Fold [class] recognized by an…[NN] predictor based-on evolutionary & structural info., w/ particle-swarm training
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24232/full
Ngaam J. Cheung,
Xue-Ming Ding,
Hong-Bin Shen
First published: 27 October 2015
DOI: 10.1002/jcc.24232
two papers for journal club:
1. What are super-enhancers? Pott et al., Nature Genetics (2015) http://www.nature.com/ng/journal/v47/n1/full/ng.3167.html
2. Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer, Heyn et al., Genome Biology (2016)
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0879-2
#Epigenomic analysis detects aberrant super-enhancer DNA methylation in human #cancer
https://GenomeBiology.biomedcentral.com/articles/10.1186/s13059-016-0879-2 hypo-Me of many large blocks
miRNA silencing for…therapy targeted to the [acidic] tumor microenviron., w/ #pHLIP
http://www.nature.com/nature/journal/v518/n7537/abs/nature13905.html miR-155 moves beyond biomarker
DREM…reconstruction of…regulatory #networks from time-series expression http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-6-104 Classic approach using 3-level IO #HMMs
Discovering TFBSs in…Repetitive Regions of #Genomes with Multi-Read
Analysis http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002111 CSEM uses EM to refine site occupancy
Chung D, Kuan PF, Li B, SanalKumar R, Liang K, Bresnick E, Dewey C, and Keles S (2011), “Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data,” PLoS Computational Biology, 7(7): e1002111
http://www.stat.wisc.edu/~keles/Software/multi-reads/
CSEM
Expanded seq. context model…explains variability in polymorphism[s] http://www.nature.com/NG/journal/vaop/ncurrent/full/ng.3511.html Reminiscent of GOR sec. structure prediction
Staying Afloat in the Rising Tide of Science by @CarlZimmer
http://www.Cell.com/cell/fulltext/S0092-8674(16)30192-1 How can this tide lift all boats & not drown us in Tb?
http://dx.doi.org/10.1093/bioinformatics/btw120
http://AlgoRun.org, #Docker-based packaging [w/ web GUI & workflow mgt] for platform-agnostic implement[ations]
http://Bioinformatics.Oxfordjournals.org/content/early/2016/03/02/bioinformatics.btw120
Hosny, A. et al. AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms. Bioinformatics Advance Access, Mar 2, 2016.
What’s the EM #algorithm?
http://www.nature.com/nbt/journal/v26/n8/full/nbt1406.html Description of its essence in simple contexts (ie coin toss) & as soft version of kmeans
What is the expectation maximization algorithm? : Article : Nature Biotechnology
Primer
Nature Biotechnology 26, 897 – 899 (2008)
doi:10.1038/nbt1406
Chuong B Do & Serafim Batzoglou
Abstract
The expectation maximization algorithm arises in many computational biology applications that involve probabilistic models. What is it good for, and how does it work?
without too much math