Thomas Rattei

According to our database1, Thomas Rattei authored at least 27 papers between 2005 and 2021.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


Online presence:



DeepNOG: fast and accurate protein orthologous group assignment.
Bioinform., 2021

scikit-hubness: Hubness Reduction and Approximate Neighbor Search.
J. Open Source Softw., 2020

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Nucleic Acids Res., 2019

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Nucleic Acids Res., 2016

probeBase - an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016.
Nucleic Acids Res., 2016

EffectiveDB - updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems.
Nucleic Acids Res., 2016

ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes.
Bioinform., 2016

NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies.
Bioinform., 2016

eggNOG v4.0: nested orthology inference across 3686 organisms.
Nucleic Acids Res., 2014

SIMAP - the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.
Nucleic Acids Res., 2014

Challenges in RNA virus bioinformatics.
Bioinform., 2014

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Nucleic Acids Res., 2012

MIPS: curated databases and comprehensive secondary data resources in 2010.
Nucleic Acids Res., 2011

Effective - a database of predicted secreted bacterial proteins.
Nucleic Acids Res., 2011

B2G-FAR, a species-centered GO annotation repository.
Bioinform., 2011

The Negatome database: a reference set of non-interacting protein pairs.
Nucleic Acids Res., 2010

SIMAP - a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.
Nucleic Acids Res., 2010

PEDANT covers all complete RefSeq genomes.
Nucleic Acids Res., 2009

SIMAP - structuring the network of protein similarities.
Nucleic Acids Res., 2008

MIPS: analysis and annotation of genome information in 2007.
Nucleic Acids Res., 2008

Beyond the "best" match: machine learning annotation of protein sequences by integration of different sources of information.
Bioinform., 2008

Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
Bioinform., 2007

The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context.
Nucleic Acids Res., 2006

SIMAP: the similarity matrix of proteins.
Nucleic Acids Res., 2006

MIPS: analysis and annotation of proteins from whole genomes in 2005.
Nucleic Acids Res., 2006

Using Public Resource Computing and Systematic Pre-calculation for Large Scale Sequence Analysis.
Proceedings of the Distributed, 2006

SIMAP - The similarity matrix of proteins.
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