Thomas Rattei

Research interests

Publications

• Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

  Nature · 2023 · https://doi.org/10.1038/s41586-022-05546-8

• eggNOG 6.0: enabling comparative genomics across 12 535 organisms

  Nucleic Acids Research · 2022 · https://doi.org/10.1093/nar/gkac1022

• The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

  Cell Host & Microbe · 2019 · https://doi.org/10.1016/j.chom.2019.08.018

• Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

  Environmental Microbiology · 2018 · https://doi.org/10.1111/1462-2920.14043

• Minimum Information about an Uncultivated Virus Genome (MIUViG)

  Nature Biotechnology · 2018 · https://doi.org/10.1038/nbt.4306

• eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

  Nucleic Acids Research · 2018 · https://doi.org/10.1093/nar/gky1085

• Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

  Nature Biotechnology · 2017 · https://doi.org/10.1038/nbt.3893

• Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

  Nature Methods · 2017 · https://doi.org/10.1038/nmeth.4458

• eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

  Nucleic Acids Research · 2015 · https://doi.org/10.1093/nar/gkv1248

• Complete nitrification by Nitrospira bacteria

  Nature · 2015 · https://doi.org/10.1038/nature16461

• Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

  The ISME Journal · 2014 · https://doi.org/10.1038/ismej.2014.208

• NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite‐oxidizing N itrospira

  Environmental Microbiology · 2013 · https://doi.org/10.1111/1462-2920.12300

• Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

  Genome biology · 2013 · https://doi.org/10.1186/gb-2013-14-2-r11

• eggNOG v4.0: nested orthology inference across 3686 organisms

  Nucleic Acids Research · 2013 · 10.1093/nar/gkt1253

• The genome of the ammonia‐oxidizing C andidatus N itrososphaera gargensis: insights into metabolic versatility and environmental adaptations

  Environmental Microbiology · 2012 · https://doi.org/10.1111/j.1462-2920.2012.02893.x

• amoA ‐based consensus phylogeny of ammonia‐oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions

  Environmental Microbiology · 2011 · https://doi.org/10.1111/j.1462-2920.2011.02666.x

• eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

  Nucleic Acids Research · 2011 · 10.1093/nar/gkr1060

• A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria

  Proceedings of the National Academy of Sciences · 2010 · 10.1073/pnas.1003860107

• The dynamic genome of Hydra

  Nature · 2010 · https://doi.org/10.1038/nature08830

• Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota

  Trends in Microbiology · 2010 · https://doi.org/10.1016/j.tim.2010.06.003

• Sequence-Based Prediction of Type III Secreted Proteins

  PLoS Pathogens · 2009 · https://doi.org/10.1371/journal.ppat.1000376

• Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts

  Environmental Microbiology · 2009 · https://doi.org/10.1111/j.1462-2920.2009.02065.x

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

  Bioinformatics · 2007 · https://doi.org/10.1093/bioinformatics/btm039

• Deciphering the evolution and metabolism of an anammox bacterium from a community genome

  Nature · 2006 · https://doi.org/10.1038/nature04647

• Illuminating the Evolutionary History of Chlamydiae

  Science · 2004 · https://doi.org/10.1126/science.1096330

Current projects

No projects listed.