OOIR: Observatory of International Research

Papers

(The TQCC of RNA is 11. 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 2020-04-01 to 2024-04-01.)

Article	Citations
Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection	401
Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols	215
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look	189
Aminoacyl-tRNA synthetases	183
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers	97
The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation	96
SARS-CoV-2 infection triggers widespread host mRNA decay leading to an mRNA export block	63
The emerging structural complexity of G-quadruplex RNAs	57
RNA partitioning into stress granules is based on the summation of multiple interactions	57
RNA in formation and regulation of transcriptional condensates	53
FISH-quant v2: a scalable and modular tool for smFISH image analysis	46
The virtual circular genome model for primordial RNA replication	39
DDX3X and DDX3Y are redundant in protein synthesis	38
Nanopore sequencing of RNA and cDNA molecules in Escherichia coli	38
Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance	38
Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads	38
Sensing of transposable elements by the antiviral innate immune system	36
Phosphodiester modifications in mRNA poly(A) tail prevent deadenylation without compromising protein expression	34
Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome	33
Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein	31
Long noncoding RNA and protein abundance in lncRNPs	31
Cyclic oligoadenylate signaling and regulation by ring nucleases during type III CRISPR defense	31
The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression	30
Are stress granules the RNA analogs of misfolded protein aggregates?	30
Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein	30

Circulating SNORD57 rather than piR-54265 is a promising biomarker for colorectal cancer: common pitfalls in the study of somatic piRNAs in cancer	28
Nuclease-mediated depletion biases in ribosome footprint profiling libraries	28
Chemical crosslinking enhances RNA immunoprecipitation for efficient identification of binding sites of proteins that photo-crosslink poorly with RNA	28
Elimination of Calm1 long 3′-UTR mRNA isoform by CRISPR–Cas9 gene editing impairs dorsal root ganglion development and hippocampal neuron activation in mice	27
The life and times of a tRNA	27
How do protein domains of low sequence complexity work?	27
RNA multimerization as an organizing force for liquid–liquid phase separation	27
Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot	25
Viral subversion of nonsense-mediated mRNA decay	25
Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA	25
A mark of disease: how mRNA modifications shape genetic and acquired pathologies	24
Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea	24
Structure and ligand binding of the ADP-binding domain of the NAD⁺ riboswitch	23
A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation	23
Recruitment of endoplasmic reticulum-targeted and cytosolic mRNAs into membrane-associated stress granules	23
Physiologic RNA targets and refined sequence specificity of coronavirus EndoU	23
Rampant C-to-U deamination accounts for the intrinsically high mutation rate in SARS-CoV-2 spike gene	23
The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions	23
Argonaute binding within human nuclear RNA and its impact on alternative splicing	23
A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly	22
Nuage condensates: accelerators or circuit breakers for sRNA silencing pathways?	21
Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context–independent	21
Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET	21
Molecular basis for the distinct cellular functions of the Lsm1–7 and Lsm2–8 complexes	21
A second riboswitch class for the enzyme cofactor NAD⁺	21
What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?	21
Cold-inducible RNA binding protein promotes breast cancer cell malignancy by regulating Cystatin C levels	20
Studies with recombinant U7 snRNP demonstrate that CPSF73 is both an endonuclease and a 5′–3′ exonuclease	20
Exploring the epitranscriptome by native RNA sequencing	20
An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7	19
Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing	19
A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs	19
A model for DHX15 mediated disassembly of A-complex spliceosomes	19
The limits of human microRNA annotation have been met	18
Requirement for cleavage factor II_m in the control of alternative polyadenylation in breast cancer cells	18
Validation strategies for antibodies targeting modified ribonucleotides	18
mRNA spindle localization and mitotic translational regulation by CPEB1 and CPEB4	17
Ago2 protects Drosophila siRNAs and microRNAs from target-directed degradation, even in the absence of 2′-O-methylation	17
Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation	17
5-methylcytosine modification of an Epstein–Barr virus noncoding RNA decreases its stability	17
RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes	17
Endosomal escape of RNA therapeutics: How do we solve this rate-limiting problem?	17
Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy	17
Correlated sequence signatures are present within the genomic 5′UTR RNA and NSP1 protein in coronaviruses	17
microRNA-seq of cartilage reveals an overabundance of miR-140-3p which contains functional isomiRs	16
Weak multivalent biomolecular interactions: a strength versus numbers tug of war with implications for phase partitioning	16
Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	16
Using quantitative reconstitution to investigate multicomponent condensates	16
A robust and versatile method for production and purification of large-scale RNA samples for structural biology	16
2′-fluoro-modified pyrimidines enhance affinity of RNA oligonucleotides to HIV-1 reverse transcriptase	16

Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis	16
PAR-TERRA is the main contributor to telomeric repeat-containing RNA transcripts in normal and cancer mouse cells	16
The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2′-O-Me sites	16
Revisiting tRNA chaperones: new players in an ancient game	16
Structure of 3′-PO₄/5′-OH RNA ligase RtcB in complex with a 5′-OH oligonucleotide	15
Pathological phase transitions in ALS-FTD impair dynamic RNA–protein granules	15
tRNA elbow modifications affect the tRNA pseudouridine synthase TruB and the methyltransferase TrmA	15
Ensemble switching unveils a kinetic rheostat mechanism of the eukaryotic thiamine pyrophosphate riboswitch	15
Ribosome profiling reveals novel regulation of C9ORF72 GGGGCC repeat-containing RNA translation	15
Allosteric regulation of U1 snRNP by splicing regulatory proteins controls spliceosomal assembly	15
Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin	15
Splicing conservation signals in plant long noncoding RNAs	15
Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder	15
Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae	15
Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmic PUS10 produce conserved pseudouridine 55 in different sets of tRNA	15
Cotranscriptional splicing efficiencies differ within genes and between cell types	15
Tob2 phosphorylation regulates global mRNA turnover to reshape transcriptome and impact cell proliferation	15
PDCD4 regulates axonal growth by translational repression of neurite growth-related genes and is modulated during nerve injury responses	14
Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis	14
The role of stress-activated RNA–protein granules in surviving adversity	14
An evolutionarily conserved RNA structure in the functional core of the lincRNA Cyrano	14
Specificity in the biosynthesis of the universal tRNA nucleoside N⁶-threonylcarbamoyl adenosine (t⁶A)—TsaD is the gatekeeper	14
Fusion protein EWS-FLI1 is incorporated into a protein granule in cells	14
In vitro studies provide insight into effects of Dicer-2 helicase mutations inDrosophila melanogaster	14
A combinatorially regulated RNA splicing signature predicts breast cancer EMT states and patient survival	14
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations	14
Alternative splicing regulation of cell-cycle genes by SPF45/SR140/CHERP complex controls cell proliferation	14
The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold	13
Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique	13
Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem–loop RNAs and their implications for functional cellular assays	13
RNase H-based analysis of synthetic mRNA 5′ cap incorporation	13
Detection and quantification of glycosylated queuosine modified tRNAs by acid denaturing and APB gels	13
A noncanonical microRNA derived from the snaR-A noncoding RNA targets a metastasis inhibitor	13
Metabolic labeling of RNA uncovers the contribution of transcription and decay rates on hypoxia-induced changes in RNA levels	13
Transfer RNA halves are found as nicked tRNAs in cells: evidence that nicked tRNAs regulate expression of an RNA repair operon	12
Human disease-associated single nucleotide polymorphism changes the orientation of DROSHA on pri-mir-146a	12
Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	12
The total mRNA concentration buffering system in yeast is global rather than gene-specific	12
Folding heterogeneity in the essential human telomerase RNA three-way junction	12
A hybrid deep clustering approach for robust cell type profiling using single-cell RNA-seq data	12
Highly specific, multiplexed isothermal pathogen detection with fluorescent aptamer readout	12
Evaluating DCA-based method performances for RNA contact prediction by a well-curated data set	12
Termi-Luc: a versatile assay to monitor full-protein release from ribosomes	12
Deflating the RNA Mg²⁺ bubble: stereochemistry to the rescue!	12
A piRNA-lncRNA regulatory network initiates responder and trailer piRNA formation during mosquito embryonic development	12
Frameshifting at collided ribosomes is modulated by elongation factor eEF3 and by integrated stress response regulators Gcn1 and Gcn20	12
RNA sequence and structure control assembly and function of RNA condensates	12
Mutations in domain IV of elongation factor EF-G confer −1 frameshifting	12
Widespread genetic heterogeneity of human ribosomal RNA genes	12
Transcription and splicing dynamics during early Drosophila development	11
T1TAdb: the database of type I toxin–antitoxin systems	11
The m⁶A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication	11
RNALigands: a database and web server for RNA–ligand interactions	11
The stem cell–specific protein TRIM71 inhibits maturation and activity of the prodifferentiation miRNA let-7 via two independent molecular mechanisms	11
DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells	11
Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses	11
Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing	11
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments	11
Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)	11
Pdc2/Pat1 increases the range of decay factors and RNA bound by the Lsm1–7 complex	11
An ancient evolutionary connection between Ribonuclease A and EndoU families	11
Validation and classification of RNA binding proteins identified by mRNA interactome capture	11