Publications

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

25. 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

DOI: 10.1038/s41591-022-01913-0

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

23. 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

DOI: 10.1099/mgen.0.000790

22. 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

DOI: 10.1038/s41591-022-01688-4

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

by Alvaro Rodriguez del Rio, Joaquin Giner-Lamia, Carlos P Cantalapiedra, ..., Luis Pedro Coelho, Jaime Huerta-Cepas

DOI: 10.1101/2022.01.26.477801

20. Extended bacterial diversity of the urinary microbiome of reproductive-age healthy European women captured by culturomics and long-read amplicon sequencing

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

18. Towards the biogeography of prokaryotic genes

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

DOI: 10.1038/s41586-021-04233-4

17. 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*

DOI: 10.1038/s41586-021-04177-9

16. An open code pledge for the neuroscience community

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

DOI: 10.31222/osf.io/vrwm7

15. 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

DOI: 10.1186/s13059-021-02393-0

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

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

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

DOI: 10.1111/1462-2920.15314

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

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

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

DOI: 10.1038/s41467-019-08844-4

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

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

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

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

DOI: 10.1038/s41586-018-0386-6

Year

Lab Member


Copyright (c) 2018-2022. Luis Pedro Coelho and other group members. All rights reserved.