Archive for the 'SciLit' Category

Evolution of the Caenorhabditis elegans Genome

August 10, 2013

this should partially explain the high insertion rate in worm: http://mbe.oxfordjournals.org/content/26/6/1199.full

QT:”
Of the new mutations observed in MA lines, more than half were short indel mutations, with fewer deletions than insertions (Denver, Morris, Lynch, and Thomas 2004). This finding on indels contrasts with previous work with C. elegans pseudogenes in which deletions are more common than insertions (Robertson 2000; Witherspoon and Robertson 2003) but is consistent with findings in C. elegansmicrosatellite mutation data (Frisse 1999; Denver, Morris, Kewalramani, et al. 2004; Seyfert et al. 2008).

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data : Nature Methods : Nature Publishing Group

August 9, 2013

http://www.nature.com/nmeth/journal/v10/n8/full/nmeth.2557.html

FYI: Another Encode Commentary Paper

August 4, 2013

Mattick & Dinger
The extent of functionality in the human genome
http://www.thehugojournal.com/content/7/1/2/

Intrinsically Disordered Proteins in Human Diseases: Introducing the D2 Concept

August 4, 2013

http://www.annualreviews.org/doi/abs/10.1146/annurev.biophys.37.032807.125924

PLOS Collections: A Primer on Regression Methods for Decoding cis-Regulatory Logic

August 4, 2013

#Regression Methods for Decoding cis-Regulatory Logic, incl. interaction terms & non-linear sigmoidal relationships
http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000269

Global Epigenomic Reconfiguration During Mammalian Brain Development

July 27, 2013

Lister… Ecker

MT @BiomedRevon: Global #epigenomic reconfiguration during mammalian #brain development http://bit.ly/16lbboa cortex methylation over time

A “map showing how methylation changes in the frontal cortex over time. During the first two years of life… a wave of methylation alters the DNA in genes ”

http://www.sciencemag.org/content/early/2013/07/05/science.1237905

PLOS Computational Biology: A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

July 27, 2013

http://www.ploscompbiol.org/article/info%253Adoi%252F10.1371%252Fjournal.pcbi.1000770

An Information-Theoretic Machine Learning Approach to Expression QTL Analysis

July 26, 2013

An Information-Theoretic Machine Learning Approach to Expression QTL Analysis Tao Huang, Yu-Dong Cai
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0067899

The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

July 20, 2013

The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology
Cancer Res July 15, 2013 73:4372-4382; Published OnlineFirst July 15, 2013; http://cancerres.aacrjournals.org/content/73/14/4372.long

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

July 18, 2013

http://www.pnas.org/content/110/29/11952