linkstream2 microblog

Data compression for sequencing data
http://www.almob.org/content/8/1/25

An Empirical Analysis of Topic Modeling for Mining Cancer Clinical Notes http://www.computer.org/csdl/proceedings/icdmw/2013/3142/00/3143a056-abs.html

Shimizu cites: Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT)
http://bioinformatics.oxfordjournals.org/content/30/9/1266.long

#Network Legos: Building Blocks of Cellular Wiring Diagrams
http://online.liebertpub.com/doi/abs/10.1089/cmb.2007.0139 Active subnets from protein interactions & co-expression

This paper describes a top-down, set-theoretic approach to comparing gene expression network dynamics under multiple conditions. The method takes an input “wiring diagram” of gene interactions as well as gene expression datasets, which are used to derive interaction profiles composed of enriched genes. Sets of these interaction profiles are used to identify statistically significant “network blocks”
representing network modules underlying the various enriched profiles. These blocks are then organized in a directed acyclic graph in order to identify “network legos”, which represent the most fundamental building blocks of the enriched gene expression networks. The authors demonstrate the utility of the method by identifying a differentially enriched pathway in various forms of leukemia and finding common network modules activated by two human cell types in response to different cellular stresses.

http://online.liebertpub.com/doi/abs/10.1089/cmb.2007.0139

The genomic landscape of #Neanderthal ancestry in…humans
http://www.nature.com/nature/journal/v507/n7492/full/nature12961.html Regions enriched & depleted in ancient alleles, from 1000G

1004 indiv. => 1000G phase 1

QT:{{”
Here, we have systematically inferred Neandertal haplotypes in the genomes of 1,004 present-day humans. Regions that harbor a high frequency of Neandertal alleles in modern humans are enriched for genes affecting keratin filaments suggesting that Neandertal alleles may have helped modern humans adapt to non-African environments. Neandertal alleles also continue to shape human biology, as we identify multiple Neandertal-derived alleles that confer risk for disease. We also identify regions of millions of base pairs that are nearly devoid of Neandertal ancestry and enriched in genes, implying selection to remove genetic material derived from Neandertals. “}}

Curation of gene–mutation relations… automated extraction &
#crowdsourcing http://database.oxfordjournals.org/content/2014/bau094.abstract?ct $AMZN’s turkers help to get 90% accuracy

http://www.biomedcentral.com/1471-2105/9/205

http://ajcn.nutrition.org/content/97/1/127.long

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3314570 as ref. to current annotation in human

http://biorxiv.org/content/early/2014/08/19/008144