OOIR: Observatory of International 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 2021-05-01 to 2025-05-01.)

Article	Citations
SV4GD: a comprehensive structural variation database specially for genetic diseases	5907
NucleoFind: a deep-learning network for interpreting nucleic acid electron density	4922
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip	4036
A method for targeting a specified segment of DNA to a bacterial microorganelle	3758
Correction to ‘Cis regulation within a cluster of viral microRNAs’	3657
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition	3174
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’	3126
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’	2013
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’	1957
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’	1889
Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution	1842
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers	1772
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis	1586
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip	1474
Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ	1466
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 telomeres	1446
Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization	1420
The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically	1326
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition	1293
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey	1255
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA	1212
Nanopores map the acid-base properties of a single site in a single DNA molecule	1170
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping	1039
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors	1014
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats	960

High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases	933
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins	877
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex	873
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase	777
Folding and persistence times of intramolecular G-quadruplexes transiently embedded in a DNA duplex	732
CoffeeProt: an online tool for correlation and functional enrichment of systems genetics data	731
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase	724
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models	678
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program	666
Systematic discovery of DNA-binding tandem repeat proteins	659
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break	656
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices	652
Cognate restriction of transposition by piggyBac-like proteins	642
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning	606
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA	601
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	532
Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions	529
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics	504
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis	495
VID22counteracts G-quadruplex-induced genome instability	488
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning	474
Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity	466
Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization	462
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing	451
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression	444
Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations	440
Human prefoldin modulates co-transcriptional pre-mRNA splicing	435
Widespread translational control regulates retinal development in mouse	427
PHF8 facilitates transcription recovery following DNA double-strand break repair	403
Correction to ‘The European Genome-phenome Archive in 2021’	403
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei	399
Flap endonuclease Rad27 cleaves the RNA of R-loop structures to suppress telomere recombination	398
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts	393
The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG	387
Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA	359
Correction to ‘EMDB—the Electron Microscopy Data Bank’	354
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR’	333
Investigating the origins of the mutational signatures in cancer	332
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy	323
Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits	307
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’	306
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide	305
Diverse targets ofSMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy	303
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions	290
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)	278
A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome	273
DriverDBv4: a multi-omics integration database for cancer driver gene research	272
Formation and persistence of polyglutamine aggregates in mistranslating cells	269
H2A mono-ubiquitination differentiates FACT’s functions in nucleosome assembly and disassembly	266
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse	265

TheS. cerevisiaem6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts	263
Discordant regulation of eIF2 kinase GCN2 and mTORC1 during nutrient stress	261
Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants	257
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools	253
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline	253
Post-replicative lesion processing limits DNA damage-induced mutagenesis	248
NCBI Taxonomy: enhanced access via NCBI Datasets	239
THUMPD3–TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates	236
Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells	230
Splitting the yeast centromere by recombination	230
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data	229
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication	227
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells	224
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins	221
pLannotate: engineered plasmid annotation	220
scQTLbase: an integrated human single-cell eQTL database	218
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro	218
ZEB1 promotes non-homologous end joining double-strand break repair	218
The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses	214
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs	205
Yeast transcription factor Msn2 binds to G4 DNA	204
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa	203
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription	201
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection	196
CPLM 4.0: an updated database with rich annotations for protein lysine modifications	188
The human telomeric proteome during telomere replication	185
Human Ageing Genomic Resources: updates on key databases in ageing research	184
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions	184
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis	184
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR	181
RefMetaPlant: a reference metabolome database for plants across five major phyla	175
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation	172
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms	170
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo	170
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels	169
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing	168
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins	166
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options	163
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress	161
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors	161
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	160
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity	159
ZYP1-mediated recruitment of PCH2 to the synaptonemal complex remodels the chromosome axis leading to crossover restriction	158
Rfam 15: RNA families database in 2025	156
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study	155
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes	152
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity	149
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity	149
Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy	148
BioSamples database: FAIRer samples metadata to accelerate research data management	145
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system	145
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery	143
ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules	140
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast	140
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB	139
Prediction of DNA i-motifs via machine learning	139
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database	137
Waves of sumoylation support transcription dynamics during adipocyte differentiation	136
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins	135
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli	134
A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes	134