Nucleic Acids Research

Article	Citations
Correction to ‘The European Genome-phenome Archive in 2021’	7893
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	6199
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	4439
SV4GD: a comprehensive structural variation database specially for genetic diseases	3437
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	2925
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	2388
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	2084
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	1993
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	1907
Correction to ‘Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development’	1804
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	1733
Correction to ‘DNA-protein Interactions at the Telomeric Repeats of Schizosaccharomyces Pombe’	1627
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons	1574
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	1570
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region	1560
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	1546
PHF8 facilitates transcription recovery following DNA double-strand break repair	1497
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	1466
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	1415
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	1405
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	1251
Correction to ‘EMDB—the Electron Microscopy Data Bank’	1099
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells	1091
Nanopores map the acid-base properties of a single site in a single DNA molecule	1087
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering	1070

Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	1070
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	1058
Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome	1011
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity	974
Investigating the origins of the mutational signatures in cancer	971
TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability	943
Splitting the yeast centromere by recombination	908
Systematic discovery of DNA-binding tandem repeat proteins	902
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system	856
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	806
In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences	797
A method for targeting a specified segment of DNA to a bacterial microorganelle	788
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR ’	775
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	760
RoCi—a single-step multi-copy integration system based on rolling-circle replication	707
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	705
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	692
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	641
METTL1 interacts with XPO5 to modulate pre-miRNA export	608
Molecular determinants for recognition of serotonylated chromatin	555
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	553
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation	543
The quantitative impact of 3′UTRs on gene expression	536
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	531
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	528
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	520
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	502
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	490
scQTLbase: an integrated human single-cell eQTL database	488
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	463
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	453
Constant trouble with prolines—navigating a global translation dilemma	453
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	430
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	416
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	415
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	411
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins	411
DriverDBv4: a multi-omics integration database for cancer driver gene research	408
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	405
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways	399
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	399
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	397
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	382
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	378
Ensembl 2024	376
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	367
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies	367
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	362
Prediction of DNA i-motifs via machine learning	358
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	346

Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	335
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	324
Human Ageing Genomic Resources: updates on key databases in ageing research	320
Rfam 15: RNA families database in 2025	312
Cas12a-assisted split crRNA complex for analysis and detection of diverse entities	305
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	305
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	303
An elevated level of the mRNA exporter Mex67-Mtr2 in nuclear mRNPs impairs nuclear mRNA export	296
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	291
EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment	288
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	288
gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics	287
Characterization of gRNA-dependent and gRNA-independent off-target binding sites of PspCas13b and RfxCas13d in mammalian cells	276
Evidence for a functional interaction between yeast Pol ε and PCNA in vivo	274
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	263
Yeast transcription factor Msn2 binds to G4 DNA	248
Diverse RNA viral effectors converge on facilitation of AGO4 degradation to promote infection	246
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	241
A transcriptomic and proteomic map of primary human cell types	239
PDBe: enhanced structural data exploration to facilitate discovery	238
SmallBARNA 2026: a kingdom-wide bacterial sRNA resource	235
GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana	232
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	230
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	230
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	229
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	220
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	220
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	208
YqeK governs the acquisition and removal of nucleoside tetraphosphate caps in Firmicutes	206
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	204
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	202
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	196
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli	192
Helical coiling of metaphase chromatids	190
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	190
The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	185
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	183
The antiSMASH database version 5	183
Metal ions govern coronavirus endoribonuclease activity	181
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments	179
Mbd4 and MutSα protect cells from spontaneous deamination of 5-methylcytosine	176
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	175
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation	173
RefMetaPlant: a reference metabolome database for plants across five major phyla	173
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research	170
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	167
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	165
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	164
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	162
Post-replicative lesion processing limits DNA damage-induced mutagenesis	161
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	160
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	157
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	157
Multisite phosphorylation of the AML-linked C-terminal of nucleophosmin (NPM1) orchestrates protein stability, DNA binding and charge block-driven phase separation	154
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	153
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	150
ZEB1 promotes non-homologous end joining double-strand break repair	150
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	149
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	147
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	145
NCBI Taxonomy: enhanced access via NCBI Datasets	143
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	143
Disruption of a six-nucleotide miRNA motif improves PKD1 dosage and ameliorates polycystic kidney disease	142
LysR-type regulator LrhA promotes CRISPR-Cas immunity in Escherichia coli	142
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	141
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	140
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	140
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery	140
Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification	139
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’	139
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’	138
GenePlexus: a web-server for gene discovery using network-based machine learning	135
Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout	133
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription	132
Correction to ‘8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα’	132
DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain	132
Molecular basis for RNA discrimination by human DNA ligase 1	132
High-throughput competitive binding assay for targeting RNA tertiary structures with small molecules: application to pseudoknots and G-quadruplexes	130
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’	130
Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD	127

