32. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments by Shaojun Pan, Chengkai Zhu, Xing-Ming Zhao, Luis Pedro Coelho in Nature Communications (2022).

31. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes by Supriya Khedkar, Georgy Smyshlyaev, Ivica Letunic, ..., Luis Pedro Coelho, ..., Thomas S B Schmidt, Orsolya Barabas, Peer Bork in Nucleic Acids Research (2022).

30. Software testing in microbial bioinformatics: a call to action by Boas C.L. van der Putten, C. I. Mendes, Brooke M. Talbot, ..., Luis Pedro Coelho, ..., Christopher A. Gulvik, Lee S. Katz, The ASM NGS 2020 Hackathon participants in Microbial Genomics (2022).

29. Microbiome and metabolome features of the cardiometabolic disease spectrum by Sebastien Fromentin, Sofia K. Forslund, Kanta Chechi, ..., Luis Pedro Coelho, ..., Marc-Emmanuel Dumas, S. Dusko Ehrlich, Oluf Pedersen in Nature Medicine (2022).

28. Functional and evolutionary significance of unknown genes from uncultivated taxa by Álvaro Rodríguez del Río, Joaquín Giner-Lamia, Carlos P. Cantalapiedra, ..., Peer Bork, Luis Pedro Coelho, Jaime Huerta-Cepas in biorXiv (PREPRINT) (2022).

27. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism by Eugeni Belda, Lise Voland, Valentina Tremaroli, ..., Luis Pedro Coelho, ..., Jeroen Raes, Karine Clément, The MetaCardis Consortium in Gut (2022).

26. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism by Eugeni Belda, Lise Voland, Valentina Tremaroli, ..., Luis Pedro Coelho, ..., Jeroen Raes, Karine Clément, The MetaCardis Consortium in Gut (2022).

25. Functional and evolutionary significance of unknown genes from uncultivated taxa by Alvaro Rodriguez del Rio, Joaquin Giner-Lamia, Carlos P Cantalapiedra, ..., Peer Bork, Luis Pedro Coelho, Jaime Huerta-Cepas in bioRxiv (2022).

24. Towards the biogeography of prokaryotic genes by Luis Pedro Coelho, Renato Alves, Álvaro Rodríguez del Río, ..., Henrik Bjørn Nielsen, Jaime Huerta-Cepas, Peer Bork in Nature (2021).

23. EXPERT: Transfer Learning-enabled context-aware microbial source tracking by Hui Chong, Qingyang Yu, Yuguo Zha, ..., Weihua Chen, Luis Pedro Coelho, Kang Ning in biorXiv (2021).

22. An open code pledge for the neuroscience community by Cooper Smout, Dawn Liu Holford, Kelly Garner, ..., Naoyuki Sunami, Sina Mansour L., Luis Pedro Coelho in MetaArXiv Preprint (2021).

21. Combinatorial, additive and dose-dependent drug–microbiome associations by Sofia K. Forslund, Rima Chakaroun, Maria Zimmermann-Kogadeeva, ..., Luis Pedro Coelho, ..., Michael Stumvoll, Peer Bork, The MetaCardis Consortium* in Nature (2021).

20. Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation by Thomas SB Schmidt, Simone S Li, Oleksandr M Maistrenko, ..., Luis Pedro Coelho, ..., Anna Glazek, Rajna Hercog, Hilde Herrema in bioRxiv (2021).

19. metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies by Senying Lai, Shaojun Pan, Luis Pedro Coelho, Wei-hua Chen, Xing-Ming Zhao in bioRxiv (2021).

18. MACREL: antimicrobial peptide screening in genomes and metagenomes by Célio Dias Santos-Junior, Shaojun Pan, Xing-Ming Zhao, Luis Pedro Coelho in PeerJ (2020).

17. GUNC: detection of chimerism and contamination in prokaryotic genomes by Askarbek Orakov, Anthony Fullam, Luis Pedro Coelho, ..., Daniel R Mende, Thomas SB Schmidt, Peer Bork in Genome Biology (2021).

