MT: Now engineering NAHR-mediated segmented microdeletion / duplication syndrome #AGBT15
2:35pm February 28th 2015 via Hootsuite
MT: Dual gRNA - could induce inversions at a couple of sites. '14 Cell Stem Cell ref http://t.co/IyuvqjaJbJ #AGBT15
2:34pm February 28th 2015 via Hootsuite
MT: Only 1/172 off-target sites enriched for mutations. Targeted CCR5 but CCR2 paralog could influence result #AGBT15
2:33pm February 28th 2015 via Hootsuite
MT: Looked for mut freq. On-target eff: 4-13%, gRNA-dep. Dual gRNA - up to 48% efficient deletion of region of interest #AGBT15
2:32pm February 28th 2015 via Hootsuite
MT: Mimic via CD34+ HPSCs (used for HIV co-inf). Used both single and dual gRNA. 1kb tiling probe capture, then deep seq #AGBT15
2:31pm February 28th 2015 via Hootsuite
MT: CRISPR brief intro, Nature 14 paper: http://t.co/hRXUCzgZDV single guide RNA; 2 guides can cause larger rearrangements #AGBT15
2:29pm February 28th 2015 via Hootsuite
MT: Looking at tissue spec in ASD now: between Mouse CTX, Human LCL and Human NPS models, Venn diagram of overlaps #AGBT15
2:28pm February 28th 2015 via Hootsuite
MT: Showed figure from this '14 Nature paper http://t.co/ukvXjLSZO2 #AGBT15
2:27pm February 28th 2015 via Hootsuite
MT: Now overlappiong with Hi-C peaks - suggests 16p interactions. The CNV's affects nuclear positioning in the genome #AGBT15
2:25pm February 28th 2015 via Hootsuite
MT: Showed Manhattan plot; positional effects in Cis; looking for significant bins (count vs. log(p-val)) Found distal CNV region #AGBT15
MT:16p11.2 recurr genomic disorder: classic example. Horev PNAS http://t.co/xStEOIsc3H Found limited dosage compensation #AGBT15
2:23pm February 28th 2015 via Hootsuite
MT:Neurodev disorders: does ASD/NDD converge on small # of shared final pathways? How to study pathogenesis of rare mut's w/N=1? #AGBT15
2:21pm February 28th 2015 via Hootsuite
MT: Will cover: xcr consequences of recurrent CNV; generation of CRISPR/Cas9 mutants #AGBT15
2:20pm February 28th 2015 via Hootsuite
Michael Talkowski Harvard Med Sch: Modeling Structural Variation and Genomic Disorders Using CRISPR/Cas9 and Integrative Genomics #AGBT15
2:19pm February 28th 2015 via Hootsuite
RT @TorontoGenomics: Mickey Williams: One of the key reasons for picking @iontorrent PGM was input material requirements #AGBT15
1:08pm February 28th 2015 via Hootsuite
LM:Q:Control animals for handling? A:3 groups - wild; 2nd all conditions w/gravity; 3rd to space. $3M missions; smpls kept #AGBT15
12:00pm February 28th 2015 via Hootsuite
LM: Sampling biodiversity; losing 1 species every 6h; "We cannot being these animals to the a lab" #AGBT15
11:59am February 28th 2015 via Hootsuite
LM: 'Neurons evolved more than once'; 9-12 ways to make a brain. 'Access 3.5B years of experiments already done by Nature' #AGBT15
11:56am February 28th 2015 via Hootsuite
LM: One of the fastest brain regeneration in the Animal Kingdom - 3-5d. 'Kings of regeneration' 2.5h wound regeneration #AGBT15
11:55am February 28th 2015 via Hootsuite
LM: No hox genes, no miRNAs, There is RNA editing in their development (!) 'There are many ways to make a neural system' #AGBT15
11:54am February 28th 2015 via Hootsuite
LM: 2014 Nature paper here: http://t.co/A70OnmnXlL Shows Centophoria, Porifera, Placozoa, Cnidaria, Bilateria: very diff 600MYa #AGBT15
11:53am February 28th 2015 via Hootsuite
LM:Shows EM photo of 'the aliens of the sea'. Blog post on ctenophores and @iontorrent PGM here http://t.co/ozI2xxPt8H #AGBT15
11:51am February 28th 2015 via Hootsuite
LM: Best astronauts are snail statocysts - 13 cells; 30/33 neuropeptides down regulated. #AGBT15
11:50am February 28th 2015 via Hootsuite
.@s_mccarroll After seeing that visual of 50%-80% affected by space sickness, um, count me out, thanks. #AGBT15
11:49am February 28th 2015 via Hootsuite in reply to
RT @s_mccarroll: The Moroz lab (U. Florida) is moving on from "Ship-Seq" to "Spaceship-Seq". Anyone up for a zero-G lab rotation? #agbt15
