Janet Jansson (Lawrence Berkeley National Lab): “Multi-omics of the human micorbiome - filling in the missing links” #ASM2014
9:58am May 20th 2014 via Hootsuite
Dorrestein:Q: Spatial resolution? A: can push to 10um, for human maps limit is swabbing, multiple cm #ASM2014
9:56am May 20th 2014 via Hootsuite
Dorrestein: (Remarkable datasets from MS combined with NGS metagenomics and human body imaging data.) #ASM2014
9:55am May 20th 2014 via Hootsuite
Dorrestein: Free fatty acid present - tested in culture, oleic and oxidized oleic acids confirming hypothesis #ASM2014
9:54am May 20th 2014 via Hootsuite
Dorrestein: Correlate 850 microbial maps + 50K molecule maps across a surface? A taxon score; illus. with propriobact. and MS data #ASM2014
9:53am May 20th 2014 via Hootsuite
Dorrestein: Found a gut-derived molecule on the bottom of the foot? Crowdsourced. Rob Knight sequenced overlaid to ID spp #ASM2014
9:51am May 20th 2014 via Hootsuite
Dorrestein: Visualized amazing movie of human body model, overlaid with molecules across the surface. Gradients #ASM2014
9:50am May 20th 2014 via Hootsuite
Dorrestein: Illustrating tool with human skin microbiome: sampled MALDI and UPLC-Q TOF from skin #ASM2014
9:49am May 20th 2014 via Hootsuite
Dorrestein: 50-70 searches/day, uploaders, wide variety of organisms. Link to GNPS: http://t.co/zeETeFoPUf #ASM2014
9:46am May 20th 2014 via Hootsuite
Dorrestein: Illustrates 2011 to 2014 dataset and computational growth. "By 2015 we need the NSA's supercomputer" #ASM2014
9:42am May 20th 2014 via Hootsuite
Dorrestein: Requests for using tool; 35pg of instruction. Recent work using their tool 2014 Nature http://t.co/3Hu8YZDLH0 #ASM2014
9:41am May 20th 2014 via Hootsuite
Dorrestein: Can annotate by organism, other attributes "I see a lot of chemistry here" in MS data #ASM2014
9:38am May 20th 2014 via Hootsuite
Dorrestein: Group by similarity, can group with edges & nodes, a map of structural space 2012 PNAS http://t.co/EG1u6b0gjs #ASM2014
9:37am May 20th 2014 via Hootsuite
Dorrestein: Gerwick cyanobacterial coll is 15M spectra! 'a long time for a PhD' to sift through #ASM2014
9:36am May 20th 2014 via Hootsuite
Dorrestein: Microbial metabolic maps using 'Microbial Imaging MS' Refer to 2012 PNAS paper http://t.co/HodFBEMVrt #ASM2014
Dorrestein: Analogy to GPS: "where's my boyfriend app" Can track pets, anti-poach, anti-theft. We need this for molecules #ASM2014
9:34am May 20th 2014 via Hootsuite
Dorrestein: Very cool animation - the 4th branch of the central dogma, what role do microbes play 2014 publ http://t.co/fb0JLQGSjK #ASM2014
9:33am May 20th 2014 via Hootsuite
Pieter C. Dorrestein (Univ CA San Diego): "GoogleMAP" - Type Molecular View of Microbes: From Culture to People #ASM2014
9:31am May 20th 2014 via Hootsuite
Church: Q&A: 'I think we can fairly easily reconstruct an ancient ancestral genome today' #ASM2014
9:26am May 20th 2014 via Hootsuite
Church: Tyr-Trp cross-feeding of evolution over time 2005 Science http://t.co/swYJWEQ0Ia Now 14 2014 PNAS http://t.co/oMYFl680qx #ASM2014
9:23am May 20th 2014 via Hootsuite
Church: Now onto new sensor/selectors against a few dozen compounds #ASM2014
9:20am May 20th 2014 via Hootsuite
Church: Has 'derisked' 2 more codons, recoded another 13 codons in ribosomal genes. Mage - 2009 Nature http://t.co/9HmxoAa0Dd #ASM2014
9:19am May 20th 2014 via Hootsuite
Church: Genome recoding - a radical change to change one codon genome-wide. (virus resistance) 2013 Science http://t.co/9BEjSiGN8s #ASM2014
9:17am May 20th 2014 via Hootsuite
Church: Looked at effect of n-term codon bias Science 2013 paper http://t.co/3nMufLoQHY #ASM2014
9:16am May 20th 2014 via Hootsuite
Church: Showed regulatory region data from 2013 PNAS Kosuri et al http://t.co/AjiKi1h5KJ #ASM2014
9:15am May 20th 2014 via Hootsuite
