Predicting peptide binding sites on protein surfaces by ACCLUSTER http://onlinelibrary.wiley.com/doi/10.1002/jcc.23771/abstract #Chemical interactions out perform pure #packing
Posts Tagged ‘from’
Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes
July 2, 2016#SingleCell Coexpression…Reveals Distinct Func. Modules [v clustering bulk RNAseq]… & Clinical Outcomes [in GBM]
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004892
QT:{{”
We found that the co-expressed genes observed in single cells and bulk tumors have little overlap and show distinct characteristics. The co-expressed genes identified in bulk tumors tend to have similar biological functions, and are enriched for intrachromosomal
interactions with synchronized promoter activity. In contrast, single-cell co-expressed genes are enriched for known protein-protein interactions, and are regulated through interchromosomal interactions. “}}
Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling: Cell
July 2, 2016Kinome-wide Decoding of #Network-Attacking Mutations Rewiring Cancer http://www.cell.com/cell/abstract/S0092-8674(15)01108-3 Mapping NAMs onto well-known signaling pathways
Tempus – Buying Time
June 18, 2016The Independent Discovery of TCP/IP, By Ants
June 18, 2016The Independent Discovery of TCP/IP, By Ants
http://priceonomics.com/the-independent-discovery-of-tcpip-by-ants/ Protocol has similarities to #ant communication; man reinventing nature
How does multiple testing correction work?
June 13, 2016How does multiple-testing correction work
http://www.nature.com/nbt/journal/v27/n12/abs/nbt1209-1135.html Intuition for teaching: genome-wide error rate on a single gene v family
The role of regulatory variation in complex traits and disease : Nature Reviews Genetics : Nature Publishing Group
June 12, 2016Reg. variation in cplx traits by @LeonidKruglyak
http://www.nature.com/nrg/journal/v16/n4/full/nrg3891.html nice teaching figure for #eQTLs, showing how mostly cis + hotspots http://www.nature.com/nrg/journal/v16/n4/full/nrg3891.html
Amazon.com: Ice to the Eskimos: How to Market a Product Nobody Wants eBook: Jon Spoelstra: Kindle Store
June 5, 2016Genome-wide association study identifies 74 loci associated with educational attainment : Nature : Nature Publishing Group
May 21, 2016GWAS identifies 74 loci associated w. educational attainment http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17671.html Described in 3 pgs of main text & 146 pgs of supplement
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17671.html
Lalonde E*, Ishkanian AS*, ….P’ng C, Collins CC, Squire JA, Jurisica I, Cooper C, Eeles R, Pintilie M, Dal Pra A, Davicioni E, Lam WL, Milosevic M, Neal DE, van der Kwast T, Boutros PC, Bristow RG (2014) “Tumour genomic a nd microenvironmental heterogeneity as integrated predictors for prostate cancer recurrence: a retrospective study” La ncet Oncology 15(13):1521-1532 (PMID: 25456371)
May 17, 2016Genomic & microenvironmental heterogeneity as integrated predictors for prostate #cancer recurrence
http://www.ncbi.nlm.nih.gov/pubmed/25456371 CNVs & hypoxia
* Lalonde E*, Ishkanian AS*, ….P’ng C, Collins CC, Squire JA, Jurisica I, Cooper C, Eeles R, Pintilie M, Dal Pra A, Davicioni E, Lam WL, Milosevic M, Neal DE, van der Kwast T, Boutros PC, Bristow RG (2014) “Tumour genomic and microenvironmental heterogeneity as integrated predictors for prostate cancer recurrence: a retrospective study” Lancet Oncology 15(13):1521-1532 (PMID: 25456371)
The novelty of the paper is that it is the first study integrating DNA-based signatures and microenviroment-based signature for cancer prognosis. The authors found four prognostic indices, i.e. cancer genomic subtype (generated from clusters of CNV profiles), genomic instability (represented by the percentage of genome alteration), DNA signature (276 genes identified from random forests), and tumor hypoxia (the microenvironment signature), to be effective in predicting patient survival in different groups. Standard clinical univariate and multivariate analyses were performed.
