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38. Quest for Orthologs in the Era of Biodiversity Genomics

[More about Quest for Orthologs in the Era of Biodiversity Genomics]

by Felix Langschied, Nicola Bordin, Salvatore Cosentino, ..., Luis Pedro Coelho, ..., Christophe Dessimoz, Ingo Ebersberger in Genome Biology and Evolution

DOI: 10.1093/gbe/evae224

37. argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)

[More about argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)]

by Svetlana Ugarcina Perovic, Vedanth Ramji, Hui Chong, Yiqian Duan, Finlay Maguire, Luis Pedro Coelho in QUT ePrints (Preprint)

DOI: 10.5204/rep.eprints.252448

36. A catalog of small proteins from the global microbiome

[More about A catalog of small proteins from the global microbiome]

by Yiqian Duan, Célio Dias Santos Júnior, Thomas S.B. Schmidt, Anthony Fullam, Breno L. S. de Almeida, Chengkai Zhu, Kuhn Michael, Xing-Ming Zhao, Peer Bork, Luis Pedro Coelho in Nature Communications

DOI: 10.1038/s41467-024-51894-6

35. Discovery of antimicrobial peptides in the global microbiome with machine learning

[More about Discovery of antimicrobial peptides in the global microbiome with machine learning]

by Célio Dias Santos Júnior, Marcelo D.T. Torres, Yiqian Duan, ..., Hui Chong, ..., Chengkai Zhu, Amy Houseman, ..., Cesar de la Fuente-Nunez, Luis Pedro Coelho in Cell

DOI: 10.1016/j.cell.2024.05.013

34. For long-term sustainable software in bioinformatics

[More about For long-term sustainable software in bioinformatics]

by Luis Pedro Coelho in PLOS Computational Biology

DOI: 10.1371/journal.pcbi.1011920

33. Challenges in computational discovery of bioactive peptides in ’omics data

[More about Challenges in computational discovery of bioactive peptides in ’omics data]

by Luis Pedro Coelho, Célio Dias Santos Júnior, Cesar de la Fuente‐Nunez in PROTEOMICS

DOI: 10.1002/pmic.202300105

32. A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer

[More about A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer]

by Marija Dmitrijeva, Janko Tackmann, João Frederico Matias Rodrigues, Jaime Huerta-Cepas, Luis Pedro Coelho, Christian von Mering in Nature Ecology & Evolution

DOI: 10.1038/s41559-024-02357-0

31. Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean

[More about Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean]

by Fabien Lombard, Lionel Guidi, Manoela C. Brandão, Luis Pedro Coelho, ..., Gabriel Gorsky, Tara Oceans Coordinators in bioRxiv (PREPRINT)

DOI: 10.1101/2024.02.09.579612

30. Functional and evolutionary significance of unknown genes from uncultivated taxa

[More about Functional and evolutionary significance of unknown genes from uncultivated taxa]

by Álvaro Rodríguez del Río, Joaquín Giner-Lamia, Carlos P. Cantalapiedra, ..., Luis Pedro Coelho, Jaime Huerta-Cepas in Nature

DOI: 10.1038/s41586-023-06955-z

29. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

[More about SPIRE: a Searchable, Planetary-scale mIcrobiome REsource]

by Thomas S B Schmidt, Anthony Fullam, Pamela Ferretti, ..., Yiqian Duan, ..., Luis Pedro Coelho, Peer Bork in Nucleic Acids Research

DOI: 10.1093/nar/gkad943

28. Towards Monitoring of Antimicrobial Resistance in the Environment: For what Reasons, How to Implement It, and What Are the Data Needs?

