linkstream2 microblog

Server for predicting damaging missense #mutations
http://www.nature.com/nmeth/journal/v7/n4/full/nmeth0410-248.html Polyphen2 uses both structure & sequence (eg ASA & conservation)

http://www.ncbi.nlm.nih.gov/pubmed/20354512

Polyphen2 includes both structural and sequence features to predict the effect of nonsynonymous substitutions on protein function. Similar to many other methods, Polyphen2 uses evolutionary conservation as one of the features to identify functionally important residues. Integration of 3D-structure, membrane-specific features (PHAT matrix for TM regions) and other features such as protein-domain and active-site are the strengths of Polyphen2 compared to other sequence-based software making it a good tool for prediction.

http://www.nytimes.com/2014/10/11/your-money/giving-back-to-your-school-in-a-big-way.html?rref=your-money&module=Ribbon&version=context&region=Header&action=click&contentCollection=Your%20Money&pgtype=article

http://www.nytimes.com/2014/10/11/your-money/the-slippery-plastic-slope-to-overspending.html?smid=tw-nytimes

Multiplatform assessment of #transcriptome profiling [w.] RNAseq http://www.nature.com/nbt/journal/v32/n9/full/nbt.2972.html Nice plots showing great effect of poly-A selection

http://yaledailynews.com/blog/2014/10/09/breaking-yale-data-server-down/

Yale’s kerberos authentication is down…. kind of bad….

http://www.nytimes.com/interactive/2014/10/08/magazine/eaters-all-over.html?_r=1

http://bd2k.nih.gov/FY14/COE/COE.html#sthash.0bCFkkg3.dpbs
http://bd2k.nih.gov/FY14/DDICC/DDICC.html#sthash.M2bAtnWw.dpbs

http://www.genomeweb.com/informatics/bina-wins-1m-va-million-veteran-program-contract

Bina Wins $1M VA Million Veteran Program Contract
October 09, 2014

Speak text with ios…
http://9to5mac.com/2014/10/04/ios-8-how-to-have-your-ios-device-read-text-for-you/

Signaling #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.