Nucleic Acids Research

Article	Citations
Correction to ‘The European Genome-phenome Archive in 2021’	6738
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	5685
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	5562
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	5210
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	4594
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	3808
Nanopores map the acid-base properties of a single site in a single DNA molecule	2386
SV4GD: a comprehensive structural variation database specially for genetic diseases	2351
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	2129
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	2071
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’	1941
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	1800
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells	1771
Correction to ‘EMDB—the Electron Microscopy Data Bank’	1738
PHF8 facilitates transcription recovery following DNA double-strand break repair	1667
Systematic discovery of DNA-binding tandem repeat proteins	1658
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	1607
VID22counteracts G-quadruplex-induced genome instability	1343
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	1287
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	1238
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	1226
Correction to ‘Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development’	1192
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’	1106
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	1080
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	1050

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	1032
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	976
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	936
gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics	914
Yeast transcription factor Msn2 binds to G4 DNA	891
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	861
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research	836
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	828
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	804
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	795
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	784
Waves of sumoylation support transcription dynamics during adipocyte differentiation	777
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase	753
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	706
DriverDBv4: a multi-omics integration database for cancer driver gene research	677
TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability	677
Investigating the origins of the mutational signatures in cancer	672
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments	671
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	663
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	628
Human Ageing Genomic Resources: updates on key databases in ageing research	617
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	611
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	599
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	567
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	554
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	530
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly	528
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	526
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection	524
The human telomeric proteome during telomere replication	472
Correction to ‘DNA-protein Interactions at the Telomeric Repeats of Schizosaccharomyces Pombe’	425
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	422
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	392
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli	392
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	388
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	376
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	369
A method for targeting a specified segment of DNA to a bacterial microorganelle	368
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	357
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	357
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation	354
In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences	350
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery	348
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning	345
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	342
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering	340
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	338
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	337
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation	332
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	327

The quantitative impact of 3′UTRs on gene expression	326
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	325
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region	319
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	318
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program	305
Helical coiling of metaphase chromatids	305
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	294
ZEB1 promotes non-homologous end joining double-strand break repair	283
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	280
Prediction of DNA i-motifs via machine learning	277
Splitting the yeast centromere by recombination	273
Molecular determinants for recognition of serotonylated chromatin	267
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	259
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	258
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning	252
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	243
TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	243
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	239
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	228
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	223
RefMetaPlant: a reference metabolome database for plants across five major phyla	219
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	218
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	214
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	213
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy	212
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	212
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	207
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	205
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	204
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	203
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	202
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	202
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	200
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	199
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	195
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	193
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	192
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	189
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	187
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	185
SmallBARNA 2026: a kingdom-wide bacterial sRNA resource	182
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways	181
Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome	181
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	174
scQTLbase: an integrated human single-cell eQTL database	172
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies	172
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	170
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	170
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	166
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	165
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins	164
Rfam 15: RNA families database in 2025	156
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	156
NCBI Taxonomy: enhanced access via NCBI Datasets	155
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	154
BioSamples database: FAIRer samples metadata to accelerate research data management	153
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity	152
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system	151
Ensembl 2024	149
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	147
The carbohydrate-active enzyme database: functions and literature	147
Post-replicative lesion processing limits DNA damage-induced mutagenesis	147
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’	146
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’	146
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity	143
Dynamic and facilitated binding of topoisomerase accelerates topological relaxation	143
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames	141
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’	141
Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification	141
BioKA: a curated and integrated biomarker knowledgebase for animals	140
GenePlexus: a web-server for gene discovery using network-based machine learning	140
Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci	138
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells	137
Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout	137
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation	137
Molecular basis for RNA discrimination by human DNA ligase 1	136
The DNA-PKcs/JNK/p53 pathway underlies changes in cell fate decision toward death during DNA replication catastrophe	135
Correction to ‘8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα’	135
Novel telomere-targeting dual-pharmacophore dinucleotide prodrugs for anticancer therapy	131
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription	131

