Standout Papers
- eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015)
- Complete nitrification by Nitrospira bacteria (2015)
- eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018)
Citation Impact
Citing Papers
Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes
2020 StandoutNobel
Protein interaction networks revealed by proteome coevolution
2019 StandoutScienceNobel
Accurate prediction of orthologs in the presence of divergence after duplication
2018
Gene essentiality and synthetic lethality in haploid human cells
2015 Science
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
2021
Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions
2009 StandoutScience
Machine learning predicts new anti-CRISPR proteins
2020 StandoutNobel
A rooted phylogeny resolves early bacterial evolution
2021 Science
Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation
2017 Science
One thousand plant transcriptomes and the phylogenomics of green plants
2019 StandoutNature
Rapid and automated design of two-component protein nanomaterials using ProteinMPNN
2024 StandoutNobel
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
2012 Standout
The future of ancient DNA: Technical advances and conceptual shifts
2014
Ammonia-Oxidising Archaea – Physiology, Ecology and Evolution
2010
Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR–Cas system
2016
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
2023 StandoutNobel
WGCNA: an R package for weighted correlation network analysis
2008 Standout
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems
2016
HINT: High-quality protein interactomes and their applications in understanding human disease
2012
Structure of a VirD4 coupling protein bound to a VirB type IV secretion machinery
2017
From conjugation to T4S systems in Gram‐negative bacteria: a mechanistic biology perspective
2019
OrthoFinder: phylogenetic orthology inference for comparative genomics
2019 Standout
A core gut microbiome in obese and lean twins
2008 StandoutNature
The technological and economic prospects for CO2 utilization and removal
2019 StandoutNature
Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without FtsZ
2013
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
2012 Standout
A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria
2016
Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME‐1 group
2009
Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis
2011
Classification and evolution of type II CRISPR-Cas systems
2014 StandoutNobel
AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment
2017
Protein Complexes in Bacteria
2015
STRING v10: protein–protein interaction networks, integrated over the tree of life
2014 Standout
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
2015 Standout
Metabolic-network-driven analysis of bacterial ecological strategies
2009
New CRISPR–Cas systems from uncultivated microbes
2016 StandoutNatureNobel
CORUM: the comprehensive resource of mammalian protein complexes—2009
2009
Complete nitrification by a single microorganism
2015 Nature
The ecology and biotechnology of sulphate-reducing bacteria
2008 Standout
Membrane-bound electron transport systems of an anammox bacterium: A complexome analysis
2016
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
2016 Standout
STRING 7--recent developments in the integration and prediction of protein interactions
2006
The Heat Shock Response: Life on the Verge of Death
2010 Standout
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold
2019
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams
2021
Defining and combating antibiotic resistance from One Health and Global Health perspectives
2019
VisANT: an integrative framework for networks in systems biology
2008
PIPs: human protein-protein interaction prediction database
2008
NOD1 and NOD2 signalling links ER stress with inflammation
2016 StandoutNature
Hieranoid: Hierarchical Orthology Inference
2013
A Cell-Penetrating Scorpion Toxin Enables Mode-Specific Modulation of TRPA1 and Pain
2019 StandoutNobel
Effects of microbial activity on perfluorinated carboxylic acids (PFCAs) generation during aerobic biotransformation of fluorotelomer alcohols in activated sludge
2017
The distinction of CPR bacteria from other bacteria based on protein family content
2019
Unusual biology across a group comprising more than 15% of domain Bacteria
2015 Nature
Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla
2019
The nitrogen cycle
2016
A Burkholderia Type VI Effector Deamidates Rho GTPases to Activate the Pyrin Inflammasome and Trigger Inflammation
2016
Hypoxia Rescues Frataxin Loss by Restoring Iron Sulfur Cluster Biogenesis
2019 StandoutNobel
How to make a living from anaerobic ammonium oxidation
2012
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
2013 StandoutNature
Targeted isolation and cultivation of uncultivated bacteria by reverse genomics
2019
Evolutionary conservation and in vitro reconstitution of microsporidian iron–sulfur cluster biosynthesis
2017
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer
2012
Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks
2020 StandoutNobel
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
2013 Standout
Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle
2017 Nature
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
2010 Standout
The Biology of CRISPR-Cas: Backward and Forward
2018 StandoutNobel
Diversity, stability and resilience of the human gut microbiota
2012 StandoutNature
Cyanate as an energy source for nitrifiers
2015 Nature
Cryo-EM structure of a type IV secretion system
2022 StandoutNatureNobel
O-GlcNAc modification of small heat shock proteins enhances their anti-amyloid chaperone activity
2021 StandoutNobel
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
2016
Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations
2012
The microbial nitrogen-cycling network
2018 Standout
