OOIR: Observatory of International Research

Papers

(The TQCC of RNA is 8. 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 2022-08-01 to 2026-08-01.)

Article	Citations
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors	148
Novel trinucleotide mRNA capping reagents: improved synthetic route and efficient cotranscriptional incorporation in mRNA	129
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	111
Motifs in SARS-CoV-2 evolution	81
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis	66
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis	49
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging	45
Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (	43
Direct RNA-seq provides evidence for an antiterminator function of the yeast Hrp1 protein on RNA polymerase II transcripts	39
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions	35
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2	34
Simultaneous detection of the AAV genomes and their transcripts in situ at the single-cell level	32
Molecular basis for GIGYF–TNRC6 complex assembly	31
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription	31
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells	30
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations	29
Molecular basis for the interactions of eIF2β with eIF5, eIF2B, and 5MP1 and their regulation by CK2	29
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast	29
Small noncoding RNA interactome capture reveals pervasive, carbon source–dependent tRNA engagement of yeast glycolytic enzymes	28
Far from home: the role of glial mRNA localization in synaptic plasticity	28
Corrigendum: Pharmacologically stabilizing RNA G-quadruplexes in coronavirus genome reduces infectivity	28
PANTHER Score: Protein-Affinity for Nucleic Target-binding, Hybridization, and Energy Regression	27
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2	27
Exploring the targeting spectrum of rocaglates among eIF4A homologs	26
Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering	25

Bioinformatic and experimental analyses revealed pathogen-derived pathoPEP candidates predicted to control plant miRNA expression and infection	25
Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity	25
mRNA COVID-19 vaccines: science versus misinformation	24
The m⁶A-binding protein YTHDF3 modulates the cardiac response to stress	23
Reconstitution of antiviral Dicer activity in vitro reveals distinct contributions of RDE-4 dsRNA-binding motifs	23
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor	23
Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion	22
Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function	22
A novel reporter for helicase activity in translation uncovers DDX3X interactions	22
Nuclear RNA-binding proteins meet cytoplasmic viruses	22
Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	21
Target-site Dynamics Explain a Large Share of Apparent MicroRNA Differential Expression	21
Comprehensive analysis of m6A-seq data reveals distinct features of conserved and unique m6A sites in mammals	21
Diversity and modularity of tyrosine-accepting tRNA-like structures	21
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	21
Site-blocking antisense oligonucleotides as a mechanism to fine-tune MeCP2 expression	20
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements	20
Human vault RNAs exhibit diverse expression patterns and inter-locus compensation	20
Adenosine deaminases that act on RNA, then and now	20
Terminal loop sequences in viral double-stranded RNAs modulate RIG-I signaling	20
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes	20
Progress and challenges in profiling protein–RNA and protein-associated RNA–RNA interactions	20
Corrigendum: Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	19
Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes	19
Novel ADAR2 variants in children with seizures, intellectual disability, and motor delay have reduced RNA editing	19
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)	18
Absolute quantification of mammalian microRNAs for therapeutic RNA cleavage and detargeting	18
Decoding Argonaute specificity: insights from C. elegans and beyond	18
PACT suppresses PKR activation through dsRNA binding and dimerization, and is a therapeutic target for triple-negative breast cancer	17
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	17
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA	17
Codon bias shapes bacterial small RNA binding sites within protein-coding sequences	16
Corrigendum: RNA partitioning into stress granules is based on the summation of multiple interactions	16
clipplotr —a comparative visualization and analysis tool for CLIP data	16
An incredible life in science: Joseph G. Gall (1928–2024)	16
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP	16
Seven wonders of RNA modification biology	16
EF-P Inhibits Ribosomal α-Hydroxy Acid Incorporation: Strategic tRNA Body Selection for Co-incorporating α-Hydroxy Acids and Nonproteinogenic Amino Acids into Depsipeptides	16
SMDesigner: a program to design sequence mutations to assess RNA structure	15
Desthiobiotin (DTB)–modified and TAMRA-modified 2″OMeNAD ⁺ are RNA 2′-phosphotransferase (Tpt1) poisons that enable affinity-tagging and fluorescence	15
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human and Drosophila cells	15
The pseudotorsional space of RNA	15
Boosting the toolbox for live imaging of translation	14
Corrigendum: No evidence for epitranscriptomic m⁵C modification of SARS-CoV-2, HIV, and MLV viral RNA	14
Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA	14
The codon context provides cis -acting immune evasion for the human papilloma virus (HPV) E6	14
Translation elongation inhibitors stabilize select short-lived transcripts	14
RNA modifications: an overview of select web-based tools	14
Genetic suppression of precocious transcription termination identifies mutations in essential subunits of the fission yeast cleavage and polyadenylation machinery	14
Localization of RNAs to the Mitochondria – Mechanisms and Functions	14