Extensive homologous recombination safeguards oocyte genome integrity in mammals	129
Influenza a virus antiparallel helical nucleocapsid-like pseudo-atomic structure	128
DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain	123
CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software	123
Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers	122
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’	120
scTML: a pan-cancer single-cell landscape of multiple mutation types	118
The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution	117
Does rapid sequence divergence preclude RNA structure conservation in vertebrates?	116
Reconstructing DNA methylation maps of ancient populations	116
Interpretable deep residual network uncovers nucleosome positioning and associated features	116
RNA/DNA-binding protein TDP43 regulates DNA mismatch repair genes with implications for genome stability	115
Kingdom-wide CRISPR guide design with ALLEGRO	114
RMVar 2.0: an updated database of functional variants in RNA modifications	111
The origin of mirror repeats in the human genome	111
Structural basis of how MGME1 processes DNA 5′ ends to maintain mitochondrial genome integrity	110
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment	110
The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity	108
Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication	107
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data	106
Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro	106
A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB	105
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA	105
Cryo-EM structure of human TUT1:U6 snRNA complex	104
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’	104
Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5′UTRs	103
Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency	102
Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers	102
Commonality and diversity in tRNA substrate recognition in t6A biogenesis by eukaryotic KEOPSs	102
ABC portal: a single-cell database and web server for blood cells	101
Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture	101
HGD: an integrated homologous gene database across multiple species	99
Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp	98
DEPCOD: a tool to detect and visualize co-evolution of protein domains	98
Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics	98
Cancer histone mutations impact protein binding and DNA repair with possible links to genomic instability	97
A-MYB substitutes for B-MYB in activating cell cycle genes and in stimulating proliferation	97
KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing	95
Accurate measurement of microsatellite length by disrupting its tandem repeat structure	93
Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil	92
G-quadruplexes as potential traps for superenhancer marker BRD4: ligand-sensitive binding and co-separation in vitro	91
SMAP design: a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation	91
DBR1 orchestrates the fate of lariat RNA: debranching-dependent turnover and function	91
Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes	90
Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA	90
Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy	90
ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner	89
SCAN: Spatiotemporal Cloud Atlas for Neural cells	89
Structural insights into RNA cleavage by a novel family of bacterial RNases	89
High-throughput competitive binding assay for targeting RNA tertiary structures with small molecules: application to pseudoknots and G-quadruplexes	89
TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice	89
Inhibition mechanisms of CRISPR-Cas9 by AcrIIA17 and AcrIIA18	88
Hypoxia stabilizes SETDB1 to maintain genome stability	88
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers	88
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design	87
Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24	87
Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A	86
PsrA is a novel regulator contributes to antibiotic synthesis, bacterial virulence, cell motility and extracellular polysaccharides production in Serratia marcescens	86
FARS2 deficiency in Drosophila reveals the developmental delay and seizure manifested by aberrant mitochondrial tRNA metabolism	86
AcrIIA28 is a metalloprotein that specifically inhibits targeted-DNA loading to SpyCas9 by binding to the REC3 domain	86
Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length	86
40S hnRNP particles are a novel class of nuclear biomolecular condensates	85
Crystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold	85
Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022	85
A rationalized definition of general tumor suppressor microRNAs excludes miR-34a	84
Cisplatin fastens chromatin irreversibly even at a high chloride concentration	84
Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin	84
Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors	84
Genome-wide screening and functional validation of methylation barriers near promoters	83
Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network	83
POT-3 preferentially binds the terminal DNA-repeat on the telomeric G-overhang	83
Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses	82
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs	82
Iron-sensitive RNA regulation by poly C-binding proteins	82
WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination	81
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes	81
Fungal chromatin remodeler Isw1 modulates translation via regulating tRNA transcription	80
Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus	80
A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction	80
Learning interpretable representations of single-cell multi-omics data with multi-output Gaussian processes	79
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells	78
A common transcriptional mechanism involving R-loop and RNA abasic site regulates an enhancer RNA of APOE	78
Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species	78
Optimized high-throughput screening of non-coding variants identified from genome-wide association studies	78
SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA	77
Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules	77
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize	77
CircaKB: a comprehensive knowledgebase of circadian genes across multiple species	77
SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data	77
Quadruplet codon decoding-based versatile genetic biocontainment system	75
RNA helicase DDX6 and scaffold protein GW182 in P-bodies promote biogenesis of stress granules	75
High-throughput identification of RNA localization elements in neuronal cells	74
A conserved viral RNA fold enables nuclease resistance across kingdoms of life	74
Oxidative events in a double helix system promote the formation of kinetically trapped G-quadruplexes	73
Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal	73