Nucleic Acids Research

Papers
(The H4-Index of Nucleic Acids Research is 132. 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 2021-04-01 to 2025-04-01.)
ArticleCitations
Correction to ‘Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs’7714
Correction to ‘Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM’5768
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’4786
Correction to ‘ATM-mediated ELL phosphorylation enhances its self-association through increased EAF1 interaction and inhibits global transcription during genotoxic stress’3833
Virus-derived siRNA: Coronavirus and influenza virus trigger antiviral RNAi immunity in birds3477
Multifaceted roles of H2B mono-ubiquitylation in D-loop metabolism during homologous recombination repair3470
Structural basis of ssDNA-guided NADase activation of prokaryotic SPARTA system3114
NEAT1-mediated regulation of proteostasis and mRNA localization impacts autophagy dysregulation in Rett syndrome2986
R2DT: a comprehensive platform for visualizing RNA secondary structure1966
A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators1886
Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase1847
Argonaute CSR-1A promotes H3K9me3 maintenance to protect somatic development in offspring1728
Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses1692
A detailed analysis of second and third-generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers1598
Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states1561
Centromeric localization of αKNL2 and CENP-C proteins in plants depends on their centromere-targeting domain and DNA-binding regions1441
SP140 represses specific loci by recruiting polycomb repressive complex 2 and NuRD complex1427
Conformational reorganization and phase separation drive hyper-editing of ADR-2–ADBP-1 complex1417
Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits1342
Eukaryotic initiation factors eIF4F and eIF4B promote translation termination upon closed-loop formation1280
Checkpoint kinases regulate the circadian clock after DNA damage by influencing chromatin dynamics1253
Correction ‘LncPepAtlas: a comprehensive resource for exploring the translational landscape of long non-coding RNA’1203
Mitochondrial exonuclease EXOG supports DNA integrity by the removal of single-stranded DNA flaps1178
The mutational landscape of Bacillus subtilis conditional hypermutators shows how proofreading skews DNA polymerase error rates1094
Correction to ‘High mobility group AT-hook 1 (HMGA1) is an important positive regulator of hepatitis B virus (HBV) that is reciprocally upregulated by HBV X protein’992
Correction to ‘In vivo analysis of Pim-1 deficiency’967
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis916
Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites881
Widespread translational control regulates retinal development in mouse812
Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI758
BFVD—a large repository of predicted viral protein structures738
Epitranscriptomic editing of the RNA N6-methyladenosine modification by dCasRx conjugated methyltransferase and demethylase703
Deep learning-assisted genome-wide characterization of massively parallel reporter assays696
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy674
Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes664
mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation633
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa620
CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells613
Regulation of PDGFR-β gene expression by targeting the G-vacancy bearing G-quadruplex in promoter612
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity594
Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics581
USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress578
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli556
Correction to ‘EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants’488
Editor's Note on ‘PCAF regulates the stability of the transcriptional regulator and cyclin-dependent kinase inhibitor p27Kip1’488
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’474
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning465
PHF8 facilitates transcription recovery following DNA double-strand break repair461
Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events456
STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading443
Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster428
Retraction of ‘DICER-dependent biogenesis of let-7 miRNAs affects human cell response to DNA damage via targeting p21/p27’411
Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates411
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’409
Expression of Concern on ‘Mutually exclusive splicing regulates the Nav 1.6 sodium channel function through a combinatorial mechanism that involves three distinct splicing regulatory elements and thei392
Expression of concern to ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’383
Novel archaeal ribosome dimerization factor facilitating unique 30S–30S dimerization379
Engineered initiator tRNAs can effectively start translation at non-AUG start codons and diversify N-terminal amino acids for mRNA Display378
The iMab antibody selectively binds to intramolecular and intermolecular i-motif structures372
Cre-Lox miRNA-delivery technology optimized for inducible microRNA and gene-silencing studies in zebrafish370
Retraction of ‘Nuclear CaMKII enhances histone H3 phosphorylation and remodels chromatin during cardiac hypertrophy’368
zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters346
Telomemore enables single-cell analysis of cell cycle and chromatin condensation325
A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis322
Large serine integrases utilise scavenged phage proteins as directionality cofactors322
Antagonistic roles by the conserved nuclear poly(A)-binding proteins PABPN1 and ZC3H14 in nuclear RNA surveillance314
