Nucleic Acids Research

Papers
(The H4-Index of Nucleic Acids Research is 141. 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 2021-11-01 to 2025-11-01.)
ArticleCitations
Correction to ‘The European Genome-phenome Archive in 2021’6738
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA5685
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey5562
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex5210
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase4594
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis3808
Nanopores map the acid-base properties of a single site in a single DNA molecule2386
SV4GD: a comprehensive structural variation database specially for genetic diseases2351
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 berghei1800
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells1771
Correction to ‘EMDB—the Electron Microscopy Data Bank’1738
PHF8 facilitates transcription recovery following DNA double-strand break repair1667
Systematic discovery of DNA-binding tandem repeat proteins1658
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics1607
VID22counteracts G-quadruplex-induced genome instability1343
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization1287
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing1238
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs1226
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 analysis1080
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition1050
Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression1032
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA976
NucleoFind: a deep-learning network for interpreting nucleic acid electron density936
gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics914
Yeast transcription factor Msn2 binds to G4 DNA891
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide861
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research836
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes828
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity804
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression795
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa784
Waves of sumoylation support transcription dynamics during adipocyte differentiation777
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase753
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping706
TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability677
DriverDBv4: a multi-omics integration database for cancer driver gene research677
Investigating the origins of the mutational signatures in cancer672
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments671
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions663
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options628
Human Ageing Genomic Resources: updates on key databases in ageing research617
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation611
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins599
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA567
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools554
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity530
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly528
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG526
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection524
The human telomeric proteome during telomere replication472
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 mouse422
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database392
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli392
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms388
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’376
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication369
A method for targeting a specified segment of DNA to a bacterial microorganelle368
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing357
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR357
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation354
In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences350
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery348
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning345
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation342
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering340
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 microscopy337
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation332
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits327
The quantitative impact of 3′UTRs on gene expression326
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity325
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region319
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution318
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program305
Helical coiling of metaphase chromatids305
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction294
ZEB1 promotes non-homologous end joining double-strand break repair283
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)280
Prediction of DNA i-motifs via machine learning277
Splitting the yeast centromere by recombination273
Molecular determinants for recognition of serotonylated chromatin267
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts259
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome258
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning252
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins243
TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts243
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro239
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes228
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination223
RefMetaPlant: a reference metabolome database for plants across five major phyla219
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors218
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells214
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes213
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy212
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants212
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions207
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline205
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining204
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats203
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins202
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB202
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions200
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically199
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling195
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress193
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices192
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy189
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ187
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo185
SmallBARNA 2026: a kingdom-wide bacterial sRNA resource182
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways181
Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome181
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break174
scQTLbase: an integrated human single-cell eQTL database172
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies172
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription170
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery170
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis166
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition165
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins164
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast156
Rfam 15: RNA families database in 2025156
NCBI Taxonomy: enhanced access via NCBI Datasets155
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models154
BioSamples database: FAIRer samples metadata to accelerate research data management153
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity152
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system151
Ensembl 2024149
Post-replicative lesion processing limits DNA damage-induced mutagenesis147
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees147
The carbohydrate-active enzyme database: functions and literature147
Editor's Note to ‘Autoregulatory circuit of human rpL3 expression requires hnRNP H1, NPM and KHSRP’146
Editor's Note on ‘Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53’146
Dynamic and facilitated binding of topoisomerase accelerates topological relaxation143
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity143
Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification141
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames141
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’141
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