Nucleic Acids Research

Article	Citations
SV4GD: a comprehensive structural variation database specially for genetic diseases	6331
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	5282
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip	4688
Correction to ‘Cis regulation within a cluster of viral microRNAs’	4618
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	4115
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’	3466
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	2161
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	2128
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	1992
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	1957
Nanopores map the acid-base properties of a single site in a single DNA molecule	1669
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	1644
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase	1601
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	1574
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	1535
Systematic discovery of DNA-binding tandem repeat proteins	1530
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning	1430
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	1403
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	1344
VID22counteracts G-quadruplex-induced genome instability	1176
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	1158
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	1101
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	1081
Correction to ‘The European Genome-phenome Archive in 2021’	1074
PHF8 facilitates transcription recovery following DNA double-strand break repair	933

Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	901
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	853
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers	826
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection	810
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	800
Correction to ‘EMDB—the Electron Microscopy Data Bank’	744
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’	724
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors	724
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	717
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	711
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	674
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning	670
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	661
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	635
TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	634
Splitting the yeast centromere by recombination	617
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	605
Widespread translational control regulates retinal development in mouse	600
NCBI Taxonomy: enhanced access via NCBI Datasets	591
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	580
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	537
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program	535
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	501
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	497
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	493
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	490
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells	477
Molecular determinants for recognition of serotonylated chromatin	470
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	463
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	463
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy	411
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	402
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	379
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	370
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	370
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	342
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	337
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	332
CPLM 4.0: an updated database with rich annotations for protein lysine modifications	323
ZEB1 promotes non-homologous end joining double-strand break repair	321
BioSamples database: FAIRer samples metadata to accelerate research data management	315
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip	315
High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases	313
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	312
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	310
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	305
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	303
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	301
Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization	301
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system	299

RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	295
Prediction of DNA i-motifs via machine learning	294
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	289
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	281
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	278
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	277
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	272
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	271
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	265
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	264
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels	262
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	255
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	250
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	246
The human telomeric proteome during telomere replication	246
Rfam 15: RNA families database in 2025	238
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	238
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study	221
Human Ageing Genomic Resources: updates on key databases in ageing research	220
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	217
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	208
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	208
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	203
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	202
A method for targeting a specified segment of DNA to a bacterial microorganelle	193
Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5′-untranslated region	187
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli	186
Waves of sumoylation support transcription dynamics during adipocyte differentiation	186
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	185
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins	185
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	181
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	178
Helical coiling of metaphase chromatids	177
THUMPD3–TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates	177
Formation and persistence of polyglutamine aggregates in mistranslating cells	177
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	177
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering	175
scQTLbase: an integrated human single-cell eQTL database	175
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	175
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research	173
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	170
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	168
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation	168
Post-replicative lesion processing limits DNA damage-induced mutagenesis	167
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region	166
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	166
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies	165
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery	164
Investigating the origins of the mutational signatures in cancer	162
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	161
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	160
The quantitative impact of 3′UTRs on gene expression	158
Yeast transcription factor Msn2 binds to G4 DNA	157
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	156
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	155
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells	154
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly	153
RefMetaPlant: a reference metabolome database for plants across five major phyla	152
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	152
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	151
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	145
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	144
The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses	144
DriverDBv4: a multi-omics integration database for cancer driver gene research	142
Ensembl 2024	142
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	141
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity	139
The carbohydrate-active enzyme database: functions and literature	139
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’	139
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’	138
A rationalized definition of general tumor suppressor microRNAs excludes miR-34a	137
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’	137
Functional redundancy in tRNA dihydrouridylation	136
The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity	136
AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation	133
Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time	133
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize	129
SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data	128
DEPCOD: a tool to detect and visualize co-evolution of protein domains	127
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA	127