Chemotherapy drugs induce pyroptosis through caspase-3 cleavage of a gasdermin
2017 StandoutNature
In vivo 3′-to-5′ exoribonuclease targetomes of Streptococcus pyogenes
2018 StandoutNobel
DeepFunc: A Deep Learning Framework for Accurate Prediction of Protein Functions from Protein Sequences and Interactions
2019
Genome-wide functional association networks: background, data & state-of-the-art resources
2019
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
2010 Standout
Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa
2015 StandoutScience
Beyond fossil fuel–driven nitrogen transformations
2018 StandoutScienceNobel
Viruses.STRING: A Virus-Host Protein-Protein Interaction Database
2018
How Biology Handles Nitrite
2014
Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution
2013 Science
Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea
2012
Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus
2017
TISSUES 2.0: an integrative web resource on mammalian tissue expression
2018
Decoupling function and taxonomy in the global ocean microbiome
2016 StandoutScience
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell‐lines
2015
De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity
2016 StandoutScienceNobel
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes
2018 StandoutScienceNobel
Imaging bacterial peptidoglycan with near-infrared fluorogenic azide probes
2014 StandoutNobel
Psychrophilic microorganisms: challenges for life
2006 Standout
Abiotic Conversion of Extracellular NH2OH Contributes to N2O Emission during Ammonia Oxidation
2017
Evolutionary-scale prediction of atomic-level protein structure with a language model
2023 StandoutScience
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest
2022 Standout
MGnify: the microbiome analysis resource in 2020
2019
Chlamydiaeinteraction with the endoplasmic reticulum: contact, function and consequences
2015
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
2018 Standout
Identification of simple arylfluorosulfates as potent agents against resistant bacteria
2021 StandoutNobel
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
2019
Nitrososphaera viennensis , an ammonia oxidizing archaeon from soil
2011
Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira
2015
Crenothrix are major methane consumers in stratified lakes
2017
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
2017
Enzymology and ecology of the nitrogen cycle
2011
Per- and polyfluoroalkyl substances in the environment
2022 StandoutScience
Towards an integrated model of bacterial conjugation
2014
Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation
2014 Science
Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota
2016
E3 ubiquitin ligase Mindbomb 1 facilitates nuclear delivery of adenovirus genomes
2020 StandoutNobel
Accurate proteome-wide missense variant effect prediction with AlphaMissense
2023 StandoutScienceNobel
VFDB 2019: a comparative pathogenomic platform with an interactive web interface
2018
De novo design of protein logic gates
2020 StandoutScienceNobel
Evolution Stings: The Origin and Diversification of Scorpion Toxin Peptide Scaffolds
2013
Cultivation of a vampire: ‘ Candidatus Absconditicoccus praedator’
2021
SAR11 bacteria linked to ocean anoxia and nitrogen loss
2016 Nature
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles
2015
Works of Thomas Rattei being referenced
Illuminating the Evolutionary History of Chlamydiae
2004 Science
Functionally relevant diversity of closely related Nitrospira in activated sludge
2014
Man-made microbial resistances in built environments
2019
The Genome of the Obligate Intracellular Parasite Trachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution
2012
The genome of Desulfotalea psychrophila , a sulfate‐reducing bacterium from permanently cold Arctic sediments
2004
Complete nitrification by Nitrospira bacteria
2015 StandoutNature
Unity in Variety--The Pan-Genome of the Chlamydiae
2011
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
2015 Standout
Metatranscriptomics of the marine sponge Geodia barretti : tackling phylogeny and function of its microbial community
2012
eggNOG v4.0: nested orthology inference across 3686 organisms
2013
Sequence-Based Prediction of Type III Secreted Proteins
2009
Metagenomic Analysis Reveals Presence of Treponema denticola in a Tissue Biopsy of the Iceman
2014
Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota
2010
Molecular recognition determinants for type IV secretion of diverse families of conjugative relaxases
2010
The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer
2013
MIPS: analysis and annotation of genome information in 2007
2007
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
2011
SIMAP: the similarity matrix of proteins
2005
SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters
2009
amoA ‐based consensus phylogeny of ammonia‐oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions
2011
SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage
2013
B2G-FAR, a species-centered GO annotation repository
2011
A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria
2010
The genome of the ammonia‐oxidizing C andidatus N itrososphaera gargensis: insights into metabolic versatility and environmental adaptations
2012
MIPS: curated databases and comprehensive secondary data resources in 2010
2010
2013
Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases
2014
Phage Morphology Recapitulates Phylogeny: The Comparative Genomics of a New Group of Myoviruses
2012
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
2018 Standout
Signature Protein of the PVC Superphylum
2013
Independent evolution of the core domain and its flanking sequences in small heat shock proteins
2010
Gepard: a rapid and sensitive tool for creating dotplots on genome scale
2007
Internalization of Pseudomonas aeruginosa Strain PAO1 into Epithelial Cells Is Promoted by Interaction of a T6SS Effector with the Microtubule Network
2015