Nucleic Acids Research

Article	Citations
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 complex	6738
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	4709
SV4GD: a comprehensive structural variation database specially for genetic diseases	4276
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 microorganelle	2273
A transcriptomic and proteomic map of primary human cell types	2241
GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana	2207
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	2129
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 monoxide	1996
Correction to ‘DNA-protein Interactions at the Telomeric Repeats of Schizosaccharomyces Pombe’	1782
Yeast transcription factor Msn2 binds to G4 DNA	1732
Diverse RNA viral effectors converge on facilitation of AGO4 degradation to promote infection	1718
Nanopores map the acid-base properties of a single site in a single DNA molecule	1657
Correction to ‘EMDB—the Electron Microscopy Data Bank’	1648
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	1489
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	1479
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering	1407
TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability	1377
Evidence for a functional interaction between yeast Pol ε and PCNA in vivo	1273
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	1230
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	1222

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 berghei	1191
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	1183
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 DNA	1075
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	1061
Helical coiling of metaphase chromatids	1059
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	1045
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region	933
Systematic discovery of DNA-binding tandem repeat proteins	860
Characterization of gRNA-dependent and gRNA-independent off-target binding sites of PspCas13b and RfxCas13d in mammalian cells	858
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	854
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	796
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 separation	776
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	714
gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics	684
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	672
EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment	650
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	646
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	628
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation	623
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	593
ZEB1 promotes non-homologous end joining double-strand break repair	587
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	585
CDCA7 targets LSH to DNA maintenance methylation in S phase and transcription regulation in interphase via two distinct DNA-binding modes	576
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery	553
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	547
Collective interactions along recombinase-bound D-loops could speed repair of double-strand breaks by destabilizing flanking homoduplex tails	539
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	532
RoCi—a single-step multi-copy integration system based on rolling-circle replication	507
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	503
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	476
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	463
RNAPII and DNA supercoiling regulate cohesin engagement in neurons	458
An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal	456
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	452
YqeK governs the acquisition and removal of nucleoside tetraphosphate caps in Firmicutes	447
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	447
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	442
PHF8 facilitates transcription recovery following DNA double-strand break repair	435
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	434
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research	416
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	416
LysR-type regulator LrhA promotes CRISPR-Cas immunity in Escherichia coli	411
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation	410
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	406
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons	399
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	389
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	372

Prediction of DNA i-motifs via machine learning	369
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	364
Disruption of a six-nucleotide miRNA motif improves PKD1 dosage and ameliorates polycystic kidney disease	363
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	351
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	336
An elevated level of the mRNA exporter Mex67-Mtr2 in nuclear mRNPs impairs nuclear mRNA export	332
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	330
Post-replicative lesion processing limits DNA damage-induced mutagenesis	328
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	326
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	324
Mbd4 and MutSα protect cells from spontaneous deamination of 5-methylcytosine	314
DriverDBv4: a multi-omics integration database for cancer driver gene research	308
METTL1 interacts with XPO5 to modulate pre-miRNA export	308
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	305
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	292
In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences	271
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	267
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	265
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	264
scQTLbase: an integrated human single-cell eQTL database	259
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells	257
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	247
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	241
Splitting the yeast centromere by recombination	235
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways	229
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments	228
Molecular determinants for recognition of serotonylated chromatin	224
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	217
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	216
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	214
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	212
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	209
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	208
Constant trouble with prolines—navigating a global translation dilemma	206
Smc5/6 uses its head-NSE module to preferentially associate with ssDNA gaps and ss-dsDNA junctions	206
The antiSMASH database version 5	204
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	203
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies	202
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	202
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	202
Cas12a-assisted split crRNA complex for analysis and detection of diverse entities	197
Investigating the origins of the mutational signatures in cancer	193
RefMetaPlant: a reference metabolome database for plants across five major phyla	190
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	187
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	182
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	177
PDBe: enhanced structural data exploration to facilitate discovery	177
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	174
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	171
The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	164
NCBI Taxonomy: enhanced access via NCBI Datasets	164
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	162
Human Ageing Genomic Resources: updates on key databases in ageing research	159
Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome	159
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	158
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	155
The quantitative impact of 3′UTRs on gene expression	153
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	153
Rfam 15: RNA families database in 2025	152
Structure and function of IWS1 in transcription elongation	152
SmallBARNA 2026: a kingdom-wide bacterial sRNA resource	152
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	151
Metal ions govern coronavirus endoribonuclease activity	151
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	150
Ensembl 2024	149
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 readout	145
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’	145
Correction to ‘8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα’	144
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription	144
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’	143
Nature-inspired engineering of an artificial ligase enzyme by domain fusion	142
Learning interpretable representations of single-cell multi-omics data with multi-output Gaussian processes	140
Type I-Fv and engineered type IV-A1 CRISPR–Cas effectors facilitate genome reduction in Escherichia coli	140
A de novo H3.2K9me2 deposition pathway establishes heterochromatin for suppressing transposon mobilization during fly somatic development	135
A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB	134
Novel telomere-targeting dual-pharmacophore dinucleotide prodrugs for anticancer therapy	134
KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing	134
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’	133
The organization principles of P. falciparum translation initiation features and their potential as drug targets	132

