Nucleic Acids Research

Article	Citations
SV4GD: a comprehensive structural variation database specially for genetic diseases	5907
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	4922
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip	4036
A method for targeting a specified segment of DNA to a bacterial microorganelle	3758
Correction to ‘Cis regulation within a cluster of viral microRNAs’	3657
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	3174
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	3126
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	2013
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’	1957
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	1889
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	1842
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers	1772
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	1586
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip	1474
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	1466
GGGCTA repeats can fold into hairpins poorly unfolded by replication protein A: a possible origin of the length-dependent instability of GGGCTA variant repeats in human telomeres	1446
Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization	1420
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	1326
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	1293
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	1255
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	1212
Nanopores map the acid-base properties of a single site in a single DNA molecule	1170
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	1039
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	1014
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	960

High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases	933
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	877
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	873
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase	777
Folding and persistence times of intramolecular G-quadruplexes transiently embedded in a DNA duplex	732
CoffeeProt: an online tool for correlation and functional enrichment of systems genetics data	731
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	724
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	678
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program	666
Systematic discovery of DNA-binding tandem repeat proteins	659
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	656
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	652
Cognate restriction of transposition by piggyBac-like proteins	642
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning	606
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	601
Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5′-untranslated region	532
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	529
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	504
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	495
VID22counteracts G-quadruplex-induced genome instability	488
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning	474
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	466
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	462
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	451
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	444
Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations	440
Human prefoldin modulates co-transcriptional pre-mRNA splicing	435
Widespread translational control regulates retinal development in mouse	427
Correction to ‘The European Genome-phenome Archive in 2021’	403
PHF8 facilitates transcription recovery following DNA double-strand break repair	403
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	399
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	398
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	393
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	387
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	359
Correction to ‘EMDB—the Electron Microscopy Data Bank’	354
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’	333
Investigating the origins of the mutational signatures in cancer	332
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy	323
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	307
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	306
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	305
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	303
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	290
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	278
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	273
DriverDBv4: a multi-omics integration database for cancer driver gene research	272
Formation and persistence of polyglutamine aggregates in mistranslating cells	269
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly	266
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	265

TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	263
Discordant regulation of eIF2 kinase GCN2 and mTORC1 during nutrient stress	261
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	257
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	253
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	253
Post-replicative lesion processing limits DNA damage-induced mutagenesis	248
NCBI Taxonomy: enhanced access via NCBI Datasets	239
THUMPD3–TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates	236
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	230
Splitting the yeast centromere by recombination	230
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data	229
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	227
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells	224
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	221
pLannotate: engineered plasmid annotation	220
scQTLbase: an integrated human single-cell eQTL database	218
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	218
ZEB1 promotes non-homologous end joining double-strand break repair	218
The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses	214
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	205
Yeast transcription factor Msn2 binds to G4 DNA	204
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	203
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	201
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection	196
CPLM 4.0: an updated database with rich annotations for protein lysine modifications	188
The human telomeric proteome during telomere replication	185
Human Ageing Genomic Resources: updates on key databases in ageing research	184
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	184
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	184
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	181
RefMetaPlant: a reference metabolome database for plants across five major phyla	175
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	172
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	170
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	170
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels	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
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	166
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	163
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	161
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors	161
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	160
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	159
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	158
Rfam 15: RNA families database in 2025	156
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study	155
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	152
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	149
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity	149
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	148
BioSamples database: FAIRer samples metadata to accelerate research data management	145
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system	145
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	143
ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules	140
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	140
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	139
Prediction of DNA i-motifs via machine learning	139
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	137
Waves of sumoylation support transcription dynamics during adipocyte differentiation	136
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins	135
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli	134
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	134
Helical coiling of metaphase chromatids	132
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	130
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	130
The carbohydrate-active enzyme database: functions and literature	129
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	129
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	128
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	127
Post-translational modification of RNA m6A demethylase ALKBH5 regulates ROS-induced DNA damage response	126
Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout	126
Ensembl 2024	126
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription	125
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’	123
Quadruplet codon decoding-based versatile genetic biocontainment system	123
Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers	122
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’	122
Improving the generalization of protein expression models with mechanistic sequence information	122
RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells	122
Influenza a virus antiparallel helical nucleocapsid-like pseudo-atomic structure	120
Intein-based thermoregulated meganucleases for containment of genetic material	119

Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’	117
Structural basis of how MGME1 processes DNA 5′ ends to maintain mitochondrial genome integrity	116
Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022	116
DNA–protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM)	116
AcrIIA28 is a metalloprotein that specifically inhibits targeted-DNA loading to SpyCas9 by binding to the REC3 domain	115
Overlapping and distinct functions of SPT6, PNUTS, and PCF11 in regulating transcription termination	114
Cisplatin fastens chromatin irreversibly even at a high chloride concentration	114
GenePlexus: a web-server for gene discovery using network-based machine learning	113
A common transcriptional mechanism involving R-loop and RNA abasic site regulates an enhancer RNA of APOE	112
Fungal chromatin remodeler Isw1 modulates translation via regulating tRNA transcription	111
Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD	111
Oxidative events in a double helix system promote the formation of kinetically trapped G-quadruplexes	111
The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution	110
Functional redundancy in tRNA dihydrouridylation	110
Genome-wide screening and functional validation of methylation barriers near promoters	110
Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase	108
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells	108
AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation	107
IAnimal: a cross-species omics knowledgebase for animals	107
The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells	106
High-throughput identification of RNA localization elements in neuronal cells	105
Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal	103
Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time	103
Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network	103
Molecular basis for RNA discrimination by human DNA ligase 1	103
Phospho-Ku70 induced by DNA damage interacts with RNA Pol II and promotes the formation of phospho-53BP1 foci to ensure optimal cNHEJ	102
Structural insights into RNA cleavage by a novel family of bacterial RNases	101
HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins	101
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation	100
Nature-inspired engineering of an artificial ligase enzyme by domain fusion	99
Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus	97
PsrA is a novel regulator contributes to antibiotic synthesis, bacterial virulence, cell motility and extracellular polysaccharides production in Serratia marcescens	96
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize	95
The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity	95
SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data	94
A rationalized definition of general tumor suppressor microRNAs excludes miR-34a	93
A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction	93
Mechanisms of mitochondrial promoter recognition in humans and other mammalian species	93
PWOs repress gene transcription by regulating chromatin structures in Arabidopsis	92
Coronaviral RNA-methyltransferases: function, structure and inhibition	91
Unmodificated stepless regulation of CRISPR/Cas12a multi-performance	90
The ‘Alu-ome’ shapes the epigenetic environment of regulatory elements controlling cellular defense	90
Constraints on error rate revealed by computational study of G•U tautomerization in translation	90
Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency	90
PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process	90
ECOD: integrating classifications of protein domains from experimental and predicted structures	89
Interpretable deep residual network uncovers nucleosome positioning and associated features	88
BioKA: a curated and integrated biomarker knowledgebase for animals	88
The European Variation Archive: a FAIR resource of genomic variation for all species	87
Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors	87
Binding of DNA origami to lipids: maximizing yield and switching via strand displacement	87
MethBank 4.0: an updated database of DNA methylation across a variety of species	86
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA	86
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming	85
Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal	85
Preferential import of queuosine-modified tRNAs into Trypanosoma brucei mitochondrion is critical for organellar protein synthesis	84
FACT interacts with Set3 HDAC and fine-tunesGAL1transcription in response to environmental stimulation	84
Commonality and diversity in tRNA substrate recognition in t6A biogenesis by eukaryotic KEOPSs	83
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design	83
TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice	83
DEPCOD: a tool to detect and visualize co-evolution of protein domains	82
Cryo-EM structure of human TUT1:U6 snRNA complex	82
Does rapid sequence divergence preclude RNA structure conservation in vertebrates?	82
ZNF598 co-translationally titrates poly(GR) protein implicated in the pathogenesis of C9ORF72-associated ALS/FTD	82
Extensive homologous recombination safeguards oocyte genome integrity in mammals	82
PseudoGA: cell pseudotime reconstruction based on genetic algorithm	81
Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1	80
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase	80
Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules	79
Downregulation of MLF1 safeguards cardiomyocytes against senescence-associated chromatin opening	79
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment	79
MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species	79
Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses	78
Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers	78
POT-3 preferentially binds the terminal DNA-repeat on the telomeric G-overhang	78
DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain	78
Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24	78
KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing	77
Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides	77
Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction	77
Accurate measurement of microsatellite length by disrupting its tandem repeat structure	77
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	76
FARS2 deficiency in Drosophila reveals the developmental delay and seizure manifested by aberrant mitochondrial tRNA metabolism	76
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’	76
Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA	75
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’	74
Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci	73
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs	73
Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA	72
A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC)	72
Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species	72
EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants	72
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes	72
Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin	72
SMAP design: a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation	71