Sabeti: Many challenges - molecular Dx moving toward Point of Care; rapid Dx working in challenging environments #AGBT16
6:25pm February 10th 2016 via Hootsuite
Sabeti: Sample collection, community engagement; ethics IRB; recruitment, Dx, sequencing, datasharing, etc. #AGBT16
Sabeti: Need incentives for datasharing. 'End-to-end involvement', starting 10y ago: spending time, close collaboration #AGBT16
6:24pm February 10th 2016 via Hootsuite
Sabeti: And then to surveillance; Ebola was tragic, and raised the alarm with WHO on datasharing. Value of genomic data (real-time) #AGBT16
6:23pm February 10th 2016 via Hootsuite
Sabeti: Of 14 BL-4 labs in the US - ability to look at emerging threats. We have an 'amazing potential' to detect #AGBT16
6:22pm February 10th 2016 via Hootsuite
RT @KMS_Meltzy: Pardis Sabeti == Rockstar. Also she is wearing a sweater with a capuchin monkey on it. #winning #AGBT16
6:21pm February 10th 2016 via Hootsuite
Sabeti: Was able to monitor viral evolution in near real-time. Informing diagnostics, vaccines, and therapies. #AGBT16
Sabeti: For Ebola, confirmed Sierra Leone, but 100's of cases in a matter of weeks. Long collab. w/Lassa - could get Ebola samples #AGBT16
6:20pm February 10th 2016 via Hootsuite
Sabeti: '12 Science https://t.co/1m9Emvx1QW is this an emerging disease, or a diagnosis of a disease long-standing? #AGBT16
6:19pm February 10th 2016 via Hootsuite
Sabeti: Suspected cases were going undetected. Analysis suggests over 1,000 yo and >200 spp 2015 Cell https://t.co/1H3lNc3T49 #AGBT16
6:17pm February 10th 2016 via Hootsuite
Sabeti: Low amount of virus in sample, can be degraded, <5% Lassa Virus. '14 publ: https://t.co/pytjnBrIB2 #AGBT16
6:16pm February 10th 2016 via Hootsuite
Sabeti: Setup in Nigeria, Sierra Leone, partnered in training (21 people in the US this year) #AGBT16
6:15pm February 10th 2016 via Hootsuite
Sabeti: Lassa is like Ebola, described as an emerging disease, not an ancient pressure. BL-4 in a remote region (!) #AGBT16
6:14pm February 10th 2016 via Hootsuite
Sabeti: ID'd the LARGE gene - critical for Lassa Virus entry (early on, from HapMap data). KO LARGE, Lassa can't enter. #AGBT16
6:13pm February 10th 2016 via Hootsuite
Sabeti RT @TorontoGenomics: PS: developed MPRA for testing regulatory variation https://t.co/RQVV7Mi5j7 #agbt16
6:12pm February 10th 2016 via Hootsuite
Sabeti: Developed a method called MPRA for testing regulatory variation, and ID mut's that change expression #AGBT16
Sabeti: The signal: high prevalence allele, over a short period of time. Using HapMap and TGP data, MB-long to KB to 100's of bp #AGBT16
6:08pm February 10th 2016 via Hootsuite
Sabeti: Goes back to Haldane 'leveraging evolution to find biology' - looking for signals of recent positive natural selection #AGBT16
6:07pm February 10th 2016 via Hootsuite
Pardis Sabeti (Harvard) “Genomic approaches for infectious disease” #AGBT16
6:05pm February 10th 2016 via Hootsuite
Pardis Sabeti makes a special appearance at #AGBT16 although on medical leave https://t.co/LjdNiFtVUA
Haussler:Q:How will this scale in add'n to 5 regions? A: 'Stay tuned'. Technology will be challenging. #AGBT16
6:02pm February 10th 2016 via Hootsuite
Haussler:Q:Danger of overfitting with packed graphs? A:"It hasn't happened yet - a huge capacity in the graph, empirically" #AGBT16
Haussler: Shows BioNano and Dovetail N50 contig data of de novo from the hummingbird. Human shows 26KB N50 scaffolds #AGBT16
5:59pm February 10th 2016 via Hootsuite
Haussler: Also working on an actionable cancer genome project with Charles Sawyer, looking at somatic mutations. #AGBT16
5:57pm February 10th 2016 via Hootsuite
Haussler: Shares a comparison of mapping methods of MHC; plots portion perfectly mapped against portion uniquely mapped #AGBT16
5:52pm February 10th 2016 via Hootsuite
