Nucleic Acids Research

Article	Citations
Correction to ‘The European Genome-phenome Archive in 2021’	8188
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	6327
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	4502
SV4GD: a comprehensive structural variation database specially for genetic diseases	3646
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	2995
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	2416
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	2130
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	2074
In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences	1987
A method for targeting a specified segment of DNA to a bacterial microorganelle	1875
A transcriptomic and proteomic map of primary human cell types	1839
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	1766
GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana	1670
SmallBARNA 2026: a kingdom-wide bacterial sRNA resource	1623
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	1570
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	1557
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	1532
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	1469
Correction to ‘Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development’	1420
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	1308
Correction to ‘DNA-protein Interactions at the Telomeric Repeats of Schizosaccharomyces Pombe’	1175
Yeast transcription factor Msn2 binds to G4 DNA	1126
Diverse RNA viral effectors converge on facilitation of AGO4 degradation to promote infection	1116
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	1105
Nanopores map the acid-base properties of a single site in a single DNA molecule	1095

Correction to ‘EMDB—the Electron Microscopy Data Bank’	1094
Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome	1076
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	1022
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	1010
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	974
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	936
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	912
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering	872
TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability	816
Evidence for a functional interaction between yeast Pol ε and PCNA in vivo	808
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	790
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	789
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR ’	731
Metal ions govern coronavirus endoribonuclease activity	721
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	677
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	613
Mbd4 and MutSα protect cells from spontaneous deamination of 5-methylcytosine	588
RoCi—a single-step multi-copy integration system based on rolling-circle replication	580
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	572
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	569
The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	563
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	543
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	539
Helical coiling of metaphase chromatids	526
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli	515
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	510
Characterization of gRNA-dependent and gRNA-independent off-target binding sites of PspCas13b and RfxCas13d in mammalian cells	505
RefMetaPlant: a reference metabolome database for plants across five major phyla	465
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	463
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	458
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	431
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	429
Post-replicative lesion processing limits DNA damage-induced mutagenesis	426
Multisite phosphorylation of the AML-linked C-terminal of nucleophosmin (NPM1) orchestrates protein stability, DNA binding and charge block-driven phase separation	425
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research	420
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	418
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	416
gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics	414
An elevated level of the mRNA exporter Mex67-Mtr2 in nuclear mRNPs impairs nuclear mRNA export	411
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	406
EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment	387
Disruption of a six-nucleotide miRNA motif improves PKD1 dosage and ameliorates polycystic kidney disease	385
LysR-type regulator LrhA promotes CRISPR-Cas immunity in Escherichia coli	383
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	376
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	368
Structure and function of IWS1 in transcription elongation	359
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments	346
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	345
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation	333
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells	323

A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	321
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	318
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity	317
The antiSMASH database version 5	313
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation	302
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	297
ZEB1 promotes non-homologous end joining double-strand break repair	296
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways	293
The quantitative impact of 3′UTRs on gene expression	286
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	282
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	267
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	257
Molecular determinants for recognition of serotonylated chromatin	254
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	252
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	251
Cas12a-assisted split crRNA complex for analysis and detection of diverse entities	247
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	246
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	243
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery	242
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	240
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	238
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	233
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	213
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	210
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	198
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	196
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	194
Constant trouble with prolines—navigating a global translation dilemma	193
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	192
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	191
scQTLbase: an integrated human single-cell eQTL database	189
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	186
METTL1 interacts with XPO5 to modulate pre-miRNA export	186
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	184
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region	183
Systematic discovery of DNA-binding tandem repeat proteins	176
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	175
PHF8 facilitates transcription recovery following DNA double-strand break repair	172
Splitting the yeast centromere by recombination	169
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	168
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	166
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons	164
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	163
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	160
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	155
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	155
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	154
Prediction of DNA i-motifs via machine learning	153
NCBI Taxonomy: enhanced access via NCBI Datasets	149
An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal	148
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	147
Human Ageing Genomic Resources: updates on key databases in ageing research	147
PDBe: enhanced structural data exploration to facilitate discovery	147
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	146
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	146
YqeK governs the acquisition and removal of nucleoside tetraphosphate caps in Firmicutes	145
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	143
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	143
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	142
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	140
DriverDBv4: a multi-omics integration database for cancer driver gene research	139
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	137
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	134
Rfam 15: RNA families database in 2025	134
Investigating the origins of the mutational signatures in cancer	134
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	133
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies	132
Ensembl 2024	132
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’	130
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’	128
Molecular basis for RNA discrimination by human DNA ligase 1	128
Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout	128
Correction to ‘8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα’	126
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription	126
DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain	125
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’	122
Nature-inspired engineering of an artificial ligase enzyme by domain fusion	121
HGD: an integrated homologous gene database across multiple species	119
Learning interpretable representations of single-cell multi-omics data with multi-output Gaussian processes	119
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames	118

Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells	118
Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus	117
Type I-Fv and engineered type IV-A1 CRISPR–Cas effectors facilitate genome reduction in Escherichia coli	116
A de novo H3.2K9me2 deposition pathway establishes heterochromatin for suppressing transposon mobilization during fly somatic development	115
Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture	115
KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing	114
Novel telomere-targeting dual-pharmacophore dinucleotide prodrugs for anticancer therapy	113
A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB	112
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’	112
Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides	111
SMAP design : a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation	109
The organization principles of P. falciparum translation initiation features and their potential as drug targets	109
KLF9 and KLF13 transcription factors boost myelin gene expression in oligodendrocytes as partners of SOX10 and MYRF	107
A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction	107
Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA	107
AcrIIA28 is a metalloprotein that specifically inhibits targeted-DNA loading to SpyCas9 by binding to the REC3 domain	106
Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24	106
Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency	106
Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil	105
Cryo-EM structure of human TUT1:U6 snRNA complex	105
Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network	105
The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation	105
Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus	105
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize	103
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs	100
The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution	100
Heteroduplex oligonucleotide technology boosts gene knockdown in cardiac and skeletal muscles	99
Proteolytic cleavage activates the mitochondrial isoform of TOP3A	99
Genome-wide screening and functional validation of methylation barriers near promoters	98
Oxidative events in a double helix system promote the formation of kinetically trapped G-quadruplexes	98
Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022	98
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs	98
Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp	97
Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules	97
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design	96
Quadruplet codon decoding-based versatile genetic biocontainment system	95
RNA helicase DDX6 and scaffold protein GW182 in P-bodies promote biogenesis of stress granules	94
MethBank 4.0: an updated database of DNA methylation across a variety of species	93
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase	92
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors	92
Functional redundancy in tRNA dihydrouridylation	91
Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA	91
Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers	91
Fungal chromatin remodeler Isw1 modulates translation via regulating tRNA transcription	91
BilboMD: a web-accessible SAXS and AlphaFold-guided modeling pipeline	90
Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires	90
PWOs repress gene transcription by regulating chromatin structures in Arabidopsis	89
Single-cell trajectory inference for detecting transient events in biological processes	89
Absence of mitochondrial SLC25A51 enhances PARP1-dependent DNA repair by increasing nuclear NAD+ levels	89
Improving the generalization of protein expression models with mechanistic sequence information	89
SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA	89
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells	88
Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase	88
Cancer histone mutations impact protein binding and DNA repair with possible links to genomic instability	88
Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers	88
RMVar 2.0: an updated database of functional variants in RNA modifications	87
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism	86
MazF endoribonuclease promotes resolution of transcription–replication conflicts at ribosomal RNA genes in Escherichia coli	86
A conserved viral RNA fold enables nuclease resistance across kingdoms of life	85
Iron-sensitive RNA regulation by poly C-binding proteins	85
Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon	85
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA	85
Hypoxia stabilizes SETDB1 to maintain genome stability	84
Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes	83
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation	83
Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin	83
Nucleotide salvage, genome instability, and potential therapeutic applications	82
CilioGenics: an integrated method and database for predicting novel ciliary genes	82
TRIP12’s role in the governance of DNA polymerase β involvement in DNA damage response and repair	81
IAnimal: a cross-species omics knowledgebase for animals	81
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	81
Unmodificated stepless regulation of CRISPR/Cas12a multi-performance	81
Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy	80
CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software	80
Optimized high-throughput screening of non-coding variants identified from genome-wide association studies	80
WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination	80
Efficient 3′-pairing renders microRNA targeting less sensitive to mRNA seed accessibility	80
Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro	79
High-throughput identification of RNA localization elements in neuronal cells	79
Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities	79
Downregulation of MLF1 safeguards cardiomyocytes against senescence-associated chromatin opening	77
ECOD: integrating classifications of protein domains from experimental and predicted structures	77
STAMarker: determining spatial domain-specific variable genes with saliency maps in deep learning	76
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data	76
A novel ψ–χ fusion protein for unravelling the contributions of χ to DNA replication and repair	75
The DNA-PKcs/JNK/p53 pathway underlies changes in cell fate decision toward death during DNA replication catastrophe	75
High-throughput competitive binding assay for targeting RNA tertiary structures with small molecules: application to pseudoknots and G-quadruplexes	75
A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum	75
Development and application of G4-Flame as a visual biosensor for G4-DNA	74
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes	74
BioKA: a curated and integrated biomarker knowledgebase for animals	74
Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1	73
Intein-based thermoregulated meganucleases for containment of genetic material	73
RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells	72
DNA binding and dimerization of the SOG1 NAC domain are functionally linked with its ability to undergo liquid–liquid phase separation	72