Coming up

28 February 2022

Deadline for remote internship applications

Publications

21. Towards the biogeography of prokaryotic genes

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by Luis Pedro Coelho, Renato Alves, Álvaro Rodríguez del Río, Pernille Neve Myers, Carlos P. Cantalapiedra, Joaquín Giner-Lamia, Thomas Sebastian Schmidt, Daniel R. Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia K. Forslund, Supriya Khedkar, Oleksandr M. Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjørn Nielsen, Jaime Huerta-Cepas, Peer Bork

DOI: 10.1038/s41586-021-04233-4

20. 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, Lajos Markó, Judith Aron-Wisnewsky, Trine Nielsen, Lucas Moitinho-Silva, Thomas S. B. Schmidt, Gwen Falony, Sara Vieira-Silva, Solia Adriouch, Renato J. Alves, Karen Assmann, Jean-Philippe Bastard, Till Birkner, Robert Caesar, Julien Chilloux, Luis Pedro Coelho, Leopold Fezeu, Nathalie Galleron, Gerard Helft, Richard Isnard, Boyang Ji, Michael Kuhn, Emmanuelle Le Chatelier, Antonis Myridakis, Lisa Olsson, Nicolas Pons, Edi Prifti, Benoit Quinquis, Hugo Roume, Joe-Elie Salem, Nataliya Sokolovska, Valentina Tremaroli, Mireia Valles-Colomer, Christian Lewinter, Nadja B. Søndertoft, Helle Krogh Pedersen, Tue H. Hansen, Chloe Amouyal, Ehm Astrid Andersson Galijatovic, Fabrizio Andreelli, Olivier Barthelemy, Jean-Paul Batisse, Eugeni Belda, Magalie Berland, Randa Bittar, Hervé Blottière, Frederic Bosquet, Rachid Boubrit, Olivier Bourron, Mickael Camus, Dominique Cassuto, Cecile Ciangura, Jean-Philippe Collet, Maria-Carlota Dao, Morad Djebbar, Angélique Doré, Line Engelbrechtsen, Soraya Fellahi, Sebastien Fromentin, Pilar Galan, Dominique Gauguier, Philippe Giral, Agnes Hartemann, Bolette Hartmann, Jens Juul Holst, Malene Hornbak, Lesley Hoyles, Jean-Sebastien Hulot, Sophie Jaqueminet, Niklas Rye Jørgensen, Hanna Julienne, Johanne Justesen, Judith Kammer, Nikolaj Krarup, Mathieu Kerneis, Jean Khemis, Ruby Kozlowski, Véronique Lejard, Florence Levenez, Lea Lucas-Martini, Robin Massey, Laura Martinez-Gili, Nicolas Maziers, Jonathan Medina-Stamminger, Gilles Montalescot, Sandrine Moute, Ana Luisa Neves, Michael Olanipekun, Laetitia Pasero Le Pavin, Christine Poitou, Francoise Pousset, Laurence Pouzoulet, Andrea Rodriguez-Martinez, Christine Rouault, Johanne Silvain, Mathilde Svendstrup, Timothy Swartz, Thierry Vanduyvenboden, Camille Vatier, Stefanie Walther, Jens Peter Gøtze, Lars Køber, Henrik Vestergaard, Torben Hansen, Jean-Daniel Zucker, Serge Hercberg, Jean-Michel Oppert, Ivica Letunic, Jens Nielsen, Fredrik Bäckhed, S. Dusko Ehrlich, Marc-Emmanuel Dumas, Jeroen Raes, Oluf Pedersen, Karine Clément, Michael Stumvoll, Peer Bork, The MetaCardis Consortium*

DOI: 10.1038/s41586-021-04177-9

19. 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, ruddy manuel illanes beyuma, Paula Andrea Martinez, Megan Ethel Janine Campbell, Ibrahim Khormi, Dylan G. E. Gomes, Johanna Margarete Marianne Bayer, Claire Bradley, Antonio Schettino, Naoyuki Sunami, Sina Mansour L., Luis Pedro Coelho

DOI: 10.31222/osf.io/vrwm7

18. 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

DOI: 10.1186/s13059-021-02393-0

17. 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

DOI: 10.1093/nar/gkab973

16. 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, Wasiu Akanni, Luis Pedro Coelho, Sibasish Dolai, Anthony Fullam, Anna M Glazek, Rajna Hercog, Hilde Herrema, Ferris Jung, Stefanie Kandels, Askarbek Orakov, Thea Van Rossum, Vladimir Benes, Thomas J Borody, Willem M de Vos, Cyriel Y Ponsioen, Max Nieuwdorp, Peer Bork

DOI: 10.1101/2021.09.30.462010

15. SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)

[More about SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)]

by Shaojun Pan, Chengkai Zhu, Xing-Ming Zhao, Luis Pedro Coelho

DOI: 10.1101/2021.08.16.456517

14. 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, Luis Pedro Coelho, Wei-Hua Chen, Xing-Ming Zhao

