February 2014

DeRisi: IRB did not allow treatment decision. Bioethicist, trtmnt. was penicillin in this case. High dose IV, 14d later discharged! #AGBT14

9:57am February 14th 2014 via Hootsuite

DeRisi: Likely got it in PR (Puerto Rico). Only 100-200/y in US, meningitis in ~15% of cases. #AGBT14

9:56am February 14th 2014 via Hootsuite

DeRisi: Find Leptospiria. Breakdown of viral and bacterial reads. 475 reads, distributed all over Leptospiria. Widespread zoonosis #AGBT14

9:55am February 14th 2014 via Hootsuite

DeRisi: Now goes to uBiome browser (UCSF Kickstarter project) produced a taxonomy browser UCSF press rel: http://t.co/aD9ULWCoSb #AGBT14

9:54am February 14th 2014 via Hootsuite

DeRisi: Breakdown of 90m of analysis, this is AGBT of course. 8.1M reads, used SNAP, 65m took non-human reads #AGBT14

9:52am February 14th 2014 via Hootsuite

DeRisi: Rapid IRB at day 42: "How fast can you do it?" Answer: 2 days on MiSeq. Metagenomic prep, 1d library, o/n run, 90m analysis #AGBT14

9:51am February 14th 2014 via Hootsuite

DeRisi: YouTube video screenshot from mother (not shown), 22 pumps going into the boy. Lab reached out to then. #AGBT14

9:50am February 14th 2014 via Hootsuite

DeRisi: Now at a critical point, put on steriods, continued decline, put into an induced coma due to seizures. #AGBT14

9:49am February 14th 2014 via Hootsuite

DeRisi:Encephalitis - could be infection or autoimmunity, with drastic treatment differences in this case. 1cm2 frontal lobe biopsy #AGBT14

9:47am February 14th 2014 via Hootsuite

DeRisi: Infectious disease workup - almost 30 of them - all negative. #AGBT14

9:46am February 14th 2014 via Hootsuite

DeRisi: Jul '13 boy had abnormal MRI - 'hyperintensity' images doesn't indicate cause. #AGBT14

9:45am February 14th 2014 via Hootsuite

DeRisi: Sharing story of 14y.o. WI boy, lot of symptoms from Sep '12 through Jul '13; exposure Aug '12 'at a FL resort' or PR visit #AGBT14

9:45am February 14th 2014 via Hootsuite

DeRisi: NGS for ICU / critical care cases? Cons are speed (incl. analysis) and cost #AGBT14

9:40am February 14th 2014 via Hootsuite

DeRisi: In CA: 7y study, 1570 cases; 63% undiag., as it can be caused by >100 pathogens (could be autoimmune also). #AGBT14

9:39am February 14th 2014 via Hootsuite

DeRisi: 20K cases/y in US, 5.8% fatal, 50% undiag. (!) Cost in '10 ($2B in US); long hospital stays. #AGBT14

9:38am February 14th 2014 via Hootsuite

DeRisi: They work on malaria, viruses, pythons; but today is '2 day's worth of work': acute encephalitis. Fever, seizures, etc. #AGBT14

9:37am February 14th 2014 via Hootsuite

Up next: Joe DeRisi (University of California, San Francisco): NGS in the Context of Critical Care: A Case Example #AGBT14

9:35am February 14th 2014 via Hootsuite

Botstein: Q: Stable mixture persistancy? A: Each mut. can't 'do it themself'. Seen physical separation, where one sticks other not #AGBT14

9:34am February 14th 2014 via Hootsuite

Botstein: Q: (S. Plos) Haploid model vs diploid? Differences? A: Rel. few rearr. in haploids; rearr = lethal. SNV's have same effect.#AGBT14

9:33am February 14th 2014 via Hootsuite

Botstein: Q: (Mardis) Chemostat cp. to body? Microenv.? A: Microenv. is 'consistently reproducible' during metastasis. #AGBT14

9:31am February 14th 2014 via Hootsuite

Botstein: Genes found repeatedly - IRA 'neg regulator of Ras'. But cell wall assembly too. #AGBT14

9:29am February 14th 2014 via Hootsuite

Botstein: Notable trajectories of passengers and drivers: many passengers, but it takes time to determine the few drivers #AGBT14

9:28am February 14th 2014 via Hootsuite

Botstein: But which one, elo1 or gas1 gene is the important one? A yeast backcross provides the answer. elo1 passenger, gas1 driver #AGBT14

