Nucleic Acids Research

Papers
(The TQCC of Nucleic Acids Research is 14. 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 2021-02-01 to 2025-02-01.)
ArticleCitations
Correction to ‘Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs’6985
Correction to ‘Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM’5291
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’4254
Correction to ‘ATM-mediated ELL phosphorylation enhances its self-association through increased EAF1 interaction and inhibits global transcription during genotoxic stress’3069
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex2935
Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes2906
Structures of pMV158 replication initiator RepB with and without DNA reveal a flexible dual-function protein2561
Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA2506
The flexible N-terminal motif of uL11 unique to eukaryotic ribosomes interacts with P-complex and facilitates protein translation1853
CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors1673
CRISPRi-based programmable logic inverter cascade for antibiotic-free selection and maintenance of multiple plasmids1569
Mapping yeast mitotic 5′ resection at base resolution reveals the sequence and positional dependence of nucleases in vivo1476
CD44 alternative splicing senses intragenic DNA methylation in tumors via direct and indirect mechanisms1399
Archaeal Hel308 suppresses recombination through a catalytic switch that controls DNA annealing1363
Human HELQ regulates DNA end resection at DNA double-strand breaks and stalled replication forks1348
Corrigendum to article “A programmable omnipotent Argonaute nuclease from mesophilic bacteria Kurthia massiliensis’’1332
Correction to ‘Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy’1271
Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression1258
Cre-Lox miRNA-delivery technology optimized for inducible microRNA and gene-silencing studies in zebrafish1176
The iMab antibody selectively binds to intramolecular and intermolecular i-motif structures1094
Novel archaeal ribosome dimerization factor facilitating unique 30S–30S dimerization1054
Engineered initiator tRNAs can effectively start translation at non-AUG start codons and diversify N-terminal amino acids for mRNA Display1032
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei1028
CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation847
Novel BRCA1–PLK1–CIP2A axis orchestrates homologous recombination-mediated DNA repair to maintain chromosome integrity during oocyte meiosis795
A tunable and reversible thermo-inducible bio-switch for streptomycetes781
Automating microbial taxonomy workflows with PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes738
Precise homology-directed installation of large genomic edits in human cells with cleaving and nicking high-specificity Cas9 variants697
Genome manipulation by guide-directed Argonaute cleavage691
To let go or not to let go: how ParA can impact the release of the chromosomal anchoring in Caulobacter crescentus626
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes608
Small-molecule compounds boost genome-editing efficiency of cytosine base editor572
An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity568
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors539
TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts528
DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides526
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA495
tatDB: a database of Ago1-mediated targets of transfer RNA fragments484
DNA Data Bank of Japan (DDBJ) update report 2022476
RNAcanvas: interactive drawing and exploration of nucleic acid structures473
Predicting functional consequences of SNPs on mRNA translation via machine learning429
Heavy metal ions exchange driven protein phosphorylation cascade functions in genomic instability in spermatocytes and male infertility426
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes426
Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics378
OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics374
Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes371
Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs361
CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer357
The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials347
Adenovirus prevents dsRNA formation by promoting efficient splicing of viral RNA341
Arena3Dweb: interactive 3D visualization of multilayered networks335
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation322
RNA-guided DNA base damage repair via DNA polymerase-mediated nick translation321
Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery312
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’304
Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation302
Correction to ‘In vivo analysis of Pim-1 deficiency’301
Structural basis for the selective methylation of 5-carboxymethoxyuridine in tRNA modification301
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes298
Distinct characteristics of two types of alternative lengthening of telomeres in mouse embryonic stem cells289
Three-way contact analysis characterizes the higher order organization of the Tcra locus277
Role of a cryptic tRNA gene operon in survival under translational stress263
Assessing base-resolution DNA mechanics on the genome scale255
