Nucleic Acids Research

Papers
(The TQCC of Nucleic Acids Research is 17. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-07-01 to 2025-07-01.)
ArticleCitations
SV4GD: a comprehensive structural variation database specially for genetic diseases6190
NucleoFind: a deep-learning network for interpreting nucleic acid electron density5163
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip4422
A method for targeting a specified segment of DNA to a bacterial microorganelle4368
Correction to ‘Cis regulation within a cluster of viral microRNAs’3963
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’3351
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’2081
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’2050
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’1958
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis1900
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ1644
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 telomeres1588
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey1544
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA1541
Nanopores map the acid-base properties of a single site in a single DNA molecule1499
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex1459
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase1380
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase1321
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models1164
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program1127
Systematic discovery of DNA-binding tandem repeat proteins1124
Cognate restriction of transposition by piggyBac-like proteins1037
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning1026
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA1008
Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5′-untranslated region847
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics824
VID22counteracts G-quadruplex-induced genome instability789
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity786
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization778
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression762
Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations728
Correction to ‘The European Genome-phenome Archive in 2021’703
PHF8 facilitates transcription recovery following DNA double-strand break repair685
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei684
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination629
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation627
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse625
Helical coiling of metaphase chromatids619
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis601
Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression570
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy561
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers557
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels553
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection549
NCBI Taxonomy: enhanced access via NCBI Datasets516
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells506
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins491
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo465
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes460
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes452
Correction to ‘EMDB—the Electron Microscopy Data Bank’447
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR443
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome440
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits437
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)414
TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts398
Splitting the yeast centromere by recombination374
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline350
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants336
Yeast transcription factor Msn2 binds to G4 DNA330
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs319
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies317
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy309
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly309
Post-replicative lesion processing limits DNA damage-induced mutagenesis300
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions300
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break293
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition291
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery288
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR286
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity286
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping284
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning284
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication281
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress277
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices276
Formation and persistence of polyglutamine aggregates in mistranslating cells271
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing267
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution257
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region256
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition255
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors254
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation253
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli250
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis247
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts246
ZEB1 promotes non-homologous end joining double-strand break repair242
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’242
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools242
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip241
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms234
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG226
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy226
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining217
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats210
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling203
Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization200
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering200
BioSamples database: FAIRer samples metadata to accelerate research data management195
High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases194
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA191
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing183
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins181
DriverDBv4: a multi-omics integration database for cancer driver gene research180
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins179
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options179
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions178
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins174
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription173
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity173
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB171
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study169
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells166
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions165
CPLM 4.0: an updated database with rich annotations for protein lysine modifications164
scQTLbase: an integrated human single-cell eQTL database163
Investigating the origins of the mutational signatures in cancer159
The quantitative impact of 3′UTRs on gene expression158
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research157
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically156
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database154
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction154
Human Ageing Genomic Resources: updates on key databases in ageing research152
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast151
Widespread translational control regulates retinal development in mouse151
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system151
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes150
RefMetaPlant: a reference metabolome database for plants across five major phyla149
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa147
Rfam 15: RNA families database in 2025145
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors145
