Archive for the ‘SciLit’ Category

hi-C for 9 cell types

Tuesday, December 16th, 2014

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of #Chromatin Looping
http://www.cell.com/cell/abstract/S0092-8674(14)01497-4 HiC data for 9 celltypes

A 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

BMC Bioinformatics | Full text | Inferring clonal evolution of tumors from single nucleotide somatic mutations

Monday, December 15th, 2014

BMC Bioinformatics | Full text | Inferring clonal evolution of tumors from single nucleotide somatic mutations
http://www.biomedcentral.com/1471-2105/15/35

interesting article

Monday, December 15th, 2014

Bioinformatics. 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

Monday, December 15th, 2014

http://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

Sunday, December 14th, 2014

A 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

Tuesday, December 9th, 2014

A 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

Monday, December 1st, 2014

Social 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.

“}}

CRE-Seq paper…

Monday, November 24th, 2014

High-throughput functional testing of ENCODE segmentation
predictionsGenome Res. October 2014 24: 1595-1602; Published in Advance July 17, 2014,

that can be used for training predicted enhancers

http://genome.cshlp.org/content/24/10/1595.full.pdf

Nuclear reaction

Saturday, November 22nd, 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

Friday, November 21st, 2014

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