KERA: analysis tool for multi-process, multi-state single-molecule data244
A novel bipartite antitermination system widespread in conjugative elements of Gram-positive bacteria239
SARS-CoV-2 nsp15 preferentially degrades AU-rich dsRNA via its dsRNA nickase activity221
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 oligomers221
CGG repeats trigger translational frameshifts that generate aggregation-prone chimeric proteins220
RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures217
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome215
Genome-wide mapping of Vibrio cholerae VpsT binding identifies a mechanism for c-di-GMP homeostasis214
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction212
Correction to ‘Optimized design of antisense oligomers for targeted rRNA depletion’203
Editor's Note on ‘PCAF regulates the stability of the transcriptional regulator and cyclin-dependent kinase inhibitor p27Kip1’202
Correction to ‘EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants’202
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’199
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA197
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically196
Monocyte chemoattractant protein-induced protein 1 directly degrades viral miRNAs with a specific motif and inhibits KSHV infection195
Transcriptome-wide profiling of A-to-I RNA editing by Slic-seq194
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip189
MultifacetedProtDB: a database of human proteins with multiple functions188
Influence of RNA circularity on Target RNA-Directed MicroRNA Degradation185
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline185
Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops177
Employing bimodal representations to predict DNA bendability within a self-supervised pre-trained framework177
Efficient detection and assembly of non-reference DNA sequences with synthetic long reads175
A method for targeting a specified segment of DNA to a bacterial microorganelle174
Evaluation of the determinants for improved pluripotency induction and maintenance by engineered SOX17174
Usage of the H3 variants during the S-phase of the cell cycle in Physarum polycephalum172
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations171
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics171
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’170
The Efg1–Bud22 dimer associates with the U14 snoRNP contacting the 5′ rRNA domain of an early 90S pre-ribosomal particle168
Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression163
Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410–DNA interaction using small angle X-ray scattering161
ZEB1 promotes non-homologous end joining double-strand break repair159
Ccr4–Not complex reduces transcription efficiency in heterochromatin150
mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation147
Aviator: a web service for monitoring the availability of web services145
Correction to ‘Bias-minimized quantification of microRNA reveals widespread alternative processing and 3′ end modification’142
Comparison of genome architecture at two stages of male germline cell differentiation inDrosophila142
Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N′- methylguanidine-bridged nucleic a141
Correction to ‘MiR-145 directly targets p70S6K1 in cancer cells to inhibit tumor growth and angiogenesis’139
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase134
Correction to ‘Stabilization of XIAP mRNA through the RNA binding protein HuR regulated by cellular polyamines’132
A multiplexed, three-dimensional pooling and next-generation sequencing strategy for creating barcoded mutant arrays: construction of a Schizosaccharomyces pombe transposon insertion library132
Long-read sequencing and de novo genome assemblies reveal complex chromosome end structures caused by telomere dysfunction at the single nucleotide level132
Correction to ‘DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion’129
Correction to ‘The European Genome-phenome Archive in 2021’129
Temperature-sensitive splicing defects in Arabidopsis mitochondria caused by mutations in the ROOT PRIMORDIUM DEFECTIVE 1 gene128
Novel insights into the role of translesion synthesis polymerase in DNA incorporation and bypass of 5-fluorouracil in colorectal cancer127
Unearthing a novel function of SRSF1 in binding and unfolding of RNA G-quadruplexes126
TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma125
Position-dependent sequence motif preferences of SpCas9 are largely determined by scaffold-complementary spacer motifs123
G-quadruplex inducer/stabilizer pyridostatin targets SUB1 to promote cytotoxicity of a transplatinum complex121
High-density generation of spatial transcriptomics with STAGE120
Translocating RNA polymerase generates R-loops at DNA double-strand breaks without any additional factors119
Two distinct pathways of RNA polymerase backtracking determine the requirement for the Trigger Loop during RNA hydrolysis118
Orphan nuclear receptors-induced ALT-associated PML bodies are targets for ALT inhibition116
rAAV capsid mutants eliminate leaky expression from DNA donor template for homologous recombination116
Interaction between a J-domain co-chaperone and a specific Argonaute protein contributes to microRNA function in animals115
DNA i-motif formation at neutral pH is driven by kinetic partitioning114
