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 2021-05-01 to 2025-05-01.)

Article	Citations
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis	95
A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3′-end processing	95
Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1	81
Molecular basis for GIGYF–TNRC6 complex assembly	70
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors	69
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)	66
RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells	62
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2	53
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis	51
Motifs in SARS-CoV-2 evolution	48
Oppositional poly(A) tail length regulation by FMRP and CPEB1	48
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging	47
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions	43
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	43
Nuclear RNA-binding proteins meet cytoplasmic viruses	43
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations	41
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2	41
The m6A binding protein YTHDF3 modulates the cardiac response to stress	40
Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity	39
RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type	38
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription	38
Far from home: the role of glial mRNA localization in synaptic plasticity	37
A novel reporter for helicase activity in translation uncovers DDX3X interactions	35
Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering	33
Small noncoding RNA interactome capture reveals pervasive, carbon source–dependent tRNA engagement of yeast glycolytic enzymes	32

The total mRNA concentration buffering system in yeast is global rather than gene-specific	30
A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication	28
Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing	28
Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria	27
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast	27
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells	26
Site-blocking antisense oligonucleotides as a mechanism to fine-tune MeCP2 expression	25
Exploring the targeting spectrum of rocaglates among eIF4A homologs	25
Adenosine deaminases that act on RNA, then and now	24
Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function	23
Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	23
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements	23
Diversity and modularity of tyrosine-accepting tRNA-like structures	23
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes	23
Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin	22
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	22
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations	22
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	21
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP	21
Corrigendum: Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	21
Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes	21
Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining	20
Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities	20
clipplotr—a comparative visualization and analysis tool for CLIP data	20
DDX3X and DDX3Y are redundant in protein synthesis	19
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA	19
Effects of transgene insertion loci and copy number on Dnmt3L gene silencing through antisense transgene-derived PIWI-interacting RNAs	19
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)	19
Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance	19
Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA	19
An incredible life in science: Joseph G. Gall (1928–2024)	19
The m⁶A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication	19
Corrigendum: RNA partitioning into stress granules is based on the summation of multiple interactions	19
Localization of RNAs to the Mitochondria – Mechanisms and Functions	19
The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to zinc toxicity	18
The limits of human microRNA annotation have been met	18
The pseudotorsional space of RNA	18
Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells	18
Boosting the toolbox for live imaging of translation	18
SMDesigner: a program to design sequence mutations to assess RNA structure	18
Functional analysis of the zinc finger modules of theSaccharomyces cerevisiaesplicing factor Luc7	18
Translation elongation inhibitors stabilize select short-lived transcripts	18
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human andDrosophilacells	18
RNA modifications: an overview of select web-based tools	17
Double-stemmed and split structural variants of fluorescent RNA Mango aptamers	17
Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription	17
A piRNA-lncRNA regulatory network initiates responder and trailer piRNA formation during mosquito embryonic development	17
Corrigendum: No evidence for epitranscriptomic m⁵C modification of SARS-CoV-2, HIV, and MLV viral RNA	17
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	17
The catalytic-dead Pcif1 regulates gene expression and fertility inDrosophila	16

Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	16
Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations	16
Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation	16
SARS-CoV-2 infection triggers widespread host mRNA decay leading to an mRNA export block	16
Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2	16
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends	15
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat	15
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex	15
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning	14
Walter Keller (1938–2023): a tribute from his mentees	14
Understanding the redundant functions of the m⁶A-binding YTHDF proteins	14
The daunting task of modifying ribosomal RNA	14
The importance of m⁶A topology in chicken embryo mRNA: a precise mapping of m⁶A at the conserved chicken β-actin zipcode	14
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability	14
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns	14
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p	14
Global analysis by LC-MS/MS ofN6-methyladenosine and inosine in mRNA reveal complex incidence	14
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity	13
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	13
Chemical manipulation of m¹A mediates its detection in human tRNA	13
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations	13
Conformational dynamics of the hepatitis C virus 3′X RNA	13
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	13
DNMT1 inhibition by pUG-fold quadruplex RNA	12
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	12
Molecular basis of human polyA polymerase recruitment by mPSF	12
Computational design and experimental verification of pseudoknotted ribozymes	12
RNA gain-of-function mechanisms in short tandem repeat diseases	12
Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs	12
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	12
ac4C: a fragile modification with stabilizing functions in RNA metabolism	12
The essential role of architectural noncoding RNANeat1in cold-induced beige adipocyte differentiation in mice	12
The unfolding landscape of RNA and disease	12
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server	11
Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs	11
The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets, by Thomas R. Cech. 2024. W.W. Norton & Company	11
IsoSplitter: identification and characterization of alternative splicing sites without a reference genome	11
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae	11
Fusion protein EWS-FLI1 is incorporated into a protein granule in cells	11
Targeting splicing factors for cancer therapy	11
Alternative splicing regulation of membrane trafficking genes during myogenesis	11
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function	11
KRGG1 function in RNA editing inTrypanosoma brucei	11
Study of the RNA splicing kinetics via in vivo 5-EU labeling	11
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis	10
SnoRNA guide activities: real and ambiguous	10
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	10
Theje ne sais quoiof 5-methylcytosine in messenger RNA	10
APOBEC1 mediated C-to-U RNA editing: target sequence and trans-acting factor contribution to 177 RNA editing events in 119 murine transcripts in vivo	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
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA	10
Cytoplasmic regulation of the poly(A) tail length as a potential therapeutic target	10
Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast	10
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea	10
TERRA ONTseq: a long-read-based sequencing pipeline to study the human telomeric transcriptome	9
Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor inSaccharomyces cerevisiae	9
Rational design yields RNA-binding zinc finger domains with altered sequence specificity	9
Localization of unlabeled bepirovirsen antisense oligonucleotide in murine tissues using in situ hybridization and CARS imaging	9
Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3′-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides	9
T1TAdb: the database of type I toxin–antitoxin systems	9
Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders	9
Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of theBDF2mRNA	9
Tribute to Yoshiro Shimura (1932–2023)	9
Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA	9
m6A-ELISA, a simple method for quantifyingN6-methyladenosine from mRNA populations	9
Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development	9
Cross-linking mass spectrometric analysis of the endogenous TREX complex fromSaccharomyces cerevisiae	9
The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression	9
Human T-cell leukemia virus type 1 uses a specific tRNA^Proisodecoder to prime reverse transcription	9
The life and times of a tRNA	9