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
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Hybrid curation of gene–mutation relations combining automated extraction and crowdsourcing
November 1, 2014Rev – Audio & Video Transcription Services | $1/min, Fast, Accurate
October 11, 2014Translation & transcription; Connected to an app & api (via zapier)
https://www.rev.com/translation/business
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nature Methods (2010) 7: 248-249.
October 11, 2014Server 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.
Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study : Nature Biotechnology : Nature Publishing Group
October 10, 2014Multiplatform 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
Bina Wins $1M VA Million Veteran Program Contract
October 9, 2014http://www.genomeweb.com/informatics/bina-wins-1m-va-million-veteran-program-contract
Bina Wins $1M VA Million Veteran Program Contract
October 09, 2014
iOS 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.
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