Structural basis of how MGME1 processes DNA 5′ ends to maintain mitochondrial genome integrity	126
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors	126
Nature-inspired engineering of an artificial ligase enzyme by domain fusion	126
Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication	126
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes	125
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs	124
Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil	124
SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA	123
Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species	121
Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics	120
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data	119
Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5′UTRs	117
Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro	117
ABC portal: a single-cell database and web server for blood cells	115
DNA–protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM)	114
Crystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold	114
Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD	113
RNA helicase DDX6 and scaffold protein GW182 in P-bodies promote biogenesis of stress granules	113
Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA	113
Constraints on error rate revealed by computational study of G•U tautomerization in translation	110
A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB	110
The origin of mirror repeats in the human genome	107
Optimized high-throughput screening of non-coding variants identified from genome-wide association studies	106
CilioGenics: an integrated method and database for predicting novel ciliary genes	106
A-MYB substitutes for B-MYB in activating cell cycle genes and in stimulating proliferation	106
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment	105
BioKA: a curated and integrated biomarker knowledgebase for animals	105
TRIP12’s role in the governance of DNA polymerase β involvement in DNA damage response and repair	104
PWOs repress gene transcription by regulating chromatin structures in Arabidopsis	103
Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture	101
T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations	100
The ‘Alu-ome’ shapes the epigenetic environment of regulatory elements controlling cellular defense	100
Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24	98
Does rapid sequence divergence preclude RNA structure conservation in vertebrates?	98
KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing	97
Accurate measurement of microsatellite length by disrupting its tandem repeat structure	96
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’	96
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’	96
Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci	95
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity	94
A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC)	94
EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants	94
Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression	94
Dynamic and facilitated binding of topoisomerase accelerates topological relaxation	92
Computational resources to define alleles and altered regulatory motifs at genomically edited candidate response elements	90
Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification	89
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames	88
Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon	87
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers	87
Reconstructing DNA methylation maps of ancient populations	86
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs	86
Hypoxia stabilizes SETDB1 to maintain genome stability	86
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism	86
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming	85
Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency	85
Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal	84
POT-3 preferentially binds the terminal DNA-repeat on the telomeric G-overhang	84
SCAN: Spatiotemporal Cloud Atlas for Neural cells	84
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells	84
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells	83
scTML: a pan-cancer single-cell landscape of multiple mutation types	83
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation	83
Single molecule/particle tracking analysis program SMTracker 2.0 reveals different dynamics of proteins within the RNA degradosome complex inBacillus subtilis	83
Absence of mitochondrial SLC25A51 enhances PARP1-dependent DNA repair by increasing nuclear NAD+ levels	83
CircaKB: a comprehensive knowledgebase of circadian genes across multiple species	83
Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin	82
Phospho-Ku70 induced by DNA damage interacts with RNA Pol II and promotes the formation of phospho-53BP1 foci to ensure optimal cNHEJ	82
ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner	81
Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1	81
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase	80
WebCSEA: web-based cell-type-specific enrichment analysis of genes	80
Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022	80
Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes	80
Unmodificated stepless regulation of CRISPR/Cas12a multi-performance	80
TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice	80
Intein-based thermoregulated meganucleases for containment of genetic material	80
GenePlexus: a web-server for gene discovery using network-based machine learning	79
Coronaviral RNA-methyltransferases: function, structure and inhibition	79
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design	79
Structural insights into RNA cleavage by a novel family of bacterial RNases	78
A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum	78
IAnimal: a cross-species omics knowledgebase for animals	78
Integration of single cell data by disentangled representation learning	77
ECOD: integrating classifications of protein domains from experimental and predicted structures	77
Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides	76
AcrIIA28 is a metalloprotein that specifically inhibits targeted-DNA loading to SpyCas9 by binding to the REC3 domain	76
OpenProt 2.0 builds a path to the functional characterization of alternative proteins	76
Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length	76
Learning interpretable representations of single-cell multi-omics data with multi-output Gaussian processes	75
SMAP design: a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation	75
Binding of DNA origami to lipids: maximizing yield and switching via strand displacement	75
PsrA is a novel regulator contributes to antibiotic synthesis, bacterial virulence, cell motility and extracellular polysaccharides production in Serratia marcescens	75
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers	75
Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses	74
High-throughput identification of RNA localization elements in neuronal cells	74