coelho - Publications

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

25/39 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
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  0.68
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  0.56
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  0.68
2019 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, et al. Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell. 179: 1084-1097.e21. PMID 31730851 DOI: 10.1016/J.Cell.2019.10.008  0.56
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.56
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  0.68
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  0.56
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  0.68
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  0.68
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  0.68
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  0.68
2017 Huerta-Cepas J, Forslund K, Pedro Coelho L, Szklarczyk D, Juhl Jensen L, von Mering C, Bork P. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Molecular Biology and Evolution. PMID 28460117 DOI: 10.1093/Molbev/Msx148  0.44
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  0.56
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  0.56
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  0.56
2015 Coelho LP, Pato C, Friães A, Neumann A, von Köckritz-Blickwede M, Ramirez M, Carriço JA. Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images. Bioinformatics (Oxford, England). 31: 2364-70. PMID 25792554 DOI: 10.1093/bioinformatics/btv156  0.56
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  0.56
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  0.56
Low-probability matches
2013 Coelho LP, Kangas JD, Naik AW, Osuna-Highley E, Glory-Afshar E, Fuhrman M, Simha R, Berget PB, Jarvik JW, Murphy RF. Determining the subcellular location of new proteins from microscope images using local features. Bioinformatics (Oxford, England). 29: 2343-9. PMID 23836142 DOI: 10.1093/Bioinformatics/Btt392  0.08
2010 Ahmed A, Arnold A, Coelho LP, Kangas J, Sheikh AS, Xing E, Cohen W, Murphy RF. Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature. Web Semantics (Online). 8: 151-154. PMID 24991197 DOI: 10.1016/J.Websem.2010.04.002  0.08
2010 Coelho LP, Peng T, Murphy RF. Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing. Bioinformatics (Oxford, England). 26: i7-12. PMID 20529939 DOI: 10.1093/bioinformatics/btq220  0.08
2010 Shariff A, Kangas J, Coelho LP, Quinn S, Murphy RF. Automated image analysis for high-content screening and analysis. Journal of Biomolecular Screening. 15: 726-34. PMID 20488979 DOI: 10.1177/1087057110370894  0.08
2010 Coelho LP, Ahmed A, Arnold A, Kangas J, Sheikh AS, Xing EP, Cohen WW, Murphy RF. Structured literature image finder: Extracting information from text and images in biomedical literature Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6004: 23-32. DOI: 10.1007/978-3-642-13131-8_4  0.08
2010 Coelho LP, Glory-Afshar E, Kangas J, Quinn S, Shariff A, Murphy RF. Principles of bioimage informatics: Focus on machine learning of cell patterns Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6004: 8-18. DOI: 10.1007/978-3-642-13131-8_2  0.08
2009 Coelho LP, Shariff A, Murphy RF. NUCLEAR SEGMENTATION IN MICROSCOPE CELL IMAGES: A HAND-SEGMENTED DATASET AND COMPARISON OF ALGORITHMS. Proceedings / Ieee International Symposium On Biomedical Imaging: From Nano to Macro. Ieee International Symposium On Biomedical Imaging. 5193098: 518-521. PMID 20628545 DOI: 10.1109/ISBI.2009.5193098  0.08
2009 Buck TE, Rao A, Coelho LP, Fuhrman MH, Jarvik JW, Berget PB, Murphy RF. Cell cycle dependence of protein subcellular location inferred from static, asynchronous images. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 1016-9. PMID 19963740 DOI: 10.1109/IEMBS.2009.5332888  0.08
2006 Chebira A, Coelho LP, Sandryhaila A, Lin S, Jenkinson WG, MacSleyne J, Hoffman C, Cuadra P, Jackson C, Püschel M, Kovačević J. An adaptive multiresolution approach to fingerprint recognition Proceedings - International Conference On Image Processing, Icip. 1. DOI: 10.1109/ICIP.2007.4378990  0.08
2020 Santos-Júnior CD, Pan S, Zhao XM, Coelho LP. Macrel: antimicrobial peptide screening in genomes and metagenomes. Peerj. 8: e10555. PMID 33384902 DOI: 10.7717/peerj.10555  0.01
2020 Coelho LP. Voices of the new generation: science in a state of benign confusion. Nature Reviews. Molecular Cell Biology. PMID 32546774 DOI: 10.1038/s41580-020-0265-5  0.01
2017 van Oort PM, Nijsen T, Weda H, Knobel H, Dark P, Felton T, Rattray NJ, Lawal O, Ahmed W, Portsmouth C, Sterk PJ, Schultz MJ, Zakharkina T, Artigas A, Povoa P, et al. BreathDx - molecular analysis of exhaled breath as a diagnostic test for ventilator-associated pneumonia: protocol for a European multicentre observational study. Bmc Pulmonary Medicine. 17: 1. PMID 28049457 DOI: 10.1186/s12890-016-0353-7  0.01
2017 Coelho LP. Jug: Software for Parallel Reproducible Computation in Python Journal of Open Research Software. 5. DOI: 10.5334/JORS.161  0.01
2015 Pinheiro-Silva R, Borges L, Coelho LP, Cabezas-Cruz A, Valdés JJ, do Rosário V, de la Fuente J, Domingos A. Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection. Parasites & Vectors. 8: 485. PMID 26395987 DOI: 10.1186/S13071-015-1079-8  0.01
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