Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. - 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; et al. (Nat., 2015)

MOCAT2: a metagenomic assembly, annotation and profiling framework. - 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 (Bioinform., 2016)

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. - Jaime Huerta-Cepas; Damian Szklarczyk; Kristoffer Forslund; Helen Cook; Davide Heller; Mathias C. Walter; Thomas Rattei; Daniel R. Mende; Shinichi Sunagawa; Michael Kuhn 004; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2016)

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. - Daniel R. Mende; Ivica Letunic; Jaime Huerta-Cepas; Simone S. Li; Kristoffer Forslund; Shinichi Sunagawa; Peer Bork (Nucleic Acids Res., 2017)

The Ocean Gene Atlas: exploring the biogeography of plankton genes online. - Emilie Villar; Thomas Vannier; Caroline Vernette; Magali Lescot; Miguelangel Cuenca; Aurélien Alexandre; Paul Bachelerie; Thomas Rosnet; Eric Pelletier; Shinichi Sunagawa; Pascal Hingamp (Nucleic Acids Res., 2018)

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. - 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; et al. (Nucleic Acids Res., 2020)

mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes. - Guillem Salazar; Hans-Joachim Ruscheweyh; Falk Hildebrand; Silvia G. Acinas; Shinichi Sunagawa (Bioinform., 2021)

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes. - Thea Van Rossum; Paul I. Costea; Lucas Paoli; Renato Alves; Roman Thielemann; Shinichi Sunagawa; Peer Bork (Bioinform., 2022)

The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. - 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; et al. (Nucleic Acids Res., 2022)

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. - Anthony Fullam; Ivica Letunic; Thomas S. B. Schmidt; Quinten R. Ducarmon; Nicolai Karcher; Supriya Khedkar; Michael Kuhn 004; Martin Larralde; Oleksandr M. Maistrenko; Lukas Malfertheiner; Alessio Milanese; João F. Matias Rodrigues; et al. (Nucleic Acids Res., 2023)

Dataset to: Environmental controls of dark CO2 fixation in wetland microbiota. - Luise Grüterich; Jason Nicholas Woodhouse; Peter Mueller; Amos Tiemann; Hans-Joachim Ruscheweyh; Shinichi Sunagawa; Hans-Peter Grossart; Wolfgang R. Streit (UHH-FDR, 2023)

Dataset to: Environmental controls of dark CO2 fixation in wetland microbiota. - Luise Grüterich; Jason Nicholas Woodhouse; Peter Mueller; Amos Tiemann; Hans-Joachim Ruscheweyh; Shinichi Sunagawa; Hans-Peter Grossart; Wolfgang R. Streit (UHH-FDR, 2023)

Dataset to: Environmental controls of dark CO2 fixation in wetland microbiomes. - Luise Grüterich; Jason Nicholas Woodhouse; Peter Mueller; Amos Tiemann; Hans-Joachim Ruscheweyh; Shinichi Sunagawa; Hans-Peter Grossart; Wolfgang R. Streit (UHH-FDR, 2023)

mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations. - Anna Sintsova; Hans-Joachim Ruscheweyh; Christopher M. Field; Lilith Feer; Bidong D. Nguyen; Benjamin Daniel; Wolf-Dietrich Hardt; Julia A. Vorholt; Shinichi Sunagawa (Bioinform., 2024)