Standout Papers
Citation Impact
Citing Papers
Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS
2018 StandoutNobel
Protein interaction networks revealed by proteome coevolution
2019 StandoutScienceNobel
Spatially resolved, highly multiplexed RNA profiling in single cells
2015 StandoutScience
A Gene Network Regulating Lysosomal Biogenesis and Function
2009 StandoutScience
In vivo aspects of protein folding and quality control
2016 Science
Systematic analysis of dynamic miRNA-target interactions during C. elegans development
2009 StandoutNobel
deepNF: deep network fusion for protein function prediction
2018
Genes2FANs: connecting genes through functional association networks
2012
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
2023 StandoutNobel
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
2009 Standout
HINT: High-quality protein interactomes and their applications in understanding human disease
2012
Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons
2013 StandoutNobel
Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions
2021 StandoutNobel
Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism
2024 StandoutNobel
Network-based stratification of tumor mutations
2013
In Situ trans Ligands of CD22 Identified by Glycan-Protein Photocross-linking-enabled Proteomics
2010
GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists
2007
DISEASES: Text mining and data integration of disease–gene associations
2014
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
2015
Control of somatic tissue differentiation by the long non-coding RNA TINCR
2012 StandoutNature
Genetic effects on gene expression across human tissues
2017 StandoutNature
Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown
2018 StandoutNobel
Systematic Identification of C. elegans miRISC Proteins, miRNAs, and mRNA Targets by Their Interactions with GW182 Proteins AIN-1 and AIN-2
2007
Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence
2012 StandoutNatureNobel
nhl-2 Modulates MicroRNA Activity in Caenorhabditis elegans
2009 StandoutNobel
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
2013
STRING v10: protein–protein interaction networks, integrated over the tree of life
2014 Standout
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics
2012
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update
2017 Standout
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
2008 Standout
Inactivation of Conserved C. elegans Genes Engages Pathogen- and Xenobiotic-Associated Defenses
2012 StandoutNobel
Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum
2015 Nature
The changing landscape of atherosclerosis
2021 StandoutNature
TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins
2016 StandoutNobel
Complete nitrification by Nitrospira bacteria
2015 StandoutNature
Machine learning for molecular and materials science
2018 StandoutNature
A genome-wide approach identifies distinct but overlapping subsets of cellular mRNAs associated with Staufen1- and Staufen2-containing ribonucleoprotein complexes
2007
STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data
2015
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
2016 Standout
eggNOG v4.0: nested orthology inference across 3686 organisms
2013
The bone marrow niche for haematopoietic stem cells
2014 StandoutNature
COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems
2014
Image-based transcriptomics in thousands of single human cells at single-molecule resolution
2013
The impact of microRNAs on protein output
2008 StandoutNature
ALDH4A1 is an atherosclerosis auto-antigen targeted by protective antibodies
2020 Nature
COMPARTMENTS: unification and visualization of protein subcellular localization evidence
2014
Protein-Protein Interactions and Prediction: A Comprehensive Overview
2013
REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms
2011 Standout
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
2008 Standout
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes
2018
A Conserved PMK-1/p38 MAPK Is Required in Caenorhabditis elegans Tissue-specific Immune Response to Yersinia pestis Infection
2010
Human diseases through the lens of network biology
2012
Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization
2013
Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors
2008
The BioGRID interaction database: 2013 update
2012
Selecting causal genes from genome-wide association studies via functionally coherent subnetworks
2014
ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data
2008
Network-based in silico drug efficacy screening
2016
Aneuploidy Underlies Rapid Adaptive Evolution of Yeast Cells Deprived of a Conserved Cytokinesis Motor
2008
Network analysis of GWAS data
2013
STITCH 4: integration of protein–chemical interactions with user data
2013
Microbial interactions: from networks to models
2012 Standout
Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways
2013
Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells
2013
limma powers differential expression analyses for RNA-sequencing and microarray studies
2015 Standout
ProOpDB: Prokaryotic Operon DataBase
2011
Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks
2020 StandoutNobel
