IsoMiRmap: a tool for profiling isomiRs in short RNA-seq datasets
All possible isomiRs of miR-151a-5p within 3 nts of the endpoints of the miRBase reference miRNA Motivation: MicroRNA (miRNA) precursor…
Research Papers
Summaries of our highlighted papers.
The expression of Ribosomal-RNA-derived fragments (rRFs) is modulated in a sex- and population-specific manner
log2 fold change of iDARs (intersection of differentially abundant rRFs) plotted as a function of significance Ribosomal RNAs (rRNAs) are…
A hormone-dependent tRNA half drives cell cycle progression by destabilizing p21 mRNA
When cells receive growth cues, they must carefully balance pro-proliferative signals with “brakes” that prevent uncontrolled division. In hormone-dependent cancers,…
RNase κ promotes piRNA production by generating 2′,3′-cyclic phosphate (cP-RNA) precursors
In our new publication [1], we show that cP-RNAs serve as piRNA precursors in mouse and silkworm. A mitochondria-associated endoribonuclease,… In vitro production and multiplex quantification of 2′,3′-cyclic phosphate-containing 5′-tRNA half molecules
We synthesized cP-containing 5′-tRNA half molecules and developed a multiplex TaqMan RT-qPCR method which can simultaneously quantify multiple cP-containing 5′-tRNA… Repetitive elements and pyknons in the genes of early development
Genes involved in pluripotency/proliferation have the opposite structure (length, exon count, Alu density and pyknons) than tissue-specific ones. Genes and… A novel role of tRNA half molecules in immune response as activators of TLR7
tRNA half molecules mediate the innate immune response by activating the toll-like receptor TLR7. When a host is infected with… Oxidative stress enhances the expression of 2′,3′-cyclic phosphate-containing RNAs (cP-RNAs)
By using our original cP-RNA-seq, we have revealed comprehensive expression profiles of 2′,3′-cyclic phosphate-containing RNAs (cP-RNAs) in human cells and… Analysis of rRNA fragments (rRFs) from five human populations reveals dependence on personal attributes
We profiled ribosomal RNA fragments (rRFs) in the RNA-seq datasets from the lymphoblastoid cell lines (LCLs) of the 1000 Genomes… First genome-wide identification of short cyclic phosphate-containing RNAs
Our comprehensive identification of 2′,3′-cyclic phosphate-containing RNAs (cP-RNAs) unraveled a novel, abundant class of non-coding RNAs which may play a…