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2020 – today
- 2023
[j28]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:
eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Res. 51(D1): 389-394 (2023)- 2021
- [j27]Roman Feldbauer, Lukas Gosch, Lukas Lüftinger, Patrick Hyden, Arthur Flexer, Thomas Rattei:
DeepNOG: fast and accurate protein orthologous group assignment. Bioinform. 36(22-23): 5304-5312 (2021) - [j26]Samuel M. Gerner, Alexandra B. Graf, Thomas Rattei:
Tamock: simulation of habitat-specific benchmark data in metagenomics. BMC Bioinform. 22(1): 227 (2021) - 2020
- [j25]Roman Feldbauer, Thomas Rattei, Arthur Flexer:
scikit-hubness: Hubness Reduction and Approximate Neighbor Search. J. Open Source Softw. 5(45): 1957 (2020)
2010 – 2019
- 2019
- [j24]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:
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47(Database-Issue): D309-D314 (2019) - [i1]Roman Feldbauer, Thomas Rattei, Arthur Flexer:
scikit-hubness: Hubness Reduction and Approximate Neighbor Search. CoRR abs/1912.00706 (2019) - 2016
- [j23]Thomas Weinmaier, Alexander Platzer, Jeroen Frank, Hans-Jörg Hellinger, Patrick Tischler, Thomas Rattei:
ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes. Bioinform. 32(21): 3327-3329 (2016) - [j22]Thomas Eder, Florian Grebien, Thomas Rattei:
NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies. Bioinform. 32(23): 3682-3684 (2016) - [j21]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:
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44(Database-Issue): 286-293 (2016) - [j20]Daniel Greuter, Alexander Loy, Matthias Horn, Thomas Rattei:
probeBase - an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016. Nucleic Acids Res. 44(Database-Issue): 586-589 (2016) - [j19]Valerie Eichinger, Thomas Nussbaumer, Alexander Platzer, Marc-André Jehl, Roland Arnold, Thomas Rattei:
EffectiveDB - updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. Nucleic Acids Res. 44(Database-Issue): 669-674 (2016) - 2015
- [j18]Roman Feldbauer, Frederik Schulz, Matthias Horn, Thomas Rattei:
Prediction of microbial phenotypes based on comparative genomics. BMC Bioinform. 16(S14): S1 (2015) - 2014
- [j17]Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer:
Challenges in RNA virus bioinformatics. Bioinform. 30(13): 1793-1799 (2014) - [j16]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:
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 42(Database-Issue): 231-239 (2014) - [j15]Roland Arnold, Florian Goldenberg, Hans-Werner Mewes, Thomas Rattei:
SIMAP - the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. Nucleic Acids Res. 42(Database-Issue): 279-284 (2014) - 2012
- [j14]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:
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 40(Database-Issue): 284-289 (2012) - 2011
- [j13]Stefan Götz, Roland Arnold, Patricia Sebastián-León, Samuel Martín-Rodríguez, Patrick Tischler, Marc-André Jehl, Joaquín Dopazo, Thomas Rattei, Ana Conesa:
B2G-FAR, a species-centered GO annotation repository. Bioinform. 27(7): 919-924 (2011) - [j12]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:
MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res. 39(Database-Issue): 220-224 (2011) - [j11]Marc-André Jehl, Roland Arnold, Thomas Rattei:
Effective - a database of predicted secreted bacterial proteins. Nucleic Acids Res. 39(Database-Issue): 591-595 (2011) - 2010
- [j10]Thomas Rattei, Patrick Tischler, Stefan Götz, Marc-André Jehl, Jonathan Hoser, Roland Arnold, Ana Conesa, Hans-Werner Mewes:
SIMAP - a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Res. 38(Database-Issue): 223-226 (2010) - [j9]Pawel Smialowski, Philipp Pagel, Philip Wong, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Thomas Rattei, Dmitrij Frishman, Andreas Ruepp:
The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res. 38(Database-Issue): 540-544 (2010)
2000 – 2009
- 2009
- [j8]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:
PEDANT covers all complete RefSeq genomes. Nucleic Acids Res. 37(Database-Issue): 408-411 (2009) - 2008
- [j7]Igor V. Tetko, Igor V. Rodchenkov, Mathias C. Walter, Thomas Rattei, Hans-Werner Mewes:
Beyond the "best" match: machine learning annotation of protein sequences by integration of different sources of information. Bioinform. 24(5): 621-628 (2008) - [j6]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:
MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res. 36(Database-Issue): 196-201 (2008) - [j5]Thomas Rattei, Patrick Tischler, Roland Arnold, Franz Hamberger, Jörg Krebs, Jan Krumsiek, Benedikt Wachinger, Volker Stümpflen, Hans-Werner Mewes:
SIMAP - structuring the network of protein similarities. Nucleic Acids Res. 36(Database-Issue): 289-292 (2008) - 2007
- [j4]Jan Krumsiek, Roland Arnold, Thomas Rattei:
Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinform. 23(8): 1026-1028 (2007) - 2006
- [j3]Hans-Werner Mewes, Dmitrij Frishman, Klaus F. X. Mayer, Martin Münsterkötter, Octave Noubibou, Philipp Pagel, Thomas Rattei, Matthias Oesterheld, Andreas Ruepp, Volker Stümpflen:
MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res. 34(Database-Issue): 169-172 (2006) - [j2]Thomas Rattei, Roland Arnold, Patrick Tischler, Dominik Lindner, Volker Stümpflen, Hans-Werner Mewes:
SIMAP: the similarity matrix of proteins. Nucleic Acids Res. 34(Database-Issue): 252-256 (2006) - [j1]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:
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res. 34(Database-Issue): 568-571 (2006) - [c2]Thomas Rattei, Mathias C. Walter, Roland Arnold, David P. Anderson, Hans-Werner Mewes:
Using Public Resource Computing and Systematic Pre-calculation for Large Scale Sequence Analysis. GCCB 2006: 11-18 - 2005
- [c1]Roland Arnold, Thomas Rattei, Patrick Tischler, Minh-Duc Truong, Volker Stümpflen, Hans-Werner Mewes:
SIMAP - The similarity matrix of proteins. ECCB/JBI 2005: 46
Coauthor Index
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