Nucleic Acids Research

Papers
(The H4-Index of Nucleic Acids Research is 140. 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 2022-05-01 to 2026-05-01.)
ArticleCitations
Correction to ‘The European Genome-phenome Archive in 2021’7893
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex6199
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis4439
SV4GD: a comprehensive structural variation database specially for genetic diseases3437
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’2925
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’2388
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization2084
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions1993
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics1907
Correction to ‘Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development’1804
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide1733
Correction to ‘DNA-protein Interactions at the Telomeric Repeats of Schizosaccharomyces Pombe’1627
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons1574
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy1570
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region1560
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination1546
PHF8 facilitates transcription recovery following DNA double-strand break repair1497
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions1466
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution1415
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing1405
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB1251
Correction to ‘EMDB—the Electron Microscopy Data Bank’1099
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells1091
Nanopores map the acid-base properties of a single site in a single DNA molecule1087
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering1070
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo1070
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins1058
Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome1011
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity974
Investigating the origins of the mutational signatures in cancer971
TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability943
Splitting the yeast centromere by recombination908
Systematic discovery of DNA-binding tandem repeat proteins902
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system856
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’806
In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences797
A method for targeting a specified segment of DNA to a bacterial microorganelle788
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR ’775
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription760
RoCi—a single-step multi-copy integration system based on rolling-circle replication707
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei705
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity692
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining641
METTL1 interacts with XPO5 to modulate pre-miRNA export608
Molecular determinants for recognition of serotonylated chromatin555
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse553
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation543
The quantitative impact of 3′UTRs on gene expression536
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing531
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models528
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors520
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction502
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation490
scQTLbase: an integrated human single-cell eQTL database488
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery463
Constant trouble with prolines—navigating a global translation dilemma453
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation453
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy430
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database416
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG415
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins411
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools411
DriverDBv4: a multi-omics integration database for cancer driver gene research408
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast405
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR399
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways399
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping397
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices382
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break378
Ensembl 2024376
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies367
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition367
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees362
Prediction of DNA i-motifs via machine learning358
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins346
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants335
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline324
Human Ageing Genomic Resources: updates on key databases in ageing research320
Rfam 15: RNA families database in 2025312
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats305
Cas12a-assisted split crRNA complex for analysis and detection of diverse entities305
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically303
An elevated level of the mRNA exporter Mex67-Mtr2 in nuclear mRNPs impairs nuclear mRNA export296
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity291
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options288
EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment288
gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics287
Characterization of gRNA-dependent and gRNA-independent off-target binding sites of PspCas13b and RfxCas13d in mammalian cells276
Evidence for a functional interaction between yeast Pol ε and PCNA in vivo274
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome263
Yeast transcription factor Msn2 binds to G4 DNA248
Diverse RNA viral effectors converge on facilitation of AGO4 degradation to promote infection246
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA241
A transcriptomic and proteomic map of primary human cell types239
PDBe: enhanced structural data exploration to facilitate discovery238
SmallBARNA 2026: a kingdom-wide bacterial sRNA resource235
GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana232
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling230
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’230
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression229
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA220
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits220
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes208
YqeK governs the acquisition and removal of nucleoside tetraphosphate caps in Firmicutes206
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs204
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins202
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity196
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli192
Helical coiling of metaphase chromatids190
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions190
The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts185
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms183
The antiSMASH database version 5183
Metal ions govern coronavirus endoribonuclease activity181
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments179
Mbd4 and MutSα protect cells from spontaneous deamination of 5-methylcytosine176
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis175
RefMetaPlant: a reference metabolome database for plants across five major phyla173
Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation173
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research170
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells167
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro165
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)164
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition162
Post-replicative lesion processing limits DNA damage-induced mutagenesis161
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ160
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts157
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey157
Multisite phosphorylation of the AML-linked C-terminal of nucleophosmin (NPM1) orchestrates protein stability, DNA binding and charge block-driven phase separation154
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase153
ZEB1 promotes non-homologous end joining double-strand break repair150
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes150
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes149
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication147
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress145
NucleoFind: a deep-learning network for interpreting nucleic acid electron density143
NCBI Taxonomy: enhanced access via NCBI Datasets143
Disruption of a six-nucleotide miRNA motif improves PKD1 dosage and ameliorates polycystic kidney disease142
LysR-type regulator LrhA promotes CRISPR-Cas immunity in Escherichia coli142
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA141
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa140
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery140
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis140
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