Posts Tagged ‘rna’

Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data: Biophysical Journal

August 18, 2018

Modeling RNA Secondary Structure with Sequence Comparison &
Experimental Mapping Data
https://www.Cell.com/biophysj/fulltext/S0006-3495(17)30689-6 combines TurboFold sec. structure prediction w/ results of SHAPE assays

Zhen Tan
Gaurav Sharma
David H. Mathews

Open Archive Published:July 20, 2017
DOI:https://doi.org/10.1016/j.bpj.2017.06.039

Jclub Paper

January 28, 2017

#RNA Struc. Determinants of Optimal Codons…by MAGESeq
http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4 Probing effect of synonymous changes; towards a better dN/dS

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4

Genome sequence-independent identification of RNA editing sites : Nature Methods : Nature Publishing Group

March 21, 2015

Genome sequence-independent identification of #RNA editing
siteshttp://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3314.html GIREMI uses LD to separate edit sites from #SNPs

Qing Zhang
& Xinshu Xiao

Nature Methods (2015) doi:10.1038/nmeth.3314Received

The go-between: Life’s unexpected messenger – life – 15 September 2014 – New Scientist

October 3, 2014

The go-between: Life’s unexpected
messengerhttp://www.newscientist.com/article/mg22329860.400-the-gobetween-lifes-unexpected-messenger.html Overview connecting many flavors of #RNA – ie RNAi, siRNA, miRNA & @exRNA

Some bits unclear though – in relation to boundaries betw. siRNA & exRNA

QT:{{”

The RNA in cells is far more mobile than we thought (Image: Renaud Vigourt)

Far from staying put, RNA – the less famous cousin of DNA – can roam far afield, carrying information to other cells in the body and even to other animals

UNDER the soil of the cornfield, the rootworm larvae emerge from their eggs and crawl in search of roots to munch on. But their mother chose the wrong field to lay her eggs in. There’s something special about the maize here – it’s armed with a smart weapon designed to target the rootworms.

As the larvae feed, this weapon is released from the plant and enters their gut cells. There it halts production of a vital protein by blocking one specific gene. In the hours that follow, this “gene silencing” weapon spreads to other cells in the larvae’s bodies. At first there is no …

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News & Analysis Cell Biology: NIH Effort Gambles on Mysterious Extracellular RNAs feedly

September 2, 2013

New $17M program exploring mysterious extracellular #RNA: defining its action, collecting #bigdata http://scim.ag/18nWSyU MT @lopezjenniferw

http://www.sciencemag.org/content/341/6149/947.full

[News & Analysis] Cell Biology: NIH Effort Gambles on Mysterious Extracellular RNAs
A $17 million research program, announced this month by the U.S. National Institutes of Health, aims to determine whether RNA molecules are deliberately released by cells as hormonelike signals—and whether such extracellular RNAs can be harnessed for diagnosis and treatment of human diseases.
Author: Mitch Leslie

HITS-CLIP: panoramic views of protein-RNA regulation in living cells

December 22, 2012

Nice overview of Clipseq/HITS-CLIP
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222227/
QT:”
This advantage relates to the mechanism of UV-mediated crosslinking, which, although incompletely understood, is believed to involve absorption of UV light by nucleic acid bases44 to induce ground state electrons to a singlet higher-energy state that enables the electron to partake in a chemical reaction in which a new covalent bond is formed…