Nucleic Acids Research

Article	Citations
Correction to ‘The European Genome-phenome Archive in 2021’	6442
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	5541
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	4910
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	4041
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	2579
Nanopores map the acid-base properties of a single site in a single DNA molecule	2407
SV4GD: a comprehensive structural variation database specially for genetic diseases	2230
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	2121
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	1808
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’	1512
Systematic discovery of DNA-binding tandem repeat proteins	1434
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	1368
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	1367
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	1271
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways	1255
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	1254
Correction to ‘Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development’	1229
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’	1204
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	1105
gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics	1096
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	996
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	965
TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability	963
Correction to ‘DNA-protein Interactions at the Telomeric Repeats of Schizosaccharomyces Pombe’	942
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	933

High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	929
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation	906
In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences	884
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	857
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation	856
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	800
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region	747
A method for targeting a specified segment of DNA to a bacterial microorganelle	742
Splitting the yeast centromere by recombination	710
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	708
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	682
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research	662
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	606
Molecular determinants for recognition of serotonylated chromatin	597
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	594
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	581
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	568
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	560
The antiSMASH database version 5	531
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	516
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	502
The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	502
Cas12a-assisted split crRNA complex for analysis and detection of diverse entities	463
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	458
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	455
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	451
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	431
PHF8 facilitates transcription recovery following DNA double-strand break repair	413
Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome	404
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	392
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	381
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program	380
Yeast transcription factor Msn2 binds to G4 DNA	376
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons	371
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery	369
EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment	368
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	360
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	353
Diverse RNA viral effectors converge on facilitation of AGO4 degradation to promote infection	353
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	346
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	345
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	320
Evidence for a functional interaction between yeast Pol ε and PCNA in vivo	317
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system	317
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	316
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	315
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	311
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	309
The quantitative impact of 3′UTRs on gene expression	294
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	278

ZEB1 promotes non-homologous end joining double-strand break repair	272
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments	268
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	267
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	261
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	258
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering	255
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	254
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	243
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	243
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	242
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	239
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	233
GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana	224
SmallBARNA 2026: a kingdom-wide bacterial sRNA resource	222
PDBe: enhanced structural data exploration to facilitate discovery	216
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning	215
Correction to ‘EMDB—the Electron Microscopy Data Bank’	215
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	200
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	196
NCBI Taxonomy: enhanced access via NCBI Datasets	196
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	193
DriverDBv4: a multi-omics integration database for cancer driver gene research	191
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	190
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	189
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	187
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	184
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	183
RefMetaPlant: a reference metabolome database for plants across five major phyla	179
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	178
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	178
scQTLbase: an integrated human single-cell eQTL database	167
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	166
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells	164
Investigating the origins of the mutational signatures in cancer	163
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli	161
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	161
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	158
Helical coiling of metaphase chromatids	156
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	154
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	153
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	147
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	144
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	142
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	141
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	140
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	138
Prediction of DNA i-motifs via machine learning	137
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	136
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies	133
Post-replicative lesion processing limits DNA damage-induced mutagenesis	133
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	130
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	130
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	127
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity	127
Waves of sumoylation support transcription dynamics during adipocyte differentiation	126
Rfam 15: RNA families database in 2025	126
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins	124
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	123
Human Ageing Genomic Resources: updates on key databases in ageing research	122
Ensembl 2024	120
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	120
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’	119
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’	119
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity	119
Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification	118
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames	117
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’	116
GenePlexus: a web-server for gene discovery using network-based machine learning	115
BioKA: a curated and integrated biomarker knowledgebase for animals	115
Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout	114
Correction to ‘8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα’	112
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription	112
Molecular basis for RNA discrimination by human DNA ligase 1	112
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’	111
DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain	111
Does rapid sequence divergence preclude RNA structure conservation in vertebrates?	111
Kingdom-wide CRISPR guide design with ALLEGRO	110
Interpretable deep residual network uncovers nucleosome positioning and associated features	110
The origin of mirror repeats in the human genome	109
Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication	106

Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro	104
A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB	103
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA	103
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’	102
Influenza a virus antiparallel helical nucleocapsid-like pseudo-atomic structure	102
KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing	100
Cancer histone mutations impact protein binding and DNA repair with possible links to genomic instability	100
Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA	99
G-quadruplexes as potential traps for superenhancer marker BRD4: ligand-sensitive binding and co-separation in vitro	99
Structural insights into RNA cleavage by a novel family of bacterial RNases	98
High-throughput competitive binding assay for targeting RNA tertiary structures with small molecules: application to pseudoknots and G-quadruplexes	98
A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction	97
Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network	97
Genome-wide screening and functional validation of methylation barriers near promoters	97
Iron-sensitive RNA regulation by poly C-binding proteins	97
MazF endoribonuclease promotes resolution of transcription–replication conflicts at ribosomal RNA genes in Escherichia coli	96
Overlapping and distinct functions of SPT6, PNUTS, and PCF11 in regulating transcription termination	96
EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants	96
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism	95
Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression	94
Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon	93
Functional redundancy in tRNA dihydrouridylation	92
DEPCOD: a tool to detect and visualize co-evolution of protein domains	91
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize	91
Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers	91
The organization principles of P. falciparum translation initiation features and their potential as drug targets	91
Proteolytic cleavage activates the mitochondrial isoform of TOP3A	90
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation	90
Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture	90
SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data	90
Intein-based thermoregulated meganucleases for containment of genetic material	89
Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes	89
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs	89
SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA	89
Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses	89
Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires	87
TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice	87
ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner	87
The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation	87
Dynamic and facilitated binding of topoisomerase accelerates topological relaxation	87
POT-3 preferentially binds the terminal DNA-repeat on the telomeric G-overhang	86
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers	86
Learning interpretable representations of single-cell multi-omics data with multi-output Gaussian processes	85
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors	84
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells	83
Fungal chromatin remodeler Isw1 modulates translation via regulating tRNA transcription	82
Optimized high-throughput screening of non-coding variants identified from genome-wide association studies	82
A rationalized definition of general tumor suppressor microRNAs excludes miR-34a	82
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	82
Reconstructing DNA methylation maps of ancient populations	81
RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells	81
Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA	81
Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022	81
Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors	81
HGD: an integrated homologous gene database across multiple species	80
RMVar 2.0: an updated database of functional variants in RNA modifications	80
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment	80
WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination	80
Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers	79
Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules	79
Novel telomere-targeting dual-pharmacophore dinucleotide prodrugs for anticancer therapy	78
DNA–protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM)	78
Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A	77
Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy	77
Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp	77
Extensive homologous recombination safeguards oocyte genome integrity in mammals	77
Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5′UTRs	77
Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD	76
scTML: a pan-cancer single-cell landscape of multiple mutation types	76
Commonality and diversity in tRNA substrate recognition in t6A biogenesis by eukaryotic KEOPSs	76
Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin	75
Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species	75
RNA/DNA-binding protein TDP43 regulates DNA mismatch repair genes with implications for genome stability	74
Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions	74
Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus	74
Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics	73
ABC portal: a single-cell database and web server for blood cells	73
STAMarker: determining spatial domain-specific variable genes with saliency maps in deep learning	73
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	73
40S hnRNP particles are a novel class of nuclear biomolecular condensates	73
SCAN: Spatiotemporal Cloud Atlas for Neural cells	72
SMAP design : a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation	72
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes	72
Oxidative events in a double helix system promote the formation of kinetically trapped G-quadruplexes	72
Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus	72
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design	72
The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells	71
Unmodificated stepless regulation of CRISPR/Cas12a multi-performance	71
Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24	71
Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency	71
Improving the generalization of protein expression models with mechanistic sequence information	70
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming	70
The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity	70
The DNA-PKcs/JNK/p53 pathway underlies changes in cell fate decision toward death during DNA replication catastrophe	70
Nature-inspired engineering of an artificial ligase enzyme by domain fusion	69