G-quadruplexes as potential traps for superenhancer marker BRD4: ligand-sensitive binding and co-separation in vitro	126
Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species	124
ABC portal: a single-cell database and web server for blood cells	124
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity	123
Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A	123
SCAN: Spatiotemporal Cloud Atlas for Neural cells	122
Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex	122
A de novo H3.2K9me2 deposition pathway establishes heterochromatin for suppressing transposon mobilization during fly somatic development	119
SSB-mediated enhancement of argonaute activity triggers SOS filamentation in bacteria	119
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames	118
Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus	118
Type I-Fv and engineered type IV-A1 CRISPR–Cas effectors facilitate genome reduction in Escherichia coli	116
Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro	114
RMVar 2.0: an updated database of functional variants in RNA modifications	112
A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB	112
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data	112
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’	112
Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil	111
Kingdom-wide CRISPR guide design with ALLEGRO	110
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize	110
Nucleotide salvage, genome instability, and potential therapeutic applications	109
Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication	109
RNA helicase DDX6 and scaffold protein GW182 in P-bodies promote biogenesis of stress granules	109
ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner	108
Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1	107
RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells	107
Development and application of G4-Flame as a visual biosensor for G4-DNA	107
Structural insights into RNA cleavage by a novel family of bacterial RNases	106
Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression	105
Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal	105
Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5′UTRs	104
TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice	104
Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase	104
Optimized high-throughput screening of non-coding variants identified from genome-wide association studies	104
Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp	103
Unmodificated stepless regulation of CRISPR/Cas12a multi-performance	103
DNA–protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM)	101
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes	101
A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC)	100
Intein-based thermoregulated meganucleases for containment of genetic material	99
A novel Queuovirinae lineage of Pseudomonas aeruginosa phages encode dPreQ0 DNA modifications with a single GA motif that provide restriction and CRISPR Cas9 protection in vitro	98
MazF endoribonuclease promotes resolution of transcription–replication conflicts at ribosomal RNA genes in Escherichia coli	98
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs	97
HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins	97
scTML: a pan-cancer single-cell landscape of multiple mutation types	96
Oxidative events in a double helix system promote the formation of kinetically trapped G-quadruplexes	96
Genome-wide screening and functional validation of methylation barriers near promoters	96
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism	95
Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules	95
Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon	94
DEPCOD: a tool to detect and visualize co-evolution of protein domains	94
Proteolytic cleavage activates the mitochondrial isoform of TOP3A	93
Novel telomere-targeting dual-pharmacophore dinucleotide prodrugs for anticancer therapy	93
Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors	93
Accurate measurement of microsatellite length by disrupting its tandem repeat structure	92
A-MYB substitutes for B-MYB in activating cell cycle genes and in stimulating proliferation	92
Microenvironment-aware spatial modeling for accurate inference of cell identity	91
The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells	91
Replication stress increases de novo CNVs across the malaria parasite genome	90
Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics	89
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’	89
Design prokaryotic cis-regulatory elements using language model	89
The origin of mirror repeats in the human genome	89
CircaKB: a comprehensive knowledgebase of circadian genes across multiple species	88
The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context	88
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells	87
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors	87
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase	87
Correction to ‘Condensins regulate resection–dependent DNA double–strand break repair pathways in replicated chromatin’	86
Learning interpretable representations of single-cell multi-omics data with multi-output Gaussian processes	86
Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture	86
Optimized CRISPR-Cas9 system for efficient engineering of ecDNA in cancer cells	85
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment	85
WebCSEA: web-based cell-type-specific enrichment analysis of genes	84
SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA	84
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs	83
Accurate detection of tandem repeats exposes ubiquitous reuse of biological sequences	83
SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data	83
Functional redundancy in tRNA dihydrouridylation	83
Absence of mitochondrial SLC25A51 enhances PARP1-dependent DNA repair by increasing nuclear NAD+ levels	83
Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires	83
Cancer histone mutations impact protein binding and DNA repair with possible links to genomic instability	82
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells	82
PWOs repress gene transcription by regulating chromatin structures in Arabidopsis	82
The organization principles of P. falciparum translation initiation features and their potential as drug targets	81
MethBank 4.0: an updated database of DNA methylation across a variety of species	81
IAnimal: a cross-species omics knowledgebase for animals	81
The ‘Alu-ome’ shapes the epigenetic environment of regulatory elements controlling cellular defense	80
40S hnRNP particles are a novel class of nuclear biomolecular condensates	80
Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus	79
Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network	79
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes	78
A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction	78
Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides	78
SMAP design : a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation	78