Archive for the 'SciLit' Category

Nuclear reaction

November 22, 2014

Nuclear reaction
http://www.economist.com/news/science-and-technology/21630959-how-complex-cells-evolved-mystery-new-idea-may-come-close Hypothesis from BMC paper on #evolution of eukaryotes from membrane blebs (http://www.biomedcentral.com/1741-7007/12/76)

An inside-out origin for the eukaryotic cell

David A Baum and Buzz Baum

BMC Biology 2014, 12:76 doi:10.1186/s12915-014-0076-2

QT:{{”

The consensus is that the first eukaryote was a prokaryote which engulfed, but failed on several occasions to digest, other
prokaryotes. One of these undigested meals was a bacterium ancestral to mitochondria. Even today mitochondria have their own genes separate from those in the nucleus. These genes, which are carried on circular DNA molecules like those in bacteria, resemble those in a group of bacteria called Rickettsiales,
…
They imagine the original host prokaryote creating small protrusions, known to microbiologists as blebs, that poked out of it, as the diagram shows, like tiny fingers. Blebs like this are known to form in certain sorts of archaea, a group of prokaryotes distinct from bacteria proper that biochemical evidence suggests were involved in the formation of eukaryotes. The job of blebs is unclear, as archaea are not a well-studied group, but they may be feeding structures. The Drs Baum suggest that, in the case of the ancestral eukaryote, the blebs grew bigger and bigger, pinning proto-mitochondria (and, on a subsequent occasion, proto-chloroplasts), into the intervening spaces. “}}

A case study for cloud based high throughput analysis of NGS data using the globus genomics system

November 21, 2014

http://www.sciencedirect.com/science/article/pii/S2001037014000427

Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer

November 20, 2014

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

Circle of life

November 15, 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

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Ori gin — ScienceDirect

November 11, 2014

– 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

Discovery and saturation analysis of cancer genes across 21 tumour … – PubMed – NCBI

November 11, 2014

“mutsig2CV”

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

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

November 11, 2014

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

Diverse mechanisms of somatic structural variations in human cancer genomes

November 11, 2014

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 – IEEE Spectrum

November 10, 2014

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

Predicting Social Security numbers from public data

November 10, 2014

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