OOIR: Observatory of International Research

Papers

(The TQCC of RNA is 9. 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 2021-12-01 to 2025-12-01.)

Article	Citations
Oppositional poly(A) tail length regulation by FMRP and CPEB1	123
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging	102
Simultaneous detection of the AAV genomes and their transcripts in situ at the single-cell level	98
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors	80
Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1	78
Molecular basis for GIGYF–TNRC6 complex assembly	60
Novel Trinucleotide mRNA Capping Reagents: Improved Synthetic Route and Efficient Co-transcriptional Incorporation in mRNA	59
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2	54
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions	48
Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (	38
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis	34
Motifs in SARS-CoV-2 evolution	33
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis	30
Constructing an active chimeric pRNA ring with a stoichiometry of six and identifying 12 domains of the pRNA ring binding to the 12-subunit channel of phi29 DNA-packaging motor	29
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription	28
The m⁶A-binding protein YTHDF3 modulates the cardiac response to stress	27
Nuclear RNA-binding proteins meet cytoplasmic viruses	27
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells	27
Exploring the targeting spectrum of rocaglates among eIF4A homologs	27
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast	26
Far from home: the role of glial mRNA localization in synaptic plasticity	25
Corrigendum: Pharmacologically stabilizing RNA G-quadruplexes in coronavirus genome reduces infectivity	25
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations	25
Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion	24
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor	24

RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type	24
Molecular basis for the interactions of eIF2β with eIF5, eIF2B, and 5MP1 and their regulation by CK2	24
Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity	23
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2	23
Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering	23
A novel reporter for helicase activity in translation uncovers DDX3X interactions	22
Small noncoding RNA interactome capture reveals pervasive, carbon source–dependent tRNA engagement of yeast glycolytic enzymes	22
Adenosine deaminases that act on RNA, then and now	22
Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	22
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements	22
Site-blocking antisense oligonucleotides as a mechanism to fine-tune MeCP2 expression	22
Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function	21
Comprehensive analysis of m6A-seq data reveals distinct features of conserved and unique m6A sites in mammals	21
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	21
Schizosaccharomyces pombe pus1mutants are temperature sensitive due to decay of tRNA^Ile(UAU)by the 5′-3′ exonuclease Dhp1, primarily targeting the unspliced pre-tRNA	20
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes	20
Corrigendum: Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	20
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations	20
Diversity and modularity of tyrosine-accepting tRNA-like structures	20
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA	19
Novel ADAR2 variants in children with seizures, intellectual disability, and motor delay have reduced RNA editing	18
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)	18
Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities	18
Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes	18
Absolute quantification of mammalian microRNAs for therapeutic RNA cleavage and detargeting	18
Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining	18
PACT suppresses PKR activation through dsRNA binding and dimerization, and is a therapeutic target for triple-negative breast cancer	18
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP	18
Corrigendum: RNA partitioning into stress granules is based on the summation of multiple interactions	17
An incredible life in science: Joseph G. Gall (1928–2024)	17
clipplotr —a comparative visualization and analysis tool for CLIP data	17
The limits of human microRNA annotation have been met	16
Effects of transgene insertion loci and copy number on Dnmt3L gene silencing through antisense transgene-derived PIWI-interacting RNAs	16
The pseudotorsional space of RNA	16
Genetic suppression of precocious transcription termination identifies mutations in essential subunits of the fission yeast cleavage and polyadenylation machinery	15
Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA	15
Translation elongation inhibitors stabilize select short-lived transcripts	15
Desthiobiotin (DTB)–modified and TAMRA-modified 2″OMeNAD ⁺ are RNA 2′-phosphotransferase (Tpt1) poisons that enable affinity-tagging and fluorescence	15
Localization of RNAs to the Mitochondria – Mechanisms and Functions	15
SMDesigner: a program to design sequence mutations to assess RNA structure	15
The codon context provides cis -acting immune evasion for the human papilloma virus (HPV) E6	15
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human and Drosophila cells	15
Implications for OLE RNA as a natural integral membrane RNA	14
RNA modifications: an overview of select web-based tools	14
Solution Structure Determination and Biophysical Studies of 7SK RNP and 7SL SRP RNAs	14
Corrigendum: No evidence for epitranscriptomic m⁵C modification of SARS-CoV-2, HIV, and MLV viral RNA	14
Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells	14
The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to zinc toxicity	14
Boosting the toolbox for live imaging of translation	14
Double-stemmed and split structural variants of fluorescent RNA Mango aptamers	13

Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	13
Functional analysis of the zinc finger modules of the Saccharomyces cerevisiae splicing factor Luc7	13
The catalytic-dead Pcif1 regulates gene expression and fertility inDrosophila	13
Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations	13
Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2	13
EDC4 C-terminal domain scaffolds P-body assembly and links P-body dynamics to p53-mediated tumor suppression	13
Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription	13
The daunting task of modifying ribosomal RNA	12
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns	12
Walter Keller (1938–2023): a tribute from his mentees	12
C. elegans FBF-1 and FBF-2 C-terminal intrinsically-disordered regions differentially regulate RNA-binding affinity	12
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends	12
OpenASO: RNA Rescue—designing splice-modulating antisense oligonucleotides through community science	12
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning	12
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	12
Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation	12
The importance of m ⁶ A topology in chicken embryo mRNA: a precise mapping of m ⁶ A at the conserv	11
Corrigendum: Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay	11
Computational design and experimental verification of pseudoknotted ribozymes	11
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p	11
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	11
Global analysis by LC-MS/MS of N6 -methyladenosine and inosine in mRNA reveal complex incidence	11
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat	11
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations	11
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity	11
Chemical manipulation of m¹A mediates its detection in human tRNA	11
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	11
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex	11
ZYS-1 is not an ADAR1 inhibitor	11
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability	11
DNMT1 inhibition by pUG-fold quadruplex RNA	11
RNA G-quadruplex structure targeting and imaging: recent advances and future directions	11
Conformational dynamics of the hepatitis C virus 3′X RNA	11
Understanding the redundant functions of the m⁶A-binding YTHDF proteins	10
Molecular basis of human polyA polymerase recruitment by mPSF	10
The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets, by Thomas R. Cech. 2024. W.W. Norton & Company	10
RNA gain-of-function mechanisms in short tandem repeat diseases	10
ac4C: a fragile modification with stabilizing functions in RNA metabolism	10
Promiscuous RNA editing in lncRNA roX1 is generally non-adaptive	10
Study of the RNA splicing kinetics via in vivo 5-EU labeling	10
The unfolding landscape of RNA and disease	10
KRGG1 function in RNA editing inTrypanosoma brucei	10
Alternative splicing regulation of membrane trafficking genes during myogenesis	10
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae	10
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	10
The essential role of architectural noncoding RNANeat1in cold-induced beige adipocyte differentiation in mice	9
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server	9
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea	9
RNA aptamers as tools for the purification and analysis of in vivo assembled ribonucleoproteins	9
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes	9
The role of nonsense-mediated mRNA decay in restricting long noncoding RNA expression has been conserved in RNAi-capable budding yeast	9
Targeting splicing factors for cancer therapy	9
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function	9
Theje ne sais quoiof 5-methylcytosine in messenger RNA	9
Splice site diversity and abundance of noncanonical introns in diplonemids (Diplonemea, Euglenozoa)	9
Cytoplasmic regulation of the poly(A) tail length as a potential therapeutic target	9
Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs	9
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	9
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA	9
Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast	9
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis	9