eggNOG 6.0: enabling comparative genomics across 12 535 organisms - Ana Hernández-Plaza; Damian Szklarczyk; Jorge Botas; Carlos P. Cantalapiedra; Joaquín Giner-Lamia; Daniel R. Mende; Rebecca Kirsch; Thomas Rattei; Ivica Letunic; Lars Juhl Jensen; Peer Bork; Christian von Mering; et al. (Nucleic Acids Res., 2023)

DeepNOG: fast and accurate protein orthologous group assignment - Roman Feldbauer; Lukas Gosch; Lukas Lüftinger; Patrick Hyden; Arthur Flexer; Thomas Rattei (Bioinform., 2021)

Tamock: simulation of habitat-specific benchmark data in metagenomics - Samuel M. Gerner; Alexandra B. Graf; Thomas Rattei (BMC Bioinform., 2021)

scikit-hubness: Hubness Reduction and Approximate Neighbor Search - Roman Feldbauer; Thomas Rattei; Arthur Flexer (J. Open Source Softw., 2020)

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses - Jaime Huerta-Cepas; Damian Szklarczyk; Davide Heller; Ana Hernández-Plaza; Sofia K. Forslund; Helen Cook; Daniel R. Mende; Ivica Letunic; Thomas Rattei; Lars Juhl Jensen; Christian von Mering; Peer Bork (Nucleic Acids Res., 2019)

scikit-hubness: Hubness Reduction and Approximate Neighbor Search - Roman Feldbauer; Thomas Rattei; Arthur Flexer (CoRR, 2019)

ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes - Thomas Weinmaier; Alexander Platzer; Jeroen Frank; Hans-Jörg Hellinger; Patrick Tischler; Thomas Rattei (Bioinform., 2016)

NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies - Thomas Eder; Florian Grebien; Thomas Rattei (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; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2016)

probeBase - an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016 - Daniel Greuter; Alexander Loy; Matthias Horn; Thomas Rattei (Nucleic Acids Res., 2016)

EffectiveDB - updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems - Valerie Eichinger; Thomas Nussbaumer; Alexander Platzer; Marc-André Jehl; Roland Arnold; Thomas Rattei (Nucleic Acids Res., 2016)

Prediction of microbial phenotypes based on comparative genomics - Roman Feldbauer; Frederik Schulz; Matthias Horn; Thomas Rattei (BMC Bioinform., 2015)

Challenges in RNA virus bioinformatics - Manja Marz; Niko Beerenwinkel; Christian Drosten; Markus Fricke; Dmitrij Frishman; Ivo L. Hofacker; Dieter Hoffmann; Martin Middendorf; Thomas Rattei; Peter F. Stadler; Armin Töpfer (Bioinform., 2014)

eggNOG v4.0: nested orthology inference across 3686 organisms - Sean Powell; Kristoffer Forslund; Damian Szklarczyk; Kalliopi Trachana; Alexander Roth; Jaime Huerta-Cepas; Toni Gabaldón; Thomas Rattei; Christopher J. Creevey; Michael Kuhn; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2014)

SIMAP - the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage - Roland Arnold; Florian Goldenberg; Hans-Werner Mewes; Thomas Rattei (Nucleic Acids Res., 2014)

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges - Sean Powell; Damian Szklarczyk; Kalliopi Trachana; Alexander Roth; Michael Kuhn; Jean Muller; Roland Arnold; Thomas Rattei; Ivica Letunic; Tobias Doerks; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2012)

B2G-FAR, a species-centered GO annotation repository - Stefan Götz; Roland Arnold; Patricia Sebastián-León; Samuel Martín-Rodríguez; Patrick Tischler; Marc-André Jehl; Joaquín Dopazo; Thomas Rattei; Ana Conesa (Bioinform., 2011)

MIPS: curated databases and comprehensive secondary data resources in 2010 - Hans-Werner Mewes; Andreas Ruepp; Fabian J. Theis; Thomas Rattei; Mathias C. Walter; Dmitrij Frishman; Karsten Suhre; Manuel Spannagl; Klaus F. X. Mayer; Volker Stümpflen; Alexey V. Antonov (Nucleic Acids Res., 2011)

