Nucleic Acids Research

Papers
(The H4-Index of Nucleic Acids Research is 128. 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 2021-12-01 to 2025-12-01.)
ArticleCitations
Correction to ‘The European Genome-phenome Archive in 2021’6085
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA5390
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex4755
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase3934
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis2497
Nanopores map the acid-base properties of a single site in a single DNA molecule2409
SV4GD: a comprehensive structural variation database specially for genetic diseases2176
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’2175
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’2100
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’1727
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei1428
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells1340
Correction to ‘EMDB—the Electron Microscopy Data Bank’1327
Systematic discovery of DNA-binding tandem repeat proteins1233
VID22counteracts G-quadruplex-induced genome instability1182
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization1180
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions1157
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline1147
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically1137
SmallBARNA 2026: a kingdom-wide bacterial sRNA resource1020
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways1019
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics917
Correction to ‘Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development’889
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’886
Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression880
NucleoFind: a deep-learning network for interpreting nucleic acid electron density878
gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics855
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide836
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity830
TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability816
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments792
Correction to ‘DNA-protein Interactions at the Telomeric Repeats of Schizosaccharomyces Pombe’740
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies702
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms691
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’689
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing686
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR666
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation656
In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences648
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’631
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation583
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits565
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region554
A method for targeting a specified segment of DNA to a bacterial microorganelle546
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity546
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research528
GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana475
Splitting the yeast centromere by recombination442
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly433
Molecular determinants for recognition of serotonylated chromatin432
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning429
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors424
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells417
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools405
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG397
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break389
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA388
The antiSMASH database version 5378
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models358
The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts358
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ357
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system357
Cas12a-assisted split crRNA complex for analysis and detection of diverse entities352
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts351
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution344
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions336
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA336
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)331
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey330
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition314
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats307
Prediction of DNA i-motifs via machine learning300
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning292
PHF8 facilitates transcription recovery following DNA double-strand break repair286
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication286
Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome266
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination265
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs259
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription253
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes249
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program244
Yeast transcription factor Msn2 binds to G4 DNA241
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons239
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery238
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection232
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation231
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction225
EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment223
Post-replicative lesion processing limits DNA damage-induced mutagenesis221
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy220
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity212
Waves of sumoylation support transcription dynamics during adipocyte differentiation212
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices207
Diverse RNA viral effectors converge on facilitation of AGO4 degradation to promote infection201
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins201
ZEB1 promotes non-homologous end joining double-strand break repair190
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants188
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome183
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy182
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins181
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes180
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering179
Investigating the origins of the mutational signatures in cancer177
The quantitative impact of 3′UTRs on gene expression173
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping172
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing163
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress162
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition160
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity159
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB156
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis155
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining155
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options153
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse153
NCBI Taxonomy: enhanced access via NCBI Datasets152
scQTLbase: an integrated human single-cell eQTL database152
Rfam 15: RNA families database in 2025151
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo146
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli145
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery144
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions140
Helical coiling of metaphase chromatids139
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression137
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins136
DriverDBv4: a multi-omics integration database for cancer driver gene research135
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes134
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis132
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro130
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