MV: Laboratory website: http://t.co/FnNU62dvE0 #PAGXXIII
5:38pm January 13th 2015 via Hootsuite
MV:Reports Lucigen mate-pair efficiency of >90%, chimera codes help reduce chimeras - have non-pairing codes #PAGXXIII
5:35pm January 13th 2015 via Hootsuite
MV: Wheat has 124k protein coding genes, alohexaploid. Using PacBio, sequenced 672 BACs, enhanced w/ long mate-pairs #PAGXXIII
5:33pm January 13th 2015 via Hootsuite
Miroslav Valarik (Inst of Exp Botany, Olomouc, Czech Republic) Mate Pair Libraries for Enhancing Wheat BAC Assemblies #PAGXXIII
5:29pm January 13th 2015 via Hootsuite
KS:Q:Relevance of miscanthus to bioenergy? A:Most benefit is to sugarcane. Miscanthus also has potential but a way to go #PAGXXIII
5:28pm January 13th 2015 via Hootsuite
KS: Est grass duplication ~70Mya. Shows data that Miscanthus genome better reference for sugarcane than Sorghum #PAGXXIII
5:19pm January 13th 2015 via Hootsuite
KS: 300 scaffolds pieced together. Resulted in 87% of scaffolds >50kb. Now 'the fun stuff' - diff in genes & their expression #PAGXXI
5:16pm January 13th 2015 via Hootsuite
KS: Some evidence of clonal redundancy, filter out wrong orientation reads, >40kb; keep all <40kb. 4-cutters worked best #PAGXXIII
5:14pm January 13th 2015 via Hootsuite
KS: Sent tissue to Lucigen, 960K fosmid clones (15x) using 5 different RE's to effectively sample fosmid ends #PAGXXIII
5:10pm January 13th 2015 via Hootsuite
KS: (NB - Lucigen's Mate Pair technology highlighted here http://t.co/MVWvS2WiOe for @iontorrent ) #PAGXXIII
5:08pm January 13th 2015 via Hootsuite
KS: With help from @Hudsonalpha have 8kb jumping libraries. Now Lucigen's 40kb NGS mate-pair fosmids: restricted size #PAGXXIII
KS: A doubled haploid Miscanthus sinensis line developed - no allelic var. Many repeats, dupl's: Need larger PE insert sizes #PAGXXIII
5:06pm January 13th 2015 via Hootsuite
Kankshita Swaminathan (Energy Biosciences Institute, IL) Construction and analysis of a Miscanthus sinensis gene space assembly #PAGXXIII
5:02pm January 13th 2015 via Hootsuite
KT: Platform has scheduler to optimize node usage; data compression uses gzip w/FPGA board; 2.5Gb/s; working on CRAM #PAGXXIII
4:53pm January 13th 2015 via Hootsuite
KT: I/O intensive processes: +processing power doesn't help. Extreme example of Casava 1730min vs 107min by caching library #PAGXXIII
4:47pm January 13th 2015 via Hootsuite
KT: GATK optimized on their Power8 system; HaplotypeCaller optimization laid out here http://t.co/przVRB5ywC #PAGXXIII
4:45pm January 13th 2015 via Hootsuite
KT: Tape drives to save energy (and highly reliable), also data compression appliance http://t.co/zek1v0CGlq w/open source apps #PAGXXIII
4:42pm January 13th 2015 via Hootsuite
Kathy Tzeng (IBM NY) "Accelerating Genomics Research Using an Integrated High Performance Computing Solution" #PAGXXIII
4:41pm January 13th 2015 via Hootsuite
RT @davidfuzzylime: Awesome correction in today's @guardian, to be filed under "why hyphens are important" http://t.co/BMHgyht6ak
3:30pm January 13th 2015 via Hootsuite
MW:Showed histogram of ID'd GNPS dataset - most in 1-5% range. But ID's are increasing over time. Now at 187 datasets #PAGXXIII
3:15pm January 13th 2015 via Hootsuite
MW: MassIVE is their MS repository. A 'continuous identification' - automatically searching db's for ID #PAGXXIII
3:09pm January 13th 2015 via Hootsuite
MW: Their solution GNPS. Note: Behind the Bench blog post from ASM http://t.co/OEI4pBkoXz #PAGXXIII
3:08pm January 13th 2015 via Hootsuite
MW:Many rediscover what has already been done. Already: NIST, MassBank, ReSpect, Metlin - but incomplete and grow slowly #PAGXXIII
3:05pm January 13th 2015 via Hootsuite
MW:Leveraging social networking for mass-spec: one problem they work on is compound ID. Normally NMR, manual interpretation #PAGXXIII
3:04pm January 13th 2015 via Hootsuite
Mingxun Wang (UC San Diego) "GNPS - The Future of Community Wide Collaboration and the Power of Social Networking in Mass Spec" #PAGXXIII
3:01pm January 13th 2015 via Hootsuite