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins111
Regulation of both transcription and RNA turnover contribute to germline specification111
Deep learning-assisted genome-wide characterization of massively parallel reporter assays111
KRCC1, a modulator of the DNA damage response109
Correction to ‘A novel 5′-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes’109
Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide108
Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems108
Assessing in vivo the impact of gene context on transcription through DNA supercoiling107
EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure107
Ribosomal collision is not a prerequisite for ZNF598-mediated ribosome ubiquitination and disassembly of ribosomal complexes by ASCC107
Molecular basis of anti-CRISPR operon repression by Aca10105
Dual genetic level modification engineering accelerate genome evolution of Corynebacterium glutamicum104
The non-telomeric evolutionary trajectory of TRF2 in zebrafish reveals its specific roles in neurodevelopment and aging103
Multiplexed in-situ mutagenesis driven by a dCas12a-based dual-function base editor102
Stable bulged G-quadruplexes in the human genome: identification, experimental validation and functionalization101
Correction to ‘Cis regulation within a cluster of viral microRNAs’101
CYCLeR—a novel tool for the full isoform assembly and quantification of circRNAs99
Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation99
UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF298
Evaluating the oral delivery of GalNAc-conjugated siRNAs in rodents and non-human primates98
Substrate specificity of Mycobacterium tuberculosis tRNA terminal nucleotidyltransferase toxin MenT398
Short 2′-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo98
Two redundant transcription factor binding sites in a single enhancer are essential for mammalian sex determination96
Implication of nucleotides near the 3′ end of 16S rRNA in guarding the translational reading frame96
eIF5 and eIF5B together stimulate 48S initiation complex formation during ribosomal scanning95
Structural basis for the allosteric regulation and dynamic assembly of DNMT3B95
Correction to ‘Activating cryptic biosynthetic gene cluster through a CRISPR–Cas12a-mediated direct cloning approach’95
A role for AKT1 in nonsense-mediated mRNA decay95
Correction to ‘The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex’94
Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses93
Fission yeast Swi2 designates cell-type specific donor and stimulates Rad51-driven strand exchange for mating-type switching93
Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM93
Small-molecule activators specific to adenine base editors through blocking the canonical TGF-β pathway92
scQTLbase: an integrated human single-cell eQTL database92
NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs91
Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome90
Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome90
Decoding dissociation of sequence-specific protein–DNA complexes with non-equilibrium simulations90
AT-specific DNA visualization revisits the directionality of bacteriophage λ DNA ejection89
Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations89
Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ϵ variants at low dNTP levels88
Inhibition of DNA replication initiation by silver nanoclusters87
PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs87
The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation87
mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability86
An archaeal transcription factor EnfR with a novel ‘eighth note’ fold controls hydrogen production of a hyperthermophilic archaeon Thermococcus onnurineus NA185
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data84
Mechanisms of spacer acquisition by sequential assembly of the adaptation module in Synechocystis84
MACC: a visual interactive knowledgebase of metabolite-associated cell communications84
Pathways of thymidine hypermodification83
DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database83
AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations82
Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II82
ADARp150 counteracts whole genome duplication81
Cryo-EM structure of DNA polymerase of African swine fever virus81
Y-switch: a spring-loaded synthetic gene switch for robust DNA/RNA signal amplification and detection80
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation80
Systematic discovery of DNA-binding tandem repeat proteins79
NucleoFind: a deep-learning network for interpreting nucleic acid electron density79
Efficient circularization of protein-encoding RNAs via a novel cis-splicing system79
RUV-III-NB: normalization of single cell RNA-seq data78
The transcription factor network ofE. colisteers global responses to shifts in RNAP concentration78
Efficacy, biodistribution and safety comparison of chemically modified antisense oligonucleotides in the retina77
PHF8 facilitates transcription recovery following DNA double-strand break repair77
Transposition with Tn3-family elements occurs through interaction with the host β-sliding clamp processivity factor77
Meiotic chromatin-associated HSF5 is indispensable for pachynema progression and male fertility77
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’76