9:27am February 14th 2014 via Hootsuite

Botstein: With NGS deep sequencing on ILMN, earlier sweeps detected; fatty acid elongation, chrom. silencing, then mating. #AGBT14

9:26am February 14th 2014 via Hootsuite

Botstein: Steriles initially spread faster than expected. Showed Desai in 2000 was right. Lang 2011 ref http://t.co/neG5Sfkw8L #AGBT14

9:25am February 14th 2014 via Hootsuite

Botstein: Start with w/t, at the end can calculate % mutated at the end, and can measure it experimentally. Can view 'sweeps' #AGBT14

9:24am February 14th 2014 via Hootsuite

Botstein: Fitness cost of constitutive signalling through the mating pathway.. Ref Lang 2009 http://t.co/pkWWD6o3UE #AGBT14

9:23am February 14th 2014 via Hootsuite

Botstein: Theoretical framework for mutations over many generations in a distribution. Ref: Desai Fisher 2007 http://t.co/oOnn5eTYiM #AGBT14

9:21am February 14th 2014 via Hootsuite

RT @GenomeNathan: Botstein: Sugar-starved yeast burn more, ferment less. Clearly, they've read Biochemistry (Stryer). #agbt14

9:18am February 14th 2014 via Hootsuite

@deannachurch D. Botstein gave a similar talk in Jan. 2012 that you can watch: http://t.co/b1PLA3iWwH #agbt14

9:18am February 14th 2014 via Hootsuite

Botstein: 3 N2 sources for yeast; different chrom. rearr.'s. Successful strains were deletions, around repeated sequences #AGBT14

9:17am February 14th 2014 via Hootsuite

Botstein: If there are four breast cancer subtypes, the path may be different; then genetic predisposition (BRCA) will be 1 subtype #AGBT14

9:15am February 14th 2014 via Hootsuite

Botstein: Data from sulfate-reduced yeast environments. Gresham 2008 paper http://t.co/Je4YzNpegi #AGBT14

9:12am February 14th 2014 via Hootsuite

Botstein: CIT1 (citrate synthase) now run by a different promoter, just like the Philadelphia Chromosome (CML) (bcr-abl / Gleevec) #AGBT14

9:10am February 14th 2014 via Hootsuite

Botstein: Using aCGH, rearranged chromosomes in this clonal evolution; transloc. in a transposon element (CIT1) #AGBT14

9:09am February 14th 2014 via Hootsuite

Botstein: Using rate-limiting glucose, reported glucose limitation 1999 Ferea paper http://t.co/irB06ajMuE Some genes up / down #AGBT14

9:08am February 14th 2014 via Hootsuite

Botstein: Photo of Leo Szilard at CSHL - invented with Monod the Chemostat, enabling single-cell organism growth in a steady-state #AGBT14

9:04am February 14th 2014 via Hootsuite

Botstein: "Yeast... has provided a remarkably high fx of our knowledge abt the functions of individual euk. genes and proteins" #AGBT14

9:03am February 14th 2014 via Hootsuite

Up first: David Botstein (Princeton University): Yeast, Evolution and Cancer #AGBT14

9:01am February 14th 2014 via Hootsuite

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types | Science ($) http://t.co/057ekmDgju

7:20am February 14th 2014 via Hootsuite

Thanks to all who introduced yourselves to me at #AGBT14. From Sharon Plon (@splon) "Do you do anything else other than Twitter?"

7:10am February 14th 2014 via Hootsuite

Interactive genetic history map | Biosci Technology http://t.co/HK9Vv3U0iE

5:25am February 14th 2014 via Hootsuite

RT @insidehighered: Record share of wives are "marrying down" educationally http://t.co/ksZBQhyvUc

4:35am February 14th 2014 via Hootsuite

Seshagiri:Used in vitro assay systems to probe ERBB3 mutants; look at cell survival as a proxy for oncogenic signalling #AGBT14

9:04pm February 13th 2014 via Hootsuite

Seshagiri:Hotspot mutations' effect on conformation? Also muts on kinase domain, but none regain kinase activity #AGBT14

9:03pm February 13th 2014 via Hootsuite

Seshagiri:Now looking at ERBB3 somatic mutations - only one of the ERBB family with a impaired kinase domain. Works w/ ERBB2 #AGBT14

9:02pm February 13th 2014 via Hootsuite

Seshagiri:Another was EIF3E-RSPO2 has a deletion, under control of a different promoter. R-spondin fusions activates Wnt #AGBT14

8:57pm February 13th 2014 via Hootsuite