List of works - Thomas Rattei

Genome sequencing and analysis of the model grass Brachypodium distachyon

scientific article

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

scientific article (publication date: 17 November 2015)

The dynamic genome of Hydra

scientific article

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

scientific article

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

scientific article published on 19 February 2007

Complete nitrification by Nitrospira bacteria

scientific article

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

scientific article

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

scientific article

eggNOG v4.0: nested orthology inference across 3686 organisms

scientific article (publication date: December 2013)

Illuminating the Evolutionary History of Chlamydiae

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

MIPS: analysis and annotation of proteins from whole genomes in 2005.

scientific article

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

scientific article published on 2 October 2017

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

scientific article

Sequence-based prediction of type III secreted proteins

scientific article

The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations.

scientific article

probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity

scientific article

Unity in variety--the pan-genome of the Chlamydiae

scientific article published on 20 June 2011

The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments

scientific article published on September 2004

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

scientific article

B2G-FAR, a species-centered GO annotation repository

scientific article

The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer

scientific article

The Genome of the Amoeba Symbiont "Candidatus Amoebophilus asiaticus" Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria

scientific article

The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution

scientific article published on 25 October 2012

MIPS: analysis and annotation of genome information in 2007

scientific article (publication date: 2008)

PEDANT covers all complete RefSeq genomes

scientific article published on 21 October 2008

Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community

scientific article

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

scientific article published on 01 January 2019

The 5300-year-old Helicobacter pylori genome of the Iceman

scientific article

Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana

scientific article

Effective--a database of predicted secreted bacterial proteins

scientific article

The Negatome database: a reference set of non-interacting protein pairs

scientific article published on 17 November 2009

NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira.

scientific article

Independent evolution of the core domain and its flanking sequences in small heat shock proteins

scientific article published on 25 May 2010

Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet

scientific article

Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

scientific article published on August 15, 2013

Internalization of Pseudomonas aeruginosa Strain PAO1 into Epithelial Cells Is Promoted by Interaction of a T6SS Effector with the Microtubule Network

scientific article published on 2 June 2015

Functionally relevant diversity of closely related Nitrospira in activated sludge.

scientific article

Complete genome sequence of Cronobacter turicensis LMG 23827, a food-borne pathogen causing deaths in neonates

scientific article

MIPS: curated databases and comprehensive secondary data resources in 2010

scientific article

Molecular recognition determinants for type IV secretion of diverse families of conjugative relaxases

scientific article published on 15 October 2010

Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing

scientific article published on 25 June 2012

Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface

scientific article published on 26 November 2014

Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture

scientific article published in October 2010

probeBase--an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016

scientific article

Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47.

scientific article published on January 2010

Minimum Information about an Uncultivated Virus Genome (MIUViG)

scientific article published on 17 December 2018

List of works by Thomas Rattei

Genome sequencing and analysis of the model grass Brachypodium distachyon

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

The dynamic genome of Hydra

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

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

Complete nitrification by Nitrospira bacteria

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

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

eggNOG v4.0: nested orthology inference across 3686 organisms

Illuminating the Evolutionary History of Chlamydiae

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

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

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

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

MIPS: analysis and annotation of proteins from whole genomes in 2005.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

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

Sequence-based prediction of type III secreted proteins

The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations.

probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity

Unity in variety--the pan-genome of the Chlamydiae

The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments

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

B2G-FAR, a species-centered GO annotation repository

The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer

The Genome of the Amoeba Symbiont "Candidatus Amoebophilus asiaticus" Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria

The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution

MIPS: analysis and annotation of genome information in 2007

PEDANT covers all complete RefSeq genomes

Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community

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

The 5300-year-old Helicobacter pylori genome of the Iceman

Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana

Effective--a database of predicted secreted bacterial proteins

The Negatome database: a reference set of non-interacting protein pairs

NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira.

Independent evolution of the core domain and its flanking sequences in small heat shock proteins

Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet

Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

Internalization of Pseudomonas aeruginosa Strain PAO1 into Epithelial Cells Is Promoted by Interaction of a T6SS Effector with the Microtubule Network

Functionally relevant diversity of closely related Nitrospira in activated sludge.

Complete genome sequence of Cronobacter turicensis LMG 23827, a food-borne pathogen causing deaths in neonates

MIPS: curated databases and comprehensive secondary data resources in 2010

Molecular recognition determinants for type IV secretion of diverse families of conjugative relaxases

Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing

Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface

Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture

probeBase--an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016

Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47.

Minimum Information about an Uncultivated Virus Genome (MIUViG)