Nucleic Acids Research

Article	Citations
Correction to ‘The European Genome-phenome Archive in 2021’	6085
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	5390
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	4755
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	3934
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	2497
Nanopores map the acid-base properties of a single site in a single DNA molecule	2409
SV4GD: a comprehensive structural variation database specially for genetic diseases	2176
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	2175
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	2100
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’	1727
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	1428
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells	1340
Correction to ‘EMDB—the Electron Microscopy Data Bank’	1327
Systematic discovery of DNA-binding tandem repeat proteins	1233
VID22counteracts G-quadruplex-induced genome instability	1182
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	1180
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	1157
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	1147
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	1137
SmallBARNA 2026: a kingdom-wide bacterial sRNA resource	1020
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways	1019
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	917
Correction to ‘Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development’	889
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’	886
Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression	880

NucleoFind: a deep-learning network for interpreting nucleic acid electron density	878
gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics	855
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	836
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	830
TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability	816
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments	792
Correction to ‘DNA-protein Interactions at the Telomeric Repeats of Schizosaccharomyces Pombe’	740
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies	702
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	691
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	689
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	686
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	666
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation	656
In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences	648
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	631
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation	583
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	565
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region	554
A method for targeting a specified segment of DNA to a bacterial microorganelle	546
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	546
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research	528
GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana	475
Splitting the yeast centromere by recombination	442
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly	433
Molecular determinants for recognition of serotonylated chromatin	432
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning	429
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	424
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	417
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	405
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	397
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	389
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	388
The antiSMASH database version 5	378
The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	358
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	358
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system	357
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	357
Cas12a-assisted split crRNA complex for analysis and detection of diverse entities	352
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	351
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	344
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	336
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	336
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	331
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	330
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	314
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	307
Prediction of DNA i-motifs via machine learning	300
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning	292
PHF8 facilitates transcription recovery following DNA double-strand break repair	286
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	286

Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome	266
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	265
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	259
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	253
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	249
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program	244
Yeast transcription factor Msn2 binds to G4 DNA	241
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons	239
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery	238
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection	232
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	231
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	225
EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment	223
Post-replicative lesion processing limits DNA damage-induced mutagenesis	221
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	220
Waves of sumoylation support transcription dynamics during adipocyte differentiation	212
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	212
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	207
Diverse RNA viral effectors converge on facilitation of AGO4 degradation to promote infection	201
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	201
ZEB1 promotes non-homologous end joining double-strand break repair	190
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	188
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	183
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	182
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	181
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	180
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering	179
Investigating the origins of the mutational signatures in cancer	177
The quantitative impact of 3′UTRs on gene expression	173
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	172
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	163
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	162
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	160
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity	159
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	156
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	155
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	155
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	153
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	153
NCBI Taxonomy: enhanced access via NCBI Datasets	152
scQTLbase: an integrated human single-cell eQTL database	152
Rfam 15: RNA families database in 2025	151
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	146
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli	145
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	144
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	140
Helical coiling of metaphase chromatids	139
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	137
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	136
DriverDBv4: a multi-omics integration database for cancer driver gene research	135
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	134
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	132
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	130
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	125
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	125
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	123
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	123
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	122
RefMetaPlant: a reference metabolome database for plants across five major phyla	119
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	119
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins	118
Human Ageing Genomic Resources: updates on key databases in ageing research	115
Ensembl 2024	115
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’	114
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’	113
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames	112
Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification	112
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity	112
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’	112
BioKA: a curated and integrated biomarker knowledgebase for animals	109
GenePlexus: a web-server for gene discovery using network-based machine learning	109
Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout	108
Correction to ‘8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα’	108
Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci	108
Molecular basis for RNA discrimination by human DNA ligase 1	108
Novel telomere-targeting dual-pharmacophore dinucleotide prodrugs for anticancer therapy	107
CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software	107
Extensive homologous recombination safeguards oocyte genome integrity in mammals	107
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription	107
DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain	106

