Publications

17. 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

16. 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

15. 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

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

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

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

11. 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

10. 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

9. 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

8. 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

7. 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

6. 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

5. 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

4. 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

3. 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

2. 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

1. 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

Year

Lab Member

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