11:48am February 28th 2015 via Hootsuite
RT @TorontoGenomics: @CIgenomics Well Kirk and Spock Transported a whole whale so a fish is easy #AGBT15
LM: Also looked at microRNAs. Did indiv neurons; 'some of the most abundant neurons are ncRNAs' #AGBT15
11:47am February 28th 2015 via Hootsuite
LM: 1000's of up and down regulated genes: neuropeptide S largest up-reg. in space. 'Activates hyperactivity, hypersexuality' #AGBT15
11:46am February 28th 2015 via Hootsuite
LM: Many animal astronauts - geckos, mice, gerbils (died), snails. Genomic analysis of vestibular system. PCA analysis #AGBT15
11:45am February 28th 2015 via Hootsuite
LM: Talks about the Russian Bion-M1. Slideshow on http://t.co/UkipKukB5q here http://t.co/QOjHfg2uWI #AGBT15
11:43am February 28th 2015 via Hootsuite
LM: The problem of gravity in exploring space: adaptation sickness affect 50-80%. Can be permanent, more than motion sickness #AGBT15
11:42am February 28th 2015 via Hootsuite
Leonid Moroz: Space Genomics: Epigenomic Mechanisms for Adaptations to Microgravity During Long-Term Orbital Flights #AGBT15
11:41am February 28th 2015 via Hootsuite
GM:Q:What is 'A' read? A:De novo, just a given read #AGBT15
11:40am February 28th 2015 via Hootsuite
GM: Hopes to get it out 'this year on the blog' here: http://t.co/OS9cvLmut4 #AGBT15
GM: Shows effect of 200x E.coli @pacbio dataset.Can use DAscrubber as 'correction-free'. 30X E.coli K12, 20% discarded. Circle assy! #AGBT15
11:38am February 28th 2015 via Hootsuite
GM: Scrubbing is to throw away any bad data; favor editing over not. Patch gaps, detect & split chimers #AGBT15
11:35am February 28th 2015 via Hootsuite
GM: Intrinsic quality values of A vs B reads; scrubbing w/good and bad thresholds. Trim bad tips (end of reads) find gaps #AGBT15
11:33am February 28th 2015 via Hootsuite
GM: Keep distance between points, keep # of differences, both space and time efficient, encoding alignments. 60x faster. #AGBT15
11:30am February 28th 2015 via Hootsuite
CM: Two bad options for aligning: space or time inefficient; 'this was a problem I wanted to work on'. Uses tracepoints #AGBT15
11:29am February 28th 2015 via Hootsuite
CM: The Pile-a-Gram concept: ends of reads stop aligning in brown, aligned portions in white. Shows examples of repeats, chimera #AGBT15
11:27am February 28th 2015 via Hootsuite
GM: And quality values are wrong - but single molecule you can't observe whether the polymerase is behaving well or not. #AGBT15
11:26am February 28th 2015 via Hootsuite
CM: Error profile of short reads (inc. Sanger) - error at start, lowers, rises toward end of read. Take the middle. @Pacbio - varies #AGBT15
11:25am February 28th 2015 via Hootsuite
GM: Edit of reads so that every read is a contiguous segment of the underlying genome (no chimers, adapters); error <20% #AGBT15
11:24am February 28th 2015 via Hootsuite
GM: Last year - an aligner daligner. This year: a scrubber DAscrub. His blog: http://t.co/aI1puua66l #AGBT15
11:23am February 28th 2015 via Hootsuite
GM: A typical generic assembler: overlap, correction, overlap, assemble, consensus. 'It takes a lot of time to build' #AGBT15
11:22am February 28th 2015 via Hootsuite
(The) Gene Myers, Max Planck Institute – CBG Low Coverage, Correction-Free Assembly for Long Reads #AGBT15
11:21am February 28th 2015 via Hootsuite
CM:More info on the twins in space and types of tests here http://t.co/9iwqU05bOu #AGBT15
CM: (Chris wrote up a nice piece here on http://t.co/jXveSmOkxM http://t.co/WRYaQSlfli ) Mentions one twin going up to ISS #AGBT15
11:19am February 28th 2015 via Hootsuite
CM: Can't use 'a little bit of anthrax' - public response in #scicomm can exaggerate #AGBT15
11:18am February 28th 2015 via Hootsuite
CM: Hospital Microbiome homepage: http://t.co/UyR2B1wFtz Future needs longer reads, greater speeds, better controls #AGBT15
11:17am February 28th 2015 via Hootsuite