Church: Synthesis of genomes: synthesis on-chips, able to error correct. Can construct many K's of cis regulatory regions #ASM2014
9:13am May 20th 2014 via Hootsuite
Church: Recent Science paper http://t.co/CTWJtW9hmZ FISSEQ in-situ RNA sequencing in 3D (Hmm - what relevance to microbiology?) #ASM2014
9:11am May 20th 2014 via Hootsuite
Church: Examples of lung and gut: in culture to include microorganisms at the interface #ASM2014
9:07am May 20th 2014 via Hootsuite
Church: His gigantic disclosure page: http://t.co/9nJzXldoEm At the human/microbial interface, organ-on-chips. #ASM2014
9:06am May 20th 2014 via Hootsuite
George M. Church (Harvard): Synthetic Ecologies #ASM2014
9:04am May 20th 2014 via Hootsuite
Hugenholtz: Estimates another 20K genomes needed to fill out the tree, 'achievable in probably 5y' #ASM2014
9:00am May 20th 2014 via Hootsuite
Hugenholtz: Broad ecological and broad phylogenetic sampling needed for evol inferences #ASM2014
8:58am May 20th 2014 via Hootsuite
Hugenholtz: UASB reactor 'is a treasure trove of candidate phyla'. Another is a hypersaline mat #ASM2014
8:57am May 20th 2014 via Hootsuite
Hugenholtz: Confirmed via phylotype-specific KSB3 FISH, Sekiguchi 2014 submitted. Clues to bulking phenotype with sensing mech #ASM2014
8:56am May 20th 2014 via Hootsuite
Hugenholtz: Culprit was KSB3 filaments: applying GroopM, 8 scaffolds ID, one 'bonus' at only 0.4% abundance #ASM2014
8:55am May 20th 2014 via Hootsuite
Hugenholtz: Another story: candidate phylum KSB3 found in an upflow anaerobic sludge blanket, clogging process #ASM2014
8:53am May 20th 2014 via Hootsuite
Hugenholtz: Low-energy lifestyle, mostly fermentative (thus reason why not culturable), clues to photosynthesis evolution #ASM2014
8:52am May 20th 2014 via Hootsuite
Hugenholtz: Their result corroborated here in human gut: nonphotosynthetic cyanobacteria http://t.co/EThXA2nLnr #ASM2014
8:51am May 20th 2014 via Hootsuite
Hugenholtz: Koala faeces, phosphate-removing sludge, anaerobic digesters: recovered six draft genomes ~2MB http://t.co/zo8wN6tpdf #ASM2014
8:49am May 20th 2014 via Hootsuite
Hugenholtz: Applied to 'dark cyanobacteria': aphotic habitats such as animal gut, deep sea sediment. Non-photosynthetic #ASM2014
8:47am May 20th 2014 via Hootsuite
Hugenholtz: Their binning called GroopM (Github repo: http://t.co/LiMThVFHu2 ) uses population abundance as a fn of sampling & seq #ASM2
8:46am May 20th 2014 via Hootsuite
Hugenholtz: 2nd aid: binning strategies, but limitations of reference datasets. #ASM2014
8:43am May 20th 2014 via Hootsuite
Hugenholtz: More accessible is via metagenomics. Varying success: only if dominant reads. 2 aids: NGS tech 'through the roof'... #ASM2014
8:42am May 20th 2014 via Hootsuite
Hugenholtz: From 16S to populations to single cells: what JGI is tackling. (Tanja Woyke's work highlighted) #ASM2014
8:41am May 20th 2014 via Hootsuite
Hugenholtz: Wu 2009 Nature paper: http://t.co/ZKCfZYXIiG Adding foliage to the tree of life Nature Rev 2014 http://t.co/zbymFPmdOU #ASM2014
8:40am May 20th 2014 via Hootsuite
Hugenholtz: Graph from Rinke 2013 http://t.co/DrqpPTwy3i in '05 the uncultured exceeded the cultured phyla. #ASM2014
8:37am May 20th 2014 via Hootsuite
Hugenholtz: "With differential coverage binning of metagenomes" - shows progress from 1998 to 2014. >60 bact phyla, 50% uncultured #ASM20
8:36am May 20th 2014 via Hootsuite
Philip Hugenholtz (U Queensland): Fast Tracking the Addition of Genomic Foliage to the Tree of Life with... Metagenomes #ASM2014
8:34am May 20th 2014 via Hootsuite
Messing: Credits Todd Micheal for 'NGS', and UC Davis / Univ MN for sending clones out free of charge #ASM2014
8:32am May 20th 2014 via Hootsuite
Messing: Free exchange of tools and materials, 'not so true today', helped develop a technique used in nearly every lab today #ASM2014
8:30am May 20th 2014 via Hootsuite
