Rosenstein: SMS optical - consider the Nyquist bandwith #NGS12
9:20am August 15th 2012 via HootSuite
Rosenstein: Fluors: 2500 photons/sec QD's: 500k photons/sec. Brightness = limiting factor. #NGS12
9:19am August 15th 2012 via HootSuite
Rosenstein: SMS = discrete, ensemble is an aggregate number. Thus SMS continuous quantities = discrete. Static quants = dynamic. #NGS12
Rosenstein: "Photons are convenient b/c they are clean." But inefficient due to signal. Transducers, PMTs etc. illustrated. #NGS12
9:17am August 15th 2012 via HootSuite
Rosenstein: Optical - 1 base/hr. Ion Torrent - 1 base/min. SM Optical - 1 base / sec. Electronic SMS - in development. #NGS12
9:15am August 15th 2012 via HootSuite
Rosenstein: Bases per second x parallel. Ensemble vs. SM - optical = thousands x 1 base / sec. #NGS12
9:14am August 15th 2012 via HootSuite
J. Rosenstein: 'Noise and Bandwidth Optimization for Nanopore Sensing at Submicrosecond Temporal Resolution'. #NGS12
9:12am August 15th 2012 via HootSuite
Drndic: A&A- Solid-state pores can't get down to 1.5nm (yet) to discriminate sizes. #NGS12
9:09am August 15th 2012 via HootSuite
Drndic: Q&A- non-canonical bases, dsDNA or ssDNA, different sizes = different signals, protein pores it works, not solid state yet. #NGS
Drndic: Q&A- everything is done in high-salt, research for the electronics industry doesn't apply there. 'Things go crazy.' #NGS12
9:07am August 15th 2012 via HootSuite
Drndic: 1 base 0.1s - 'slow'. Much faster, need to improve the electronics. Rosenstein Nature Methods 2012 (up later). #NGS12
9:03am August 15th 2012 via HootSuite
Drndic: Simulates ssDNA with 3ns and 1.5nm pore size. Serpentine and springy (my words!) #NGS12
9:02am August 15th 2012 via HootSuite
Drndic: Lowers noise via TiO2 deposition. Shows 400bp and 3kb DNA events. #NGS12
9:01am August 15th 2012 via HootSuite
Drndic: e-beam can anneal pores. Multi-layered: Si layer, SiO2, SiN, graphene at top. #NGS12
8:59am August 15th 2012 via HootSuite
Drndic: Graphene control illus., single atom knocked out. Other work on graphene, bridge, chain, other shapes, other electronic apps. #NGS12
8:58am August 15th 2012 via HootSuite
Drndic: Wafer has graphene sheet on it, diced. Can control # of layers of the sheets. Lines, holes. SiNx hole = 20nm, Graphene = 3nm. #NGS12
8:57am August 15th 2012 via HootSuite
Drndic: Video of graphene growth - a deposition layer on a polymer layer, otherwise invisible. #NGS12
8:54am August 15th 2012 via HootSuite
Drndic: One base is 0.3nm - so atomically-thin substrate can detect with better resolution. pore = 3-10nm diameter. #NGS12
Drndic: 15min. genome: 1 base in 100ns, 10^9 bases = 1000 sec. #NGS12
8:53am August 15th 2012 via HootSuite
Drndic: Able to discriminate between hmC, C and mC, occupies larger volume and create larger amplitude signals. #NGS12
8:52am August 15th 2012 via HootSuite
Drndic: Working with NEB - counting microRNA, miRNA122a from rat liver, refer to Nature Nanotech. 2010. #NGS12
8:51am August 15th 2012 via HootSuite
Drndic: Shows signals of 25bp DNA, 22bp RNA, tRNA, all with different signals. 1-100molecules / sec rates, can tune parameters #NGS12
8:50am August 15th 2012 via HootSuite
Drndic: Silica nitrite - first SS nanopores. Thinned to a few nm, can detect to 10bp. #NGS12
8:49am August 15th 2012 via HootSuite
Drndic: Refer to Gundlach and Akeson's work with first DNA seq with protein pores. Her work - solid-state nanopores. #NGS12
8:48am August 15th 2012 via HootSuite
Here in Providence it's an adventure to escape the SBUX, minor flooding... http://t.co/JvWKfkrF
8:33am August 15th 2012 via HootSuite
Commentary via PacBio RT @thenanoporesite: http://t.co/YfRr8Ayv Going beyond five bases in DNA sequencing
8:25am August 15th 2012 via HootSuite
RT @whatdnatest: Gene deletion drives more than a quarter of breast cancers http://t.co/NI7ahO77
7:25am August 15th 2012 via HootSuite
As a dog lover I approve this video. MT @naturenews: A little treat: Scientists do the wet-dog shake http://t.co/SbwH5J3T
6:07am August 15th 2012 via HootSuite
MT @Symbionticism: Which profession drinks the most coffee? Yup, scientists! - I Love Coffee http://t.co/CCLLUvTQ #2 - Marketers!