GeneTrail--advanced gene set enrichment analysis
2007
Analysis of Cell Surface Proteome Changes via Label-free, Quantitative Mass Spectrometry
2008
FunCoup 3.0: database of genome-wide functional coupling networks
2013
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
2007 Standout
Bone progenitor dysfunction induces myelodysplasia and secondary leukaemia
2010 Nature
Equivalent Mutations in the Eight Subunits of the Chaperonin CCT Produce Dramatically Different Cellular and Gene Expression Phenotypes
2010
HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores
2012
g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments
2007
Chromatin remodeller SMARCA4 recruits topoisomerase 1 and suppresses transcription-associated genomic instability
2016 StandoutNobel
Application of text mining in the biomedical domain
2015
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
2008
20 years of the SMART protein domain annotation resource
2017
SMART 7: recent updates to the protein domain annotation resource
2011
MetaboAnalyst 3.0—making metabolomics more meaningful
2015 Standout
Lysosome-targeting chimaeras for degradation of extracellular proteins
2020 StandoutNatureNobel
A miRNA Signature of Prion Induced Neurodegeneration
2008
Analyzing and interpreting genome data at the network level with ConsensusPathDB
2016
The prognostic landscape of genes and infiltrating immune cells across human cancers
2015 Standout
Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite
2007
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
2012
The Polycomb complex PRC2 and its mark in life
2011 StandoutNature
N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions
2015 StandoutNature
Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry
2013
Advances in mass spectrometry driven O-glycoproteomics
2014
EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species
2007
Human gene correlation analysis (HGCA): A tool for the identification of transcriptionally co-expressed genes
2012
Towards revealing the functions of all genes in plants
2013
In vivo 3′-to-5′ exoribonuclease targetomes of Streptococcus pyogenes
2018 StandoutNobel
Mapping of Protein-Protein Interactions: Web-Based Resources for Revealing Interactomes
2018
Viruses.STRING: A Virus-Host Protein-Protein Interaction Database
2018
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system
2016 StandoutNobel
Thiouracil Cross-Linking Mass Spectrometry: a Cell-Based Method To Identify Host Factors Involved in Viral Amplification
2013
Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development
2016 StandoutNobel
A General Mechanism for Network-Dosage Compensation in Gene Circuits
2010 StandoutScienceNobel
Functional association networks as priors for gene regulatory network inference
2014
STAMS: STRING-assisted module search for genome wide association studies and application to autism
2016
Comprehensive comparison of large-scale tissue expression datasets
2015
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest
2022 Standout
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
2018 Standout
Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling
2012 StandoutNobel
Messenger RNA Degradation in Bacterial Cells
2014
Network-assisted analysis to prioritize GWAS results: principles, methods and perspectives
2013
Candidate autism gene screen identifies critical role for cell-adhesion molecule CASPR2 in dendritic arborization and spine development
2012 StandoutNobel
Links between genetics and pathophysiology in the autism spectrum disorders
2011
Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation
2015
GeneMANIA Prediction Server 2013 Update
2013
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence
2014
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets
2020 Standout
Transcription factor and chromatin features predict genes associated with eQTLs
2012
Immunopurification of Ago1 miRNPs selects for a distinct class of microRNA targets
2009 StandoutNobel
Liquid phase condensation in cell physiology and disease
2017 StandoutScience
Chemical Glycoproteomics
2016 StandoutNobel
Eukaryotic LYR Proteins Interact with Mitochondrial Protein Complexes
2015
Works of Pablo Mínguez being referenced
Operon structure and cotranslational subunit association direct protein assembly in bacteria
2015 Science
Deciphering a global network of functionally associated post‐translational modifications
2012
From genes to functional classes in the study of biological systems
2007
Complement C5 Protein as a Marker of Subclinical Atherosclerosis
2020
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
2012 Standout
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
2007
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins
2014
Next station in microarray data analysis: GEPAS
2006
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments
2005
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments
2006
GEPAS, a web-based tool for microarray data analysis and interpretation
2008
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
2005
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
2010 Standout
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments
2012