Volume 53, Issue D1
6 January 2025
Cover image
Cover image
The cover figure showcases the updated MAP of the drug-molecule interaction atlas in DrugMAP. It illustrates the interactions between drugs (indicated by blue landmarks) and a diverse range of interacting molecules, each represented by distinct colored landmarks. The previous version of DrugMAP focused on pharmacokinetic data related to drug therapeutic targets (orange), drug transporters (red), and drug-metabolizing enzymes (green). In this current version, additional elements have been incorporated, including combinatorial drugs (strong blue), repurposed drugs (sky blue), off-target effects (purple), and diseases (brown). The gray regions of the map represent the vast exploratory space within the chemical landscape and drug-molecule interaction network. Solid lines depict interactions between drugs and various types of molecules, while dashed lines illustrate the interactions among different molecular entities.
EISSN 1362-4962
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Volume 53, Issue D1, 6 January 2025
EDITORIAL
The 2025 Nucleic Acids Research database issue and the online molecular biology database collection
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1–D9, https://doi.org/10.1093/nar/gkae1220
MAJOR MULTI-DATABASE RESOURCES
EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2024
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D10–D19, https://doi.org/10.1093/nar/gkae1089
Database resources of the National Center for Biotechnology Information in 2025
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D20–D29, https://doi.org/10.1093/nar/gkae979
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2025
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D30–D44, https://doi.org/10.1093/nar/gkae978
DDBJ update in 2024: the DDBJ Group Cloud service for sharing pre-publication data
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D45–D48, https://doi.org/10.1093/nar/gkae882
The European Nucleotide Archive in 2024
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D49–D55, https://doi.org/10.1093/nar/gkae975
GenBank 2025 update
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D56–D61, https://doi.org/10.1093/nar/gkae1114
The international nucleotide sequence database collaboration (INSDC): enhancing global participation
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D62–D66, https://doi.org/10.1093/nar/gkae1058
NUCLEIC ACID SEQUENCE, STRUCTURE AND REGULATION
CircaKB: a comprehensive knowledgebase of circadian genes across multiple species
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D67–D78, https://doi.org/10.1093/nar/gkae817
EXPRESSO: a multi-omics database to explore multi-layered 3D genomic organization
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D79–D90, https://doi.org/10.1093/nar/gkae999
G4LDB 3.0: a database for discovering and studying G-quadruplex and i-motif ligands
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D91–D98, https://doi.org/10.1093/nar/gkae835
iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D99–D106, https://doi.org/10.1093/nar/gkae1009
LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D107–D115, https://doi.org/10.1093/nar/gkae947
MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D116–D128, https://doi.org/10.1093/nar/gkae1094
miRNATissueAtlas 2025: an update to the uniformly processed and annotated human and mouse non-coding RNA tissue atlas
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D129–D137, https://doi.org/10.1093/nar/gkae1036
miRStart 2.0: enhancing miRNA regulatory insights through deep learning-based TSS identification
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D138–D146, https://doi.org/10.1093/nar/gkae1086
miRTarBase 2025: updates to the collection of experimentally validated microRNA–target interactions
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D147–D156, https://doi.org/10.1093/nar/gkae1072
NAIRDB: a database of Fourier transform infrared (FTIR) data for nucleic acids
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D157–D162, https://doi.org/10.1093/nar/gkae885
oriTDB: a database of the origin-of-transfer regions of bacterial mobile genetic elements
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D163–D168, https://doi.org/10.1093/nar/gkae869
PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D169–D178, https://doi.org/10.1093/nar/gkae952
PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D179–D188, https://doi.org/10.1093/nar/gkae930
The PLSDB 2025 update: enhanced annotations and improved functionality for comprehensive plasmid research
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D189–D196, https://doi.org/10.1093/nar/gkae1095
PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D197–D204, https://doi.org/10.1093/nar/gkae1043
qPrimerDB 2.0: an updated comprehensive gene-specific qPCR primer database for 1172 organisms
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D205–D210, https://doi.org/10.1093/nar/gkae684
RASP v2.0: an updated atlas for RNA structure probing data
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D211–D219, https://doi.org/10.1093/nar/gkae1117
