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 2021-02-01 to 2025-02-01.)

Article	Citations
A Role for SNU66 in Maintaining 5’ Splice Site Identity During Spliceosome Assembly	74
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity	72
Turn-on RNA Mango Beacons fortrans-acting fluorogenic nucleic acid detection	68
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors	52
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability	51
Cellular translational enhancer elements that recruit eukaryotic initiation factor 3	49
The daunting task of modifying ribosomal RNA	48
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p	46
RNA in biological condensates	45
Walter Keller (1938–2023): a tribute from his mentees	43
In vitro methylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome	40
Direct dsRNA preparation by promoter-free RCT and RNase H cleavage using one circular dsDNA template with a mismatched bubble	38
Unique anticodon loop conformation with the flipped-out wobble nucleotide in the crystal structure of unbound tRNA^Val	37
Splicing efficiency of minor introns in a mouse model of SMA predominantly depends on their branchpoint sequence and can involve the contribution of major spliceosome components	37
Recollections: Yasuhiro Furuichi (1940–2022)	37
HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs	36
Suppression of theEscherichia coli rnpA49conditionally lethal phenotype by different compensatory mutations	30
A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3′-end processing	30
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis	29
A crescendo of competent coding (c3) contains the Standard Genetic Code	29
Motifs in SARS-CoV-2 evolution	29
Genome-wide kinetic profiling of pre-mRNA 3′ end cleavage	28
Tho2 is critical for the recruitment of Rrp6 to chromatin in response to perturbed mRNP biogenesis	27
Impact on splicing inSaccharomyces cerevisiaeof random 50-base sequences inserted into an intron	26
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning	25

Rational design of eukaryotic riboswitches that up-regulate IRES-mediated translation initiation with high switching efficiency through a kinetic trapping mechanism in vitro	24
Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia	24
Single-molecule RNA in situ detection in clinical FFPE tissue sections by vsmCISH	23
Computational design and experimental verification of pseudoknotted ribozymes	23
Enhanced ac4C detection in RNA via chemical reduction and cDNA synthesis with modified dNTPs	23
The importance of m⁶A topology in chicken embryo mRNA: a precise mapping of m⁶A at the conserved chicken β-actin zipcode	23
Erratum: Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	23
Molecular basis for GIGYF–TNRC6 complex assembly	23
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	21
What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?	20
Oppositional poly(A) tail length regulation by FMRP and CPEB1	20
A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its function in hematopoietic differentiation	19
Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3′ splice site usage	19
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2	18
Function and mechanism of action of the small regulatory RNA ArcZ inEnterobacterales	18
Structural analysis of MALAT1 long noncoding RNA in cells and in evolution	18
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis	18
Molecular basis for the recognition of the AUUAAA polyadenylation signal by mPSF	18
The Prp19C subunit Syf2 and the Prp19C-associated protein Cwc15 function in TREX occupancy and transcription elongation	18
Hammerhead ribozyme-based U-insertion and deletion RNA editing assays for multiplexing in HTS applications	18
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex	17
Balanced cell division is secured by two different regulatory sites in OxyS RNA	17
Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions	17
Correlated sequence signatures are present within the genomic 5′UTR RNA and NSP1 protein in coronaviruses	17
RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions	16
Widespread destabilization ofCaenorhabditis elegansmicroRNAs by the E3 ubiquitin ligase EBAX-1	16
Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis	16
VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets	15
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	15
Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data	15
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments	15
N6-methyladenosine reader YTHDF2 in cell state transition and antitumor immunity	15
RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells	15
Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1	15
RNA therapeutics	15
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions	15
Processing and decay of 6S-1 and 6S-2 RNAs inBacillus subtilis	15
Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes inBacillus subtilis	15
Applications and future of aptamers that achieve rapid-onset anticoagulation	14
ac4C: a fragile modification with stabilizing functions in RNA metabolism	14
Structure and mechanism of Mycobacterium smegmatis polynucleotide phosphorylase	14
Conformational dynamics of the hepatitis C virus 3′X RNA	14
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)	14
A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammals	14
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends	14
Chemical manipulation of m¹A mediates its detection in human tRNA	14
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat	14
Widespread genetic heterogeneity of human ribosomal RNA genes	14
Alternative splicing factors and cardiac disease: more than just mis-splicing?	13
Global analysis by LC-MS/MS of N6-methyladenosine and inosine in mRNA reveal complex incidence	13

