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A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments by Shaojun Pan et al. at Nature Communications (2022)
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26. EXPERT: Transfer Learning-enabled context-aware microbial source tracking
by Hui Chong, Yuguo Zha, Qingyang Yu, ..., Luis Pedro Coelho, Kang Ning
DOI: 10.1093/bib/bbac396
25. 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
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
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
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
20. Extended bacterial diversity of the urinary microbiome of reproductive-age healthy European women captured by culturomics and long-read amplicon sequencing
by Svetlana Ugarcina Perovic, Magdalena Ksiezarek, Joana Rocha, Elisabete Alves Cappelli, Márcia Sousa, Teresa Gonçalves Ribeiro, Filipa Grosso, Luísa Peixe
19. 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
18. Towards the biogeography of prokaryotic genes
by Luis Pedro Coelho, Renato Alves, Álvaro Rodríguez del Río, ..., Shaojun Pan, ..., Jaime Huerta-Cepas, Peer Bork
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*
16. An open code pledge for the neuroscience community
by Cooper Smout, Dawn Liu Holford, Kelly Garner, ..., Sina Mansour L., Luis Pedro Coelho
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
14. 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
DOI: 10.1093/nar/gkab973
13. 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
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
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
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
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
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
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
5. 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
DOI: 10.1093/nar/gkz1002
4. 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
3. Extensive transmission of microbes along the gastrointestinal tract
by Thomas SB Schmidt, Matthew R Hayward, Luis Pedro Coelho, ..., Paul Wilmes, Peer Bork
DOI: 10.7554/elife.42693
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, ..., Qinghong Li, Peer Bork
1. Structure and function of the global topsoil microbiome
by Mohammad Bahram, Falk Hildebrand, Sofia K. Forslund, ..., Luis Pedro Coelho, ..., Leho Tedersoo, Peer Bork
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