RBPWorld for exploring functions and disease associations of RNA-binding proteins across species
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D220–D232, https://doi.org/10.1093/nar/gkae1028
REDIportal: toward an integrated view of the A-to-I editing
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D233–D242, https://doi.org/10.1093/nar/gkae1083
NCBI RefSeq: reference sequence standards through 25 years of curation and annotation
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D243–D257, https://doi.org/10.1093/nar/gkae1038
Rfam 15: RNA families database in 2025
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D258–D267, https://doi.org/10.1093/nar/gkae1023
RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D268–D274, https://doi.org/10.1093/nar/gkae1020
RMVar 2.0: an updated database of functional variants in RNA modifications
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D275–D283, https://doi.org/10.1093/nar/gkae924
RNALocate v3.0: Advancing the Repository of RNA Subcellular Localization with Dynamic Analysis and Prediction
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D284–D292, https://doi.org/10.1093/nar/gkae872
RPFdb v3.0: an enhanced repository for ribosome profiling data and related content
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D293–D298, https://doi.org/10.1093/nar/gkae808
RPS 2.0: an updated database of RNAs involved in liquid–liquid phase separation
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D299–D309, https://doi.org/10.1093/nar/gkae951
Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D310–D317, https://doi.org/10.1093/nar/gkae972
TransmiR v3.0: an updated transcription factor-microRNA regulation database
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D318–D323, https://doi.org/10.1093/nar/gkae1081
VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D324–D330, https://doi.org/10.1093/nar/gkae940
PROTEIN SEQUENCE AND STRUCTURE, MOTIFS AND DOMAINS
ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D331–D339, https://doi.org/10.1093/nar/gkae1018
BFVD—a large repository of predicted viral protein structures
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D340–D347, https://doi.org/10.1093/nar/gkae1119
CATH v4.4: major expansion of CATH by experimental and predicted structural data
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D348–D355, https://doi.org/10.1093/nar/gkae1087
COG database update 2024
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D356–D363, https://doi.org/10.1093/nar/gkae983
dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D364–D376, https://doi.org/10.1093/nar/gkae1019
dbPTM 2025 update: comprehensive integration of PTMs and proteomic data for advanced insights into cancer research
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D377–D386, https://doi.org/10.1093/nar/gkae1005
DIONYSUS: a database of protein–carbohydrate interfaces
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D387–D395, https://doi.org/10.1093/nar/gkae890
DNAproDB: an updated database for the automated and interactive analysis of protein–DNA complexes
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D396–D402, https://doi.org/10.1093/nar/gkae970
DRAMP 4.0: an open-access data repository dedicated to the clinical translation of antimicrobial peptides
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D403–D410, https://doi.org/10.1093/nar/gkae1046
ECOD: integrating classifications of protein domains from experimental and predicted structures
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D411–D418, https://doi.org/10.1093/nar/gkae1029
Update of the FANTOM web resource: enhancement for studying noncoding genomes
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D419–D424, https://doi.org/10.1093/nar/gkae1047
GPCRdb in 2025: adding odorant receptors, data mapper, structure similarity search and models of physiological ligand complexes
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D425–D435, https://doi.org/10.1093/nar/gkae1065
The Immune Epitope Database (IEDB): 2024 update
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D436–D443, https://doi.org/10.1093/nar/gkae1092
InterPro: the protein sequence classification resource in 2025
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D444–D456, https://doi.org/10.1093/nar/gkae1082
The 2024 IPD-MHC database update: a comprehensive resource for major histocompatibility complex studies
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D457–D461, https://doi.org/10.1093/nar/gkae932
jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D462–D467, https://doi.org/10.1093/nar/gkae1032
LncPepAtlas: a comprehensive resource for exploring the translational landscape of long non-coding RNAs
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D468–D476, https://doi.org/10.1093/nar/gkae905
MDRepo—an open data warehouse for community-contributed molecular dynamics simulations of proteins
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D477–D486, https://doi.org/10.1093/nar/gkae1109
MFIB 2.0: a major update of the database of protein complexes formed by mutual folding of the constituting protein chains
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D487–D494, https://doi.org/10.1093/nar/gkae976
MOBIDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D495–D503, https://doi.org/10.1093/nar/gkae969
OrgXenomics: an integrated proteomic knowledge base for patient-derived organoid and xenograft
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D504–D515, https://doi.org/10.1093/nar/gkae861
OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D516–D522, https://doi.org/10.1093/nar/gkae987
The Pfam protein families database: embracing AI/ML
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D523–D534, https://doi.org/10.1093/nar/gkae997
PLAbDab-nano: a database of camelid and shark nanobodies from patents and literature
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D535–D542, https://doi.org/10.1093/nar/gkae881
The PRIDE database at 20 years: 2025 update
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D543–D553, https://doi.org/10.1093/nar/gkae1011
PTMD 2.0: an updated database of disease-associated post-translational modifications
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D554–D563, https://doi.org/10.1093/nar/gkae850
Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D564–D574, https://doi.org/10.1093/nar/gkae1091
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D575–D581, https://doi.org/10.1093/nar/gkae965
scProAtlas: an atlas of multiplexed single-cell spatial proteomics imaging in human tissues
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D582–D594, https://doi.org/10.1093/nar/gkae990
SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D595–D603, https://doi.org/10.1093/nar/gkae893
TCR3d 2.0: expanding the T cell receptor structure database with new structures, tools and interactions
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D604–D608, https://doi.org/10.1093/nar/gkae840
UniProt: the Universal Protein Knowledgebase in 2025
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D609–D617, https://doi.org/10.1093/nar/gkae1010
METABOLIC AND SIGNALLING PATHWAYS, ENZYMES
BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D618–D624, https://doi.org/10.1093/nar/gkae953
CAZac: an activity descriptor for carbohydrate-active enzymes
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D625–D633, https://doi.org/10.1093/nar/gkae1045
COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D634–D643, https://doi.org/10.1093/nar/gkae1063
Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D644–D650, https://doi.org/10.1093/nar/gkae1085
CORUM in 2024: protein complexes as drug targets
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D651–D657, https://doi.org/10.1093/nar/gkae1033
FunCoup 6: advancing functional association networks across species with directed links and improved user experience
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D658–D671, https://doi.org/10.1093/nar/gkae1021
KEGG: biological systems database as a model of the real world
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D672–D677, https://doi.org/10.1093/nar/gkae909
MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D678–D690, https://doi.org/10.1093/nar/gkae1115
The Natural Products Atlas 3.0: extending the database of microbially derived natural products
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D691–D699, https://doi.org/10.1093/nar/gkae1093
The Natural Products Magnetic Resonance Database (NP-MRD) for 2025
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D700–D708, https://doi.org/10.1093/nar/gkae1067
RDBSB: a database for catalytic bioparts with experimental evidence
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D709–D716, https://doi.org/10.1093/nar/gkae844
The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D717–D723, https://doi.org/10.1093/nar/gkae1060
StreptomeDB 4.0: a comprehensive database of streptomycetes natural products enriched with protein interactions and interactive spectral visualization
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D724–D729, https://doi.org/10.1093/nar/gkae1030
The STRING database in 2025: protein networks with directionality of regulation
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D730–D737, https://doi.org/10.1093/nar/gkae1113
SubCELL: the landscape of subcellular compartment-specific molecular interactions
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D738–D747, https://doi.org/10.1093/nar/gkae863
VIRUSES, BACTERIA, PROTOZOA AND FUNGI
BacDive in 2025: the core database for prokaryotic strain data
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D748–D756, https://doi.org/10.1093/nar/gkae959
EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D757–D762, https://doi.org/10.1093/nar/gkae902
GCM and gcType in 2024: comprehensive resources for microbial strains and genomic data
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D763–D771, https://doi.org/10.1093/nar/gkae1057
GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D772–D782, https://doi.org/10.1093/nar/gkae1007
gutMGene v2.0: an updated comprehensive database for target genes of gut microbes and microbial metabolites
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D783–D788, https://doi.org/10.1093/nar/gkae1002
MicrobiomeNet: exploring microbial associations and metabolic profiles for mechanistic insights
