RT @iontorrent: POSTER: Rapid Detection of Aneuploidy from Multiplexed Single Cell Samples #AGBT15 http://t.co/pOyaabcbgo
10:45pm February 28th 2015 via Hootsuite
.@DShaywitz Not to me - I wrote this up a few weeks ago (though not for #AGBT15) about Google X Life Sciences http://t.co/0zTC15pgIY
10:24pm February 28th 2015 via Hootsuite in reply to
RT @iontorrent: #AGBT15: Getting Swept away by an avalanche of data with Dr. Adam Harris http://t.co/gaCsEYRWgU http://t.co/EBMnrTTwEY
7:15pm February 28th 2015 via Hootsuite
.@westr Agreed on the quality organization of #AGBT15. Great conversations all the way to RSW airport. #cantstop
6:55pm February 28th 2015 via Hootsuite in reply to
.@CIgenomics I'd write a guest post, sure. In the meantime, for #AGBT15 catch my updates at http://t.co/dwLvBExeyt @LifeTech blog
6:51pm February 28th 2015 via Hootsuite in reply to
RT @bffo: Thank you all tweet-friends at #AGBT15 | It’s been a great tweet-fest, and I really enjoyed reading all of you! http://t.co/jqrmZ…
6:38pm February 28th 2015 via Twitter Web Client
RT @FastCoLead: The super simple change to become a better listener that most of us find impossible http://t.co/7HjDYGczVh
6:25pm February 28th 2015 via Hootsuite
RT @BillGates: Kids love dinosaurs. This research may help dinosaurs return the favor: http://t.co/u2KGma1R4U http://t.co/4Fa8Zwg6AV
5:55pm February 28th 2015 via Hootsuite
Great to meet so many at #AGBT15 this year! Check the Behind the Bench blog at http://t.co/dwLvBExeyt for AGBT posts & video interviews.
4:01pm February 28th 2015 via Hootsuite
RT @obahcall: Also see Nature issue in #AGBT15 bag & SUPERB collection & Threads http://t.co/zaCnBt0De6 all THANKS to @Magda_Skippe
4:00pm February 28th 2015 via Twitter Web Client
MK:Concl: epigenomics reveal weak but functional variation #AGBT15
3:59pm February 28th 2015 via Hootsuite
MT: Variation of FTO ass'd with obesity in multiple pop's. Most active var's in adipocytes, mesenchyme cells. #AGBT15
3:51pm February 28th 2015 via Hootsuite
MK: Non-coding variation sitting in tissue-spec enhancers. HaploReg2 tool at MIT http://t.co/XWbDa2Zpbq #AGBT15
3:50pm February 28th 2015 via Hootsuite
MK: Can revisit GWAS and determine which tissues the non-coding variation is enriched #AGBT15
3:49pm February 28th 2015 via Hootsuite
MK: #RoadMapEpigenomics Project: module-based linking of enhancers and target genes. Hi-C, ChIA-PET. Can det regulatory motifs #AGBT15
3:48pm February 28th 2015 via Hootsuite
MK: Regulatory genomics: from loci to mechanism to pathways to therapeutics #AGBT15
3:45pm February 28th 2015 via Hootsuite
Last one: Manolis Kellis, MIT “Regulatory Genomics and Epigenomics of Common and Rare Variants” #AGBT15
3:43pm February 28th 2015 via Hootsuite
JG:Q:Base modifications, esp w/bacteria? A:Want to look at it (methylation) #AGBT15
3:42pm February 28th 2015 via Hootsuite
JG:Q:Representation bias? A:Homopolymers is an issue, working on self-correction #AGBT15
JG:Q:Did you try Phrap? (Elaine M "You're too young to remember") #AGBT15
3:41pm February 28th 2015 via Hootsuite
RT @mason_lab: #AGBT15 our MinION 2D run from this morning had 13-14% error http://t.co/pj0N8epvP4
3:39pm February 28th 2015 via Hootsuite
JG: 'Future of @nanopore looks pretty bright'. Will be scaling with PromethION. #AGBT15
JG:'I've heard a lot of grumbling about N50 at this meeting'. Graph of completeness of longer elements #AGBT15
3:36pm February 28th 2015 via Hootsuite
JG:Showed bar chart w/ increase in quality. For a N50 of 58kb (short) to 585kb (ONT) #AGBT15
3:35pm February 28th 2015 via Hootsuite
