February 2018

There is proprietary, and there are trade secrets. Speed-looking up references at #AGBT18 is in the latter. :) https://t.co/rv2NxAMZmY

10:08am February 13th 2018 via Hootsuite

RT @TorontoGenomics: @laxvid @DaleYuzuki I've been bugging Dale for his secret for a couple years now. He's not sharing....

10:07am February 13th 2018 via Hootsuite

Shen: Pediatric cancers are 'relatively quiet'. Shows figure from '13 Nature Gen https://t.co/0CGpyEwsKW #AGBT18

10:05am February 13th 2018 via Twitter Web Client

Shen: They've compiled their data and have shared it with CiVIC at WashU https://t.co/Ftd3B1GhRU #AGBT18

10:02am February 13th 2018 via Hootsuite

Shen: Parallel research effort; their project described here last year '16 ref https://t.co/r8AosSZm59 #AGBT18

9:59am February 13th 2018 via Hootsuite

Shen: Pediatric cancer overview; started 'Personalized OncoGenomics Project'. Std Rx, off-label, clinical trials, repurposed drugs #AGBT18

9:57am February 13th 2018 via Hootsuite

Yaoqing Shen (BC Cancer Agency CAN): Integration of whole genome and RNA sequencing for personalized therapy in pediatric cancer #AGBT18

9:56am February 13th 2018 via Hootsuite

Q: (Manolis) Is neutral evol more common in CRC? Curtis: Large lumen to expand; tissue architecture limits time, critical item #AGBT18

9:48am February 13th 2018 via Hootsuite

Curtis: Concludes: clonal evolution 'is highly constrained' in metastasis. #AGBT18

9:47am February 13th 2018 via Hootsuite

Curtis: Interesting PNAS '17 https://t.co/qw9TgQ8CNi of colon organoids seeding metastasis, and the drivers involved #AGBT18

9:46am February 13th 2018 via Hootsuite

Curtis: Their model - SCIMET, accounts for spatial heterogeneity. Could get individual, pt-specific mutation rates and timing. #AGBT18

9:44am February 13th 2018 via Hootsuite

Curtis: Clades are monophyletic; brain seeded by the lung, can recapitulate the seeding patterns. Lymph node mets - independent #AGBT18

9:43am February 13th 2018 via Hootsuite

Curtis: "Driver events are highly concordant". Most 'drivers' arise prior to transformation. Shared, truncal, ubiquitous #AGBT18

9:41am February 13th 2018 via Hootsuite

Curtis: Paired CRCs and mets to the brain, liver, lung, lymph. Rare Dx (from CRC to met), single individual, reconstructed phylogeny #AGBT18

9:41am February 13th 2018 via Hootsuite

Curtis: #AGBT18 A recent review on intra-tumor heterogeneity '17 ref https://t.co/qMeGP6WbYz

9:40am February 13th 2018 via Hootsuite

Curtis: #AGBT18 '17 Nature Gen https://t.co/8SbeAOTrKU Can distinguish between 'effective neutrality and selection'

9:38am February 13th 2018 via Hootsuite

Curtis: Now wants to look at spatial simulation of tumor evol; a stochastic death model. 10% fitness advantage, billions of cells #AGBT18

9:37am February 13th 2018 via Hootsuite

Curtis: Sequential clonal expansion and successive sweeps - '13 ref https://t.co/HqYYo4lMgZ Several newer models #AGBT18

9:35am February 13th 2018 via Hootsuite

Curtis: Elements of somatic clonal evolution: mutation, genetic drift, and non-random selection. First two are neutral. #AGBT18

9:34am February 13th 2018 via Hootsuite

Curtis: ITT: intratrumor heterogeneity. One of several refs, NEJM https://t.co/eEjZx4K6Cq Passenger events - https://t.co/yQsu9DHrHB #AGBT18

9:33am February 13th 2018 via Hootsuite

Curtis: Clonal evolution in tumors: we only sample at the end, when it is biopsied/resected. Motivating liquid biopsy #AGBT18

9:31am February 13th 2018 via Hootsuite

Christina Curtis (Stanford Univ) Quantifying the evolutionary dynamics of metastasis #AGBT18

9:31am February 13th 2018 via Hootsuite

A2 Myers: The hardest part is getting a medical professional to allow it. #AGBT18

