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
Archive for the 'SciLit' Category
PLOS Computational Biology: Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
April 3, 2016Discovering 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
An expanded sequence context model broadly explains variability in polymorphism levels across the human genome : Nature Genetics : Nature Publishing Group
March 26, 2016Expanded 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
Use and mis-use of supplementary material in science publications | BMC Bioinformatics | Full Text
March 23, 2016Staying Afloat in the Rising Tide of Science: Cell
March 19, 2016Staying 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?
AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms
March 19, 2016http://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.
EM algorithm
March 11, 2016What’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
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription: Cell
March 4, 2016CTCF-Mediated…3D Genome Architecture
http://www.cell.com/cell/abstract/S0092-8674(15)01504-4 SNPs give different #chromatin topologies, including strong #allelic effects
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins : Nature Genetics : Nature Publishing Group
March 3, 2016Gene-gene & gene-env interactions…by #transcriptome…in twins by @dermitzakis lab
http://www.nature.com/ng/journal/v47/n1/full/ng.3162.html Nice model for ASE HT @cjieming
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins
Alfonso Buil, Andrew Anand Brown, Tuuli Lappalainen, Ana Viñuela, Matthew N Davies, Hou-Feng Zheng, J Brent Richards, Daniel Glass, Kerrin S Small, Richard Durbin, Timothy D Spector & Emmanouil T Dermitzakis
linkstream2 microblog 