5:25pm August 14th 2012 via HootSuite
Edge Bio's take on the platform comparison paper. Ion Torrent PGM, Miseq, PacBio RS Comparison | EdgeBio http://t.co/XvFTUVLe
4:20pm August 14th 2012 via HootSuite
RT @InSequence: BGI Reviews Next-Gen Sequencing Platforms, Highlighting Advantages of Each System http://t.co/pVPsDn0K
3:40pm August 14th 2012 via HootSuite
V. Lemmon: They can estimate level of heterogeneity in sample due to % heterozygotes by position, although no spec/sens measure. #NGS12
2:18pm August 14th 2012 via HootSuite
V. Lemmon: Use 150 common SNPs in genes for quick sample fingerprinting through exome, transcriptome and whole-genome. #NGS12
2:15pm August 14th 2012 via HootSuite
V. Lemmon, Univ Miami: For every cancer sample selected, they do 5-15x WGS, 70-100x WES (tumor & normal), RNA-Seq, with 30d turn. #NGS12
2:13pm August 14th 2012 via HootSuite
RT @atulbutte: "Omes" make it to page A1 of @WSJ today! Congrats Zak @cbmi @mbeisen http://t.co/kGSZwPYg #genome #exposome
2:08pm August 14th 2012 via HootSuite
RT @lifecorporation: RT @AppliedBio: Congrats to @neuraustralia on their huge RNA-seq study: http://t.co/ZIMfD1Q2 #SOLiDsequencing
1:35pm August 14th 2012 via HootSuite
RT @pathogenomenick: Novoalign compared with Bowtie2 and tmap for mapping PGM data http://t.co/r2moIwdF
12:20pm August 14th 2012 via HootSuite
RT @ElementoLab: Q&A with Eric Schadt in Nature Biotech http://t.co/0nNN1XAV
11:10am August 14th 2012 via HootSuite
S. Liu shows a nice "personal recombination map" and recomb rate as a fn of position to xcr start site (TSS) #NGS12
10:25am August 14th 2012 via HootSuite
S. Liu from Sunny Xie's lab presents a new method MALBAC for single cell WGA, seq. single sperm cells. #NGS12
10:21am August 14th 2012 via HootSuite
@gholsonlyon Suganthi told me this morning she didn't agree with that number (she's at Yale too), as too little is known about WGS variation
10:03am August 14th 2012 via HootSuite in reply to
@gholsonlyon Shrikant didn't document where that number was from, only made the statement on a slide. Speaking with S. Balasubramanian con't
10:01am August 14th 2012 via HootSuite in reply to
From Cambridge Assoc.: Top 2 reasons for online community: access info found nowhere else, and 2nd to showcase themselves.
8:01am August 14th 2012 via HootSuite
RT @justcoachit: RT @matthiasrascher: Van Gogh parodies. http://t.co/WOYQ2uY6 #art #funny
6:05am August 14th 2012 via HootSuite
S. Mane (Yale Genomics Core) 85% of disease causing mutations are in exomes. 1k exomes/mo., zero Human WGS. #NGS12
4:57pm August 13th 2012 via HootSuite
#NGS12 - S. Fields (Broad Inst) states that 2M PGM reads for ChIP are equivalent to 10M reads using 'another MPS' system (not specified).
3:51pm August 13th 2012 via HootSuite
Bacterial Community Shift in Treated Periodontitis PLoS One. #PGM #metagenomics paper 2012 NCBI http://t.co/ta3pEGf2
2:25pm August 13th 2012 via HootSuite
Ion World 2012 - free 2-day conference in the SF Bay Area. Anyone interested in #iontorrent welcome to attend! http://t.co/5u8dOw5z
12:58pm August 13th 2012 via HootSuite
From a Nature Conference announcement: #Lego warriors made into a #DNA model. http://t.co/5X4KZ629 http://t.co/QPzdtDMI
11:35am August 13th 2012 via HootSuite
RT @dgmacarthur: Researchers doing small-scale sequencing in complex diseases should get used to headlines like this: http://t.co/A4GDuw5U
10:20am August 13th 2012 via HootSuite
