Archive for the 'SciLit' Category

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Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer | Genome Biology | Full Text

April 17, 2016

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

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MicroRNA silencing for cancer therapy targeted to the tumour microenvironment : Nature : Nature Publishing Group

April 8, 2016

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

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DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data | BMC Systems Biology | Full Text

April 8, 2016

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

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PLOS Computational Biology: Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

April 3, 2016

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

https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=e18c78b20646a2aa&tool_config=database%2Fcommunity_files%2F000%2Frepo_83%2Fcsem.xml&changeset_revision=1438767ad92f

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An expanded sequence context model broadly explains variability in polymorphism levels across the human genome : Nature Genetics : Nature Publishing Group

March 26, 2016

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

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Use and mis-use of supplementary material in science publications | BMC Bioinformatics | Full Text

March 23, 2016

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0668-z

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Staying Afloat in the Rising Tide of Science: Cell

March 19, 2016

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?

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AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms

March 19, 2016

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.

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EM algorithm

March 11, 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

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CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription: Cell

March 4, 2016

CTCF-Mediated…3D Genome Architecture
http://www.cell.com/cell/abstract/S0092-8674(15)01504-4 SNPs give different #chromatin topologies, including strong #allelic effects

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