BMC Bioinformatics | Full text | Inferring clonal evolution of tumors from single nucleotide somatic mutations
http://www.biomedcentral.com/1471-2105/15/35
Archive for the 'SciLit' Category
BMC Bioinformatics | Full text | Inferring clonal evolution of tumors from single nucleotide somatic mutations
December 15, 2014interesting 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
twin ASEs
December 15, 2014http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3162.html
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins
Alfonso Buil,
Andrew Anand Brown,
Tuuli Lappalainen,
Ana Viñuela,
Matthew N Davies,
Hou-Feng Zheng,
J Brent Richards,
Daniel Glass,
Kerrin S Small,
Richard Durbin,
Timothy D Spector
& Emmanouil T Dermitzakis
hi-C for 9 cell types
December 14, 2014A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Suhas S.P. Rao
,Miriam H. Huntley
Neva C. Durand
Elena K. Stamenova
Ivan D. Bochkov
James T. Robinson
Adrian L. Sanborn
Ido Machol
Arina D. Omer
Eric S. Lander
Erez Lieberman Aiden
DOI: http://dx.doi.org/10.1016/j.cell.2014.11.021
http://www.cell.com/cell/abstract/S0092-8674(14)01497-4
A load driver device for engineering modularity in biological networks : Nature Biotechnology : Nature Publishing Group
December 9, 2014A load driver device for engineering modularity in…#networks http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3044.html Allows joining components w/o downstream retroactivity
Twitter “Exhaust” Reveals Patterns of Unemployment | MIT Technology Review
December 1, 2014Social media fingerprints of unemployment, from detecting network components in tweet mining arxiv.org/abs/1411.3140 +
http://www.technologyreview.com/view/532746/twitter-exhaust-reveals-patterns-of-unemployment
Lots of press for an arxiv paper, viz:
Twitter “Exhaust” Reveals Patterns of Unemployment | MIT Technology Review
QT:{{”
So the team analysed the rate at which messages were exchanged between regions using a standard community detection algorithm. This revealed 340 independent areas of economic activity, which largely coincide with other measures of geographic and economic distribution. “This result shows that the mobility detected from geolocated tweets and the communities obtained are a good description of economical areas,” they say.
Finally, they looked at the unemployment figures in each of these regions and then mined their database for correlations with twitter activity.
“}}
Nuclear reaction
November 22, 2014Nuclear 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, 2014Whole-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
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