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
RT @CIgenomics: CM: Following the Kellys into space and generating AllData...official poster @mason_lab #AGBT15 http://t.co/0zTcVC4thE
11:28am February 28th 2015 via Twitter Web Client
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
CM: Shows the DC metro - does the person cleaning actually work there? (!) Precision metagenomics: hosp settings #AGBT
11:16am February 28th 2015 via Hootsuite
CM: A forest fire of the microbiome - after it gets washed. Then repopulated from people. #AGBT
CM: 'Should I ride the subway?' - quotes online comments. 'This is like an ad for Uber' (!) Shows movie of subway cleaned #AGBT
11:15am February 28th 2015 via Hootsuite
RT @illumina: CM: @mason_lab "let's just start looking" http://t.co/h2g7jFEnwm #AGBT15
11:14am February 28th 2015 via Hootsuite
CM: 2010 census data by ancestry, and then can map in their Pathomap data to show movement #AGBT
CM: Mentions this '08 Nature from J Novembre http://t.co/0U1bzoK4Wt connecting genotypes to geography. Also mentions STR markers #AGBT
11:13am February 28th 2015 via Hootsuite
CM: Mus musculus - as much as 8% of all DNA. Human DNA - 'no pants' day missed this year... #AGBT
11:12am February 28th 2015 via Hootsuite
CM: Corrected link to timecourse movie: http://t.co/Z6HsscjhIE #AGBT
11:11am February 28th 2015 via Hootsuite
CM: Look at hourly dynamic risks. Shows a map of ticket machine online her: http://t.co/OKs76dYA9C #AGBT15 h
CM: Flooding traces, antarctic spp. 'Licking subway poles "probably fine" says Expert' (another #scicomm reference) #AGBT15
11:10am February 28th 2015 via Hootsuite
CM: 'The subway looks like skin' - matching to HMP. Log2 of obs/expected. WSJ Interactive map of kimchi http://t.co/QktrAu3OUH #AGBT15
11:09am February 28th 2015 via Hootsuite
Chris Mason, Weill Cornell Med Coll City-Scale DNA Dynamics, Disease Surveillance, and Metagenomics Profiling #AGBT15
11:07am February 28th 2015 via Hootsuite
RT @bioinformer: Great quote from JM Tanner #AGBT15 http://t.co/W40BuFavxI
10:36am February 28th 2015 via Hootsuite
RT @johnpharmd: Have much respect for Jeff @rosenfeldja and Chris @mason_lab, co-founders of @GenomeLiberty. Looking fwd to their next proj…
10:20am February 28th 2015 via Twitter Web Client
DE: <No twitter activity as the 10K hour rule has been debunked, no matter that Malcolm is his running buddy> http://t.co/wVAwX2V7Zc #
10:18am February 28th 2015 via Hootsuite
David Epstein, ProPublica: Dangerous Dichotomies: How Sports Harm Genetic Research #AGBT15
10:10am February 28th 2015 via Hootsuite
RK: The GNPS website at UCSD: http://t.co/b7d7dMCGgV #AGBT15
RK: Is in transition to UCSD Mentions GNPS - I blogged about other work at UCSD microbiome work here http://t.co/I1OgqnRneE #AGBT15
10:09am February 28th 2015 via Hootsuite
RK: In 10y - applications of DNA seq. Future - 3D PCA software demo, called 'cheetah', can trace phylogeny per treatment #AGBT15
10:06am February 28th 2015 via Hootsuite
RK: In 1-2d, the shift to the healthy state and stays there for months. Look for disruption, healthy state. A 'smart toilet'? #AGBT15
10:03am February 28th 2015 via Hootsuite
RK: Effect of gut microbiome - now onto C.diff. Distribution of microbiomes of the recipient pt vs. donor. Shift dramatic #AGBT15
10:02am February 28th 2015 via Hootsuite
RK: American Gut project: where are you on the map? http://t.co/rXrn5SnBbT $1.1M raised for this project #AGBT15
10:01am February 28th 2015 via Hootsuite
RK: 90% of bacteria on skin 'come from beauty products'. A tremendous impact on skin microbiome #AGBT15
9:59am February 28th 2015 via Hootsuite
RK: Kwashiorkor acute malnutrition, examined effect of microbiome (Science ref: http://t.co/NDqa0i5muq ) #AGBT15
9:58am February 28th 2015 via Hootsuite
RK: Germ-free mice to look at obesity in mice. ob/ob mice, leptin mutants, transplant feces. Data shows it was feces #AGBT15
9:56am February 28th 2015 via Hootsuite
RK: But does this diversity matter? Commercialization potential of obesity: 50% via human genes; 90% via microbiome #AGBT15
9:53am February 28th 2015 via Hootsuite
RK: $173M of HMP is only a fraction of the diversity in adults in geography, age Fig from 2012 Nature http://t.co/XtEBnPP0X1 #AGBT15
9:51am February 28th 2015 via Hootsuite
RK:Traces microbiome of a newborn via this PCA representation: from birth (meconium) through 2.5y #AGBT15
9:49am February 28th 2015 via Hootsuite
RK: Points out differences across body sites - only 10% similarities. #AGBT15
9:46am February 28th 2015 via Hootsuite