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro144
The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses144
The human telomeric proteome during telomere replication144
THUMPD3–TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates143
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery141
The carbohydrate-active enzyme database: functions and literature138
Waves of sumoylation support transcription dynamics during adipocyte differentiation138
Ensembl 2024134
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide134
Prediction of DNA i-motifs via machine learning134
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation134
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees132
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription132
Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout132
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity132
Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers131
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’131
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’130
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’128
Overlapping and distinct functions of SPT6, PNUTS, and PCF11 in regulating transcription termination127
GenePlexus: a web-server for gene discovery using network-based machine learning126
Mechanisms of mitochondrial promoter recognition in humans and other mammalian species124
A rationalized definition of general tumor suppressor microRNAs excludes miR-34a124
Cisplatin fastens chromatin irreversibly even at a high chloride concentration123
Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network121
The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity121
Fungal chromatin remodeler Isw1 modulates translation via regulating tRNA transcription121
Functional redundancy in tRNA dihydrouridylation120
Oxidative events in a double helix system promote the formation of kinetically trapped G-quadruplexes120
Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase120
Molecular basis for RNA discrimination by human DNA ligase 1120
The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells118
AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation116
A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction116
Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time115
RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize114
Structural insights into RNA cleavage by a novel family of bacterial RNases114
SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data113
Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus111
Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA110
DEPCOD: a tool to detect and visualize co-evolution of protein domains108
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors108
Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A108
Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication107
Correction to ‘8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα’106
BioKA: a curated and integrated biomarker knowledgebase for animals106
Nature-inspired engineering of an artificial ligase enzyme by domain fusion106
The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution105
Structural basis of how MGME1 processes DNA 5′ ends to maintain mitochondrial genome integrity105
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs102
Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil102
Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes102
SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA101
Inhibition mechanisms of CRISPR-Cas9 by AcrIIA17 and AcrIIA18101
Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species98
STAMarker: determining spatial domain-specific variable genes with saliency maps in deep learning98
High-throughput identification of RNA localization elements in neuronal cells98
Constraints on error rate revealed by computational study of G•U tautomerization in translation96
Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics96
Quadruplet codon decoding-based versatile genetic biocontainment system95
Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro95
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data95
ZNF598 co-translationally titrates poly(GR) protein implicated in the pathogenesis of C9ORF72-associated ALS/FTD94
Does rapid sequence divergence preclude RNA structure conservation in vertebrates?94
Extensive homologous recombination safeguards oocyte genome integrity in mammals94
Cryo-EM structure of human TUT1:U6 snRNA complex94
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment92
PseudoGA: cell pseudotime reconstruction based on genetic algorithm92
DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain90
Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF2490
Accurate measurement of microsatellite length by disrupting its tandem repeat structure89
KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing89
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’89
Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA87
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’86
Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci86
A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC)84
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity84
EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants84
SMAP design: a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation84
Dynamic and facilitated binding of topoisomerase accelerates topological relaxation83
Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA83
Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression83
Computational resources to define alleles and altered regulatory motifs at genomically edited candidate response elements81
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames81
Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification81
Reconstructing DNA methylation maps of ancient populations80
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers80
Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon80
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism79
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase79
Integration of single cell data by disentangled representation learning79
Commonality and diversity in tRNA substrate recognition in t6A biogenesis by eukaryotic KEOPSs79
LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs79
Hypoxia stabilizes SETDB1 to maintain genome stability79
Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency78
Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses78
DNA–protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM)78
Coronaviral RNA-methyltransferases: function, structure and inhibition78
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming78
Crystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold77
SCAN: Spatiotemporal Cloud Atlas for Neural cells76
Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal76
The European Variation Archive: a FAIR resource of genomic variation for all species76
MethBank 4.0: an updated database of DNA methylation across a variety of species75
RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data75
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells74
ECOD: integrating classifications of protein domains from experimental and predicted structures74
Preferential import of queuosine-modified tRNAs into Trypanosoma brucei mitochondrion is critical for organellar protein synthesis74
HGD: an integrated homologous gene database across multiple species74
RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells73
POT-3 preferentially binds the terminal DNA-repeat on the telomeric G-overhang73
40S hnRNP particles are a novel class of nuclear biomolecular condensates73
Absence of mitochondrial SLC25A51 enhances PARP1-dependent DNA repair by increasing nuclear NAD+ levels72
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation72
Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector72
FARS2 deficiency in Drosophila reveals the developmental delay and seizure manifested by aberrant mitochondrial tRNA metabolism71
Single molecule/particle tracking analysis program SMTracker 2.0 reveals different dynamics of proteins within the RNA degradosome complex inBacillus subtilis71
KLF9 and KLF13 transcription factors boost myelin gene expression in oligodendrocytes as partners of SOX10 and MYRF71
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