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions76
Yeast transcription factor Msn2 binds to G4 DNA76
Dr.Nod: computational framework for discovery of regulatory non-coding drivers in tissue-matched distal regulatory elements75
Correction to ‘CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells’75
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription74
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip74
CMAUP database update 2024: extended functional and association information of useful plants for biomedical research74
Correction to ‘Four additional natural 7-deazaguanine derivatives in phages and how to make them’74
AlphaFind: discover structure similarity across the proteome in AlphaFold DB73
TTSBBC: triplex target site biomarkers and barcodes in cancer73
SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data73
PROSCA: an online platform for humanized scaffold mining facilitating rational protein engineering72
GCMS-ID: a webserver for identifying compounds from gas chromatography mass spectrometry experiments71
DNAforge: a design tool for nucleic acid wireframe nanostructures71
Accuratein silicoconfirmation of rare copy number variant calls from exome sequencing data using transfer learning70
Bioorthogonal labeling and profiling of N6-isopentenyladenosine (i6A) modified RNA70
Stochastic scanning events on the GCN4 mRNA 5’ untranslated region generate cell-to-cell heterogeneity in the yeast nutritional stress response70
Correction to ‘hnRNPA1 couples nuclear export and translation of specific mRNAs downstream of FGF-2/S6K2 signalling’70
Multivalency of nucleosome recognition by LEDGF70
The MukB-topoisomerase IV interaction mutually suppresses their catalytic activities69
AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation inArabidopsis thaliana69
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers69
A critical role for linker DNA in higher-order folding of chromatin fibers69
Sustained pigmentation causes DNA damage and invokes translesion polymerase Polκ for repair in melanocytes68
Origin, evolution, and maintenance of gene-strand bias in bacteria68
Editor's Note on ‘Influence of correct secondary and tertiary RNA folding on the binding of cellular factors to the HCV IRES’68
Dimerization of an umbravirus RNA genome activates subgenomic mRNA transcription68
Targeted de novo phasing and long-range assembly by template mutagenesis68
Dynamic accumulation of cyclobutane pyrimidine dimers and its response to changes in DNA conformation68
Correction to ‘Clerocidin interacts with the cleavage complex of Streptococcus pneumoniae topoisomerase IV to induce selective irreversible DNA damage’67
DNA methylation by CcrM contributes to genome maintenance in the Agrobacterium tumefaciens plant pathogen67
Human Thg1 displays tRNA-inducible GTPase activity67
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity66
RNA-directed peptide synthesis across a nicked loop66
SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions65
CRISPR screening uncovers nucleolar RPL22 as a heterochromatin destabilizer and senescence driver65
BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures65
Phage defence loci of Streptococcus thermophilus—tip of the anti-phage iceberg?65
LAP2alpha facilitates myogenic gene expression by preventing nucleoplasmic lamin A/C from spreading to active chromatin regions65
Chem-CRISPR/dCas9FCPF: a platform for chemically induced epigenome editing65
Correction to ‘Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch’63
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA63
Striving for clarity in language about gene expression63
Correction to ‘Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R’63
PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful63
Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS62
Structural characterization of a new subclass of panicum mosaic virus-like 3′ cap-independent translation enhancer62
Defective transfer of parental histone decreases frequency of homologous recombination by increasing free histone pools in budding yeast62
A single fiber view of the nucleosome organization in eukaryotic chromatin61
Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes61
Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis61
A new assay capturing chromosome fusions shows a protection trade-off at telomeres and NHEJ vulnerability to low-density ionizing radiation61
Mutations in the non-codingRNU4ATACgene affect the homeostasis and function of the Integrator complex61
scPlantDB: a comprehensive database for exploring cell types and markers of plant cell atlases60
In vivotargets ofSalmonellaFinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid60
Functional integration of a semi-synthetic azido-queuosine derivative into translation and a tRNA modification circuit60
Plasmid replication based on the T7 origin of replication requires a T7 RNAP variant and inactivation of ribonuclease H60
Measuring nonhomologous end-joining, homologous recombination and alternative end-joining simultaneously at an endogenous locus in any transfectable human cell60
Saturation mutagenesis charts the functional landscape ofSalmonellaProQ and reveals a gene regulatory function of its C-terminal domain60
A novel HPV16 splicing enhancer critical for viral oncogene expression and cell immortalization60
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