List of works by Thomas Rattei

A Bioinformatics Guide to Plant Microbiome Analysis

scientific article published on 23 October 2019

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

scientific article

A comparative metagenome survey of the fecal microbiota of a breast- and a plant-fed Asian elephant reveals an unexpectedly high diversity of glycoside hydrolase family enzymes

scientific article

A distinct microbiota composition is associated with protection from food allergy in an oral mouse immunization model

scientific article

A promiscuous beta-glucosidase is involved in benzoxazinoid deglycosylation in Lamium galeobdolon

scientific article published on 15 October 2018

A proteotranscriptomic study of silk-producing glands from the orb-weaving spiders

scientific article published on 01 August 2019

A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses

scientific article published on 8 December 2015

Antiviral immune response reveals host-specific virus infections in natural ant populations

scientific article published in 2023

Asian horses deepen the MSY phylogeny

scientific article published on 15 January 2018

Assessment of urban microbiome assemblies with the help of targeted in silico gold standards

scientific article published on 12 October 2018

B2G-FAR, a species-centered GO annotation repository

scientific article

Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae)

scientific article

Beyond the 'best' match: machine learning annotation of protein sequences by integration of different sources of information.

scientific article

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

scientific article published on 26 November 2014

Cellulose as an extracellular matrix component present in Enterobacter sakazakii biofilms.

scientific article

Challenges in RNA virus bioinformatics

scientific article published on 03 March 2014

Characterization of 19 new microsatellite loci for the Omani barb Garra barreimiae from 454 sequences

scientific article

Characterization of a community-acquired-MRSA USA300 isolate from a river sample in Austria and whole genome sequence based comparison to a diverse collection of USA300 isolates.

scientific article published on 21 June 2018

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta

scientific article published on 25 July 2019

Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment.

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

Comparative analysis of benzoxazinoid biosynthesis in monocots and dicots: independent recruitment of stabilization and activation functions

scientific article published on 13 March 2012

Complete Genome Sequence of Listeria monocytogenes LL195, a Serotype 4b Strain from the 1983-1987 Listeriosis Epidemic in Switzerland

scientific article published on 31 January 2013

Complete Genome Sequence of Listeria monocytogenes Lm60, a Strain with an Enhanced Cold Adaptation Capacity

scientific article published on 4 December 2014

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

scientific article

Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T

scientific article

Complete nitrification by Nitrospira bacteria

scientific article

Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization

scientific article

Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae

scientific article

ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes

scientific article

Conserved Secondary Structures in Viral mRNAs.

scientific article published on 29 April 2019

Coral-associated viral communities show high levels of diversity and host auxiliary functions

scientific article

Correction: Sequence-Based Prediction of Type III Secreted Proteins.

scientific article published on 28 April 2009

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

scientific article published in February 2018

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

article

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

article

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

scientific article published on 2 October 2017

DNA-foraging bacteria in the seafloor

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

scientific article

Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies

scientific article

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

scientific article

DeepNOG: Fast and accurate protein orthologous group assignment

scientific article published on 26 December 2020

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

scientific article

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

scientific article

Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. P22, Isolated from Populus

scientific article published on 10 April 2014

Draft genome sequence of Lactobacillus casei W56.

scientific article

Effective--a database of predicted secreted bacterial proteins

scientific article

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

scientific article published on 20 November 2015

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

Exploring Actinobacteria Associated With Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium nivale Subspecies alpinum

scientific article published on 08 November 2019

Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea

scientific article published on 16 November 2020

Functional analysis of the finO distal region of plasmid R1.

scientific article published on 8 December 2010

Functionally relevant diversity of closely related Nitrospira in activated sludge.

scientific article

Genetic diversity of the obligate intracellular bacterium Chlamydophila pneumoniae by genome-wide analysis of single nucleotide polymorphisms: evidence for highly clonal population structure

scientific article

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

scientific article

Genome sequencing and analysis of the model grass Brachypodium distachyon

scientific article

Genome sequencing of Chlamydia trachomatis serovars E and F reveals substantial genetic variation

scientific article

Genomic factors related to tissue tropism in Chlamydia pneumoniae infection

scientific article published on 7 April 2015

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments

scientific article published on 14 June 2021

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

scientific article

Genomic insights into the metabolic potential of the polycyclic aromatic hydrocarbon degrading sulfate-reducing Deltaproteobacterium N47.

scientific article published on 22 December 2010

Genotyping of evolving prokaryotic populations

Genotyping of evolving prokaryotic populations

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

scientific article published on 19 February 2007

Great Cause-Small Effect: Undeclared Genetically Engineered Orange Petunias Harbor an Inefficient Dihydroflavonol 4-Reductase.

scientific article published on 28 February 2018

Growth of Chlamydia pneumoniae Is Enhanced in Cells with Impaired Mitochondrial Function

scientific article published on 5 December 2017

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

scientific article published on 13 October 2021

Helicobacter pylori in ancient human remains

scientific article published on 01 November 2019

High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved

scientific article

Highly variable mRNA half-life time within marine bacterial taxa and functional genes

scientific article published on 25 July 2019

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

scientific article published on 9 June 2016

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

scientific article published in October 2010

Illuminating the Evolutionary History of Chlamydiae

scientific article

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

scientific article

In vitro inhibition activity of different bacteriocin-producing Escherichia coli against Salmonella strains isolated from clinical cases

scientific article published on 17 April 2009

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

scientific article published on 25 May 2010

Insecticidal Toxicity of Involves the Novel Enterotoxin YacT

article

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

scientific article

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

Interplay between gut microbiota metabolism and inflammation in HIV infection

article

Learning From Limited Data: Towards Best Practice Techniques for Antimicrobial Resistance Prediction From Whole Genome Sequencing Data

publication published on 15 February 2021

Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota.