An evolved, orthogonal ssDNA generator for targeted hypermutation of multiple genomic loci309
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’296
Correction to ‘MiR-145 directly targets p70S6K1 in cancer cells to inhibit tumor growth and angiogenesis’294
Correction to ‘Stabilization of XIAP mRNA through the RNA binding protein HuR regulated by cellular polyamines’289
Correction to ‘The European Genome-phenome Archive in 2021’275
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes270
NPASS database update 2023: quantitative natural product activity and species source database for biomedical research266
Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly260
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database259
BioSamples database: FAIRer samples metadata to accelerate research data management258
A dual-activity topoisomerase complex promotes both transcriptional activation and repression in response to starvation255
MediaDive: the expert-curated cultivation media database250
CaeNDR, the Caenorhabditis Natural Diversity Resource249
Paralogous translation factors target distinct mRNAs to differentially regulate tolerance to oxidative stress in yeast242
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide241
A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort241
ALS-associated FUS mutation reshapes the RNA and protein composition of stress granules239
Phage defence loci of Streptococcus thermophilus—tip of the anti-phage iceberg?233
p53-dependent crosstalk between DNA replication integrity and redox metabolism mediated through a NRF2-PARP1 axis227
Histone chaperone Nap1 dismantles an H2A/H2B dimer from a partially unwrapped nucleosome225
Correction to ‘Activating cryptic biosynthetic gene cluster through a CRISPR–Cas12a-mediated direct cloning approach’220
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’215
Correction to ‘CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells’215
Correction to ‘hnRNPA1 couples nuclear export and translation of specific mRNAs downstream of FGF-2/S6K2 signalling’210
Correction to ‘Four additional natural 7-deazaguanine derivatives in phages and how to make them’210
Editor's Note on ‘Influence of correct secondary and tertiary RNA folding on the binding of cellular factors to the HCV IRES’208
Correction to ‘Clerocidin interacts with the cleavage complex of Streptococcus pneumoniae topoisomerase IV to induce selective irreversible DNA damage’207
Correction to ‘Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R’207
Correction to ‘Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch’206
Correction to ‘EMDB—the Electron Microscopy Data Bank’205
Large-scale expansions of Friedreich's ataxia GAA•TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers200
Comprehensive characterization of somatic variants associated with intronic polyadenylation in human cancers199
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing197
Human TRUB1 is a highly conserved pseudouridine synthase responsible for the formation of Ψ55 in mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro193
RAP80 phase separation at DNA double-strand break promotes BRCA1 recruitment185
KRCC1, a modulator of the DNA damage response182
SUMO protease and proteasome recruitment at the nuclear periphery differently affect replication dynamics at arrested forks175
snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets175
Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes175
Ribosomal collision is not a prerequisite for ZNF598-mediated ribosome ubiquitination and disassembly of ribosomal complexes by ASCC167
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection166
Correction to ‘Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases’164
Correction to ‘ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation’163
Correction to ‘Characterization of an interplay between a Mycobacterium tuberculosis MazF homolog, Rv1495 and its sole DNA topoisomerase I’163
Correction to ‘Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome’162
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’161
Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolution160
Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells158
A new level of RNA-based plant protection: dsRNAs designed from functionally characterized siRNAs highly effective against Cucumber mosaic virus156
Genome-wide transcriptional silencing and mRNA stabilization allow the coordinated expression of the meiotic program in mice154
Optimizing gRNA selection for high-penetrance F0 CRISPR screening for interrogating disease gene function153
APE1 condensation in nucleoli of non-cancer cells depends on rRNA transcription and forming G-quadruplex RNA structures153
mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability151
Translational fidelity screens in mammalian cells reveal eIF3 and eIF4G2 as regulators of start codon selectivity150
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline148
Lysine 27 dimethylation of Drosophila linker histone dH1 contributes to heterochromatin organization independently of H3K9 methylation148
Comprehensive profiling of L1 retrotransposons in mouse144
BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures144
HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia142
Correction to ‘Mechanistic insights into the alternative ribosome recycling by HflXr’142
Correction to ‘Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data’141
Correction to ‘Genome manipulation by guide-directed Argonaute cleavage’138
Correction to ‘Click display: a rapid and efficient in vitro protein display method for directed evolution’136
Identification of a novel endogenous long non-coding RNA that inhibits selenoprotein P translation136
In vivotargets ofSalmonellaFinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid135
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions132
RNA-guided DNA base damage repair via DNA polymerase-mediated nick translation132
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