linkstream2 microblog

Dataset of 100 freely available STAD T/N pairs

http://www.nature.com/ng/journal/v46/n6/full/ng.2983.html#affil-auth

Kai Wang,
Siu Tsan Yuen,
Jiangchun Xu,
Siu Po Lee,
Helen H N Yan,
Stephanie T Shi,
Hoi Cheong Siu,
Shibing Deng,
Kent Man Chu,
Simon Law,
Kok Hoe Chan,
Annie S Y Chan,
Wai Yin Tsui,
Siu Lun Ho,
Anthony K W Chan,
Jonathan L K Man,
Valentina Foglizzo,
Man Kin Ng,
April S Chan,
Yick Pang Ching,
Grace H W Cheng,
Tao Xie,
Julio Fernandez,
Vivian S W Li,
Hans Clevers,
Paul A Rejto,
Mao Mao
& Suet Yi Leung

Nature Genetics 46, 573–582 (2014) doi:10.1038/ng.2983Received 01 August 2013 Accepted 18 April 2014 Published online 11 May 2014

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

– how to expand beyond 12 tumors?
– reclassification of lung squam. lung adeno. & subdivisions of breast cancer

Hoadley et al. … Stuart

http://www.sciencedirect.com/science/article/pii/S0092867414008769?via=ihub

“mutsig2CV”

http://www.ncbi.nlm.nih.gov/pubmed/24390350

MutSig – 1.0 – Getz et al. Science 2007
MutSigCV – CV – covariates
mutations need to cluster at hotspots & in functional regions

http://www.sciencemag.org/content/317/5844/1500.2

Science 14 September 2007:
Vol. 317 no. 5844 p. 1500
DOI: 10.1126/science.1138764

TECHNICAL COMMENTS

Comment on “The Consensus Coding Sequences of Human Breast and Colorectal Cancers”

Gad Getz1,*,†,
Holger Höfling2,*,
Jill P. Mesirov1,
Todd R. Golub1,3,4,5,6,
Matthew Meyerson1,3,
Robert Tibshirani2,7,
Eric S. Lander1,6,8

contains a mechanisms pipeline, similar to breakseq

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704973/#!po=42.5926

Cell. Author manuscript; available in PMC May 9, 2014.
Cell. May 9, 2013; 153(4): 919–929.
doi: 10.1016/j.cell.2013.04.010
PMCID: PMC3704973
NIHMSID: NIHMS475485

Diverse mechanisms of somatic structural variations in human cancer genomes Lixing Yang,1 Lovelace J. Luquette,1 Nils Gehlenborg,1,2 Ruibin Xi,1 Psalm S. Haseley,1,3 Chih-Heng Hsieh,4Chengsheng Zhang,4 Xiaojia Ren,3 Alexei Protopopov,5 Lynda Chin,5 Raju Kucherlapati,3,6 Charles Lee,4 and Peter J. Park1,3,7,*

The DNA Data Deluge
http://spectrum.ieee.org/biomedical/devices/the-dna-data-deluge

Predicting Social Security numbers from public data
http://www.pnas.org/content/106/27/10975.abstract

Global Alliance for Genomics and Health Github
https://github.com/ga4gh

http://genomebiology.com/2010/11/8/r83