http://www.genomeweb.com/informatics/bina-wins-1m-va-million-veteran-program-contract
Bina Wins $1M VA Million Veteran Program Contract
October 09, 2014
Posts Tagged ‘from’
Bina Wins $1M VA Million Veteran Program Contract
October 9, 2014iOS 8 How-to: Have your iOS device read text for you | 9to5Mac
October 9, 2014Speak text with ios…
http://9to5mac.com/2014/10/04/ios-8-how-to-have-your-ios-device-read-text-for-you/
Signaling hypergraphs: Trends in Biotechnology
October 9, 2014Signaling #hypergraphs
http://www.cell.com/trends/biotechnology/abstract/S0167-7799(14)00071-7 Edges from interactions of 2 sets of nodes. Better representation of assemblies & #complexes.
QT:{{”
each edge is defined not by interaction of 2 nodes (as in graphs), but 2 sets of nodes (known as hypernodes in hypergraphs)……The use of hypernodes also represents three concepts better than directed or non-directed graphs: protein complexes, protein assemblies and regulation (especially involving complexes/assemblies).
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Signaling hypergraphs. Ritz et al. (2014) TIB
This opinion paper advocates the use of hypergraphs to complement graph-based signaling network and pathway analyses, where each edge is defined not by interaction of 2 nodes (as in graphs), but 2 sets of nodes (known as hypernodes in hypergraphs). They argue that
hypergraphs is a set-based method that acts like a more general version of a graph. The use of hypernodes also represents three concepts better than directed or non-directed graphs: protein complexes, protein assemblies and regulation (especially involving complexes/assemblies). They propose that hypergraphs can be very useful in situations where the effects of individual proteins might be neglected in graphs but will have a noticeable effect when these proteins are included in protein complexes as hypernodes. They use 3 applications as examples: pathway enrichment, pathway reconstruction, and pathway crosstalk.
Analysis of noncoding regulatory mutations in cancer
September 29, 2014http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3101.html
An interesting report of potential non-coding drivers without actually doing any wet lab work.
“These methods identify recurrent mutations in regulatory elements upstream of PLEKHS1, WDR74 and SDHD, as well as previously identified mutations in the TERT promoter”. In the text they mention “Khurana et al. also reported WDR74 promoter mutations in 2 of the 20 prostate cancer genomes analyzed”.
Bina QC Report for Single Sample
September 29, 2014Nice viz of the quality of a single sequencing run
{Disclaimer I’m a consultant to this company.}
Blood transciptome paper
September 28, 2014Splicing changes along the blood lineage, good ex. of the
state-of-the-art in human transcriptomics
http://www.sciencemag.org/content/345/6204/1251033.abstract
Science 26 September 2014:
Vol. 345 no. 6204
DOI: 10.1126/science.1251033
Transcriptional diversity during lineage commitment of human blood progenitors
Chen et al.
BoxPlotR: a web tool for generation of box plots
September 21, 2014They published a paper on a web tool to generate box plots !! http://www.nature.com/nmeth/journal/v11/n2/full/nmeth.2811.html QT:{{”
Despite the obvious advantages of the box plot for simultaneous representation of data set and statistical parameters, this method is not in common use, in part because few available software tools allow the facile generation of box plots. For example, the standard spreadsheet tool Excel is unable to generate box plots.
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M.S. and J.W. conceived of the box plot tool
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Related:
http://bioinformatics.oxfordjournals.org/content/early/2014/01/21/bioinformatics.btu038.abstract
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