linkstream2 microblog

Large-scale genomic datasets can easily be transformed into various networks. The authors aimed to infer for each particular edge, whether or not it shows up in a particular tissue by training a model based on well curated tissue-specific expression as gold standards. The algorithm arrives at different tissue-specific networks from large-scale genomics datasets; without surprise, tissue-specific networks are more informative in predicting genes corresponding to diseases related to that particular tissue. For instance, a
testis-specific network performs better in predicting genes associated with male fertility phenotypes.

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002694 PLoS Comput Biol. 2012 Sep;8(9):e1002694.
doi: 10.1371/journal.pcbi.1002694. Epub 2012 Sep 27.
Tissue-specific functional networks for prioritizing phenotype and disease genes.
Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MA, Bult CJ, Hibbs MA, Troyanskaya O

http://www.nytimes.com/2012/10/16/science/affective-programming-grows-in-effort-to-read-faces.html?_r=2&ref=science&pagewanted=all&

This paper introduces a new method for detecting copy number variants in cancer genomes that addresses deficiencies of previous detection methods. The new method, dubbed HHCRF by the authors, adds the use of sequential correlations in selecting classification features for inferring copy numbers and identifying clinically relevant genes. This improvement results in higher accuracy on noisy data, and the identification of more clinically relevant genes, relative to previous methods. These results were obtained by testing HHCRF on both simulated array-CGH microarray data, and on actual breast cancer, uveal melanoma, and bladder tumor datasets.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677736/
Bioinformatics. 2009 May 15;25(10):1307-13. Epub 2008 Dec 3. Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.
Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG.

http://www.artinfo.com/news/story/838275/after-the-flood-how-will-hurricane-sandy-change-new-yorks-art

http://pubs.acs.org/doi/abs/10.1021/cen-v088n014.p036

lots of GC & nmr on things like wine

http://gigaom.com/data/graph-startup-neo-raises-11m-as-specialized-databases-take-hold
see open-source graph nosql DB : http://neo4j.org/

http://nymag.com/nymag/letters/hurricane-sandy-editors-letter-2012-11

http://www.ncbi.nlm.nih.gov/pubmed/22825316

Hum Genet. 2012 Oct 10.
Ostrer H, Skorecki K.
Departments of Pathology and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
http://www.ncbi.nlm.nih.gov/pubmed/23052947

Admixture analysis

http://gigaom.com/data/graph-startup-neo-raises-11m-as-specialized-databases-take-hold