Nucleic Acids Research

Papers
(The H4-Index of Nucleic Acids Research is 134. 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 2021-06-01 to 2025-06-01.)
ArticleCitations
SV4GD: a comprehensive structural variation database specially for genetic diseases6059
NucleoFind: a deep-learning network for interpreting nucleic acid electron density5042
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip4245
A method for targeting a specified segment of DNA to a bacterial microorganelle4073
Correction to ‘Cis regulation within a cluster of viral microRNAs’3817
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’3240
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’2018
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’1942
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’1933
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers1842
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis1618
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ1539
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 telomeres1504
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition1478
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically1478
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey1394
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA1333
Nanopores map the acid-base properties of a single site in a single DNA molecule1250
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins1241
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex1085
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase1070
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase1012
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models1007
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program980
Systematic discovery of DNA-binding tandem repeat proteins942
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices771
Cognate restriction of transposition by piggyBac-like proteins761
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning755
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA754
Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5′-untranslated region726
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions708
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics699
VID22counteracts G-quadruplex-induced genome instability676
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning664
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity631
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization617
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression577
Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations572
Human prefoldin modulates co-transcriptional pre-mRNA splicing537
Correction to ‘The European Genome-phenome Archive in 2021’535
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei531
PHF8 facilitates transcription recovery following DNA double-strand break repair531
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination517
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA498
Correction to ‘EMDB—the Electron Microscopy Data Bank’494
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’483
Investigating the origins of the mutational signatures in cancer482
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy480
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome450
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits432
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)428
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide416
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly413
TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts403
Splitting the yeast centromere by recombination398
Post-replicative lesion processing limits DNA damage-induced mutagenesis392
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data335
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline333
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants325
The human telomeric proteome during telomere replication324
scQTLbase: an integrated human single-cell eQTL database319
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro312
Yeast transcription factor Msn2 binds to G4 DNA297
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs297
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo288
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity286
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB282
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system282
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa278
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy275
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies273
RefMetaPlant: a reference metabolome database for plants across five major phyla270
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing270
Widespread translational control regulates retinal development in mouse269
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts260
Waves of sumoylation support transcription dynamics during adipocyte differentiation259
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress255
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis247
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition241
ZEB1 promotes non-homologous end joining double-strand break repair241
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis240
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription238
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins233
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells232
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools231
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip230
BioSamples database: FAIRer samples metadata to accelerate research data management226
THUMPD3–TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates226
Formation and persistence of polyglutamine aggregates in mistranslating cells222
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing219
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction218
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling215
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation213
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity208
Helical coiling of metaphase chromatids203
NCBI Taxonomy: enhanced access via NCBI Datasets193
High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases192
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes190
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats182
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database182
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels182
Prediction of DNA i-motifs via machine learning177
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors175
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation174
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG174
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells172
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions170
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy169
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins169
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining168
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’166
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast165
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms165
CPLM 4.0: an updated database with rich annotations for protein lysine modifications160
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering156
The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses156
Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization154
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli149
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery149
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication148
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break147
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options147
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping147
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection146
Human Ageing Genomic Resources: updates on key databases in ageing research144
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study144
Rfam 15: RNA families database in 2025143
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions142
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors141
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes140
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR139
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity137
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes136
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse135
DriverDBv4: a multi-omics integration database for cancer driver gene research134
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