[More about Towards Monitoring of Antimicrobial Resistance in the Environment: For what Reasons, How to Implement It, and What Are the Data Needs?]

by Johan Bengtsson-Palme, Anna Abramova, Thomas U. Berendonk, Luis Pedro Coelho, ..., Svetlana Ugarcina Perovic, ..., Astrid Louise Wester, Rabaab Zahra in Environment International

DOI: 10.1016/j.envint.2023.108089

27. SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing

[More about SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing]

by Shaojun Pan, Xing-Ming Zhao, Luis Pedro Coelho in Bioinformatics

DOI: 10.1093/bioinformatics/btad209

26. ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics

[More about ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics]

by Rémi Gschwind, Svetlana Ugarcina Perovic, Maja Weiss, Marie Petitjean, Julie Lao, Luis Pedro Coelho, Etienne Ruppé in Nucleic Acids Research

DOI: 10.1093/nar/gkad384

25. Urinary Microbiome of Reproductive-Age Asymptomatic European Women

[More about Urinary Microbiome of Reproductive-Age Asymptomatic European Women]

by Svetlana Ugarcina Perovic, Magdalena Ksiezarek, Joana Rocha, Elisabete Alves Cappelli, Márcia Sousa, Teresa Gonçalves Ribeiro, Filipa Grosso, Luísa Peixe in Microbiology Spectrum

DOI: 10.1128/spectrum.01308-22

24. metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies

[More about metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies]

by Senying Lai, Shaojun Pan, Chuqing Sun, Luis Pedro Coelho, Wei-Hua Chen, Xing-Ming Zhao in Genome biology

DOI: 10.1101/2021.06.22.449514

23. EXPERT: Transfer Learning-enabled context-aware microbial source tracking

[More about EXPERT: Transfer Learning-enabled context-aware microbial source tracking]

by Hui Chong, Yuguo Zha, Qingyang Yu, ..., Luis Pedro Coelho, Kang Ning in Briefings in Bioinformatics

DOI: 10.1093/bib/bbac396

22. Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation

[More about Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation]

by Thomas SB Schmidt, Simone S Li, Oleksandr M Maistrenko, ..., Luis Pedro Coelho, ..., Max Nieuwdorp, Peer Bork in Nature Medicine

DOI: 10.1038/s41591-022-01913-0

21. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments

[More about 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

DOI: 10.1038/s41467-022-29843-y

20. Software testing in microbial bioinformatics: a call to action

[More about Software testing in microbial bioinformatics: a call to action]

by Boas C.L. van der Putten, C. I. Mendes, Brooke M. Talbot, Jolinda de Korne-Elenbaas, Rafael Mamede, Pedro Vila-Cerqueira, Luis Pedro Coelho, Christopher A. Gulvik, Lee S. Katz, The ASM NGS 2020 Hackathon participants in Microbial Genomics

DOI: 10.1099/mgen.0.000790

19. Microbiome and metabolome features of the cardiometabolic disease spectrum

[More about Microbiome and metabolome features of the cardiometabolic disease spectrum]

by Sebastien Fromentin, Sofia K. Forslund, Kanta Chechi, ..., Luis Pedro Coelho, ..., S. Dusko Ehrlich, Oluf Pedersen in Nature Medicine

DOI: 10.1038/s41591-022-01688-4

18. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism

[More about 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, ..., Karine Clément, The MetaCardis Consortium in Gut

DOI: 10.1136/gutjnl-2021-325753

17. Towards the biogeography of prokaryotic genes

[More about Towards the biogeography of prokaryotic genes]

by Luis Pedro Coelho, Renato Alves, Álvaro Rodríguez del Río, ..., Shaojun Pan, ..., Jaime Huerta-Cepas, Peer Bork in Nature

DOI: 10.1038/s41586-021-04233-4

16. Combinatorial, additive and dose-dependent drug–microbiome associations

[More about Combinatorial, additive and dose-dependent drug–microbiome associations]

by Sofia K. Forslund, Rima Chakaroun, Maria Zimmermann-Kogadeeva, ..., Luis Pedro Coelho, ..., Peer Bork, The MetaCardis Consortium* in Nature

DOI: 10.1038/s41586-021-04177-9

15. An open code pledge for the neuroscience community

[More about An open code pledge for the neuroscience community]

by Cooper Smout, Dawn Liu Holford, Kelly Garner, ..., Sina Mansour L., Luis Pedro Coelho in Preprint