SMAP design : a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation	132
KLF9 and KLF13 transcription factors boost myelin gene expression in oligodendrocytes as partners of SOX10 and MYRF	131
Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA	130
AcrIIA28 is a metalloprotein that specifically inhibits targeted-DNA loading to SpyCas9 by binding to the REC3 domain	128
The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation	127
Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus	125
Cryo-EM structure of human TUT1:U6 snRNA complex	125
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize	125
Heteroduplex oligonucleotide technology boosts gene knockdown in cardiac and skeletal muscles	124
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs	123
Quadruplet codon decoding-based versatile genetic biocontainment system	122
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase	121
Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA	120
Fungal chromatin remodeler Isw1 modulates translation via regulating tRNA transcription	118
Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires	116
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells	115
PWOs repress gene transcription by regulating chromatin structures in Arabidopsis	115
SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA	115
Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers	114
MazF endoribonuclease promotes resolution of transcription–replication conflicts at ribosomal RNA genes in Escherichia coli	111
Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase	111
Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes	110
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA	110
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism	110
Hypoxia stabilizes SETDB1 to maintain genome stability	110
Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon	110
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	109
Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro	109
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data	108
High-throughput competitive binding assay for targeting RNA tertiary structures with small molecules: application to pseudoknots and G-quadruplexes	107
A novel ψ–χ fusion protein for unravelling the contributions of χ to DNA replication and repair	106
A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum	105
BioKA: a curated and integrated biomarker knowledgebase for animals	104
Mapping the phenotypic landscape of a transcriptional repressor using deep mutational scanning and growth-based quantitative sequencing	104
DNA binding and dimerization of the SOG1 NAC domain are functionally linked with its ability to undergo liquid–liquid phase separation	104
Intein-based thermoregulated meganucleases for containment of genetic material	104
RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells	104
Correction to ‘Single-cell imaging of N 4-acetylcytidine-modified RNA using fluorine metabolic labeling mediated proximity ligation assay’	103
SCAN: Spatiotemporal Cloud Atlas for Neural cells	103
Replication stress increases de novo CNVs across the malaria parasite genome	103
Microenvironment-aware spatial modeling for accurate inference of cell identity	102
Accurate measurement of microsatellite length by disrupting its tandem repeat structure	102
Design prokaryotic cis-regulatory elements using language model	101
scTML: a pan-cancer single-cell landscape of multiple mutation types	101
Correction to ‘Condensins regulate resection–dependent DNA double–strand break repair pathways in replicated chromatin’	100
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’	99
SSB-mediated enhancement of argonaute activity triggers SOS filamentation in bacteria	99
DNA–protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM)	99
IAnimal: a cross-species omics knowledgebase for animals	99
Successive waves of transcriptional repression and de-repression license cell cycle progression in an archaeon	99
A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction	97
DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain	97
The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells	96
Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin	95
Genome-wide screening and functional validation of methylation barriers near promoters	93
TRIP12’s role in the governance of DNA polymerase β involvement in DNA damage response and repair	93
A conserved viral RNA fold enables nuclease resistance across kingdoms of life	92
Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network	92
Structural insights into RNA cleavage by a novel family of bacterial RNases	91
ABC portal: a single-cell database and web server for blood cells	91
Sequence-directed covalent protein–RNA linkages in a single step using engineered HUH-tags	91
Overlapping and distinct functions of SPT6, PNUTS, and PCF11 in regulating transcription termination	90
Accurate detection of tandem repeats exposes ubiquitous reuse of biological sequences	90
Optimized CRISPR-Cas9 system for efficient engineering of ecDNA in cancer cells	90
Kingdom-wide CRISPR guide design with ALLEGRO	90
Histone variant H2A.X represses deposition of active H3K4me3 marks and restricts H2A.W incorporation	89
RNA/DNA-binding protein TDP43 regulates DNA mismatch repair genes with implications for genome stability	89
POT-3 preferentially binds the terminal DNA-repeat on the telomeric G-overhang	89
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs	88
Iron-sensitive RNA regulation by poly C-binding proteins	88
Downregulation of MLF1 safeguards cardiomyocytes against senescence-associated chromatin opening	87
Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5′UTRs	86
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity	86
A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC)	86
ATRX inactivation disrupts global chromatin state and topology to dysregulate neurodevelopmental pathways in glioma pathogenesis	85
HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins	85
WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination	84
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes	84
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design	84
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation	84
Extensive homologous recombination safeguards oocyte genome integrity in mammals	84
The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution	84
Development and application of G4-Flame as a visual biosensor for G4-DNA	83
Absence of mitochondrial SLC25A51 enhances PARP1-dependent DNA repair by increasing nuclear NAD+ levels	83
DBR1 orchestrates the fate of lariat RNA: debranching-dependent turnover and function	83
G-quadruplexes as potential traps for superenhancer marker BRD4: ligand-sensitive binding and co-separation in vitro	82
Oxidative events in a double helix system promote the formation of kinetically trapped G-quadruplexes	81
RMVar 2.0: an updated database of functional variants in RNA modifications	81
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells	80
Interpretable deep residual network uncovers nucleosome positioning and associated features	80
Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy	79
Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil	79
Efficient 3′-pairing renders microRNA targeting less sensitive to mRNA seed accessibility	79
ECOD: integrating classifications of protein domains from experimental and predicted structures	79
The origin of mirror repeats in the human genome	79