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

35. For long-term sustainable software in bioinformatics

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

33. 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

32. 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

31. A catalogue 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 biorXiv (PREPRINT)

DOI: 10.1101/2023.12.27.573469

30. 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

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?

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

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

25. 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

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

22. 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

20. 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

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

17. 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

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

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

DOI: 10.31222/

14. 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

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

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

10. 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

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

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

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

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

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

3. 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

1. 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


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