posts aggrigation for "The biology of genomes" (1)

Jason Ernst on chromatin state dynamics in 9 cell types published as http://www.ncbi.nlm.nih.gov/pubmed/21441907 #BG2011

2011-05-11 11:00:31

Jason Ernst is using epigenomic data from 9 human cell types to make diagrams with lots of arrows and coloured boxes. #bg2011

2011-05-11 11:03:21

JE: Use chromatin marks to model chromatin state and infer function "active promotor", "strong enhancer" etc #BG2011

2011-05-11 11:04:06

Jeff Kiefer @jeffk8900

Can't believe speakers do not allow tweeting of talks. In that case don't present! #BG2011

2011-05-11 11:04:14

Keith Bradnam 📈 @kbradnam

Most speakers are giving the okay to let their talks be covered via twitter, which is good to see. #bg2011

2011-05-11 11:06:24

Shoa L. Clarke @ShoaClarke

Jason Ernst: measure enhancer markers & gene expression in multiple cell lines to infer correct gene target of enhancers. #BG2011

2011-05-11 11:06:52

JE: Correlate these functional annotations with TF binding sites to find what TFs are activators of which cell types #BG2011

2011-05-11 11:08:44

JE overlays GWAS SNPs with disrupted enhancer motifs. Would be nice to see this for gene-diet interacting SNPs. #BG2011

2011-05-11 11:09:32

JE overlays GWAS SNPs with disrupted enhancer motifs. Would be nice to see this for gene-diet interacting SNPs. #BG2011

2011-05-11 11:09:33

JE is assigning function to non-coding regions, which can help determine which SNP in a GWAS region is causal #bg2011

2011-05-11 11:10:35

Keith Bradnam 📈 @kbradnam

That was the first talk to finish under 15 minutes. Two more talks to go. I think that many people here are sleep deprived #bg2011

2011-05-11 11:13:33

JE's talk is a good reminder of just how hard it is to integrate complex genomic data-sets to predict function. My head hurts. #bg2011

2011-05-11 11:14:19

Next Ross Hardison. Hypothesis: Chromatin profiles laid down at lineage commitment, setting the stage for TF binding #BG2011

2011-05-11 11:20:54

RH: Epigenetic changes at/near GATA1 binding sites over the 72 hrs of erythroid cell differentiation #BG2011 Just 72 hrs!

2011-05-11 11:23:48

RH: Epigenetic changes at/near GATA1 binding sites over the 72 hrs of erythroid cell differentiation #BG2011 Just 72 hrs!

2011-05-11 11:23:48

Chris Gunter @girlscientist

Thanks again all on good wishes for surgery. Now resemble beaten piñata, but made it through. Living genomics vicariously thru #bg2011, tx!

2011-05-11 11:34:31

RH: In erythrocyte differentiation, post commitment, chromatin state doesn't change much, but TFs move around a lot #BG2011

2011-05-11 11:36:04

Hey, not bad - 6/8 speakers have been tweetable. Vincent Magrini talking about PacBio sequencing of the worm. #bg2011

2011-05-11 11:40:24

Vincent Magrini is talking about evaluating the PacBio machine for sequencing C elegans. Ooh hybrid assembly. #BG2011

2011-05-11 11:41:15

VM: 3 types of PacBio seq: circular consensus for accurate small fragments, strobe seq for long, interrupted reads, or standard. #bg2011

2011-05-11 11:43:51

VM: sequenced worm to 30x, got 99.98% consensus accuracy, average reads length ~700 bp, raw read error rate 15%. #bg2011

2011-05-11 11:47:34

VM: For hybrid assembly, generated 95X illumina plus 2.2X strobed PacBio. I think PacBio increased N50 by about 50%. #BG2011

2011-05-11 11:53:46

VM's data makes PacBio look pretty attractive for small genome sequencing. #bg2011

2011-05-11 11:53:52