Nucleic Acids Research

Papers
(The H4-Index of Nucleic Acids Research is 144. 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 2022-08-01 to 2026-08-01.)
ArticleCitations
Correction to ‘The European Genome-phenome Archive in 2021’8971
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex6738
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis4709
SV4GD: a comprehensive structural variation database specially for genetic diseases4276
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’3188
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’2488
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’2428
A method for targeting a specified segment of DNA to a bacterial microorganelle2273
A transcriptomic and proteomic map of primary human cell types2241
GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana2207
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics2129
Correction to ‘Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development’2042
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide1996
Correction to ‘DNA-protein Interactions at the Telomeric Repeats of Schizosaccharomyces Pombe’1782
Yeast transcription factor Msn2 binds to G4 DNA1732
Diverse RNA viral effectors converge on facilitation of AGO4 degradation to promote infection1718
Nanopores map the acid-base properties of a single site in a single DNA molecule1657
Correction to ‘EMDB—the Electron Microscopy Data Bank’1648
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo1489
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms1479
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering1407
TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability1377
Evidence for a functional interaction between yeast Pol ε and PCNA in vivo1273
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome1230
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically1222
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR ’1204
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei1191
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity1183
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’1106
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA1075
NucleoFind: a deep-learning network for interpreting nucleic acid electron density1061
Helical coiling of metaphase chromatids1059
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline1045
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region933
Systematic discovery of DNA-binding tandem repeat proteins860
Characterization of gRNA-dependent and gRNA-independent off-target binding sites of PspCas13b and RfxCas13d in mammalian cells858
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ854
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro796
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)780
Multisite phosphorylation of the AML-linked C-terminal of nucleophosmin (NPM1) orchestrates protein stability, DNA binding and charge block-driven phase separation776
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells714
gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics684
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options672
EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment650
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis646
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase628
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation623
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes593
ZEB1 promotes non-homologous end joining double-strand break repair587
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression585
CDCA7 targets LSH to DNA maintenance methylation in S phase and transcription regulation in interphase via two distinct DNA-binding modes576
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery553
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors547
Collective interactions along recombinase-bound D-loops could speed repair of double-strand breaks by destabilizing flanking homoduplex tails539
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse532
RoCi—a single-step multi-copy integration system based on rolling-circle replication507
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization503
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG476
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA463
RNAPII and DNA supercoiling regulate cohesin engagement in neurons458
An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal456
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions452
YqeK governs the acquisition and removal of nucleoside tetraphosphate caps in Firmicutes447
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast447
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition442
PHF8 facilitates transcription recovery following DNA double-strand break repair435
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation434
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research416
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing416
LysR-type regulator LrhA promotes CRISPR-Cas immunity in Escherichia coli411
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation410
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins406
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons399
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination389
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits372
Prediction of DNA i-motifs via machine learning369
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining364
Disruption of a six-nucleotide miRNA motif improves PKD1 dosage and ameliorates polycystic kidney disease363
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation351
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR336
An elevated level of the mRNA exporter Mex67-Mtr2 in nuclear mRNPs impairs nuclear mRNA export332
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs330
Post-replicative lesion processing limits DNA damage-induced mutagenesis328
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing326
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy324
Mbd4 and MutSα protect cells from spontaneous deamination of 5-methylcytosine314
DriverDBv4: a multi-omics integration database for cancer driver gene research308
METTL1 interacts with XPO5 to modulate pre-miRNA export308
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats305
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions292
In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences271
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa267
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy265
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction264
scQTLbase: an integrated human single-cell eQTL database259
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells257
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins247
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication241
Splitting the yeast centromere by recombination235
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways229
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments228
Molecular determinants for recognition of serotonylated chromatin224
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity217
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA216
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins214
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution212
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break209
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models208
Smc5/6 uses its head-NSE module to preferentially associate with ssDNA gaps and ss-dsDNA junctions206
Constant trouble with prolines—navigating a global translation dilemma206
The antiSMASH database version 5204
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping203
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes202
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies202
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB202
Cas12a-assisted split crRNA complex for analysis and detection of diverse entities197
Investigating the origins of the mutational signatures in cancer193
RefMetaPlant: a reference metabolome database for plants across five major phyla190
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription187
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes182
PDBe: enhanced structural data exploration to facilitate discovery177
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices177
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling174
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants171
NCBI Taxonomy: enhanced access via NCBI Datasets164
The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts164
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity162
Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome159
Human Ageing Genomic Resources: updates on key databases in ageing research159
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools158
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis155
The quantitative impact of 3′UTRs on gene expression153
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database153
Structure and function of IWS1 in transcription elongation152
SmallBARNA 2026: a kingdom-wide bacterial sRNA resource152
Rfam 15: RNA families database in 2025152
Metal ions govern coronavirus endoribonuclease activity151
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees151
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery150
Ensembl 2024149
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’147
Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout145
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’145
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription144
Correction to ‘8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα’144
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