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D789–D796, https://doi.org/10.1093/nar/gkae944
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D797–D805, https://doi.org/10.1093/nar/gkae1004
PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D806–D818, https://doi.org/10.1093/nar/gkae1042
PhageDive: the comprehensive strain database of prokaryotic viral diversity
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D819–D825, https://doi.org/10.1093/nar/gkae878
PHI-base – the multi-species pathogen–host interaction database in 2025
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D826–D838, https://doi.org/10.1093/nar/gkae1084
PneumoBrowse 2: an integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D839–D851, https://doi.org/10.1093/nar/gkae923
ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D852–D863, https://doi.org/10.1093/nar/gkae955
A new framework for SubtiWiki, the database for the model organism Bacillus subtilis
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D864–D870, https://doi.org/10.1093/nar/gkae957
VFDB 2025: an integrated resource for exploring anti-virulence compounds
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D871–D877, https://doi.org/10.1093/nar/gkae968
HUMAN GENOME, MODEL ORGANISMS, COMPARATIVE GENOMICS
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D878–D885, https://doi.org/10.1093/nar/gkae1118
CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D886–D900, https://doi.org/10.1093/nar/gkae1142
CRISPRepi: a multi-omic atlas for CRISPR-based epigenome editing
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D901–D913, https://doi.org/10.1093/nar/gkae1039
CRISPRoffT: comprehensive database of CRISPR/Cas off-targets
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D914–D924, https://doi.org/10.1093/nar/gkae1025
The evolution of dbSNP: 25 years of impact in genomic research
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D925–D931, https://doi.org/10.1093/nar/gkae977
Rediscovering publicly available single-cell data with the DISCO platform
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D932–D938, https://doi.org/10.1093/nar/gkae1108
Dog10K: an integrated Dog10K database summarizing canine multi-omics
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D939–D947, https://doi.org/10.1093/nar/gkae928
Ensembl 2025
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D948–D957, https://doi.org/10.1093/nar/gkae1071
FlyRNAi.org 2025 update—expanded resources for new technologies and species
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D958–D965, https://doi.org/10.1093/nar/gkae917
GENCODE 2025: reference gene annotation for human and mouse
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D966–D975, https://doi.org/10.1093/nar/gkae1078
GoFCards: an integrated database and analytic platform for gain of function variants in humans
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D976–D988, https://doi.org/10.1093/nar/gkae1079
Genomes OnLine Database (GOLD) v.10: new features and updates
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D989–D997, https://doi.org/10.1093/nar/gkae1000
The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D998–D1005, https://doi.org/10.1093/nar/gkae1070
GWAShug: a comprehensive platform for decoding the shared genetic basis between complex traits based on summary statistics
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1006–D1015, https://doi.org/10.1093/nar/gkae873
Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1016–D1028, https://doi.org/10.1093/nar/gkae1080
HSCGD: a comprehensive database of single-cell whole-genome data and metadata
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1029–D1038, https://doi.org/10.1093/nar/gkae971
iDog: a multi-omics resource for canids study
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1039–D1046, https://doi.org/10.1093/nar/gkae1031
Immunosenescence Inventory—a multi-omics database for immune aging research
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1047–D1054, https://doi.org/10.1093/nar/gkae1102
MAPbrain: a multi-omics atlas of the primate brain
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1055–D1065, https://doi.org/10.1093/nar/gkae911
miRNASNP-v4: a comprehensive database for miRNA-related SNPs across 17 species
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1066–D1074, https://doi.org/10.1093/nar/gkae888
MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1075–D1086, https://doi.org/10.1093/nar/gkae1026
Pairpot: a database with real-time lasso-based analysis tailored for paired single-cell and spatial transcriptomics
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1087–D1098, https://doi.org/10.1093/nar/gkae986
PerturBase: a comprehensive database for single-cell perturbation data analysis and visualization
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1099–D1111, https://doi.org/10.1093/nar/gkae858
PerturbAtlas: a comprehensive atlas of public genetic perturbation bulk RNA-seq datasets
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1112–D1119, https://doi.org/10.1093/nar/gkae851
PerturbDB for unraveling gene functions and regulatory networks
