Shinichi Sunagawa

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2024 J jnl
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations.
Bioinform.
Anna Sintsova, Hans-Joachim Ruscheweyh, Christopher M. Field, Lilith Feer, Bidong D. Nguyen, Benjamin Daniel, Wolf-Dietrich Hardt, Julia A. Vorholt, Shinichi Sunagawa
2023 J jnl
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Nucleic Acids Res.
Anthony Fullam, Ivica Letunic, Thomas S. B. Schmidt, Quinten R. Ducarmon, Nicolai Karcher, Supriya Khedkar, Michael Kuhn, Martin Larralde, Oleksandr M. Maistrenko, Lukas Malfertheiner, Alessio Milanese, João F. Matias Rodrigues, Claudia Sanchis-López, Christian Schudoma, Damian Szklarczyk, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Christian von Mering, Peer Bork, Daniel R. Mende
2022 J jnl
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.
Nucleic Acids Res.
Caroline Vernette, Julien Lecubin, Pablo Sánchez, Silvia G. Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Gabriel Gorsky, Lionel Guidi, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels-Lewis, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole Poulton, Stephane Pesant, Christian Sardet, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker, Tom O. Delmont, Eric Pelletier, Magali Lescot
2022 J jnl
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes.
Bioinform.
Thea Van Rossum, Paul I. Costea, Lucas Paoli, Renato Alves, Roman Thielemann, Shinichi Sunagawa, Peer Bork
2021 J jnl
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes.
Bioinform.
Guillem Salazar, Hans-Joachim Ruscheweyh, Falk Hildebrand, Silvia G. Acinas, Shinichi Sunagawa
2020 J jnl
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Nucleic Acids Res.
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, Luís Pedro Coelho, Peer Bork
2018 J jnl
The Ocean Gene Atlas: exploring the biogeography of plankton genes online.
Nucleic Acids Res.
Emilie Villar, Thomas Vannier, Caroline Vernette, Magali Lescot, Miguelangel Cuenca, Aurélien Alexandre, Paul Bachelerie, Thomas Rosnet, Eric Pelletier, Shinichi Sunagawa, Pascal Hingamp
2017 J jnl
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Nucleic Acids Res.
Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
2016 J jnl
MOCAT2: a metagenomic assembly, annotation and profiling framework.
Bioinform.
Jens Roat Kultima, Luís Pedro Coelho, Kristoffer Forslund, Jaime Huerta-Cepas, Simone S. Li, Marja Driessen, Anita Yvonne Voigt, Georg Zeller, Shinichi Sunagawa, Peer Bork
2016 J jnl
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Nucleic Acids Res.
Jaime Huerta-Cepas, Damian Szklarczyk, Kristoffer Forslund, Helen Cook, Davide Heller, Mathias C. Walter, Thomas Rattei, Daniel R. Mende, Shinichi Sunagawa, Michael Kuhn, Lars Juhl Jensen, Christian von Mering, Peer Bork
2015 J jnl
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Nat.
Kristoffer Forslund, Falk Hildebrand, Trine Nielsen, Gwen Falony, Emmanuelle Le Chatelier, Shinichi Sunagawa, Edi Prifti, Sara Vieira-Silva, Valborg Gudmundsdottir, Helle Krogh Pedersen, Manimozhiyan Arumugam, Karsten Kristiansen, Anita Yvonne Voigt, Henrik Vestergaard, Rajna Hercog, Paul I. Costea, Jens Roat Kultima, Junhua Li, Torben Jørgensen, Florence Levenez, Joël Dore, Henrik Bjørn Nielsen, Søren Brunak, Jeroen Raes, Torben Hansen, Jun Wang, S. Dusko Ehrlich, Peer Bork, Oluf Pedersen