MF: Carotenoids from Gram-pos, APEs Gram-neg have >1000 clusters. "No one ever thought it was this wide" #AGBT15
9:21am February 28th 2015 via Hootsuite
MF:One of the most widely distributed biochemical synthetic pathways on the planet. Onto cartenoid pigments - 870 clusters #AGBT15
9:20am February 28th 2015 via Hootsuite
MF: APE ec/vf the largest family in the database; both discovered previously never connected. 'A chemical marker' for xanthomonadin #AGBT15
MF: What are the biosynth functions most unknown, not seen before for active biomolecules? Gram-neg 'large family of gene clusters' #AGBT15
9:18am February 28th 2015 via Hootsuite
MF: Oligosacch - hard to study, hard to char, but via MS/NMR the 'payoff is going to be huge'. Perh most impt molecules synthesized #AGBT15
MF: A broader view of the biosynthetic world - edge and node graph between genes, you can see largest network oligosaccharides #AGBT15
9:17am February 28th 2015 via Hootsuite
MF: 30K putative biosynt gene clusters (!!), via their bioinformatic method 2014 Cell paper http://t.co/uhDrwJurtL : #AGBT15
9:16am February 28th 2015 via Hootsuite
MF: 'Genomics reveals cryptic natural products' - sequence reveals what it is doing, rather than going to the corners of the earth #AGBT15
9:15am February 28th 2015 via Hootsuite
MF:Justification of forward genetics method - for erythromycin, 2007 Nature Biotech http://t.co/EfaSIntPDR #AGBT15
9:14am February 28th 2015 via Hootsuite
MF: From gene cluster to molecule - genes, domains mapped, make high res predictions, then pred structure 'all on the computer' #AGBT15
9:13am February 28th 2015 via Hootsuite
MF: Connecting molecules to genes - 750 known examples. Very slow, also we learn about known molecules, not unk ones #AGBT15
9:11am February 28th 2015 via Hootsuite
MF: Recently forward genetics. 150 examples where genes have been discovered '98 pub http://t.co/6ublnr04LK Chloroeremomycin #AGBT15
MF: The old paradigm - quite alive today, similar to when penicillin discovered; chemical purified from supernatants then screened #AGBT15
9:09am February 28th 2015 via Hootsuite
MF: Daptomycin synthetase - ~3000 kDa (!) 37 proteins, to make 1 small molecule. Why this kind of devotion! #AGBT15
9:08am February 28th 2015 via Hootsuite
MF: How to microbes interact w/each other, and w/human hosts? And - nature products- 2003 Newman review http://t.co/6pyXgGoe97 #AGBT15
Michael Fischback, UCSF: Insights From a Global View of Secondary Metabolism: Small Molecules From the Human Microbiota #AGBT15
9:06am February 28th 2015 via Hootsuite
MT @OmicsOmicsBlog: @GenomeNathan no, protocol from @nanopore, leverages His tags already on protein that binds hairpin (not pore) #AGBT15
7:01am February 28th 2015 via Hootsuite in reply to
RT @CLCbio: Aaand, the official Arcade Champ of #AGBT15 is... Miguel from Vanderbilt! By a large margin, even. Congratulations! http://t.co…
6:58am February 28th 2015 via Hootsuite
.@h2so4hurts @gsaldanha @OmicsOmicsBlog ‘What is shared at a #AGBT15 tweetup is a Marco Island secret’ #truthcomesouteventually
6:58am February 28th 2015 via Hootsuite in reply to
.@euanashley Thank you for the shout-out! <humbled actually> #AGBT15
6:52am February 28th 2015 via Hootsuite in reply to
Part 3 - first goats, then sheep. RT @washingtonpost: Map: Llamas are literally everywhere http://t.co/i5iOd7C6R2 http://t.co/6GIFkgPWSW
6:20am February 28th 2015 via Hootsuite
fMRI in PNAS RT @wef: How the language you speak changes your brain http://t.co/fdFexk2BUy #neuroscience http://t.co/3emMVRvbdy
5:15am February 28th 2015 via Hootsuite
RT @vocativ: Here's NASA's First Global Map of Rainfall and Snowfall by @JoshKrisch http://t.co/WMdOPmmihx http://t.co/xfwOx7UUWX
4:10am February 28th 2015 via Hootsuite
RT @OmicsOmicsBlog: The ability of @DaleYuzuki to live tweet with URLs to key references never fails to impress me #agbt15
1:10am February 28th 2015 via Hootsuite
The 6 Issues That Will Guide the Future of Museums http://t.co/giXHjdVhFk
11:45pm February 27th 2015 via Hootsuite
RT @ibmwatsonbot: IBM’s Watson morphs into big business- via USA Today http://t.co/u2KapUQHCE
10:55pm February 27th 2015 via Hootsuite in reply to
VM:Q:Ever notice chimeric Pacbio reads? A:No, but something to look at #AGBT15
9:22pm February 27th 2015 via Hootsuite
.@nelsondl Didn't realize this - thanks for the correction!
