Nucleic Acids Research

Article	Citations
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation	5163
UniProt: the universal protein knowledgebase in 2021	4601
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets	4299
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models	3981
Pfam: The protein families database in 2021	3177
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences	3014
TIMER2.0 for analysis of tumor-infiltrating immune cells	2533
The Gene Ontology resource: enriching a GOld mine	2411
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights	2304
KEGG: integrating viruses and cellular organisms	2282
PubChem in 2021: new data content and improved web interfaces	2141
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)	1854
KEGG for taxonomy-based analysis of pathways and genomes	1584
antiSMASH 6.0: improving cluster detection and comparison capabilities	1571
UniProt: the Universal Protein Knowledgebase in 2023	1448
The InterPro protein families and domains database: 20 years on	1421
Ensembl 2021	1232
Ensembl 2022	1179
Search and sequence analysis tools services from EMBL-EBI in 2022	1139
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest	1070
The reactome pathway knowledgebase 2022	1003
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	992
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API	991
Database resources of the national center for biotechnology information	985
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties	981

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles	963
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	930
SMART: recent updates, new developments and status in 2020	922
The carbohydrate-active enzyme database: functions and literature	878
HMDB 5.0: the Human Metabolome Database for 2022	800
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes	784
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations	781
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis	776
PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA	738
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy	715
InterPro in 2022	708
The Human Phenotype Ontology in 2021	679
GENCODE 2021	666
PubChem 2023 update	633
Comparative Toxicogenomics Database (CTD): update 2021	621
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes	603
Database resources of the National Center for Biotechnology Information	550
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation	544
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures	538
WikiPathways: connecting communities	533
Rfam 14: expanded coverage of metagenomic, viral and microRNA families	505
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment	496
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts	462
miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology	460
COG database update: focus on microbial diversity, model organisms, and widespread pathogens	458
Dali server: structural unification of protein families	453
The IPD-IMGT/HLA Database	453
A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase	438
DRAM for distilling microbial metabolism to automate the curation of microbiome function	432
VFDB 2022: a general classification scheme for bacterial virulence factors	425
MODOMICS: a database of RNA modification pathways. 2021 update	397
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource	375
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update	374
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022	373
FlyBase: updates to theDrosophila melanogasterknowledge base	366
BRENDA, the ELIXIR core data resource in 2021: new developments and updates	360
The UCSC Genome Browser database: 2021 update	355
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users	349
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes	349
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities	331
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents	328
miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions	328
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update	312
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation	310
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics	306
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center	281
CATH: increased structural coverage of functional space	278
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine	276
Open Targets Platform: supporting systematic drug–target identification and prioritisation	276
Genenames.org: the HGNC and VGNC resources in 2021	273

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database	272
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation	271
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR	264
GPCRdb in 2021: integrating GPCR sequence, structure and function	260
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics	245
CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting	244
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses	244
Correction to ‘The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets’	232
iProX in 2021: connecting proteomics data sharing with big data	223
GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA	221
Ensembl 2023	217
Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology	204
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models	204
The Transporter Classification Database (TCDB): 2021 update	201
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements	198
GenBank	197
The ProteomeXchange consortium at 10 years: 2023 update	196
A comprehensive review of m6A/m6Am RNA methyltransferase structures	195
m6A-Atlas: a comprehensive knowledgebase for unraveling theN6-methyladenosine (m6A) epitranscriptome	189
MobiDB: intrinsically disordered proteins in 2021	183
LitCovid: an open database of COVID-19 literature	180
The UCSC Genome Browser database: 2022 update	180
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study	179
Proksee: in-depth characterization and visualization of bacterial genomes	179
Dynamic landscape and evolution of m6A methylation in human	176
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments	174
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	174
Phosphorothioate modified oligonucleotide–protein interactions	171
CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data	167
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants	167
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases	166
Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data	163
Comparative Toxicogenomics Database (CTD): update 2023	162
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021	158
The UCSC Genome Browser database: 2023 update	156
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples	154
The Eukaryotic Linear Motif resource: 2022 release	150
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates	150
Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue	150
HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets	149
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data	147
Database resources of the National Center for Biotechnology Information in 2023	144
Genomes OnLine Database (GOLD) v.8: overview and updates	143
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more	143
Aging Atlas: a multi-omics database for aging biology	142
Targeted mRNA demethylation using an engineered dCas13b-ALKBH5 fusion protein	142
Investigating the pharmacodynamic durability of GalNAc–siRNA conjugates	142
SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update)	140
Decoding the epitranscriptional landscape from native RNA sequences	140
The international nucleotide sequence database collaboration	139
DNA G-quadruplex structures: more than simple roadblocks to transcription?	139
FATCAT 2.0: towards a better understanding of the structural diversity of proteins	138
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems	137
PredictProtein - Predicting Protein Structure and Function for 29 Years	137
GTRD: an integrated view of transcription regulation	135
MutationTaster2021	135
The Sequence Read Archive: a decade more of explosive growth	135
Chemistry, structure and function of approved oligonucleotide therapeutics	132
Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services	131
BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking	130
BiG-FAM: the biosynthetic gene cluster families database	128
PROTAC-DB: an online database of PROTACs	128
DrugCentral 2021 supports drug discovery and repositioning	127
iLearnPlus:a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization	127
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy	126
GenBank	126
Genenames.org: the HGNC resources in 2023	123
DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools	122
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation	119
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes	119
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining	116
The Natural Products Atlas 2.0: a database of microbially-derived natural products	115
The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease	115
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals	114
RMVar: an updated database of functional variants involved in RNA modifications	113
TCRD and Pharos 2021: mining the human proteome for disease biology	113
BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy	113
Mechanisms of replication and repair in mitochondrial DNA deletion formation	111
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters	111
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years	110

CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication	110
CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics	110
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean	109
DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides	107
Extracellular vesicles engineered with valency-controlled DNA nanostructures deliver CRISPR/Cas9 system for gene therapy	107
The Human Disease Ontology 2022 update	106
jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population	106
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	106
On the expanding roles of tRNA fragments in modulating cell behavior	106
PML nuclear bodies and chromatin dynamics: catch me if you can!	103
The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials	103
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes	103
OrthoDB in 2020: evolutionary and functional annotations of orthologs	103
Detection of genomic G-quadruplexes in living cells using a small artificial protein	103
PhycoCosm, a comparative algal genomics resource	102
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt	102
Unbiased investigation of specificities of prime editing systems in human cells	102
Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back	101
Unraveling the interaction between doxorubicin and DNA origami nanostructures for customizable chemotherapeutic drug release	100
SpaGE: Spatial Gene Enhancement using scRNA-seq	99
scIGANs: single-cell RNA-seq imputation using generative adversarial networks	98
PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants	98
g:Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)	98
A unified model for the G1/S cell cycle transition	98
dbCAN3: automated carbohydrate-active enzyme and substrate annotation	97
METTL3 counteracts premature aging via m6A-dependent stabilization of MIS12 mRNA	97
RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility	97
Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires	96
The European Nucleotide Archive in 2020	96
The current state of SubtiWiki, the database for the model organism Bacillus subtilis	96
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata	96
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins	96
OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer	96
MNDR v3.0: mammal ncRNA–disease repository with increased coverage and annotation	95
BRAD V3.0: an upgraded Brassicaceae database	95
DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism	95
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types	94
Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-ExoN domain reveals an exoribonuclease with both structural and functional integrity	94
Post-translational modification of RNA m6A demethylase ALKBH5 regulates ROS-induced DNA damage response	94
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023	93
Synthetic promoter design in Escherichia coli based on a deep generative network	93
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models	92
OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity	92
Dynamics and competition of CRISPR–Cas9 ribonucleoproteins and AAV donor-mediated NHEJ, MMEJ and HDR editing	90
Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation	90
The IntAct database: efficient access to fine-grained molecular interaction data	89
Rhea, the reaction knowledgebase in 2022	89
PLSDB: advancing a comprehensive database of bacterial plasmids	88
RNA G-quadruplexes (rG4s): genomics and biological functions	88
Expression Atlas update: gene and protein expression in multiple species	88
UFold: fast and accurate RNA secondary structure prediction with deep learning	88
Ribosomal stress-surveillance: three pathways is a magic number	88
FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations	87
The IMG/M data management and analysis system v.7: content updates and new features	87
The conserved domain database in 2023	87
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment	87
Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation	86
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning	86
exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids	85
BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models	85
MGnify: the microbiome sequence data analysis resource in 2023	85
REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments	85
Recombination machinery engineering facilitates metabolic engineering of the industrial yeast Pichia pastoris	84
miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets	84
Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations	84
G-quadruplex–R-loop interactions and the mechanism of anticancer G-quadruplex binders	84
SUMOylation of YTHDF2 promotes mRNA degradation and cancer progression by increasing its binding affinity with m6A-modified mRNAs	84
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research	82
The oncofetal RNA-binding protein IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression in cancer	82
InsectBase 2.0: a comprehensive gene resource for insects	81
NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses	80
Diverse high-affinity DNA aptamers for wild-type and B.1.1.7 SARS-CoV-2 spike proteins from a pre-structured DNA library	80
LncSEA: a platform for long non-coding RNA related sets and enrichment analysis	80
Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6	80
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data	79
BacDive in 2022: the knowledge base for standardized bacterial and archaeal data	79
G-Quadruplexes as pathogenic drivers in neurodegenerative disorders	79
catRAPIDomics v2.0: going deeper and wider in the prediction of protein–RNA interactions	79
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases	79
KLIFS: an overhaul after the first 5 years of supporting kinase research	78
Seeker: alignment-free identification of bacteriophage genomes by deep learning	77
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles	77
miRTargetLink 2.0—interactive miRNA target gene and target pathway networks	76
Genome-wide mapping of G-quadruplex structures with CUT&Tag	76
SIRT3 consolidates heterochromatin and counteracts senescence	76
CRISPR–Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning	75
Histone sumoylation and chromatin dynamics	75
Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter	75
PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs	73
The role of FACT in managing chromatin: disruption, assembly, or repair?	73
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes	73
The involvement of nucleotide excision repair proteins in the removal of oxidative DNA damage	73
The N 6-methyladenosine RNA-binding protein YTHDF1 modulates the translation of TRAF6 to mediate the intestinal immune response	72
eQuilibrator 3.0: a database solution for thermodynamic constant estimation	72
gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites	72