Tomasetti & Volgenstein
Science 2 January 2015:
Vol. 347 no. 6217 pp. 78-81
DOI: 10.1126/science.1260825
It’s a correlation between aggressiveness, mutations and cell division http://www.sciencemag.org/content/347/6217/78
Posts Tagged ‘cancer’
Variation in cancer risk among tissues can be explained by the number of stem cell divisions
January 12, 2015Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types : Nature Genetics : Nature Publishing Group
January 8, 2015Analysis of noncoding somatic mutations &…expression alterations http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html 505 WGS variants w. RNAseq, #TCGA as of Mar ’14
all of what’s in TCGA as of spring ’14
505 TCGA WGS Somatic mutations, Expression Calls, CNA
via
https://www.synapse.org/#!Synapse:syn2882200
Orthogonal to PCAWG-607 (Alexandrov et al + 100 "public" stomach cancers)
Cereal killer: Are you eating too much iron? – health – 04 December 2014 – Test – New Scientist
December 31, 2014Cereal killer: Are you eating too much iron? http://www.newscientist.com/article/mg22429980.500-cereal-killer-are-you-eating-too-much-iron.html Too much from vitamins is potentially linked to heart disease, cancer &c
Can AIDS Be Cured? | The New Yorker
December 24, 2014Can #AIDS Be Cured? http://www.newyorker.com/magazine/2014/12/22/can-aids-cured Now a chronic disease, treatable w/ HAART cocktails? Parallels w/ cancer evolution & resistance
MEDICAL DISPATCH DECEMBER 22, 2014 ISSUE
CAN AIDS BE CURED?
Researchers get closer to outwitting a killer.
BY JEROME GROOPMAN
BMC Bioinformatics | Abstract | Sensitive detection of pathway perturbations in cancers
December 23, 2014Sensitive detection of pathway perturbations in #cancers
http://www.biomedcentral.com/1471-2105/13/S3/S9/abstract Differential expression of #pathways (in toto or a sub-part)
** Sensitive detection of pathway perturbations in cancers. Rivera et al. BMC Bioinfo (2014)
In this paper, the authors introduce a new computational method that identifies subsets of pathways that exhibit differential gene expression between cancer and normal tissue. Some previous methods only considered differential expression in sets of genes without considering the structure of interactions between the genes or their protein products. Other previous methods looked at pathway
perturbations, but required all members of a pathway to exhibit differential gene expression in order for the pathway to appear significant. The authors demonstrate the general superiority of their method to these previous methods, as well as the robustness of their method to missing data. The authors also consider future enhancements, such as taking into account the direction of differential expression, using more information on the nature of each gene interaction involved, and using universal protein interaction networks to incorporate data beyond what is found in curated pathway databases.
interesting article
December 15, 2014Bioinformatics. Sep 15, 2013; 29(18): 2223–2230.
Published online Jul 9, 2013. doi: 10.1093/bioinformatics/btt375 PMCID: PMC3753564
A comparative analysis of algorithms for somatic SNV detection in cancer
Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer
November 20, 2014Dataset 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
Phenotypic impact of genomic structural variation: insights from and for human disease : Abstract : Nature Reviews Genetics
October 13, 2014Clonal evolution in breast cancer revealed by single nucleus genome sequencing : Nature : Nature Publishing Group
October 13, 2014Realizing the promise of cancer predisposition genes : Nature : Nature Publishing Group
October 13, 2014Realizing the promise of cancer predisposition genes : Nature : Nature Publishing Group
http://www.nature.com/nature/journal/v505/n7483/full/nature12981.html
@markgerstein: .@rahman_nazneen mentions: Realizing the promise of cancer predisposition genes [of which there’s >100]
http://t.co/BbGNK6VJko #BTGCG14
linkstream2 microblog 