OOIR: Observatory of International Research

Papers

(The H4-Index of Nucleic Acids Research is 141. 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 2021-08-01 to 2025-08-01.)

Article	Citations
SV4GD: a comprehensive structural variation database specially for genetic diseases	6331
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	5282
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip	4688
Correction to ‘Cis regulation within a cluster of viral microRNAs’	4618
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	4115
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’	3466
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	2161
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	2128
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	1992
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	1957
Nanopores map the acid-base properties of a single site in a single DNA molecule	1669
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	1644
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase	1601
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	1574
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	1535
Systematic discovery of DNA-binding tandem repeat proteins	1530
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning	1430
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	1403
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	1344
VID22counteracts G-quadruplex-induced genome instability	1176
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	1158
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	1101
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	1081
Correction to ‘The European Genome-phenome Archive in 2021’	1074
PHF8 facilitates transcription recovery following DNA double-strand break repair	933

Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	901
Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression	853
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers	826
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection	810
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	800
Correction to ‘EMDB—the Electron Microscopy Data Bank’	744
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors	724
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’	724
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	717
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	711
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	674
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning	670
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	661
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	635
TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	634
Splitting the yeast centromere by recombination	617
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	605
Widespread translational control regulates retinal development in mouse	600
NCBI Taxonomy: enhanced access via NCBI Datasets	591
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	580
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	537
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program	535
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	501
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	497
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	493
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	490
Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells	477
Molecular determinants for recognition of serotonylated chromatin	470
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	463
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	463
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy	411
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	402
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	379
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	370
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	370
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	342
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	337
Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling	332
CPLM 4.0: an updated database with rich annotations for protein lysine modifications	323
ZEB1 promotes non-homologous end joining double-strand break repair	321
BioSamples database: FAIRer samples metadata to accelerate research data management	315
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip	315
High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases	313
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	312
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining	310
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	305
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	303
Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization	301
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	301
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system	299

RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	295
Prediction of DNA i-motifs via machine learning	294
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	289
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	281
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	278
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	277
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	272
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	271
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	265
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	264
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels	262
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	255
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	250
The human telomeric proteome during telomere replication	246
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	246
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	238
Rfam 15: RNA families database in 2025	238
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study	221
Human Ageing Genomic Resources: updates on key databases in ageing research	220
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	217
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	208
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation	208
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	203
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	202
A method for targeting a specified segment of DNA to a bacterial microorganelle	193
Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5′-untranslated region	187
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli	186
Waves of sumoylation support transcription dynamics during adipocyte differentiation	186
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins	185
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	185
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	181
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	178
Helical coiling of metaphase chromatids	177
THUMPD3–TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates	177
Formation and persistence of polyglutamine aggregates in mistranslating cells	177
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	177
CapBuild: a cloud-native tool for adeno-associated virus capsid engineering	175
scQTLbase: an integrated human single-cell eQTL database	175
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	175
Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research	173
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	170
Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation	168
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	168
Post-replicative lesion processing limits DNA damage-induced mutagenesis	167
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	166
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region	166
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies	165
The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery	164
Investigating the origins of the mutational signatures in cancer	162
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	161
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	160
The quantitative impact of 3′UTRs on gene expression	158
Yeast transcription factor Msn2 binds to G4 DNA	157
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	156
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	155
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells	154
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly	153
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes	152
RefMetaPlant: a reference metabolome database for plants across five major phyla	152
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	151
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	145
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	144
The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses	144
Ensembl 2024	142
DriverDBv4: a multi-omics integration database for cancer driver gene research	142
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	141