9:21pm February 27th 2015 via Hootsuite in reply to
.@AndyLarrea Yes I did enjoy meeting you too Andy! I see there are no less than 7 events going on now!
VM: Tried via @nanopore as well - only alignments across, also amplification bias for larger 3 segments still remain #AGBT15
9:19pm February 27th 2015 via Hootsuite
VM: Able to get large amounts of avian virus to develop better methods of representation; template switch, 8 segments as multiplex #AGBT15
9:18pm February 27th 2015 via Hootsuite
VM:Now: used @Pacbio to CCS to close gaps from short-read assembly. Found uneven coverage in regions. #AGBT15
9:17pm February 27th 2015 via Hootsuite
VM:Used multiplex, degenerate and polyA primers; clinical monitoring over the years matched the seq data #AGBT15
9:14pm February 27th 2015 via Hootsuite
VM:Describes biology of influenza recombination of H and N subtypes and worldwide outbreaks. Samples collected 09 and 13-14 #AGBT15
9:13pm February 27th 2015 via Hootsuite
Vince Magrini WashU (Introduced by K Dewar as a 'clever undergraduate') Influenza viral RNA-Seq by PacBio #AGBT15
9:09pm February 27th 2015 via Hootsuite
TS: Now want to improve pig genome as existing reference based on Sanger is 'a mess'. Today - N50 3MB #AGBT15
9:04pm February 27th 2015 via Hootsuite
TS: N50 is now 4.4MB w/add'l scaffolding. First assembly to go the highest quality you can. Want to do RNA-Seq and Iso-Seq #AGBT15
TS: Polished w/Quiver tool. Cp assemblies it's clear there are inversions / deletions missing from original assembly #AGBT15
9:01pm February 27th 2015 via Hootsuite
TS: Assembly: 194GB sequence, 38M reads; 5.1kb mean; max 40.3kb. 20x coverage of high-quality read went into Celera Assembler #AGBT15
8:59pm February 27th 2015 via Hootsuite
TS: Generated 57x coverage, P5/C3 w/309 cells, 11 libraries; about $120K cost in 78 machine-days. Collab w/S Koren at NBACC #AGBT15
8:58pm February 27th 2015 via Hootsuite
TS: 15K feral goats in only 57 sq miles; reduced to 250, Papadum goat in MD died unfortunately due to East Coast weather. #AGBT15
8:57pm February 27th 2015 via Hootsuite
TS: Tested for high homozygosity breed - chose San Clemente Island goat - 1875 brought to Calif island #AGBT15
8:56pm February 27th 2015 via Hootsuite
TS: Not bad for short-read; but GWAS evidenced problems - Tad Sonstegard & Curt Van Tassel (ARS in MD) - used 454 + ILMN mate-pair #AGBT
8:55pm February 27th 2015 via Hootsuite
TS:Goats had a single domestication event; 604 documented breeds worldwide. 2.9GB 2013 Nature Biotech http://t.co/lFDPKm4Oy1 #AGBT15
8:54pm February 27th 2015 via Hootsuite
TS:90% of goats are unimproved varieties. Introd genetically-selected goats into Africa have failed. Improve native goat populat'n #AGBT15
8:52pm February 27th 2015 via Hootsuite
TS: Funded by 'feed the future', USDA/USAID. Why goat? Leading source of income & protein 830M worldwide #AGBT15
Tim Smith, U.S. Meat Animal Research Center: A Genome Assembly of the Domestic Goat from 70x Coverage of SMRT Sequence #AGBT15
8:51pm February 27th 2015 via Hootsuite
SG:Q:How to correct a 2D read? A:Sorry - proprietary to @nanopore #AGBT15
8:50pm February 27th 2015 via Hootsuite
SG:Q:Cost of generating data? A:Can't talk about how much they pay; ~500MB at 90x coverage, 4 flowcells #AGBT15
8:47pm February 27th 2015 via Hootsuite
SG: Found 10K annotated transcripts; 5' TSS accuracy good #AGBT15
8:45pm February 27th 2015 via Hootsuite
