linkstream2 microblog

CRAVAT
Cancer-Related Analysis of VAriants Toolkit
http://www.cravat.us/

Carter H, Douville C, Yeo G, Stenson PD, Cooper DN, Karchin R (2013) Identifying Mendelian disease genes with the Variant Effect Scoring Tool
BMC Genomics. In press

VAAST
http://www.yandell-lab.org/software/vaast.html
(explicit acknowledgement of VAT)

CHASM and SNVBox:
toolkit for detecting biologically important single nucleotide mutations in cancer.
http://www.ncbi.nlm.nih.gov/pubmed/21685053
http://www.chasmsoftware.org

==
http://lane.compbio.cmu.edu/meetings/apga/

http://ecerami.github.io/vogelstein-v-lander-round1.html
Short list of 140 drivers v an ever growing list

Science. 2013 Mar 29;339(6127):1546-58. doi: 10.1126/science.1235122. Cancer genome landscapes.
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW. QT:”
To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance.
”

Lessons from the Cancer Genome
http://www.cell.com/abstract/S0092-8674(13)00288-2
QT:”
Systematic studies of the cancer genome have exploded in recent years. These studies have revealed scores of new cancer genes, including many in processes not previously known to be causal targets in cancer. “

http://www.nytimes.com/2013/05/02/health/dna-research-points-to-new-insight-into-cancers.html?pagewanted=all&_r=0

http://ecerami.github.io/vogelstein-v-lander-round1.html

http://www.nature.com/nature/journal/v497/n7447/full/nature12065.html

http://www.nytimes.com/2013/04/22/health/patients-genes-seen-as-future-of-cancer-care.html Features new WCMC Belfer building

http://www.nytimes.com/2013/04/28/business/in-cancer-treatment-new-dna-tools.html?smid=tw-nytimesscience&seid=auto&_r=0

http://www.nytimes.com/2013/04/22/health/patients-genes-seen-as-future-of-cancer-care.html

http://genome.cshlp.org/content/21/12/2004.long
initial cnv eqtls

Gencode perspective on massspec of pseudogenes
http://www.nature.com/nmeth/journal/v8/n6/full/nmeth0611-448b.html