linkstream2 microblog

the "circle of life"

http://www.sciencedirect.com/science/article/pii/S0960982214001547#

Volume 24, Issue 6, pR238–R240, 17 March 2014

Evolution: Dynamics of De Novo Gene Emergence

Rafik Neme
Diethard Tautz

DOI: http://dx.doi.org/10.1016/j.cub.2014.02.016

Server for predicting damaging missense #mutations
http://www.nature.com/nmeth/journal/v7/n4/full/nmeth0410-248.html Polyphen2 uses both structure & sequence (eg ASA & conservation)

http://www.ncbi.nlm.nih.gov/pubmed/20354512

Polyphen2 includes both structural and sequence features to predict the effect of nonsynonymous substitutions on protein function. Similar to many other methods, Polyphen2 uses evolutionary conservation as one of the features to identify functionally important residues. Integration of 3D-structure, membrane-specific features (PHAT matrix for TM regions) and other features such as protein-domain and active-site are the strengths of Polyphen2 compared to other sequence-based software making it a good tool for prediction.

http://www.nature.com/nature/journal/v505/n7483/full/nature12981.html?WT.ec_id=NATURE-20140116

NYT recently ran an article as well:
http://www.nytimes.com/2014/04/08/business/cancer-analysis-tools-circumvent-biopsies.html

http://www.nature.com/nm/journal/v20/n4/abs/nm.3511.html

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage
http://www.nature.com/nm/journal/vaop/ncurrent/abs/nm.3519.html

http://stm.sciencemag.org/content/6/224/224ra24
http://www.nejm.org/doi/full/10.1056/NEJMoa1213261

http://stm.sciencemag.org/content/4/162/162ra154.full
DIAGNOSTICS: Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing

Variant Association Tools for Quality Control and Analysis of Large-Scale Sequence and Genotyping Array Data

http://www.cell.com/ajhg/abstract/S0002-9297(14)00176-1

vs

http://papers.gersteinlab.org/papers/vat

http://www.nature.com/ncomms/2014/140409/ncomms4644/full/ncomms4644.html

From the following article:
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium
Nature 409, 860-921(15 February 2001)
doi:10.1038/35057062

Alu age distribution

http://www.nature.com/nature/journal/v409/n6822/fig_tab/409860a0_F18.html

Integrating genotype from many callers & indication of where they differ. Might be useful for the personal diploid genome.
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2835.html

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001744

http://www.gigasciencejournal.com/content/2/1/15