OOIR: Observatory of International Research

Papers

(The TQCC of RNA is 10. 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
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)	106
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis	103
Motifs in SARS-CoV-2 evolution	83
Oppositional poly(A) tail length regulation by FMRP and CPEB1	83
Molecular basis for GIGYF–TNRC6 complex assembly	72
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging	69
Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1	61
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis	55
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	53
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions	52
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors	51
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2	48
Nuclear RNA-binding proteins meet cytoplasmic viruses	47
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells	47
Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering	46
RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type	43
Small noncoding RNA interactome capture reveals pervasive, carbon source–dependent tRNA engagement of yeast glycolytic enzymes	41
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription	41
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast	40
Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion	39
A novel reporter for helicase activity in translation uncovers DDX3X interactions	33
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations	32
Exploring the targeting spectrum of rocaglates among eIF4A homologs	29
The m⁶A-binding protein YTHDF3 modulates the cardiac response to stress	29
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2	28

Molecular basis for the interactions of eIF2β with eIF5, eIF2B, and 5MP1 and their regulation by CK2	27
A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication	25
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor	25
Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria	25
Far from home: the role of glial mRNA localization in synaptic plasticity	25
Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity	25
Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	24
Site-blocking antisense oligonucleotides as a mechanism to fine-tune MeCP2 expression	24
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements	24
Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function	23
Comprehensive analysis of m6A-seq data reveals distinct features of conserved and unique m6A sites in mammals	23
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations	23
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes	23
Diversity and modularity of tyrosine-accepting tRNA-like structures	23
Corrigendum: Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	22
Adenosine deaminases that act on RNA, then and now	22
Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities	22
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	22
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA	21
Novel ADAR2 variants in children with seizures, intellectual disability and motor delay have reduced RNA editing.	21
Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining	21
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)	21
Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes	20
Absolute quantification of mammalian microRNAs for therapeutic RNA cleavage and detargeting	20
DDX3X and DDX3Y are redundant in protein synthesis	20
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
Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance	20
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP	20
clipplotr—a comparative visualization and analysis tool for CLIP data	20
Corrigendum: RNA partitioning into stress granules is based on the summation of multiple interactions	20
The pseudotorsional space of RNA	19
An incredible life in science: Joseph G. Gall (1928–2024)	19
Translation elongation inhibitors stabilize select short-lived transcripts	19
Localization of RNAs to the Mitochondria – Mechanisms and Functions	18
Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA	18
Boosting the toolbox for live imaging of translation	18
Effects of transgene insertion loci and copy number on Dnmt3L gene silencing through antisense transgene-derived PIWI-interacting RNAs	18
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human andDrosophilacells	18
SMDesigner: a program to design sequence mutations to assess RNA structure	17
RNA modifications: an overview of select web-based tools	17
The limits of human microRNA annotation have been met	17
Corrigendum: No evidence for epitranscriptomic m⁵C modification of SARS-CoV-2, HIV, and MLV viral RNA	17
Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells	16
Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation	16
Three critical regions of the erythromycin resistance methyltransferase, ErmE, are required for function supporting a model for the interaction of Erm family enzymes with substrate rRNA	16
The catalytic-dead Pcif1 regulates gene expression and fertility inDrosophila	16
Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2	16
Implications for OLE RNA as a natural integral membrane RNA	15
Double-stemmed and split structural variants of fluorescent RNA Mango aptamers	15
The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to zinc toxicity	15

Functional analysis of the zinc finger modules of theSaccharomyces cerevisiaesplicing factor Luc7	15
Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription	15
Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations	14
Walter Keller (1938–2023): a tribute from his mentees	14
EDC4 C-terminal domain scaffolds P-body assembly and links P-body dynamics to p53-mediated tumor suppression	14
Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	14
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning	14
OpenASO: RNA Rescue—designing splice-modulating antisense oligonucleotides through community science	14
Solution Structure Determination and Biophysical Studies of 7SK RNP and 7SL SRP RNAs	14
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex	14
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability	13
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations	13
DNMT1 inhibition by pUG-fold quadruplex RNA	13
Corrigendum: Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay	13
Chemical manipulation of m¹A mediates its detection in human tRNA	13
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	13
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	13
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat	13
The importance of m⁶A topology in chicken embryo mRNA: a precise mapping of m⁶A at the conserved chicken β-actin zipcode	13
The daunting task of modifying ribosomal RNA	13
RNA G-quadruplex structure targeting and imaging: recent advances and future directions	12
Conformational dynamics of the hepatitis C virus 3′X RNA	12
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	12
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity	12
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends	12
Global analysis by LC-MS/MS ofN6-methyladenosine and inosine in mRNA reveal complex incidence	12
The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets, by Thomas R. Cech. 2024. W.W. Norton & Company	11
The unfolding landscape of RNA and disease	11
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns	11
Molecular basis of human polyA polymerase recruitment by mPSF	11
Targeting splicing factors for cancer therapy	11
Alternative splicing regulation of membrane trafficking genes during myogenesis	11
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	11
ac4C: a fragile modification with stabilizing functions in RNA metabolism	11
Computational design and experimental verification of pseudoknotted ribozymes	11
Study of the RNA splicing kinetics via in vivo 5-EU labeling	11
KRGG1 function in RNA editing inTrypanosoma brucei	11
Understanding the redundant functions of the m⁶A-binding YTHDF proteins	11
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p	11
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae	10
Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs	10
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function	10
Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast	10
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	10
Rational design yields RNA-binding zinc finger domains with altered sequence specificity	10
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis	10
The essential role of architectural noncoding RNANeat1in cold-induced beige adipocyte differentiation in mice	10
RNA gain-of-function mechanisms in short tandem repeat diseases	10
Cytoplasmic regulation of the poly(A) tail length as a potential therapeutic target	10
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes	10
RNA sequence and structure control assembly and function of RNA condensates	10
RNA aptamers as tools for the purification and analysis of in vivo assembled Ribonucleoproteins	10
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server	10
Promiscuous RNA editing in lncRNA roX1 is generally non-adaptive	10
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea	10
SnoRNA guide activities: real and ambiguous	10
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA	10
Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of theBDF2mRNA	10