The landscape of translational stall sites in bacteria revealed by monosome and disome profiling	13
Weak multivalent biomolecular interactions: a strength versus numbers tug of war with implications for phase partitioning	13
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns	13
RNA sensing at the crossroads of autoimmunity and autoinflammation	13
RNALigands: a database and web server for RNA–ligand interactions	13
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	13
bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling	12
Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein	12
Histone lysine demethylase KDM5B facilitates proliferation and suppresses apoptosis in human acute myeloid leukemia cells through the miR-140-3p/BCL2 axis	12
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations	12
DNMT1 inhibition by pUG-fold quadruplex RNA	12
Understanding the redundant functions of the m⁶A-binding YTHDF proteins	12
The ribosome epitranscriptome: inert—or a platform for functional plasticity?	12
The role of stress-activated RNA–protein granules in surviving adversity	12
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging	11
Nanopore sequencing of internal 2′-PO₄modifications installed by RNA repair	11
Kinetic dissection of pre-crRNA binding and processing by CRISPR–Cas12a	11
New reporters for monitoring cellular NMD	11
Meeting report ASOBIOTICS 2024: an interdisciplinary symposium on antisense-based programmable RNA antibiotics	11
The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets, by Thomas R. Cech. 2024. W.W. Norton & Company	11
Characterization of tRNA splicing enzymes RNA ligase and tRNA 2′-phosphotransferase from the pathogenic fungi Mucorales	11
Alternative splicing regulation of cell-cycle genes by SPF45/SR140/CHERP complex controls cell proliferation	11
Study of the RNA splicing kinetics via in vivo 5-EU labeling	11
bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures	10
Vault RNA1–1 riboregulates the autophagic function of p62 by binding to lysine 7 and arginine 21, both of which are critical for p62 oligomerization	10
KRGG1 function in RNA editing inTrypanosoma brucei	10
AptaDB: a comprehensive database integrating aptamer–target interactions	10
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast	10
Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing inC. elegans	10
Annotation of the local context of RNA secondary structure improves the classification and prediction of A-minors	10
Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria	10
Exploring the targeting spectrum of rocaglates among eIF4A homologs	10
Molecular basis of human polyA polymerase recruitment by mPSF	10
Corrigendum: Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity	10
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	10
Phase-separated ribosome-nascent chain complexes in genotoxic stress response	9
Evolutionary divergence of Firre localization and expression	9
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells	9
IsoSplitter: identification and characterization of alternative splicing sites without a reference genome	9
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations	9
Mouse nuclear RNAi-defective 2 promotes splicing of weak 5′ splice sites	9
miR-7 is recruited to the high molecular weight RNA-induced silencing complex in CD8⁺T cells upon activation and suppresses IL-2 signaling	9
Ancestry of RNA/RNA interaction regions within segmented ribosomes	9
Fission yeast poly(A) polymerase active site mutation Y86D alleviates therad24Δasp1-H397Asynthetic growth defect and up-regulates mRNAs targeted by MTREC and Mmi1	9
Corrigendum: Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells	9
A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication	9
Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA	9
Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance	9
Analysis of GTP addition in the reverse (3′–5′) direction by human tRNA^His guanylyltransferase	9
A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex	9
Fusion protein EWS-FLI1 is incorporated into a protein granule in cells	8
High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules	8
NUCLEAR RNA-BINDING PROTEINS MEET CYTOPLASMIC VIRUSES	8
Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms	8
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae	8
Biochemical and genetic dissection of the RNA-binding surface of the FinO domain ofEscherichia coliProQ	8
Alternative splicing regulation of membrane trafficking genes during myogenesis	8
In vivo PIWI slicing in mouse testes deviates from rules established in vitro	8
A novel reporter for helicase activity in translation uncovers DDX3X interactions	8
Extracellular N⁶-isopentenyladenosine (i⁶A) addition induces cotranscriptional i⁶A incorporation into ribosomal RNAs	8
Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing	8
Methylation guide RNAs without box C/D motifs	8
Thermodynamic control of mismatch discrimination for extensive splicing regulation of PKM pre-mRNA	8
Positive strand RNA viruses differ in the constraints they place on the folding of their negative strand	8