Thomas Rattei

According to our database, Thomas Rattei authored at least 30 papers between 2005 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

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, Jaime Huerta-Cepas

Nucleic Acids Res., January, 2023

2021

Tamock: simulation of habitat-specific benchmark data in metagenomics.

Samuel M. Gerner, Alexandra B. Graf, Thomas Rattei

BMC Bioinform., 2021

DeepNOG: fast and accurate protein orthologous group assignment.

Roman Feldbauer, Lukas Gosch, Lukas Lüftinger, Patrick Hyden, Arthur Flexer, Thomas Rattei

Bioinform., 2021

2020

scikit-hubness: Hubness Reduction and Approximate Neighbor Search.

Roman Feldbauer, Thomas Rattei, Arthur Flexer

J. Open Source Softw., 2020

2019

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

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, Peer Bork

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

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

2015

Prediction of microbial phenotypes based on comparative genomics.

Roman Feldbauer, Frederik Schulz, Matthias Horn, Thomas Rattei

BMC Bioinform., December, 2015

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, Peer Bork

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

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

2012

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, Peer Bork

Nucleic Acids Res., 2012

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

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

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

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

2009

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, Hans-Werner Mewes, Dmitrij Frishman

Nucleic Acids Res., 2009

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

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

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

2007

Gepard: a rapid and sensitive tool for creating dotplots on genome scale.

Jan Krumsiek, Roland Arnold, Thomas Rattei

Bioinform., 2007

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, M. Louise Riley, Dmitrij Frishman, Dimitrij Surmeli, Igor V. Tetko, Matthias Oesterheld, Volker Stümpflen, Hans-Werner Mewes

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

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

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

Proceedings of the Distributed, 2006

2005

SIMAP - The similarity matrix of proteins.

Roland Arnold, Thomas Rattei, Patrick Tischler, Minh-Duc Truong, Volker Stümpflen, Hans-Werner Mewes

Proceedings of the 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, 2005