Tweets from Hootsuite

JF: 8 Ewing Sarcoma samples; EWSR1 'poking' the assembly to illus how easy to assemble and learn things #AGBT15

7:40pm February 26th 2015 via Hootsuite

DJ: Describing DISCOVAR and 'crazy-quilt' rearrangement. 2014 Nature Genetics http://t.co/yF1HpRY9zg #AGBT15

7:37pm February 26th 2015 via Hootsuite

David Jaffe (Broad Inst) "De novo identification of somatic mutations in cancer" #AGBT15

7:35pm February 26th 2015 via Hootsuite

JB:Pleads for an 'outstanding bioinformatics post-doc' - apply http://t.co/C3ewHrjl0f @jaybradner #AGBT15

5:05pm February 26th 2015 via Hootsuite

JB:Also looking at super-enhancers for studying medullo-blastoma in press. #AGBT15

4:59pm February 26th 2015 via Hootsuite

JB:Their super-enhancers: more readily displaced; short xcr and protein half-life of myc shown. #AGBT15

4:56pm February 26th 2015 via Hootsuite

JB: About 10x the size of regular enhancers; 2014 Nature Biotech http://t.co/Yvhu88cSMd Different than locus ctrl regions. #AGBT15

4:54pm February 26th 2015 via Hootsuite

JB: Cell 2013 http://t.co/5WB7SkSoGR #AGBT15

4:52pm February 26th 2015 via Hootsuite

JB: Developed BRD4 to study MYC. Thought it could facilitate MYC's effect to turn off gene exp #AGBT15

4:49pm February 26th 2015 via Hootsuite

JB: Nature '10 paper: http://t.co/AFJ0f0ZMfX Can test BRD4 compound w/ primary xenografts #AGBT15

4:47pm February 26th 2015 via Hootsuite

JB: 3D figure - large patch for a landing zone; H3K27ac binding site illustrated. BrDr4 (small molecule) called JQ1 described #AGBT15

4:45pm February 26th 2015 via Hootsuite

JB: Shows Lys27 neutralized via HAT adding an acetyl 'cap'. Shows bromodomains - disrupt the readers of lys acetylation #AGBT15

4:44pm February 26th 2015 via Hootsuite

JB: Illus RNAPII that seed recruitment; mentioned Brad Bernstein and Stam group at UW - H3K27me3 a repressor. H3K27ac activation #AGBT15

4:43pm February 26th 2015 via Hootsuite

JB: His bias: cancer a disease of regulatory regions, and regulatory factors. c-myc, TP53 work at the enhancer regions #AGBT15

4:41pm February 26th 2015 via Hootsuite

JB: Discovery chemistry lab: ability to measure genome-wide gene exp and protein measurements; new insights to cell biology #AGBT15

4:40pm February 26th 2015 via Hootsuite

James Bradner, Dana Farber Cancer Institute. “Disruption of Super Enhancers” #AGBT15

4:39pm February 26th 2015 via Hootsuite

JA:Found many types of reg variation; gene dupl. and protein-coding change at longer timescale. #AGBT15

4:36pm February 26th 2015 via Hootsuite

JA:Looking at ~800 gene paralogs - in 20% of gene pairs, found tissue-spec differences. Tn element 5' insertion up-regulates #AGBT15

4:33pm February 26th 2015 via Hootsuite

JA: Found 5x more gene duplications in radiation ancestral lineages; no sig functions enriched. #AGBT15

4:32pm February 26th 2015 via Hootsuite

JA: Now onto Cichlid: tiilapia. From Lake Victoria 500spp, to L Tanganyika 250spp, to L Malawi 500spp, to rivers. #AGBT15

4:31pm February 26th 2015 via Hootsuite

JA: Looking at 1500y of domestication: many more non-coding than coding changes. Not one gene inactivation. #AGBT15

4:30pm February 26th 2015 via Hootsuite

JA:Mentioned Pope Gregory declaring rabbits could be eaten during Lent in 600AD b/c they resemble fish (!) #AGBT15

4:28pm February 26th 2015 via Hootsuite

JA: Found 100 selective sweep loci; 'almost none of them are fixed'; many SNPs show large freq difference betw. wild & domestic #AGBT15

4:27pm February 26th 2015 via Hootsuite

JA: Began with rabbits, their history. Thorbeck NZ white, via Sanger. 20 European rabbit populations & 1 hare via NGS. #AGBT15

4:26pm February 26th 2015 via Hootsuite

Jessica Alfoldi, Broad Institute. “Evolution Two Ways: Natural and Artificial Selection in Vertebrate Genomes” #AGBT15

