February 2015

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

RT @bioinfomagician: This t-shirt from @iontorrent is very true considering my twitter handle. #AGBT15 http://t.co/jmObJafO2C

3:11pm February 26th 2015 via Hootsuite

DP: Two Y chr BACs from 1 male: over 105kb overlap, 161kb + 178kb. 11 nt subst in 105kb; 99.99% identity; opposite arms. #AGBT15

3:10pm February 26th 2015 via Hootsuite

DP: Avoid assembly confounding problems; seq only 1 chr. Capture a few differences w/BACs from one indiv. Seq & map as 1 activty #AGBT15

3:09pm February 26th 2015 via Hootsuite

DP: The Y-ch has 8 massive palindromes. 2003 Nature http://t.co/Yvsosvvffs Arms more similar than alleles #AGBT15

3:08pm February 26th 2015 via Hootsuite

David Page, Whitehead Institute “What SHIMS (Single Haplotype Iterative Mapping and Sequencing) Has Taught Us About Sex Chromosomes” #AGBT15

3:05pm February 26th 2015 via Hootsuite

EG:Cites beginning of the HGP in Feb 1990, the early days. Ends with a call from the White House asking for >his< DNA model... #AGBT15

12:01pm February 26th 2015 via Hootsuite

EG: Interim workshop report in Sept 15. Main site: http://t.co/fz1gKU8r5N White House Blog: http://t.co/w4i24BokTT #AGBT15

11:59am February 26th 2015 via Hootsuite

EG: Posted video archive, 'the first of many workshops'. White papers, lots of issues to deal with. #AGBT15

11:57am February 26th 2015 via Hootsuite

EG:Need new ways to engage participants; new way for multi-disciplinary work; NIH workshop website here http://t.co/dH6MGfpEUd #AGBT15

11:57am February 26th 2015 via Hootsuite

EG: Also data science has matured; also the patient partnerships (existing cohorts, citizen science, crowdsourcing) #AGBT15

11:55am February 26th 2015 via Hootsuite

EG: Collins piece from 2004 http://t.co/JAXPhV8Mni calling for basically the same thing. Why now? Genomics, EHR, tech (sensors) #AGBT15

11:54am February 26th 2015 via Hootsuite

EG: EHR 'is key to this', >1M US volunteers, numerous existing cohorts and new ones. Forge new model for 'doing science' #AGBT15

11:53am February 26th 2015 via Hootsuite

EG:The vision - near term, longer term, and policy changes. Points to E Lander's NEJM piece http://t.co/OR6iUhN5fJ #AGBT15

11:52am February 26th 2015 via Hootsuite

EG: Shared political support quoted in the NYT http://t.co/AntLadEbTT Invited everyone to read this NEJM http://t.co/k1RVPZOLHd #AGBT15

11:49am February 26th 2015 via Hootsuite

EG: A photo from F Collin’s living room when the SOTU address made about #PrecisionMedicine http://t.co/Jw4j6jlmoR #AGBT15

11:48am February 26th 2015 via Hootsuite

EG: Great photo from Francis Collin's living room, some 15 people all around the TV at that moment. #AGBT15

11:45am February 26th 2015 via Hootsuite

EB: (Okay, maybe it was 6 sentences.) Included shot of standing ovation from both sides of the aisle. 'Rarely' does that happen. #AGBT15

11:44am February 26th 2015 via Hootsuite