Does rapid sequence divergence preclude RNA structure conservation in vertebrates?	104
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’	104
Kingdom-wide CRISPR guide design with ALLEGRO	101
Interpretable deep residual network uncovers nucleosome positioning and associated features	101
The origin of mirror repeats in the human genome	100
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment	98
Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication	97
Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro	96
A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB	96
Downregulation of MLF1 safeguards cardiomyocytes against senescence-associated chromatin opening	95
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’	95
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA	95
WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination	95
Proteolytic cleavage activates the mitochondrial isoform of TOP3A	94
Intein-based thermoregulated meganucleases for containment of genetic material	93
Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture	93
Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp	93
A common transcriptional mechanism involving R-loop and RNA abasic site regulates an enhancer RNA of APOE	91
Efficient 3′-pairing renders microRNA targeting less sensitive to mRNA seed accessibility	91
Cryo-EM structure of human TUT1:U6 snRNA complex	91
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation	91
Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency	90
Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5′UTRs	90
Accurate measurement of microsatellite length by disrupting its tandem repeat structure	89
KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing	89
DEPCOD: a tool to detect and visualize co-evolution of protein domains	89
G-quadruplexes as potential traps for superenhancer marker BRD4: ligand-sensitive binding and co-separation in vitro	89
Cancer histone mutations impact protein binding and DNA repair with possible links to genomic instability	89
Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy	88
Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA	88
High-throughput competitive binding assay for targeting RNA tertiary structures with small molecules: application to pseudoknots and G-quadruplexes	87
Structural insights into RNA cleavage by a novel family of bacterial RNases	87
Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24	86
Hypoxia stabilizes SETDB1 to maintain genome stability	86
Genome-wide screening and functional validation of methylation barriers near promoters	85
Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network	85
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes	83
Iron-sensitive RNA regulation by poly C-binding proteins	83
A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction	83
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize	82
SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data	82
A conserved viral RNA fold enables nuclease resistance across kingdoms of life	82
Influenza a virus antiparallel helical nucleocapsid-like pseudo-atomic structure	81
Functional redundancy in tRNA dihydrouridylation	81
Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal	81
RMVar 2.0: an updated database of functional variants in RNA modifications	81
EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants	80
Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides	80
A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC)	79
Overlapping and distinct functions of SPT6, PNUTS, and PCF11 in regulating transcription termination	79
The organization principles of P. falciparum translation initiation features and their potential as drug targets	78
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism	78
Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon	78
MazF endoribonuclease promotes resolution of transcription–replication conflicts at ribosomal RNA genes in Escherichia coli	78
Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression	78
A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum	78
Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions	77
Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers	76
FARS2 deficiency in Drosophila reveals the developmental delay and seizure manifested by aberrant mitochondrial tRNA metabolism	76
The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells	76
Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD	76
Mechanisms of mitochondrial promoter recognition in humans and other mammalian species	76
Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A	75
SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA	75
Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers	74
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs	74
Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses	74
scTML: a pan-cancer single-cell landscape of multiple mutation types	73
The ProteomeXchange consortium in 2026: making proteomics data FAIR	73
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data	73
ABC portal: a single-cell database and web server for blood cells	73
FANCD2 and RAD51 recombinase directly inhibit DNA2 nuclease at stalled replication forks and FANCD2 acts as a novel RAD51 mediator in strand exchange to promote genome stability	72
Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA	72
Quadruplet codon decoding-based versatile genetic biocontainment system	72
Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules	72
Nature-inspired engineering of an artificial ligase enzyme by domain fusion	72
Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1	72
RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells	72
Commonality and diversity in tRNA substrate recognition in t6A biogenesis by eukaryotic KEOPSs	71
Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors	71
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design	71
SCAN: Spatiotemporal Cloud Atlas for Neural cells	71
KLF9 and KLF13 transcription factors boost myelin gene expression in oligodendrocytes as partners of SOX10 and MYRF	71
Dynamic and facilitated binding of topoisomerase accelerates topological relaxation	70
The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution	70
The ‘Alu-ome’ shapes the epigenetic environment of regulatory elements controlling cellular defense	70
POT-3 preferentially binds the terminal DNA-repeat on the telomeric G-overhang	69
Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes	69
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers	69
ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner	69
The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity	69
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase	69
Learning interpretable representations of single-cell multi-omics data with multi-output Gaussian processes	68
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors	68
Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length	68