4:25pm February 26th 2015 via Hootsuite

EJ: a tree of 7k genes across spp. Publ 2014 Science http://t.co/Y8ns1nSuBh Convergent expression of 55 genes; bird RA & human LMC #AGBT

3:53pm February 26th 2015 via Hootsuite

EJ:Laid out vocal learning in birds compared to humans '04 Jarvis et al http://t.co/CeCV1A6PiP Now with Allen Brain Inst... #AGBT15

3:51pm February 26th 2015 via Hootsuite

EJ: And complex trait genomics - Pfenning 2014 Science http://t.co/OAcnSfGqap 5 gps of mammals, 3 gps of birds. Audio of bird mimic #AGBT15

3:47pm February 26th 2015 via Hootsuite

EJ: Contrasts two genes - one slowly evolving gene (GC increase w/body size); another evolving fast #AGBT15

3:45pm February 26th 2015 via Hootsuite

RT @monbons: EJ: 30 papers published in @sciencemagazine http://t.co/8qBtwpnr0D. #AGBT15

3:43pm February 26th 2015 via Hootsuite

EJ: Jarvis et al Science 14 http://t.co/DjYMr7cmVo 98% of prior birds wiped out 66MYA Predatory trait lost twice #AGBT15

3:42pm February 26th 2015 via Hootsuite

EJ: 40 papers, 28 publ in Dec '14 Science (only 1 example) http://t.co/WOVv4vUkzu #AGBT15

3:38pm February 26th 2015 via Hootsuite

EJ: >200 researchers, >120 institutions (quite the visual slide of logos!) #AGBT15

3:37pm February 26th 2015 via Hootsuite

EJ: Bird genomes more compact - should be easier. 48 avian spp - w/BGI's support, representing nearly all bird orders #AGBT15

3:36pm February 26th 2015 via Hootsuite

EJ:Avian Phylogenomics: resolve family tree of modern birds. Songbirds, hummingbirds & parrots - different trees frustrating #AGBT15

3:35pm February 26th 2015 via Hootsuite

EJ:Study learning of vocalization in songbirds, vocal learning disorders. Genome 10K zebrafish, parrotfish, chicken. Not enough. #AGBT15

3:34pm February 26th 2015 via Hootsuite

Erich Jarvis, Duke University. “Challenges for Sequencing and Analyses of Representative Genomes for an Entire Vertebrate Lineage” #AGBT15

3:32pm February 26th 2015 via Hootsuite

DP:Q:Long arms & bull:effect of domestication? A:Tested 16 different spp going back 17M years; all there (via FISH) #AGBT15

3:31pm February 26th 2015 via Hootsuite

DP:Q:W/Cas9 can it be tested? A:Still challenging to take out 100's of copies of these genes #AGBT15

3:30pm February 26th 2015 via Hootsuite

DP: Progressive Circos plots at 99%, 99.9%, 99.99%: a 7MB dupl. region at 99.999% identity. SHIMS on Sanger cp to NGS #AGBT15

3:29pm February 26th 2015 via Hootsuite

DP:In humans? VCY and VCX genes '00 Hum Mol Gen ref: http://t.co/D53IDnu3nk #AGBT15

3:27pm February 26th 2015 via Hootsuite

DP:Now on bovine (unpubl), the bull Y sees similar amplification on long arm, testis-exp genes #AGBT15

3:24pm February 26th 2015 via Hootsuite

DP:Thus X and Y gene pairs are co-amplified in an 'evolutionary arms race' #AGBT15

3:23pm February 26th 2015 via Hootsuite

DP:A 'dirty side' to X/Y chr - a selfish competition for transmission. "Indep acq & amplified testicular germ-cell spec genes #AGBT15

3:23pm February 26th 2015 via Hootsuite

DP: And 100's of copies of these genes acquired in rodent lineage. Gene families amplified too; so often they look like barcodes #AGBT15

3:21pm February 26th 2015 via Hootsuite

DP:Found 180 copies of a 500kb repeat unit. "Vendors, I'm putting before you a challenging substrate". No homology to humY #AGBT15

3:19pm February 26th 2015 via Hootsuite

DP:Dots are placed with 100% identity in 200bp windows; short arm of mouse Y is condensed replica of humY. #AGBT15

3:18pm February 26th 2015 via Hootsuite

DP:For Bos taurus / mus musculus: mouse Y. Cell '14 ref: http://t.co/khnOn9MgiM Showed dot plots, chimp Y vs mouse Y #AGBT15

3:17pm February 26th 2015 via Hootsuite

DP:Cp 3 'finished' primate chrY: Human, chimp, rhesus: 'the most rapidly evolving, most structurally complex chromosome' #AGBT15

3:14pm February 26th 2015 via Hootsuite