Haussler:Shows a funny tangled line graph of MHC using a 'cactus' method. (Not surprised.) #AGBT16
5:49pm February 10th 2016 via Hootsuite
RT @jgreid: DH: Sharing is good (JGR:Funny, Mom always said the same thing...) #AGBT16
5:48pm February 10th 2016 via Hootsuite
RT @KMS_Meltzy: Haussler: The more variation you put in the graph, the better it is. #AGBT16 PREACH IT
RT @EpigenomeHacker: Haussler: goal is to create rosetta stone of the human genome: for all inconsistencies & varied interpretations #AG
5:47pm February 10th 2016 via Hootsuite
RT @LAbizar: #AGBT16 Haussler, merging diverse genomes into one graph reflecting total diversity with unique base level identifiers
5:46pm February 10th 2016 via Hootsuite
Haussler: Shows red, green lines on a graph; with Unique Identifiers, that are permanent. Nodes, edges combining sides of sequence #AGBT16
5:42pm February 10th 2016 via Hootsuite
Haussler: Lists GRCh38, TCGA, TGP, dbSNP, dbVar, DGV, dbGaP, ClinVa, OMIM, Human Variome: the problem is lack of common language #AGBT16
5:39pm February 10th 2016 via Hootsuite
Haussler: 3rd project: human genome variation map. Proposing a graph genome structure to represent variation worldwide. #AGBT16
5:38pm February 10th 2016 via Hootsuite
Haussler: Stephen Chanock (NCI), Sir John Burn co-chairs of project. Public sharing of BRCA1/2 at https://t.co/d2aCcGvGUz #AGBT16
5:37pm February 10th 2016 via Hootsuite
Haussler: Another project - 'BRCA Challenge' - 12K coding var's in these genes already, scattered everywhere. Myriad's private one #AGBT16
5:35pm February 10th 2016 via Hootsuite
Haussler: And the answer - a Y/N answer. Busy slide of all the beacons (Wellcome Trust, Broad, ISB, OICR, SFARI etc) #AGBT16
Haussler: Want interoperability. The 'Beacon Project' - the simplest atomic query - does your repository have a A base at loc 'X'? #AGBT16
5:34pm February 10th 2016 via Hootsuite
Haussler: @ga4gh the Global Alliance for Genomics and Health Github repo here: https://t.co/4NTdMOG6AQ #AGBT16
5:33pm February 10th 2016 via Hootsuite
David Haussler (UC Santa Cruz) "Global sharing of better and more genomes" #AGBT16
5:31pm February 10th 2016 via Hootsuite
RT @Becky_Kusko: Eddy: r2r produces beautiful pictures of RNA pair wise corr, NOT for telling if things are statistically supported #AGBT16
5:18pm February 10th 2016 via Hootsuite
Eddy: Color-coding conserved seq - Refers to this tool from '11 BMC Bioinf https://t.co/LNDkHDRD1F w/caveats #AGBT16
5:17pm February 10th 2016 via Hootsuite
Eddy: One paper - '15 Mol Cell on HOTAIR https://t.co/sloHXneipr 'If there's a structure there's a fn RNA' #AGBT16
5:14pm February 10th 2016 via Hootsuite
Eddy: Goes back to '92 Gutell NAR paper https://t.co/2iYRXG0YXX to controversy today about conserved fn #AGBT16
5:13pm February 10th 2016 via Hootsuite
Sean Eddy (Harvard) "Genome Evolution: the future of deciphering the past" Woese "this probably needs no explanation" #AGBT16
5:10pm February 10th 2016 via Hootsuite
Your ‘official blogger’ #AGBT16 team, @cigenomics @salisburymw and @DaleYuzuki with Leisa Zigman of @AGBT https://t.co/tZ8ev5xBUw
5:06pm February 10th 2016 via Hootsuite
Rick Wilson kicking off #AGBT16 https://t.co/uaKPD1oUfw
5:02pm February 10th 2016 via Hootsuite
Twist Bio's hard-charging CEO hit by claims she stole Agilent's trade secrets - FierceBiotech https://t.co/USjt27EJzp
4:03pm February 10th 2016 via Hootsuite
Human evolution is more a muddy delta than a branching tree | Aeon https://t.co/KFZtJesSf0
3:02pm February 10th 2016 via Hootsuite
Qiagen Aims to Broadly Occupy Liquid Biopsy Space with Technologies, Platforms | GenomeWeb Premium ($) https://t.co/MKqgcXjz1U
2:45pm February 10th 2016 via Hootsuite
Some nice #AGBT16 swag via @Fluidigm @nanostring @nygenome @genologix @affymetrix and @Roche https://t.co/3u7cd94p9o
1:15pm February 10th 2016 via Hootsuite