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1120–D1131, https://doi.org/10.1093/nar/gkae777
PWAS Hub: exploring gene-based associations of complex diseases with sex dependency
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1132–D1143, https://doi.org/10.1093/nar/gkae1125
The RodentGPOmics Atlas: a comprehensive database of rodent biology for genomes and pathogens
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1144–D1150, https://doi.org/10.1093/nar/gkae1074
sc2GWAS: a comprehensive platform linking single cell and GWAS traits of human
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1151–D1161, https://doi.org/10.1093/nar/gkae1008
scImmOmics: a manually curated resource of single-cell multi-omics immune data
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1162–D1172, https://doi.org/10.1093/nar/gkae985
scLTdb: a comprehensive single-cell lineage tracing database
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1173–D1185, https://doi.org/10.1093/nar/gkae913
scMMO-atlas: a single cell multimodal omics atlas and portal for exploring fine cell heterogeneity and cell dynamics
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1186–D1194, https://doi.org/10.1093/nar/gkae821
scTWAS Atlas: an integrative knowledgebase of single-cell transcriptome-wide association studies
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1195–D1204, https://doi.org/10.1093/nar/gkae931
SPathDB: a comprehensive database of spatial pathway activity atlas
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1205–D1214, https://doi.org/10.1093/nar/gkae1041
SpatialRef: a reference of spatial omics with known spot annotation
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1215–D1223, https://doi.org/10.1093/nar/gkae892
stSNV: a comprehensive resource of SNVs in spatial transcriptome
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1224–D1234, https://doi.org/10.1093/nar/gkae945
TranscriptDB: a transcript-centric database to study eukaryotic transcript conservation and evolution
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1235–D1242, https://doi.org/10.1093/nar/gkae995
The UCSC Genome Browser database: 2025 update
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1243–D1249, https://doi.org/10.1093/nar/gkae974
VDGE: a data repository of variation database for gene-edited animals across multiple species
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1250–D1260, https://doi.org/10.1093/nar/gkae956
webTWAS 2.0: update platform for identifying complex disease susceptibility genes through transcriptome-wide association study
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1261–D1269, https://doi.org/10.1093/nar/gkae1022
xQTLatlas: a comprehensive resource for human cellular-resolution multi-omics genetic regulatory landscape
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1270–D1277, https://doi.org/10.1093/nar/gkae837
GENOMIC VARIATION, DISEASES AND DRUGS
CancerSCEM 2.0: an updated data resource of single-cell expression map across various human cancers
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1278–D1286, https://doi.org/10.1093/nar/gkae954
canSAR 2024—an update to the public drug discovery knowledgebase
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1287–D1294, https://doi.org/10.1093/nar/gkae1050
CAUSALdb2: an updated database for causal variants of complex traits
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1295–D1301, https://doi.org/10.1093/nar/gkae1096
ChiTaRS 8.0: the comprehensive database of chimeric transcripts and RNA-seq data with applications in liquid biopsy
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1302–D1312, https://doi.org/10.1093/nar/gkae1126
ClinVar: updates to support classifications of both germline and somatic variants
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1313–D1321, https://doi.org/10.1093/nar/gkae1090
CovalentInDB 2.0: an updated comprehensive database for structure-based and ligand-based covalent inhibitor design and screening
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1322–D1327, https://doi.org/10.1093/nar/gkae946
Comparative Toxicogenomics Database’s 20th anniversary: update 2025
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1328–D1334, https://doi.org/10.1093/nar/gkae883
CTR-DB 2.0: an updated cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1335–D1347, https://doi.org/10.1093/nar/gkae993
CVD Atlas: a multi-omics database of cardiovascular disease
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1348–D1355, https://doi.org/10.1093/nar/gkae848
DDInter 2.0: an enhanced drug interaction resource with expanded data coverage, new interaction types, and improved user interface
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1356–D1362, https://doi.org/10.1093/nar/gkae726
DMRdb: a disease-centric Mendelian randomization database for systematically assessing causal relationships of diseases with genes, proteins, CpG sites, metabolites and other diseases
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1363–D1371, https://doi.org/10.1093/nar/gkae853
DrugMAP 2.0: molecular atlas and pharma-information of all drugs
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1372–D1382, https://doi.org/10.1093/nar/gkae791
