Nucleic Acids Research

Article	Citations
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation	4641
UniProt: the universal protein knowledgebase in 2021	4417
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets	4039
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models	3525
Pfam: The protein families database in 2021	2953
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences	2637
TIMER2.0 for analysis of tumor-infiltrating immune cells	2381
The Gene Ontology resource: enriching a GOld mine	2282
KEGG: integrating viruses and cellular organisms	2197
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights	2130
PubChem in 2021: new data content and improved web interfaces	2040
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)	1612
antiSMASH 6.0: improving cluster detection and comparison capabilities	1470
KEGG for taxonomy-based analysis of pathways and genomes	1353
The InterPro protein families and domains database: 20 years on	1351
Ensembl 2021	1197
UniProt: the Universal Protein Knowledgebase in 2023	1118
Ensembl 2022	1047
Search and sequence analysis tools services from EMBL-EBI in 2022	990
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API	951
NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data	923
The reactome pathway knowledgebase 2022	885
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, bio	880
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties	871
SMART: recent updates, new developments and status in 2020	867

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles	847
Database resources of the national center for biotechnology information	841
The carbohydrate-active enzyme database: functions and literature	773
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest	761
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations	715
HMDB 5.0: the Human Metabolome Database for 2022	710
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes	698
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis	687
PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA	656
The Human Phenotype Ontology in 2021	629
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy	627
GENCODE 2021	600
Comparative Toxicogenomics Database (CTD): update 2021	595
InterPro in 2022	564
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes	538
Database resources of the National Center for Biotechnology Information	526
SynergyFinder 2.0: visual analytics of multi-drug combination synergies	521
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation	503
WikiPathways: connecting communities	502
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures	493
PubChem 2023 update	479
Rfam 14: expanded coverage of metagenomic, viral and microRNA families	462
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment	447
miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology	439
A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase	422
COG database update: focus on microbial diversity, model organisms, and widespread pathogens	421
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts	421
Dali server: structural unification of protein families	397
DRAM for distilling microbial metabolism to automate the curation of microbiome function	395
The IPD-IMGT/HLA Database	366
FlyBase: updates to theDrosophila melanogasterknowledge base	355
MODOMICS: a database of RNA modification pathways. 2021 update	353
VFDB 2022: a general classification scheme for bacterial virulence factors	344
The UCSC Genome Browser database: 2021 update	336
BRENDA, the ELIXIR core data resource in 2021: new developments and updates	332
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022	330
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities	321
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes	317
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users	316
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents	301
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update	298
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update	298
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource	285
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics	285
miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions	276
Genenames.org: the HGNC and VGNC resources in 2021	264
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center	258
CATH: increased structural coverage of functional space	257
Open Targets Platform: supporting systematic drug–target identification and prioritisation	257
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine	253

IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation	250
GPCRdb in 2021: integrating GPCR sequence, structure and function	248
SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics	239
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses	234
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics	226
Correction to ‘The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets’	213
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation	210
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR	208
CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting	205
GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA	203
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database	194
GenBank	193
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements	188
m6A-Atlas: a comprehensive knowledgebase for unraveling theN6-methyladenosine (m6A) epitranscriptome	183
The Transporter Classification Database (TCDB): 2021 update	182
iProX in 2021: connecting proteomics data sharing with big data	181
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization	181
LitCovid: an open database of COVID-19 literature	178
A comprehensive review of m6A/m6Am RNA methyltransferase structures	178
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models	176
MobiDB: intrinsically disordered proteins in 2021	172
Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology	171
The UCSC Genome Browser database: 2022 update	169
Dynamic landscape and evolution of m6A methylation in human	164
PAM recognition by miniature CRISPR–Cas12f nucleases triggers programmable double-stranded DNA target cleavage	164
The ProteomeXchange consortium at 10 years: 2023 update	161
Phosphorothioate modified oligonucleotide–protein interactions	159
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants	159
Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data	158
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments	157
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases	156
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021	154
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study	152
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning	142
Genomes OnLine Database (GOLD) v.8: overview and updates	138
HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets	136
Decoding the epitranscriptional landscape from native RNA sequences	136
The Eukaryotic Linear Motif resource: 2022 release	135
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates	135
NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data	135
Targeted mRNA demethylation using an engineered dCas13b-ALKBH5 fusion protein	135
SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update)	134
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more	134
Comparative Toxicogenomics Database (CTD): update 2023	134
Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue	134
The UCSC Genome Browser database: 2023 update	133
Investigating the pharmacodynamic durability of GalNAc–siRNA conjugates	133
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems	133
The international nucleotide sequence database collaboration	132
Ensembl 2023	132
Aging Atlas: a multi-omics database for aging biology	132
FATCAT 2.0: towards a better understanding of the structural diversity of proteins	131
MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization	131
GTRD: an integrated view of transcription regulation	130
ProteinsPlus: interactive analysis of protein–ligand binding interfaces	129
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data	129
DNA G-quadruplex structures: more than simple roadblocks to transcription?	128
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples	128
CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data	128
PredictProtein - Predicting Protein Structure and Function for 29 Years	126
BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking	126
DrugCentral 2021 supports drug discovery and repositioning	125
PROTAC-DB: an online database of PROTACs	123
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy	121
The Sequence Read Archive: a decade more of explosive growth	120
Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services	120
MutationTaster2021	119
iLearnPlus:a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization	119
GenBank	117
BiG-FAM: the biosynthetic gene cluster families database	117
Proksee: in-depth characterization and visualization of bacterial genomes	116
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining	115
DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools	115
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation	111
Database resources of the National Center for Biotechnology Information in 2023	110
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes	107
RMVar: an updated database of functional variants involved in RNA modifications	106
The Natural Products Atlas 2.0: a database of microbially-derived natural products	106
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals	106
TCRD and Pharos 2021: mining the human proteome for disease biology	105

