Research Papers | Computational Medicine Center at Thomas Jefferson University

Archive by category "Research 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

Our unique RNA-seq method (left panel) revealed RNase κ-engaged piRNA biogenesis pathway, in which the generation of cyclic phosphate-RNAs promotes robust piRNA production (right pabel).

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

Multiplex quantification of 5'-tRNA halves

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 with highest expression at the blastocyst stage are short and dense in Alu elements

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

A proposed model for 5′-tRNA half-mediated immune response

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)

Identification of stress-induced 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

Graphical representations of the length abundances of rRFs for five LCL populations from the 1KG Project

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

Diagram of Generation of cP RNAs and its Age-Dependent Decrease

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…

Mining tRNA-seq data revealed the expression of novel mitochondrial non-coding RNAs

By utilizing YAMAT-seq data, we discovered the expression of novel mitochondrial non-coding RNAs whose expression is regulated by CCA-adding enzyme.…

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