DOI: 10.1101/2021.06.22.449514

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

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

by Hui Chong, Qingyang Yu, Yuguo Zha, Guangzhou Xiong, Nan Wang, Xinhe Huang, Shijuan Huang, Chuqing Sun, Sicheng Wu, Weihua Chen, Luis Pedro Coelho, Kang Ning

DOI: 10.1101/2021.01.29.428751

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

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

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, Falk Hildebrand, Thomas S. B. Schmidt, Simone S. Li, Joao F. Matias Rodrigues, Christian von Mering, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork

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

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, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Alves, Paul I Costea, Luis Pedro Coelho, Thomas S. B. Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D. Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller, Shinichi Sunagawa

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, Jaime Huerta-Cepas, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Christopher M. Field, Luis Pedro Coelho, Corinne Cruaud, Stefan Engelen, Ann C. Gregory, Karine Labadie, Claudie Marec, Eric Pelletier, Marta Royo-Llonch, Simon Roux, Pablo Sanchez, Hideya Uehara, Ahmed A. Zayed, Georg Zeller, Margaux Carmichael, Celine Dimier, Joannie Ferland, Stefanie Kandels, Marc Picheral, Sergey Pisarev, Julie Poulain, Silvia G. Acinas, Marcel Babin, Peer Bork, Chris Bowler, Colomban de Vargas, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Lee Karp-Boss, Eric Karsenti, Hiroyuki Ogata, Stephane Pesant, Sabrina Speich, Matthew B. Sullivan, Patrick Wincker, Shinichi Sunagawa, Silvia G. Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Michael Follows, Gabriel Gorsky, Nigel Grimsley, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels-Lewis, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Stephane Pesant, Nicole Poulton, Jeroen Raes, Christian Sardet, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker

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, Severine Martini, Greta Busseni, Hannah Byrne, Luis Pedro Coelho, Hisashi Endo, Josep M. Gasol, Ann C. Gregory, Frederic Mahe, Janaina Rigonato, Marta Royo-Llonch, Guillem Salazar, Isabel Sanz-Saez, Eleonora Scalco, Dodji Soviadan, Ahmed A. Zayed, Adriana Zingone, Karine Labadie, Joannie Ferland, Claudie Marec, Stefanie Kandels, Marc Picheral, Celine Dimier, Julie Poulain, Sergey Pisarev, Margaux Carmichael, Stephane Pesant, Marcel Babin, Emmanuel Boss, Daniele Iudicone, Olivier Jaillon, Silvia G. Acinas, Hiroyuki Ogata, Eric Pelletier, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Laurent Bopp, Colomban de Vargas, Lee Karp-Boss, Patrick Wincker, Fabien Lombard, Chris Bowler, Lucie Zinger, Silvia G. Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Mick Follows, Gabriel Gorsky, Nigel Grimsley, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Stephane Pesant, Nicole Poulton, Jeroen Raes, Christian Sardet, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, 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

[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, Thomas S B Schmidt, Alessio Milanese, Lucas Paoli, Ana Hernández-Plaza, Askarbek N Orakov, Sofia K Forslund, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, 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

[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, Konrad Zych, Alireza Kashani, Alessio Milanese, Jonas S. Fleck, Anita Y. Voigt, Albert Palleja, Ruby Ponnudurai, Shinichi Sunagawa, Luis Pedro Coelho, Petra Schrotz-King, Emily Vogtmann, Nina Habermann, Emma Nimeus, Andrew M. Thomas, Paolo Manghi, Sara Gandini, Davide Serrano, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Levi Waldron, Alessio Naccarati, Nicola Segata, Rashmi Sinha, Cornelia M. Ulrich, Hermann Brenner, Manimozhiyan Arumugam, Peer Bork, Georg Zeller

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, Simone S Li, Paul I Costea, Anita Y Voigt, Jakob Wirbel, Oleksandr M Maistrenko, Renato JC Alves, Emma Bergsten, Carine de Beaufort, Iradj Sobhani, Anna Heintz-Buschart, Shinichi Sunagawa, Georg Zeller, 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

[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, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Robert Hayward, Sofia K. Forslund, Thomas Sebastian Benedikt Schmidt, Patrick Descombes, Janet R. Jackson, Qinghong Li, Peer Bork

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, Jennifer L. Anderson, Nadejda A. Soudzilovskaia, Peter M. Bodegom, Johan Bengtsson-Palme, Sten Anslan, Luis Pedro Coelho, Helery Harend, Jaime Huerta-Cepas, Marnix H. Medema, Mia R. Maltz, Sunil Mundra, Pal Axel Olsson, Mari Pent, Sergei Polme, Shinichi Sunagawa, Martin Ryberg, Leho Tedersoo, Peer Bork

DOI: 10.1038/s41586-018-0386-6