Effective - a database of predicted secreted bacterial proteins - Marc-André Jehl; Roland Arnold; Thomas Rattei (Nucleic Acids Res., 2011)

SIMAP - a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters - Thomas Rattei; Patrick Tischler; Stefan Götz; Marc-André Jehl; Jonathan Hoser; Roland Arnold; Ana Conesa; Hans-Werner Mewes (Nucleic Acids Res., 2010)

The Negatome database: a reference set of non-interacting protein pairs - Pawel Smialowski; Philipp Pagel; Philip Wong; Barbara Brauner; Irmtraud Dunger; Gisela Fobo; Goar Frishman; Corinna Montrone; Thomas Rattei; Dmitrij Frishman; Andreas Ruepp (Nucleic Acids Res., 2010)

PEDANT covers all complete RefSeq genomes - Mathias C. Walter; Thomas Rattei; Roland Arnold; Ulrich Güldener; Martin Münsterkötter; Karamfilka Nenova; Gabi Kastenmüller; Patrick Tischler; Andreas Wölling; Andreas Volz; Norbert Pongratz; Ralf Jost; et al. (Nucleic Acids Res., 2009)

Beyond the "best" match: machine learning annotation of protein sequences by integration of different sources of information - Igor V. Tetko; Igor V. Rodchenkov; Mathias C. Walter; Thomas Rattei; Hans-Werner Mewes (Bioinform., 2008)

MIPS: analysis and annotation of genome information in 2007 - Hans-Werner Mewes; Sabine Dietmann; Dmitrij Frishman; Richard Gregory; Gertrud Mannhaupt; Klaus F. X. Mayer; Martin Münsterkötter; Andreas Ruepp; Manuel Spannagl; Volker Stümpflen; Thomas Rattei (Nucleic Acids Res., 2008)

SIMAP - structuring the network of protein similarities - Thomas Rattei; Patrick Tischler; Roland Arnold; Franz Hamberger; Jörg Krebs; Jan Krumsiek; Benedikt Wachinger; Volker Stümpflen; Hans-Werner Mewes (Nucleic Acids Res., 2008)

Gepard: a rapid and sensitive tool for creating dotplots on genome scale - Jan Krumsiek; Roland Arnold; Thomas Rattei (Bioinform., 2007)

MIPS: analysis and annotation of proteins from whole genomes in 2005 - Hans-Werner Mewes; Dmitrij Frishman; Klaus F. X. Mayer; Martin Münsterkötter; Octave Noubibou; Philipp Pagel; Thomas Rattei; Matthias Oesterheld; Andreas Ruepp; Volker Stümpflen (Nucleic Acids Res., 2006)

SIMAP: the similarity matrix of proteins - Thomas Rattei; Roland Arnold; Patrick Tischler; Dominik Lindner; Volker Stümpflen; Hans-Werner Mewes (Nucleic Acids Res., 2006)

The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context - Andreas Ruepp; Octave Noubibou Doudieu; Jos van den Oever; Barbara Brauner; Irmtraud Dunger-Kaltenbach; Gisela Fobo; Goar Frishman; Corinna Montrone; Christine Skornia; Steffi Wanka; Thomas Rattei; Philipp Pagel; et al. (Nucleic Acids Res., 2006)

Using Public Resource Computing and Systematic Pre-calculation for Large Scale Sequence Analysis - Thomas Rattei; Mathias C. Walter; Roland Arnold; David P. Anderson; Hans-Werner Mewes (Distributed, High-Performance and Grid Computing in Computational Biology , International Workshop, GCCB 2006, Eilat, Israel, January 21, 2007, Proceeding, 2006)

SIMAP - The similarity matrix of proteins - Roland Arnold; Thomas Rattei; Patrick Tischler; Minh-Duc Truong; Volker Stümpflen; Hans-Werner Mewes (ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28 - October 1, 2005, 2005)