Nucleic Acids Research

Article	Citations
SV4GD: a comprehensive structural variation database specially for genetic diseases	6454
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	5379
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip	4980
Correction to ‘Cis regulation within a cluster of viral microRNAs’	4832
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	4280
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’	3589
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	2224
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	2205
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	2031
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	2011
Nanopores map the acid-base properties of a single site in a single DNA molecule	1696
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	1693
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase	1660
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	1604
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	1603
Systematic discovery of DNA-binding tandem repeat proteins	1547
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	1537
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	1492
VID22counteracts G-quadruplex-induced genome instability	1491
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	1204
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	1182
Correction to ‘The European Genome-phenome Archive in 2021’	1134
PHF8 facilitates transcription recovery following DNA double-strand break repair	1118
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	1025
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers	963

A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	923
Correction to ‘EMDB—the Electron Microscopy Data Bank’	892
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’	832
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	820
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy	820
Molecular determinants for recognition of serotonylated chromatin	765
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	754
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	752
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	749
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program	738
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels	722
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	722
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	721
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	696
TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	666
Splitting the yeast centromere by recombination	652
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	648
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning	617
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	608
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	560
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	559
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	546
A method for targeting a specified segment of DNA to a bacterial microorganelle	533
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells	527
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	511
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	498
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region	492
The quantitative impact of 3′UTRs on gene expression	490
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	489
Investigating the origins of the mutational signatures in cancer	472
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research	453
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies	434
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering	427
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery	407
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	382
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation	357
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	353
ZEB1 promotes non-homologous end joining double-strand break repair	338
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	333
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	330
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip	330
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	328
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	328
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	323
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	322
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	322
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	319
Prediction of DNA i-motifs via machine learning	318
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	311
The human telomeric proteome during telomere replication	308

NCBI Taxonomy: enhanced access via NCBI Datasets	307
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	307
Widespread translational control regulates retinal development in mouse	306
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	297
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	292
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	292
Formation and persistence of polyglutamine aggregates in mistranslating cells	290
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	287
BioSamples database: FAIRer samples metadata to accelerate research data management	287
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	284
Helical coiling of metaphase chromatids	264
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study	260
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly	252
Yeast transcription factor Msn2 binds to G4 DNA	251
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	248
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	242
DriverDBv4: a multi-omics integration database for cancer driver gene research	234
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	232
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	224
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	223
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	219
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	217
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	216
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	209
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	205
THUMPD3–TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates	204
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	203
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	194
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	193
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	193
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection	192
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning	192
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	191
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	189
scQTLbase: an integrated human single-cell eQTL database	188
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	187
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity	186
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	185
RefMetaPlant: a reference metabolome database for plants across five major phyla	185
The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses	184
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	182
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	181
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli	181
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	179
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	179
Rfam 15: RNA families database in 2025	178
Post-replicative lesion processing limits DNA damage-induced mutagenesis	176
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system	176
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	174
Waves of sumoylation support transcription dynamics during adipocyte differentiation	173
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	172
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	172
CPLM 4.0: an updated database with rich annotations for protein lysine modifications	165
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	165
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	161
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins	158
Human Ageing Genomic Resources: updates on key databases in ageing research	158
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	157
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	156
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	153
High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases	151
Ensembl 2024	150
The carbohydrate-active enzyme database: functions and literature	148
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	147
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’	146
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’	145
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’	145
The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity	142
A rationalized definition of general tumor suppressor microRNAs excludes miR-34a	142
Functional redundancy in tRNA dihydrouridylation	141
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize	141
SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data	139
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA	138
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors	135
DEPCOD: a tool to detect and visualize co-evolution of protein domains	135
Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication	134
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs	132
Structural basis of how MGME1 processes DNA 5′ ends to maintain mitochondrial genome integrity	132
Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species	132
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data	131

Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro	130
DNA–protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM)	130
Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA	128
Constraints on error rate revealed by computational study of G•U tautomerization in translation	127
A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB	126
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment	125
The origin of mirror repeats in the human genome	125
TRIP12’s role in the governance of DNA polymerase β involvement in DNA damage response and repair	124
The ‘Alu-ome’ shapes the epigenetic environment of regulatory elements controlling cellular defense	122
PWOs repress gene transcription by regulating chromatin structures in Arabidopsis	122
Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time	121
ZNF598 co-translationally titrates poly(GR) protein implicated in the pathogenesis of C9ORF72-associated ALS/FTD	121
Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus	120
RMVar 2.0: an updated database of functional variants in RNA modifications	120
MethBank 4.0: an updated database of DNA methylation across a variety of species	120
KLF9 and KLF13 transcription factors boost myelin gene expression in oligodendrocytes as partners of SOX10 and MYRF	117
Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network	115
The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells	113
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells	113
Kingdom-wide CRISPR guide design with ALLEGRO	112
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes	111
HGD: an integrated homologous gene database across multiple species	111
Binding of DNA origami to lipids: maximizing yield and switching via strand displacement	109
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design	109
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	109
scTML: a pan-cancer single-cell landscape of multiple mutation types	109
Nature-inspired engineering of an artificial ligase enzyme by domain fusion	108
Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal	107
WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination	106
Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1	106
Commonality and diversity in tRNA substrate recognition in t6A biogenesis by eukaryotic KEOPSs	104
MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species	102
Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil	102
Coronaviral RNA-methyltransferases: function, structure and inhibition	101
Efficient 3′-pairing renders microRNA targeting less sensitive to mRNA seed accessibility	100
Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5′UTRs	100
Intein-based thermoregulated meganucleases for containment of genetic material	100
HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins	99
Does rapid sequence divergence preclude RNA structure conservation in vertebrates?	98
SMAP design: a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation	98
Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24	97
KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing	96
Accurate measurement of microsatellite length by disrupting its tandem repeat structure	95
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’	95
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’	95
EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants	94
A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC)	93
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity	92
Dynamic and facilitated binding of topoisomerase accelerates topological relaxation	91
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames	91
Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression	91
Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification	91
Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon	90
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers	89
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism	89
Reconstructing DNA methylation maps of ancient populations	89
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs	88
Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency	88
Hypoxia stabilizes SETDB1 to maintain genome stability	88
Inhibition mechanisms of CRISPR-Cas9 by AcrIIA17 and AcrIIA18	87
PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process	87
Cisplatin fastens chromatin irreversibly even at a high chloride concentration	87
SCAN: Spatiotemporal Cloud Atlas for Neural cells	87
Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal	87
40S hnRNP particles are a novel class of nuclear biomolecular condensates	86
Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A	86
Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA	86
A common transcriptional mechanism involving R-loop and RNA abasic site regulates an enhancer RNA of APOE	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	84
Interpretable deep residual network uncovers nucleosome positioning and associated features	84
POT-3 preferentially binds the terminal DNA-repeat on the telomeric G-overhang	84
Genome-wide screening and functional validation of methylation barriers near promoters	84
Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector	83
TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice	83
PsrA is a novel regulator contributes to antibiotic synthesis, bacterial virulence, cell motility and extracellular polysaccharides production in Serratia marcescens	83
Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy	82
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation	81
Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci	81
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming	81
Absence of mitochondrial SLC25A51 enhances PARP1-dependent DNA repair by increasing nuclear NAD+ levels	81
Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp	81
Learning interpretable representations of single-cell multi-omics data with multi-output Gaussian processes	81
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes	81
G-quadruplexes as potential traps for superenhancer marker BRD4: ligand-sensitive binding and co-separation in vitro	81
BioKA: a curated and integrated biomarker knowledgebase for animals	81
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells	80
Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022	79
Phospho-Ku70 induced by DNA damage interacts with RNA Pol II and promotes the formation of phospho-53BP1 foci to ensure optimal cNHEJ	79
Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin	79
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase	79
CircaKB: a comprehensive knowledgebase of circadian genes across multiple species	79
GenePlexus: a web-server for gene discovery using network-based machine learning	78
Structural insights into RNA cleavage by a novel family of bacterial RNases	78
A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum	78
Integration of single cell data by disentangled representation learning	77