AB:Proteomic analysis problem - 2D gels may have multiple forms (i.e. glutamine de-amidation); 40 spots for 5 isoforms #PAGXXIII
2:56pm January 13th 2015 via Hootsuite
AB:Shows data from transgenic plants where the secalin protein ID'd and down-regulated. Tested mixing, data for stickiness #PAGXXIII
2:50pm January 13th 2015 via Hootsuite
AB:Rye translocations in wheat cause stickiness - ID omega secalins (storage protein of rye). Test via RNAi #PAGXXIII
2:45pm January 13th 2015 via Hootsuite
Ann Blechl (USDA-ARS Albany) Using Proteomics in Transgenic Wheat... RNA Interference Targets a Family of Seed Storage Proteins #PAGXXIII
2:43pm January 13th 2015 via Hootsuite
YL:Looked at relationships between 147 ID'd genes; edges show 19 correlated with fiber length #PAGXXIII
2:25pm January 13th 2015 via Hootsuite
YL:In multi-year field trial - 474 GFL genes; 2y used in field trial; each gene had small effect; 11.4% pos effect when up-reg #PAGXXIII
2:20pm January 13th 2015 via Hootsuite
YL: Using forward genetics approach: high thruput, can be done reference-free. ID new gene Gossypium Fiber Length (GFL) #PAGXXIII
2:19pm January 13th 2015 via Hootsuite
YL:500K ESTs; 1K QTLs controlling fiber quality; only 151 related to fiber length. Goal to ID mechanism, improve lengths #PAGXXIII
2:17pm January 13th 2015 via Hootsuite
Yun-Hua Liu (Texas A&M) Molec. Mech of Crop Quality: Cloning and Systems Analysis of 474 Cotton Genes Controlling Fiber Length #PAGXXIII
2:15pm January 13th 2015 via Hootsuite
HZ:Concl: host-pathogen interaction is complex, nuanced, where genetics do play an important role #PAGXXIII
2:11pm January 13th 2015 via Hootsuite
New Post: TaqMan Universal PCR Master Mix - Accept No Substitutes | Behind the Bench http://t.co/msOBN9kfER
2:10pm January 13th 2015 via Hootsuite
HZ:Using LC MS/MS, can ID thousands of proteins between two groups. 2-3K proteins ID'd. Diff expression. Better overlap cp to RNA #PAGXXIII
2:08pm January 13th 2015 via Hootsuite
HZ:Pathway analysis with subtle diff gene exp levels: RIG-I-like receptor signalling in trachea. Also gene-gene interactions #PAGXXIII
2:06pm January 13th 2015 via Hootsuite
HZ:Looking at RNA-Seq data to look at differential expression between tissues; wanted larger systems biology approach #PAGXXIII
2:03pm January 13th 2015 via Hootsuite
HZ: Looked at HTP proteomics and RNA-Seq both host proteins and viral proteins from infected tissues. Fayoumi more resistant #PAGXXIII
1:59pm January 13th 2015 via Hootsuite
HZ: Promising alternative approach is genetic selection for AIV resistance. Two diverse inbred chicken lines Legorn Fayoumi #PAGXXIII
1:58pm January 13th 2015 via Hootsuite
HZ: AIV is type A. HA attaches, NA releases virions from cells. 2y ago H7N9 from China: dozens of fatalities. Major econ loss #PAGXXIII
1:54pm January 13th 2015 via Hootsuite
HZ: Influenza - Avian bird flu is a human health concern. Highly pathogenic strains arise sporadically in CA, WA #PAGXXIII
1:53pm January 13th 2015 via Hootsuite
Huaijun Zhou (UC Davis) Systems Biology Analysis of Mechanism of Host Response to Avian Influenza Virus in Two Chicken Lines #PAGXXIII
1:50pm January 13th 2015 via Hootsuite
RT @KristaTernus: .@mike_schatz is describing his Oxford Nanopore MinION work. Learn more in his preprint http://t.co/1EhkUGCb0O #PAGXXIII
1:46pm January 13th 2015 via Hootsuite
SH:Methylation patterns in both gene-body and intergenic regions; evidence for tissue-spec gene exp #PAGXIII
1:45pm January 13th 2015 via Hootsuite
SH:Looking at single-cell epigenetic modification, BS-Seq w/heat stress. DMR's changes in both single- and multi-cells #PAGXIII
SH: Describing novel miRNAs called gma-miR171 targeting GRAS1, nodulation phenotype #PAGXIII
1:41pm January 13th 2015 via Hootsuite
Shakhawat Hossain (U Missouri) Soybean Root Hair, a Single Cell Model to Study Plant-Microbe Interactions, Epigenetic Regulation #PAGXXIII
1:40pm January 13th 2015 via Hootsuite
MG: Not a problem of more markers or WGS - just a problem of many markers of very small effect #PAGXXIII
12:15pm January 13th 2015 via Hootsuite
