linkstream2 microblog

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

#Enhancer Evolution across 20 Mammal[s is faster than for promoters] by @PaulFlicek lab http://www.cell.com/cell/abstract/S0092-8674(15)00007-0 H3K27ac & H3K4me3 #chipseq

http://www.cell.com/cell/abstract/S0092-8674(15)00007-0

#Singlecell ChIPseq reveals…subpopulations defined by chromatin statehttp://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3383.html Sparse data: on order of 1K uniq. reads/cell

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3383.html

DUX4 binding to #retroelements creates promoters that are active… Highlights #chipseq binding sites in #repeats
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003947 http://www.ncbi.nlm.nih.gov/pubmed/?term=24278031
PLoS Genet. 2013 Nov;9(11):e1003947. doi:
10.1371/journal.pgen.1003947. Epub 2013 Nov 21.
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis.
Young JM, Whiddon JL, Yao Z, Kasinathan B, Snider L, Geng LN, Balog J, Tawil R, van der Maarel SM, Tapscott SJ.