The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to zinc toxicity	14
Functional analysis of the zinc finger modules of the Saccharomyces cerevisiae splicing factor Luc7	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
Double-stemmed and split structural variants of fluorescent RNA Mango aptamers	13
Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2	13
Dual Role of 3′ UTR Length in Modulating Translation Termination Efficiency	13
The catalytic-dead Pcif1 regulates gene expression and fertility inDrosophila	13
Solution Structure Determination and Biophysical Studies of 7SK RNP and 7SL SRP RNAs	13
miRNA regulation in brain tissue space: the 3′UTR perspective	13
RK-33 inhibits the OC43 Coronavirus and induces stress granules via DDX3X-independent mechanisms	13
Implications for OLE RNA as a natural integral membrane RNA	13
Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation	12
Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations	12
Walter Keller (1938–2023): a tribute from his mentees	12
OpenASO: RNA Rescue—designing splice-modulating antisense oligonucleotides through community science	12
Ancestral intronic splicing regulatory elements in the SCNα gene family	12
A continuum-based reaction-diffusion model for spread of gene silencing in chromosomal inactivation	12
4MRNA: a new approach for nucleic acid molecular replacement using models with diverse parameter patterns	12
Editing-independent effects of Drosophila Adar on heterochromatin silencing	12
Reconfigured immunity in Adar heterozygous and Adar Mavs Eif2ak2 (PKR) triple mutant mice	12
Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	12
Corrigendum: Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay	11
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations	11
The daunting task of modifying ribosomal RNA	11
Conformational dynamics of the hepatitis C virus 3′X RNA	11
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex	11
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning	11
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p	11
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	11
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity	11
ZYS-1 is not an ADAR1 inhibitor	11
C. elegans FBF-1 and FBF-2 C-terminal intrinsically-disordered regions differentially regulate RNA-binding affinity	11
The importance of m ⁶ A topology in chicken embryo mRNA: a precise mapping of m ⁶ A at the conserv	11
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	11
Computational design and experimental verification of pseudoknotted ribozymes	11
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	11
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends	10
Understanding the redundant functions of the m⁶A-binding YTHDF proteins	10
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability	10
ac4C: a fragile modification with stabilizing functions in RNA metabolism	10
DNMT1 inhibition by pUG-fold quadruplex RNA	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 G-quadruplex structure targeting and imaging: recent advances and future directions	10
Global analysis by LC-MS/MS of N6 -methyladenosine and inosine in mRNA reveal complex incidence	10
Chemical manipulation of m¹A mediates its detection in human tRNA	10
The role of nonsense-mediated mRNA decay in restricting long noncoding RNA expression has been conserved in RNAi-capable budding yeast	9
Promiscuous RNA editing in lncRNA roX1 is generally non-adaptive	9
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae	9
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server	9
Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast	9
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	9
Study of the RNA splicing kinetics via in vivo 5-EU labeling	9
KRGG1 function in RNA editing inTrypanosoma brucei	9
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function	9
The essential role of architectural noncoding RNANeat1in cold-induced beige adipocyte differentiation in mice	9
The unfolding landscape of RNA and disease	9
RNA gain-of-function mechanisms in short tandem repeat diseases	9
Targeting splicing factors for cancer therapy	9
Onconeural antigen NOVA1 dysregulates RNA alternative splicing in breast cancer	9
Cancer-associated synonymous mutations reveal stress signal-dependent mRNA folding that selectively modulates protein function.	8
Rational design yields RNA-binding zinc finger domains with altered sequence specificity	8
Cytoplasmic regulation of the poly(A) tail length as a potential therapeutic target	8
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	8
Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops	8
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA	8
Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor in Saccharomyces cerevisiae	8
How tailored Ribo-seq methods probe unique translation events	8
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis	8
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea	8
Cross-linking mass spectrometric analysis of the endogenous TREX complex fromSaccharomyces cerevisiae	8
Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders	8
RNA aptamers as tools for the purification and analysis of in vivo assembled ribonucleoproteins	8
Splice site diversity and abundance of noncanonical introns in diplonemids (Diplonemea, Euglenozoa)	8
Comparative analysis of the m6A epitranscriptome in HeLa-expressed HPV18 early transcripts reveals its potential impact on splicing	8