16. Metagenomic assessment of the global diversity and distribution of bacteria and fungi by Mohammad Bahram, Tarquin Netherway, Clémence Frioux, ..., Luis Pedro Coelho, ..., Stefan Geisen, Peer Bork, Falk Hildebrand in Environmental Microbiology (2021).

15. Voices of the new generation: science in a state of benign confusion by Luis Pedro Coelho in Nature Reviews Molecular Cell Biology (2020).

14. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis by Sara Vieira-Silva, Gwen Falony, Eugeni Belda, ..., Luis Pedro Coelho, ..., Fredrik Bäckhed, Karine Clément, Jeroen Raes in Nature (2020).

13. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity by Oleksandr M Maistrenko, Daniel R Mende, Mechthild Luetge, ..., Luis Pedro Coelho, ..., Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork in The ISME Journal (2020).

12. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome by Guillem Salazar, Lucas Paoli, Adriana Alberti, ..., Luis Pedro Coelho, ..., Matthew B. Sullivan, Patrick Wincker, Shinichi Sunagawa in Cell (2019).

11. Global trends in marine plankton diversity across kingdoms of life by Federico M Ibarbalz, Nicolas Henry, Manoela C Brandão, ..., Luis Pedro Coelho, ..., Hisashi Endo, Josep M Gasol, Ann C Gregory in Cell (2019).

10. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes by Daniel R Mende, Ivica Letunic, Oleksandr M Maistrenko, ..., Jaime Huerta-Cepas, Luis Pedro Coelho, Peer Bork in Nucleic acids research (2020).

9. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer by Jakob Wirbel, Paul Theodor Pyl, Ece Kartal, ..., Luis Pedro Coelho, ..., Manimozhiyan Arumugam, Peer Bork, Georg Zeller in Nature medicine (2019).

8. Microbial abundance, activity and population genomic profiling with mOTUs2 by Alessio Milanese, Daniel R Mende, Lucas Paoli, ..., Luis Pedro Coelho, ..., Peer Bork, Georg Zeller, Shinichi Sunagawa in Nature Communications (2019).

7. Community‐Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems by Luigi Caputi, Quentin Carradec, Damien Eveillard, ..., Luis Pedro Coelho, ..., Patrick Wincker, Chris Bowler, Daniele Iudicone in Global Biogeochemical Cycles (2019).

6. Extensive transmission of microbes along the gastrointestinal tract by Thomas Sebastian Benedikt Schmidt, Matthew Robert Hayward, Luis Pedro Coelho, ..., Georg Zeller, Paul Wilmes, Peer Bork in eLife (2019).

5. Recovery of gut microbiota of healthy adults following antibiotic exposure by Albert Palleja, Kristian H Mikkelsen, Sofia K Forslund, ..., Luis Pedro Coelho, ..., Filip K. Knop, Manimozhiyan Arumugam, Oluf Pedersen in Nature microbiology (2018).

4. Structure and function of the global topsoil microbiome by Mohammad Bahram, Falk Hildebrand, Sofia K Forslund, ..., Luis Pedro Coelho, ..., Martin Ryberg, Leho Tedersoo, Peer Bork in Nature (2018).

3. NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language by Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork in Microbiome (2019).

2. Similarity of the dog and human gut microbiomes in gene content and response to diet by Luis Pedro Coelho, Jens Roat Kultima, Paul Igor Costea, ..., Janet R. Jackson, Qinghong Li, Peer Bork in Microbiome (2018).

1. Selective maternal seeding and environment shape the human gut microbiome by Katri Korpela, Paul Igor Costea, Luis Pedro Coelho, ..., Dorret I Boomsma, Nicola Segata, Peer Bork in Genome Research (2018).


Copyright (c) 2009-2021. Luis Pedro Coelho and other group members. All rights reserved.