Nucleic Acids Research

Article	Citations
SV4GD: a comprehensive structural variation database specially for genetic diseases	6059
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	5042
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip	4245
A method for targeting a specified segment of DNA to a bacterial microorganelle	4073
Correction to ‘Cis regulation within a cluster of viral microRNAs’	3817
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	3240
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	2018
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’	1942
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	1933
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers	1842
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	1618
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	1539
GGGCTA repeats can fold into hairpins poorly unfolded by replication protein A: a possible origin of the length-dependent instability of GGGCTA variant repeats in human telomeres	1504
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	1478
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	1478
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	1394
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	1333
Nanopores map the acid-base properties of a single site in a single DNA molecule	1250
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	1241
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	1085
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase	1070
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	1012
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	1007
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program	980
Systematic discovery of DNA-binding tandem repeat proteins	942

A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	771
Cognate restriction of transposition by piggyBac-like proteins	761
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning	755
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	754
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	726
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	708
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	699
VID22counteracts G-quadruplex-induced genome instability	676
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning	664
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	631
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	617
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	577
Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations	572
Human prefoldin modulates co-transcriptional pre-mRNA splicing	537
Correction to ‘The European Genome-phenome Archive in 2021’	535
PHF8 facilitates transcription recovery following DNA double-strand break repair	531
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	531
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	517
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	498
Correction to ‘EMDB—the Electron Microscopy Data Bank’	494
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’	483
Investigating the origins of the mutational signatures in cancer	482
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy	480
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	450
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	432
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	428
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	416
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly	413
TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	403
Splitting the yeast centromere by recombination	398
Post-replicative lesion processing limits DNA damage-induced mutagenesis	392
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data	335
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	333
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	325
The human telomeric proteome during telomere replication	324
scQTLbase: an integrated human single-cell eQTL database	319
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	312
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	297
Yeast transcription factor Msn2 binds to G4 DNA	297
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	288
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	286
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system	282
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	282
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	278
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	275
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies	273
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	270
RefMetaPlant: a reference metabolome database for plants across five major phyla	270
Widespread translational control regulates retinal development in mouse	269
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	260

Waves of sumoylation support transcription dynamics during adipocyte differentiation	259
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	255
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	247
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	241
ZEB1 promotes non-homologous end joining double-strand break repair	241
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	240
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	238
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	233
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	232
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	231
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip	230
THUMPD3–TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates	226
BioSamples database: FAIRer samples metadata to accelerate research data management	226
Formation and persistence of polyglutamine aggregates in mistranslating cells	222
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	219
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	218
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	215
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	213
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	208
Helical coiling of metaphase chromatids	203
NCBI Taxonomy: enhanced access via NCBI Datasets	193
High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases	192
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	190
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels	182
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	182
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	182
Prediction of DNA i-motifs via machine learning	177
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors	175
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	174
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	174
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells	172
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	170
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	169
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	169
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	168
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	166
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	165
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	165
CPLM 4.0: an updated database with rich annotations for protein lysine modifications	160
The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses	156
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering	156
Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization	154
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	149
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli	149
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	148
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	147
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	147
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	147
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection	146
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study	144
Human Ageing Genomic Resources: updates on key databases in ageing research	144
Rfam 15: RNA families database in 2025	143
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	142
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	141
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	140
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	139
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity	137
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	136
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	135
DriverDBv4: a multi-omics integration database for cancer driver gene research	134
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins	133
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	132
Ensembl 2024	131
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	131
The carbohydrate-active enzyme database: functions and literature	131
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	130
Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout	130
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription	129
Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers	128
Improving the generalization of protein expression models with mechanistic sequence information	128
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’	128
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’	127
Structural basis of how MGME1 processes DNA 5′ ends to maintain mitochondrial genome integrity	126
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’	126
Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022	125
Overlapping and distinct functions of SPT6, PNUTS, and PCF11 in regulating transcription termination	124
GenePlexus: a web-server for gene discovery using network-based machine learning	122
A rationalized definition of general tumor suppressor microRNAs excludes miR-34a	120
Mechanisms of mitochondrial promoter recognition in humans and other mammalian species	120
Cisplatin fastens chromatin irreversibly even at a high chloride concentration	119

Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network	116
The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity	116
Phospho-Ku70 induced by DNA damage interacts with RNA Pol II and promotes the formation of phospho-53BP1 foci to ensure optimal cNHEJ	115
Genome-wide screening and functional validation of methylation barriers near promoters	115
Fungal chromatin remodeler Isw1 modulates translation via regulating tRNA transcription	114
Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase	113
Functional redundancy in tRNA dihydrouridylation	112
Molecular basis for RNA discrimination by human DNA ligase 1	110
The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution	110
A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction	109
The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells	109
Oxidative events in a double helix system promote the formation of kinetically trapped G-quadruplexes	109
AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation	108
Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time	106
Structural insights into RNA cleavage by a novel family of bacterial RNases	105
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize	104
SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data	103
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming	102
Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus	102
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA	102
Unmodificated stepless regulation of CRISPR/Cas12a multi-performance	101
Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency	100
The ‘Alu-ome’ shapes the epigenetic environment of regulatory elements controlling cellular defense	100
DEPCOD: a tool to detect and visualize co-evolution of protein domains	99
OpenProt 2.0 builds a path to the functional characterization of alternative proteins	99
Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A	97
Coronaviral RNA-methyltransferases: function, structure and inhibition	96
Binding of DNA origami to lipids: maximizing yield and switching via strand displacement	96
Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication	96
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors	96
Correction to ‘8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα’	94
BioKA: a curated and integrated biomarker knowledgebase for animals	94
CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software	93
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes	93
Nature-inspired engineering of an artificial ligase enzyme by domain fusion	92
Does rapid sequence divergence preclude RNA structure conservation in vertebrates?	91
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment	91
ZNF598 co-translationally titrates poly(GR) protein implicated in the pathogenesis of C9ORF72-associated ALS/FTD	91
Extensive homologous recombination safeguards oocyte genome integrity in mammals	91
Cryo-EM structure of human TUT1:U6 snRNA complex	91
PseudoGA: cell pseudotime reconstruction based on genetic algorithm	91
Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules	90
Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24	89
DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain	89
MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species	89
Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses	88
KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing	87
Accurate measurement of microsatellite length by disrupting its tandem repeat structure	86
Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides	85
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	85
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’	84
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs	82
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’	82
Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci	82
Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA	82
Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA	81
EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants	81
Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species	81
A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC)	81
Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression	80
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity	80
Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA	80
SMAP design: a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation	80
Dynamic and facilitated binding of topoisomerase accelerates topological relaxation	79
Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5′UTRs	79
Computational resources to define alleles and altered regulatory motifs at genomically edited candidate response elements	79
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers	78
SCAN: Spatiotemporal Cloud Atlas for Neural cells	78
Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification	78
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames	78
CircaKB: a comprehensive knowledgebase of circadian genes across multiple species	78
Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon	78
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data	78
ABC portal: a single-cell database and web server for blood cells	77
Reconstructing DNA methylation maps of ancient populations	76
Integration of single cell data by disentangled representation learning	75
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism	75
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs	74
ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner	74
Hypoxia stabilizes SETDB1 to maintain genome stability	73
Crystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold	72
T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations	72
Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro	72
Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil	72
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers	72
AcrIIA28 is a metalloprotein that specifically inhibits targeted-DNA loading to SpyCas9 by binding to the REC3 domain	72
Inhibition mechanisms of CRISPR-Cas9 by AcrIIA17 and AcrIIA18	71
Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA	71
Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers	71
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells	71
Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics	70
Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes	70
40S hnRNP particles are a novel class of nuclear biomolecular condensates	70
Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length	70
Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors	70