linkstream2 microblog

http://www.ncbi.nlm.nih.gov/pubmed/23247980

http://genome.cshlp.org/content/early/2012/11/01/gr.141382.112
analysis of 95 tumor genomes

QT:”
Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans….Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes.
”
http://www.nature.com/nature/journal/v491/n7426/full/nature11650.html?WT.ec_id=NATURE-20121129

Bioinformatics. 2012 Jan 1;28(1):56-62. doi:
10.1093/bioinformatics/btr614. Epub 2011 Nov 8.
Epigenetic priors for identifying active transcription factor binding sites. Cuellar-Partida G, Buske FA, McLeay RC, Whitington T, Noble WS, Bailey TL.

Score (posterior, at position i in the genome) = PWM for TF t at position i + priors at i (H3K4me + Dnase), gets 60% sens. at FPR of 1% averaged over all i & t, using essentially equal weighting on each functional genomics track. One issue here is because of the huge size of the genome the 1% FPR actually turns into a very low PPV, giving 5 FPs for each TP in practice.
http://www.ncbi.nlm.nih.gov/pubmed/22072382

http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.164.6687

http://ideas.repec.org/p/ces/ceswps/_1948.html

http://genome.cshlp.org/content/22/12/2529.full

http://www.ncbi.nlm.nih.gov/PubMed/23176822Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation.
by Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev SR, McCarroll SA on 11/28/12

Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation.
Am J Hum Genet. 2012 Nov 20

http://genomemedicine.com/content/4/11/88

associated with transFIC method

http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html