Nucleic Acids Research

Papers
(The H4-Index of Nucleic Acids Research is 142. 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 2021-09-01 to 2025-09-01.)
ArticleCitations
SV4GD: a comprehensive structural variation database specially for genetic diseases6454
NucleoFind: a deep-learning network for interpreting nucleic acid electron density5379
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip4980
Correction to ‘Cis regulation within a cluster of viral microRNAs’4832
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’4280
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’3589
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’2224
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis2205
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ2031
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey2011
Nanopores map the acid-base properties of a single site in a single DNA molecule1696
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex1693
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase1660
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase1604
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models1603
Systematic discovery of DNA-binding tandem repeat proteins1547
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA1537
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics1492
VID22counteracts G-quadruplex-induced genome instability1491
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity1204
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization1182
Correction to ‘The European Genome-phenome Archive in 2021’1134
PHF8 facilitates transcription recovery following DNA double-strand break repair1118
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination1025
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers963
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes923
Correction to ‘EMDB—the Electron Microscopy Data Bank’892
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’832
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA820
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy820
Molecular determinants for recognition of serotonylated chromatin765
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts754
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast752
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome749
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program738
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels722
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis722
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction721
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)696
TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts666
Splitting the yeast centromere by recombination652
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline648
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning617
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping608
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices560
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication559
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG546
A method for targeting a specified segment of DNA to a bacterial microorganelle533
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells527
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy511
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins498
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region492
The quantitative impact of 3′UTRs on gene expression490
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’489
Investigating the origins of the mutational signatures in cancer472
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research453
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies434
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering427
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery407
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits382
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation357
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei353
ZEB1 promotes non-homologous end joining double-strand break repair338
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’333
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms330
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip330
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining328
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats328
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically323
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins322
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription322
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro319
Prediction of DNA i-motifs via machine learning318
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution311
The human telomeric proteome during telomere replication308
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options307
NCBI Taxonomy: enhanced access via NCBI Datasets307
Widespread translational control regulates retinal development in mouse306
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis297
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity292
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes292
Formation and persistence of polyglutamine aggregates in mistranslating cells290
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation287
BioSamples database: FAIRer samples metadata to accelerate research data management287
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition284
Helical coiling of metaphase chromatids264
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study260
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly252
Yeast transcription factor Msn2 binds to G4 DNA251
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions248
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa242
DriverDBv4: a multi-omics integration database for cancer driver gene research234
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins232
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse224
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions223
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions219
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells217
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR216
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation209
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs205
THUMPD3–TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates204
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression203
Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression194
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing193
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling193
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection192
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning192
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing191
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity189
scQTLbase: an integrated human single-cell eQTL database188
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools187
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity186
RefMetaPlant: a reference metabolome database for plants across five major phyla185
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition185
The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses184
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide182
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli181
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB181
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break179
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy179
Rfam 15: RNA families database in 2025178
Post-replicative lesion processing limits DNA damage-induced mutagenesis176
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system176
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress174
Waves of sumoylation support transcription dynamics during adipocyte differentiation173
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants172
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors172
CPLM 4.0: an updated database with rich annotations for protein lysine modifications165
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database165
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery161
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins158
Human Ageing Genomic Resources: updates on key databases in ageing research158
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA157
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes156
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo153
High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases151
Ensembl 2024150
The carbohydrate-active enzyme database: functions and literature148
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees147
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’146
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’145
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’145
A rationalized definition of general tumor suppressor microRNAs excludes miR-34a142
The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity142
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