Mechanisms of replication and repair in mitochondrial DNA deletion formation	105
CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics	102
On the expanding roles of tRNA fragments in modulating cell behavior	102
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years	100
jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population	100
Chemistry, structure and function of approved oligonucleotide therapeutics	100
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean	99
CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication	98
Genenames.org: the HGNC resources in 2023	98
OrthoDB in 2020: evolutionary and functional annotations of orthologs	98
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes	98
The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials	98
Unbiased investigation of specificities of prime editing systems in human cells	98
Detection of genomic G-quadruplexes in living cells using a small artificial protein	98
BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy	97
Extracellular vesicles engineered with valency-controlled DNA nanostructures deliver CRISPR/Cas9 system for gene therapy	97
Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back	97
The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease	96
PhycoCosm, a comparative algal genomics resource	95
DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides	95
The European Nucleotide Archive in 2020	95
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins	94
Unraveling the interaction between doxorubicin and DNA origami nanostructures for customizable chemotherapeutic drug release	94
METTL3 counteracts premature aging via m6A-dependent stabilization of MIS12 mRNA	92
The Human Disease Ontology 2022 update	92
PML nuclear bodies and chromatin dynamics: catch me if you can!	92
scIGANs: single-cell RNA-seq imputation using generative adversarial networks	91
MNDR v3.0: mammal ncRNA–disease repository with increased coverage and annotation	89
Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-ExoN domain reveals an exoribonuclease with both structural and functional integrity	89
SpaGE: Spatial Gene Enhancement using scRNA-seq	89
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters	88
DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism	88
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types	88
PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants	87
Post-translational modification of RNA m6A demethylase ALKBH5 regulates ROS-induced DNA damage response	87
Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires	86
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models	86
A unified model for the G1/S cell cycle transition	86
The current state of SubtiWiki, the database for the model organism Bacillus subtilis	86
RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility	86
Synthetic promoter design in Escherichia coli based on a deep generative network	85
RNA G-quadruplexes (rG4s): genomics and biological functions	84
The IntAct database: efficient access to fine-grained molecular interaction data	83
OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer	83
BRAD V3.0: an upgraded Brassicaceae database	82
Dynamics and competition of CRISPR–Cas9 ribonucleoproteins and AAV donor-mediated NHEJ, MMEJ and HDR editing	82
REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments	82
Rhea, the reaction knowledgebase in 2022	81
Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations	81
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt	81
Ribosomal stress-surveillance: three pathways is a magic number	80
Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation	79
G-quadruplex–R-loop interactions and the mechanism of anticancer G-quadruplex binders	78
The IMG/M data management and analysis system v.7: content updates and new features	78
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research	78
Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation	78
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023	78
Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6	77
miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets	77
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data	76
NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses	76
PLSDB: advancing a comprehensive database of bacterial plasmids	76
Recombination machinery engineering facilitates metabolic engineering of the industrial yeast Pichia pastoris	76
exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids	75
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata	75
The oncofetal RNA-binding protein IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression in cancer	75
LncSEA: a platform for long non-coding RNA related sets and enrichment analysis	75
Diverse high-affinity DNA aptamers for wild-type and B.1.1.7 SARS-CoV-2 spike proteins from a pre-structured DNA library	75
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning	75
Seeker: alignment-free identification of bacteriophage genomes by deep learning	74
UFold: fast and accurate RNA secondary structure prediction with deep learning	74
catRAPIDomics v2.0: going deeper and wider in the prediction of protein–RNA interactions	74
BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models	73
SUMOylation of YTHDF2 promotes mRNA degradation and cancer progression by increasing its binding affinity with m6A-modified mRNAs	73
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles	73
Expression Atlas update: gene and protein expression in multiple species	73
OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity	73
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment	72
G-Quadruplexes as pathogenic drivers in neurodegenerative disorders	72
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases	72
PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs	71
InsectBase 2.0: a comprehensive gene resource for insects	71
Genome-wide mapping of G-quadruplex structures with CUT&Tag	71
The role of FACT in managing chromatin: disruption, assembly, or repair?	71
KLIFS: an overhaul after the first 5 years of supporting kinase research	70
The N 6-methyladenosine RNA-binding protein YTHDF1 modulates the translation of TRAF6 to mediate the intestinal immune response	70
HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA	70
The involvement of nucleotide excision repair proteins in the removal of oxidative DNA damage	70
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes	70
Histone sumoylation and chromatin dynamics	69
PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins	69
BacDive in 2022: the knowledge base for standardized bacterial and archaeal data	69
miRTargetLink 2.0—interactive miRNA target gene and target pathway networks	69
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	68
FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations	68