Thomas Rattei

32 papers Journal 30Unranked 2
YearRankTypeTitle / Venue / Authors
2024 J jnl
PyCoMo: a python package for community metabolic model creation and analysis.
Bioinform.
Michael Predl, Marianne Mießkes, Thomas Rattei, Jürgen Zanghellini
2023 J jnl
eggNOG 6.0: enabling comparative genomics across 12 535 organisms.
Nucleic Acids Res.
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, Jaime Huerta-Cepas
2021 J jnl
DeepNOG: fast and accurate protein orthologous group assignment.
Bioinform.
Roman Feldbauer, Lukas Gosch, Lukas Lüftinger, Patrick Hyden, Arthur Flexer, Thomas Rattei
2021 J jnl
Tamock: simulation of habitat-specific benchmark data in metagenomics.
BMC Bioinform.
Samuel M. Gerner, Alexandra B. Graf, Thomas Rattei
2020 J jnl
scikit-hubness: Hubness Reduction and Approximate Neighbor Search.
J. Open Source Softw.
Roman Feldbauer, Thomas Rattei, Arthur Flexer
2019 J jnl
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Nucleic Acids Res.
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
2019 J jnl
scikit-hubness: Hubness Reduction and Approximate Neighbor Search.
CoRR
Roman Feldbauer, Thomas Rattei, Arthur Flexer
2016 J jnl
ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes.
Bioinform.
Thomas Weinmaier, Alexander Platzer, Jeroen Frank, Hans-Jörg Hellinger, Patrick Tischler, Thomas Rattei
2016 J jnl
EffectiveDB - updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems.
Nucleic Acids Res.
Valerie Eichinger, Thomas Nussbaumer, Alexander Platzer, Marc-André Jehl, Roland Arnold, Thomas Rattei
2016 J jnl
NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies.
Bioinform.
Thomas Eder, Florian Grebien, Thomas Rattei
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
2016 J jnl
probeBase - an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016.
Nucleic Acids Res.
Daniel Greuter, Alexander Loy, Matthias Horn, Thomas Rattei
2015 J jnl
Prediction of microbial phenotypes based on comparative genomics.
BMC Bioinform.
Roman Feldbauer, Frederik Schulz, Matthias Horn, Thomas Rattei
2014 J jnl
Challenges in RNA virus bioinformatics.
Bioinform.
Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer
2014 J jnl
SIMAP - the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.
Nucleic Acids Res.
Roland Arnold, Florian Goldenberg, Hans-Werner Mewes, Thomas Rattei
2014 J jnl
eggNOG v4.0: nested orthology inference across 3686 organisms.
Nucleic Acids Res.
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, Peer Bork
2012 J jnl
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Nucleic Acids Res.
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, Peer Bork
2011 J jnl
B2G-FAR, a species-centered GO annotation repository.
Bioinform.
Stefan Götz, Roland Arnold, Patricia Sebastián-León, Samuel Martín-Rodríguez, Patrick Tischler, Marc-André Jehl, Joaquín Dopazo, Thomas Rattei, Ana Conesa
2011 J jnl
Effective - a database of predicted secreted bacterial proteins.
Nucleic Acids Res.
Marc-André Jehl, Roland Arnold, Thomas Rattei
2011 J jnl
MIPS: curated databases and comprehensive secondary data resources in 2010.
Nucleic Acids Res.
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
2010 J jnl
SIMAP - a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.
Nucleic Acids Res.
Thomas Rattei, Patrick Tischler, Stefan Götz, Marc-André Jehl, Jonathan Hoser, Roland Arnold, Ana Conesa, Hans-Werner Mewes
2010 J jnl
The Negatome database: a reference set of non-interacting protein pairs.
Nucleic Acids Res.
Pawel Smialowski, Philipp Pagel, Philip Wong, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Thomas Rattei, Dmitrij Frishman, Andreas Ruepp
2009 J jnl
PEDANT covers all complete RefSeq genomes.
Nucleic Acids Res.
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, Hans-Werner Mewes, Dmitrij Frishman
2008 J jnl
Beyond the "best" match: machine learning annotation of protein sequences by integration of different sources of information.
Bioinform.
Igor V. Tetko, Igor V. Rodchenkov, Mathias C. Walter, Thomas Rattei, Hans-Werner Mewes
2008 J jnl
MIPS: analysis and annotation of genome information in 2007.
Nucleic Acids Res.
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
2008 J jnl
SIMAP - structuring the network of protein similarities.
Nucleic Acids Res.
Thomas Rattei, Patrick Tischler, Roland Arnold, Franz Hamberger, Jörg Krebs, Jan Krumsiek, Benedikt Wachinger, Volker Stümpflen, Hans-Werner Mewes
2007 J jnl
Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
Bioinform.
Jan Krumsiek, Roland Arnold, Thomas Rattei
2006 J jnl
MIPS: analysis and annotation of proteins from whole genomes in 2005.
Nucleic Acids Res.
Hans-Werner Mewes, Dmitrij Frishman, Klaus F. X. Mayer, Martin Münsterkötter, Octave Noubibou, Philipp Pagel, Thomas Rattei, Matthias Oesterheld, Andreas Ruepp, Volker Stümpflen
2006 J jnl
SIMAP: the similarity matrix of proteins.
Nucleic Acids Res.
Thomas Rattei, Roland Arnold, Patrick Tischler, Dominik Lindner, Volker Stümpflen, Hans-Werner Mewes
2006 J jnl
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context.
Nucleic Acids Res.
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, M. Louise Riley, Dmitrij Frishman, Dimitrij Surmeli, Igor V. Tetko, Matthias Oesterheld, Volker Stümpflen, Hans-Werner Mewes
2006 — conf
Using Public Resource Computing and Systematic Pre-calculation for Large Scale Sequence Analysis.
GCCB
Thomas Rattei, Mathias C. Walter, Roland Arnold, David P. Anderson, Hans-Werner Mewes
2005 — conf
SIMAP - The similarity matrix of proteins.
ECCB/JBI
Roland Arnold, Thomas Rattei, Patrick Tischler, Minh-Duc Truong, Volker Stümpflen, Hans-Werner Mewes