DOI: 10.31222/osf.io/vrwm7

14. GUNC: detection of chimerism and contamination in prokaryotic genomes

[More about GUNC: detection of chimerism and contamination in prokaryotic genomes]

by Askarbek Orakov, Anthony Fullam, Luis Pedro Coelho, Supriya Khedkar, Damian Szklarczyk, Daniel R. Mende, Thomas S. B. Schmidt, Peer Bork in Genome Biology

DOI: 10.1186/s13059-021-02393-0

13. mBodyMap: a curated database for microbes across human body and their associations with health and diseases

[More about mBodyMap: a curated database for microbes across human body and their associations with health and diseases]

by Hanbo Jin, Guoru Hu, Chuqing Sun, Yiqian Duan, Zhenmo Zhang, Zhi Liu, Xing-Ming Zhao, Wei-Hua Chen in Nucleic Acids Research

DOI: 10.1093/nar/gkab973

12. Metagenomic assessment of the global diversity and distribution of bacteria and fungi

[More about Metagenomic assessment of the global diversity and distribution of bacteria and fungi]

by Mohammad Bahram, Tarquin Netherway, Clemence Frioux, Pamela Ferretti, Luis Pedro Coelho, Stefan Geisen, Peer Bork, Falk Hildebrand in Environmental Microbiology

DOI: 10.1111/1462-2920.15314

11. Macrel: antimicrobial peptide screening in genomes and metagenomes

[More about Macrel: antimicrobial peptide screening in genomes and metagenomes]

by Célio Dias Santos Júnior, Shaojun Pan, Xing-Ming Zhao, Luis Pedro Coelho in PeerJ

DOI: 10.7717/peerj.10555

10. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

[More about 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, ..., Shinichi Sunagawa, Peer Bork in The ISME Journal

DOI: 10.1038/s41396-020-0600-z

9. NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

[More about 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

DOI: 10.1186/s40168-019-0684-8

8. Microbial abundance, activity and population genomic profiling with mOTUs2

[More about Microbial abundance, activity and population genomic profiling with mOTUs2]

by Alessio Milanese, Daniel R Mende, Lucas Paoli, ..., Luis Pedro Coelho, ..., Georg Zeller, Shinichi Sunagawa in Nature Communications

DOI: 10.1038/s41467-019-08844-4

7. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

[More about Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome]

by Guillem Salazar, Lucas Paoli, Adriana Alberti, ..., Luis Pedro Coelho, ..., Shinichi Sunagawa, Patrick Wincker in Cell

DOI: 10.1016/j.cell.2019.10.014

6. Global Trends in Marine Plankton Diversity across Kingdoms of Life

[More about Global Trends in Marine Plankton Diversity across Kingdoms of Life]

by Federico M. Ibarbalz, Nicolas Henry, Manoela C. Brandao, ..., Luis Pedro Coelho, ..., Shinichi Sunagawa, Patrick Wincker in Cell

DOI: 10.1016/j.cell.2019.10.008

5. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

[More about 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, ..., Luis Pedro Coelho, Peer Bork in Nucleic Acids Research

DOI: 10.1093/nar/gkz1002

4. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

[More about 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, ..., Peer Bork, Georg Zeller in Nature Medicine

DOI: 10.1038/s41591-019-0406-6

3. Extensive transmission of microbes along the gastrointestinal tract

[More about Extensive transmission of microbes along the gastrointestinal tract]

by Thomas SB Schmidt, Matthew R Hayward, Luis Pedro Coelho, ..., Paul Wilmes, Peer Bork in eLife

DOI: 10.7554/elife.42693

2. Similarity of the dog and human gut microbiomes in gene content and response to diet

[More about 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, ..., Qinghong Li, Peer Bork in Microbiome

DOI: 10.1186/s40168-018-0450-3

1. Structure and function of the global topsoil microbiome

[More about Structure and function of the global topsoil microbiome]

by Mohammad Bahram, Falk Hildebrand, Sofia K. Forslund, ..., Luis Pedro Coelho, ..., Leho Tedersoo, Peer Bork in Nature

DOI: 10.1038/s41586-018-0386-6