Posts Tagged ‘#genomics’

Genome-wide signals of positive selection in human evolution

April 6, 2014

http://genome.cshlp.org/content/early/2014/03/11/gr.164822.113.abstract

“We further demonstrate that the observed signatures of positive selection correlate better with the presence of regulatory sequences, as predicted by the ENCODE Project Consortium, than with the positions of amino acid substitutions. Our results suggest that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson that adaptive divergence is primarily driven by regulatory changes.”

Similar to conclusion positive-section section in FunSeq paper

paper on cancer driver genes in RECOMB 2014

April 6, 2014

paper from RECOMB 2014 might be interesting to you, which uses
hitting time in random walk to identify cancer drivers.

http://link.springer.com/chapter/10.1007%2F978-3-319-05269-4_23

HIT.nDRIVE: Multi-Driver Gene Prioritization based on Hitting Time

Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas
Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin,
Colin Collins, Gholamreza Haffari and S. Cenk Sahinalp.

GigaDB Dataset – DOI 10.5524/100034 – Hepatocellular carcinoma genomic data from the Asia Cancer Research Group.

March 28, 2014

Looks like 88 freely available liver cancer genome datasets
http://gigadb.org/dataset/100034

GigaScience | Full text | The rise of a digital immune system

March 27, 2014

http://www.gigasciencejournal.com/content/1/1/4

2 new FANTOM papers

March 27, 2014

QT:{{”
The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify
cell-type-specific and ubiquitous enhancers.
“}}

A promoter-level mammalian expression atlas
http://www.nature.com/nature/journal/v507/n7493/full/nature13182.html

An atlas of active enhancers across human cell types and tissues http://www.nature.com/nature/journal/v507/n7493/full/nature12787.html

het/hom

March 24, 2014

het/hom ratio = ~1.5
in the sequencing of many Asian individuals (Table 1)

http://www.nature.com/ng/journal/v43/n8/fig_tab/ng.872_T1.html

From
Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals
Nature Genetics 43, 745-752 (2011) doi:10.1038/ng.872

Technology: The $1,000 genome : Nature News & Comment

March 22, 2014

Big success for an NHGRI program

http://www.nature.com/news/technology-the-1-000-genome-1.14901

Nature’s Second Act | September 2, 2013 Issue – Vol. 91 Issue 35 | Chemical & Engineering News

March 17, 2014

Nature’s Second Act: Nice overview of the resurgence in
#pharmaceutical discovery from meta & microbial #genomics
http://cen.acs.org/articles/91/i35/Natures-Second-Act.html

Broad Institute’s Firehose Dashboard

March 17, 2014

Contains information on analysis pipelines and datasets produced from Broad’s Firehose. Access to the protected pages requires an NCI login.

https://confluence.broadinstitute.org/display/GDAC/Home

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

March 3, 2014

PARADIGM-SHIFT predicts… function of mutations in… #cancers using pathway[s]. #Network-based gene prioritization
http://bioinformatics.oxfordjournals.org/content/28/18/i640