JG: Their GitHub page for NanoCorr: http://t.co/hg82VKi9wU #AGBT15
3:34pm February 28th 2015 via Hootsuite
JG:PacBio error correction algorithms didn't work well for ONT reads; developed their own called NanoCorr #AGBT15
3:33pm February 28th 2015 via Hootsuite
JG:Read once, about 65% identity; so-called 2D base-calling improves to 77% #AGBT15
3:31pm February 28th 2015 via Hootsuite
JG:Yeast W303, best produces 445MB of sequence. 6kb mean readlength. Charted readlength vs % identity #AGBT15
3:30pm February 28th 2015 via Hootsuite
JG:Initial read is k-mers passed through HMM 'can be quite difficult' #AGBT15
3:28pm February 28th 2015 via Hootsuite
James Gurtowski, Cold Spring Harbor Lab. “Error Correction and de novo Assembly of Oxford Nanopore Sequencing” #AGBT15
3:26pm February 28th 2015 via Hootsuite
HJ: Ji Laboratory website at Stanford: http://t.co/KbnxllvTJ7 #AGBT15
3:25pm February 28th 2015 via Hootsuite
HJ:Q:Chromothrypsis? A:May need other types of analysis, suspect clonal in nature #AGBT15
3:24pm February 28th 2015 via Hootsuite
HJ:Q:What orthogonal validation? A:Nuclear trio did @PacBio and single primer extension. FP's were in repetitive regions #AGBT15
HJ: Another example, 17p haplotype and TP53 - one haplotype completely reduced. Yet another: 5q #AGBT15
3:22pm February 28th 2015 via Hootsuite
RT @erlichya: This #AGBT15 meeting is one of the strongest that I can remember in the last few years.
3:18pm February 28th 2015 via Hootsuite
HJ: Showed one example haplotypes being reduced even with 20% normal stroma #AGBT15
HJ: Can use barcode counts as a signal - can use to locate CNV by density along a given chr (i.e. chr8p) #AGBT15
3:17pm February 28th 2015 via Hootsuite
HJ:Phasing metrics: 95%. Copy number plot shows major instability genome-wide. #AGBT15
3:16pm February 28th 2015 via Hootsuite
.@cshperspectives Interesting question, yes term is not ideal. Can't think of better term though at the moment... #AGBT15
3:13pm February 28th 2015 via Hootsuite in reply to
HJ:Used to analyze primary colorectal cancer. Samples are var quality, cellularity, mixture of stroma & normal #AGBT15
3:11pm February 28th 2015 via Hootsuite
HJ: 126K barcodes, 99.0% SNPs phased; longest phased block 11.5MB. Long switch error rate 0.00023 #AGBT15
3:10pm February 28th 2015 via Hootsuite
HJ:Adv is HMW DNA. Var + indexing code. 100K droplet partitions, 100's of thousands of barcodes, 300 genome equivalents #AGBT15
3:09pm February 28th 2015 via Hootsuite
HJ: 'Quantum genetics' - interrogate individual molecules in partitions. Collaboration w/10X Genomics about 1.5y ago #AGBT15
3:08pm February 28th 2015 via Hootsuite
HJ: Implications of phased genomes: cancer rearr, loci w/dense variation (HLA), haplotypes in familial diseases; aneuploidy. #AGBT15
Hanlee Ji (Stanford) "Megabase phasing of genetic aberrations from primary colorectal tumors" #AGBT15
3:07pm February 28th 2015 via Hootsuite
RT @bioinfomagician: Drop-Seq: WANT! #AGBT15 http://t.co/t7der7zMfg
3:05pm February 28th 2015 via Hootsuite
EM:Q:Doublet rates? A:Species mixing expt's very impt. Concentrations adjusted carefully #AGBT15
3:03pm February 28th 2015 via Hootsuite
EM:Q:How are cells handled in device, effect on exp? A:Retina data confirms w/in-situ data #AGBT15
EM:Q:Can I buy one? A:Will provide designs to fabricate devices, company to make beads #AGBT15
3:01pm February 28th 2015 via Hootsuite
EM:Equipment: inverted microscope and 3 syringe pumps. Aspiration: cellular diversity, understand pathological states #AGBT15
3:00pm February 28th 2015 via Hootsuite
