Nucleic Acids Research

Papers
(The H4-Index of Nucleic Acids Research is 134. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-11-01 to 2024-11-01.)
ArticleCitations
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation6420
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets4962
UniProt: the universal protein knowledgebase in 20214928
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models4861
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences3818
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights2732
The Gene Ontology resource: enriching a GOld mine2604
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)2553
UniProt: the Universal Protein Knowledgebase in 20232451
PubChem in 2021: new data content and improved web interfaces2367
KEGG for taxonomy-based analysis of pathways and genomes2169
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest1981
antiSMASH 6.0: improving cluster detection and comparison capabilities1757
The InterPro protein families and domains database: 20 years on1565
Search and sequence analysis tools services from EMBL-EBI in 20221518
Ensembl 20221391
Database resources of the national center for biotechnology information1347
Ensembl 20211316
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties1252
The reactome pathway knowledgebase 20221243
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles1174
The carbohydrate-active enzyme database: functions and literature1135
InterPro in 20221116
PubChem 2023 update1072
HMDB 5.0: the Human Metabolome Database for 20221046
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API1045
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bio1036
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes991
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis964
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy954
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations954
PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA916
GENCODE 2021820
The Human Phenotype Ontology in 2021773
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes759
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation645
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures634
The IPD-IMGT/HLA Database627
Rfam 14: expanded coverage of metagenomic, viral and microRNA families614
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation613
VFDB 2022: a general classification scheme for bacterial virulence factors607
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource604
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment601
WikiPathways: connecting communities593
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update554
COG database update: focus on microbial diversity, model organisms, and widespread pathogens546
Dali server: structural unification of protein families543
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts542
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database489
MODOMICS: a database of RNA modification pathways. 2021 update484
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022465
miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions456
Ensembl 2023454
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users428
BRENDA, the ELIXIR core data resource in 2021: new developments and updates426
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes413
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR405
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents390
Proksee: in-depth characterization and visualization of bacterial genomes386
CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting384
FlyBase: updates to theDrosophila melanogasterknowledge base383
The UCSC Genome Browser database: 2021 update377
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation331
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center328
iProX in 2021: connecting proteomics data sharing with big data323
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine320
CATH: increased structural coverage of functional space319
Open Targets Platform: supporting systematic drug–target identification and prioritisation310
The ProteomeXchange consortium at 10 years: 2023 update303
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics303
g:Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)292
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning290
CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data287
Genenames.org: the HGNC and VGNC resources in 2021283
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models283
GPCRdb in 2021: integrating GPCR sequence, structure and function280
GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA270
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses267
Comparative Toxicogenomics Database (CTD): update 2023266
Correction to ‘The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets’266
Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology264
The UCSC Genome Browser database: 2023 update257
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study255
A comprehensive review of m6A/m6Am RNA methyltransferase structures249
The Transporter Classification Database (TCDB): 2021 update244
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees242
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples239
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments233
The conserved domain database in 2023230
Chemistry, structure and function of approved oligonucleotide therapeutics225
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements216
GenBank210
The UCSC Genome Browser database: 2022 update207
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates196
MobiDB: intrinsically disordered proteins in 2021195
LitCovid: an open database of COVID-19 literature194
dbCAN3: automated carbohydrate-active enzyme and substrate annotation193
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants193
Database resources of the National Center for Biotechnology Information in 2023192
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data191
Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data187
The Eukaryotic Linear Motif resource: 2022 release187
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters186
The Sequence Read Archive: a decade more of explosive growth176
The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease174
DNA G-quadruplex structures: more than simple roadblocks to transcription?172
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021168
Genenames.org: the HGNC resources in 2023166
GTRD: an integrated view of transcription regulation166
MutationTaster2021165
PredictProtein - Predicting Protein Structure and Function for 29 Years164
BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy163
Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services163
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt161
OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity161
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more158
Genomes OnLine Database (GOLD) v.8: overview and updates156
Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool154
The international nucleotide sequence database collaboration152
iLearnPlus:a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization151
The Natural Products Atlas 2.0: a database of microbially-derived natural products147
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment147
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences147
FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations143
GenBank142
DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides142
CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication141
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy139
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata138
The IntAct database: efficient access to fine-grained molecular interaction data138
DrugCentral 2021 supports drug discovery and repositioning137
The Human Disease Ontology 2022 update135
The IMG/M data management and analysis system v.7: content updates and new features135
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years135
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