Nucleic Acids Research

Papers
(The H4-Index of Nucleic Acids Research is 132. 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 2020-05-01 to 2024-05-01.)
ArticleCitations
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation5163
UniProt: the universal protein knowledgebase in 20214601
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets4299
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models3981
Pfam: The protein families database in 20213177
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences3014
TIMER2.0 for analysis of tumor-infiltrating immune cells2533
The Gene Ontology resource: enriching a GOld mine2411
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights2304
KEGG: integrating viruses and cellular organisms2282
PubChem in 2021: new data content and improved web interfaces2141
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 genomes1584
antiSMASH 6.0: improving cluster detection and comparison capabilities1571
UniProt: the Universal Protein Knowledgebase in 20231448
The InterPro protein families and domains database: 20 years on1421
Ensembl 20211232
Ensembl 20221179
Search and sequence analysis tools services from EMBL-EBI in 20221139
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest1070
The reactome pathway knowledgebase 20221003
NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data992
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API991
Database resources of the national center for biotechnology information985
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties981
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles963
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, bio930
SMART: recent updates, new developments and status in 2020922
The carbohydrate-active enzyme database: functions and literature878
HMDB 5.0: the Human Metabolome Database for 2022800
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes784
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations781
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis776
PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA738
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy715
InterPro in 2022708
The Human Phenotype Ontology in 2021679
GENCODE 2021666
PubChem 2023 update633
Comparative Toxicogenomics Database (CTD): update 2021621
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes603
Database resources of the National Center for Biotechnology Information550
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation544
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures538
WikiPathways: connecting communities533
Rfam 14: expanded coverage of metagenomic, viral and microRNA families505
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment496
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts462
miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology460
COG database update: focus on microbial diversity, model organisms, and widespread pathogens458
Dali server: structural unification of protein families453
The IPD-IMGT/HLA Database453
A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase438
DRAM for distilling microbial metabolism to automate the curation of microbiome function432
VFDB 2022: a general classification scheme for bacterial virulence factors425
MODOMICS: a database of RNA modification pathways. 2021 update397
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource375
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update374
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022373
FlyBase: updates to theDrosophila melanogasterknowledge base366
BRENDA, the ELIXIR core data resource in 2021: new developments and updates360
The UCSC Genome Browser database: 2021 update355
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users349
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes349
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities331
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents328
miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions328
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update312
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation310
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics306
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center281
CATH: increased structural coverage of functional space278
Open Targets Platform: supporting systematic drug–target identification and prioritisation276
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine276
Genenames.org: the HGNC and VGNC resources in 2021273
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database272
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation271
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR264
GPCRdb in 2021: integrating GPCR sequence, structure and function260
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics245
CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting244
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses244
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 data223
GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA221
Ensembl 2023217
Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology204
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models204
The Transporter Classification Database (TCDB): 2021 update201
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements198
GenBank197
The ProteomeXchange consortium at 10 years: 2023 update196
A comprehensive review of m6A/m6Am RNA methyltransferase structures195
m6A-Atlas: a comprehensive knowledgebase for unraveling theN6-methyladenosine (m6A) epitranscriptome189
MobiDB: intrinsically disordered proteins in 2021183
LitCovid: an open database of COVID-19 literature180
The UCSC Genome Browser database: 2022 update180
Proksee: in-depth characterization and visualization of bacterial genomes179
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study179
Dynamic landscape and evolution of m6A methylation in human176
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning174
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments174
Phosphorothioate modified oligonucleotide–protein interactions171
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants167
CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data167
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases166
Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data163
Comparative Toxicogenomics Database (CTD): update 2023162
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021158
The UCSC Genome Browser database: 2023 update156
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples154
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates150
Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue150
The Eukaryotic Linear Motif resource: 2022 release150
HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets149
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data147
Database resources of the National Center for Biotechnology Information in 2023144
Genomes OnLine Database (GOLD) v.8: overview and updates143
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more143
Aging Atlas: a multi-omics database for aging biology142
Targeted mRNA demethylation using an engineered dCas13b-ALKBH5 fusion protein142
Investigating the pharmacodynamic durability of GalNAc–siRNA conjugates142
Decoding the epitranscriptional landscape from native RNA sequences140
SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update)140
The international nucleotide sequence database collaboration139
DNA G-quadruplex structures: more than simple roadblocks to transcription?139
FATCAT 2.0: towards a better understanding of the structural diversity of proteins138
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems137
PredictProtein - Predicting Protein Structure and Function for 29 Years137
MutationTaster2021135
The Sequence Read Archive: a decade more of explosive growth135
GTRD: an integrated view of transcription regulation135
Chemistry, structure and function of approved oligonucleotide therapeutics132
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