scientific article published on 31 January 2017

Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member

scientific article published in 2019

Long-term transcriptional activity at zero growth by a cosmopolitan rare biosphere member

MIPS: analysis and annotation of genome information in 2007

scientific article (publication date: 2008)

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

scientific article

MIPS: curated databases and comprehensive secondary data resources in 2010

scientific article

MScDB: a mass spectrometry-centric protein sequence database for proteomics

scientific article published on 14 May 2013

Man-made microbial resistances in built environments

article published in 2019

Massive expansion of Ubiquitination-related gene families within the Chlamydiae

scientific article

Metagenomic analysis reveals presence of Treponema denticola in a tissue biopsy of the Iceman

scientific article (publication date: 2014)

Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota

scientific article

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

scientific article

Minimum Information about an Uncultivated Virus Genome (MIUViG)

scientific article published on 17 December 2018

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

scientific article

Modification of the in vitro release profile of Cetrorelix by complexation with biophilic partners

scientific article

Molecular causes of an evolutionary shift along the parasitism-mutualism continuum in a bacterial symbiont

scientific article published on 19 August 2020

Molecular characterization of the alpha-glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism.

scientific article published on 24 March 2006

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

scientific article published on 15 October 2010

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

scientific article

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling

scientific article published on 12 May 2021

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

scientific article

PEDANT covers all complete RefSeq genomes

scientific article published on 21 October 2008

Peatland Acidobacteria with a dissimilatory sulfur metabolism

scientific article published on 23 February 2018

Peatland Acidobacteria with a dissimilatory sulfur metabolism

article published in 2017

Peripheral blood vessels are a niche for blood-borne meningococci.

scientific article

Phage morphology recapitulates phylogeny: the comparative genomics of a new group of myoviruses

scientific article published in 2012

Phenotypic and transcriptomic analyses of Sigma L-dependent characteristics in Listeria monocytogenes EGD-e.

scientific article published on 25 May 2012

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

scientific article

Plasmid DNA contaminant in molecular reagents

scientific article published in Scientific Reports

Prebiotic Effects of Partially Hydrolyzed Guar Gum on the Composition and Function of the Human Microbiota-Results from the PAGODA Trial

scientific article published on 28 April 2020

Prediction of microbial phenotypes based on comparative genomics.

scientific article published on 2 October 2015

Proteome Changes Paralleling the Olfactory Conditioning in the Forager Honey Bee and Provision of a Brain Proteomics Dataset

scientific article published on 24 June 2019

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

scientific article published in 2023

Recombination drives evolution of the Clostridium difficile 16S-23S rRNA intergenic spacer region

scientific article

Reef invertebrate viromics: diversity, host specificity and functional capacity.

scientific article published on 25 March 2018

Revealing the venomous secrets of the spider's web

scientific article published on 15 June 2020

SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters

scientific article

SIMAP--structuring the network of protein similarities

scientific article

SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

scientific article

SIMAP--the similarity matrix of proteins.

scientific article published in September 2005

SIMAP: the similarity matrix of proteins

scientific article

Sequence-based prediction of type III secreted proteins

scientific article

Shotgun sequencing of Yersinia enterocolitica strain W22703 (biotype 2, serotype O:9): genomic evidence for oscillation between invertebrates and mammals

scientific article

Signature protein of the PVC superphylum

scientific article

Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets

scientific article published on 8 September 2017

Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut

scientific article published on 31 March 2021

Tamock: simulation of habitat-specific benchmark data in metagenomics

scientific article published on 01 May 2021

Targeting effectors: the molecular recognition of Type III secreted proteins

scientific article published on 21 February 2010

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

scientific article

The Genetic Transformation of Chlamydia pneumoniae

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 Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals

article

The Intraperitoneal Transcriptome of the Opportunistic Pathogen Enterococcus faecalis in Mice

scientific article published on 15 May 2015

The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context

scientific article

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

scientific article published on 17 November 2009

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

scientific article published on 10 October 2019

The dynamic genome of Hydra

scientific article

The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks

scientific article

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

scientific article published on September 2004

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

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

The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements

scientific article published on 12 May 2015

The horse Y chromosome as an informative marker for tracing sire lines

scientific article published on 15 April 2019

The morphology, systematic position and inferred biology of Spirematospermum — An extinct genus of Zingiberales

Thermal stress modifies the marine sponge virome

scientific article published on 28 July 2019

Transcriptome Profiling of the Endophyte Burkholderia phytofirmans PsJN Indicates Sensing of the Plant Environment and Drought Stress

scientific article

Transcriptomic and Proteomic Analysis of Arion vulgaris--Proteins for Probably Successful Survival Strategies? ⬇️

scientific article

Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs

scientific article published on 03 February 2014

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

scientific article published on 20 June 2011

Unraveling the microbial processes of black band disease in corals through integrated genomics

scientific article published on 17 January 2017

VOGDB—Database of Virus Orthologous Groups

scientific article published on 25 July 2024

Variant profiling of evolving prokaryotic populations

scientific article published on 16 February 2017

Viral ecogenomics across the Porifera

scientific article published on 02 October 2020

Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples

scientific article published on 8 February 2017

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

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)

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

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

scientific article

eggNOG v4.0: nested orthology inference across 3686 organisms

scientific article (publication date: December 2013)

pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils

scientific article published on 12 December 2014

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

scientific article

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

scientific article

scikit-hubness: Hubness Reduction and Approximate Neighbor Search

scientific article published on 17 January 2020

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