9:26am February 13th 2018 via Hootsuite

Q: With undiagnosed disease, do you rec. WGS? Myers: These are research projects but also clinical. Elaine Mardis does too. #AGBT18

9:24am February 13th 2018 via Hootsuite

Myers: And now targeting multiple regions with CRISPR-guided mutations in cis. #AGBT18

9:23am February 13th 2018 via Hootsuite

Myers: ATAC-seq (open chrom), DNAse hypersens. 1MB to HTT promoter - shows lots of data w/cis-acting elements #AGBT18

9:22am February 13th 2018 via Hootsuite

Myers: Idea: deliver allele-specific repressors via cerebrospinal fluid or cannula. 2MB region over HTT (Huntington's gene) #AGBT18

9:21am February 13th 2018 via Hootsuite

Myers: In Huntington's: a mini-ENCODE project, promoters, enh, insulators. Target activating cis-acting elements w/repressors #AGBT18

9:20am February 13th 2018 via Hootsuite

Myers: Analyzing cis-mutations' effect on transcription, ref from '85. Now neurodegenerative disease: we know they are dominant #AGBT18

9:19am February 13th 2018 via Hootsuite

Myers: Developmental disability, EBF3 gene https://t.co/zlWSNsOZiV Encodes a transcription factor #AGBT18

9:17am February 13th 2018 via Hootsuite

Myers: Shifting to mutations - shows PNAS from 1989 https://t.co/Qf9EJg2MRU Now at HudsonAlpha, shout out to Shawn Levy #AGBT18

9:10am February 13th 2018 via Hootsuite

Myers: #AGBT18 Shows figure ref https://t.co/OrHXYmednU Many loops = many TF's? Co-occupancy can occur. NuRD complex, txn initiation

9:08am February 13th 2018 via Hootsuite

Myers: CETCh-Seq: CRISPR epitope tagging ChIP-Seq of DNA binding proteins. 208 TF's. 3D methods of protein interactions. #AGBT18

9:07am February 13th 2018 via Hootsuite

Myers: Epitope tagging TF's via ChIP: '15 Genome Res https://t.co/EYU8hJEZXc Online: https://t.co/AZy8xt58uP #AGBT18

9:06am February 13th 2018 via Hootsuite

Myers: Starts with a footprinting autoradiogram from the '80's. (Those who remember those / performed them will feel nostalgia.) #AGBT18

9:04am February 13th 2018 via Hootsuite

Rick Myers (HudsonAlpha AL) Human gene regulation: A journey from basic research to biomedical applications #AGBT18

9:03am February 13th 2018 via Hootsuite

RT @bioinformer: ATHENA source code here: https://t.co/ajgd44IU0c PREPRINT @biorxivpreprint here: https://t.co/LpTeA7AQoj #agbt18

7:18am February 13th 2018 via Hootsuite

#AGBT18 irony: reading an apocalyptic “the US devolves into chaos and FL is written off” novel (‘The Final Day’) and the power goes out...

7:12am February 13th 2018 via Hootsuite

Great to meet @chenghlee IRL at #agbt18 last night at the mixer - Lab7 in Austin for data management worth checking out.

7:10am February 13th 2018 via Hootsuite

RT @mason_lab: Charting the unknown epitranscriptome at #AGBT18, as mentioned by @DaleYuzuki and @GarvanInstitute John Mattick, paper is he…

10:57pm February 12th 2018 via Hootsuite

RT @mason_lab: “With CaptureSeq, we didn’t increase the number of protein coding genes, but we found 10s of 1000s of missing genes and almo…

6:44pm February 12th 2018 via Twitter Web Client

Mattick: Charting the unk epitranscriptome - phage-display antibodies, mismatch sequencing, and ONT direct RNA #AGBT18

6:41pm February 12th 2018 via Hootsuite

Mattick: Shows interesting splice-junction diagram - coding and non-coding almost the same, highly conserved. #AGBT18

6:26pm February 12th 2018 via Hootsuite

Mattick: 'Public databases are vastly incomplete' regarding ncRNAs, 'just not deep enough'. #AGBT18

6:25pm February 12th 2018 via Hootsuite

Mattick: Last week ref: https://t.co/ukGUORi0eY More work using CaptureSeq of ncRNAs and isoforms #AGBT18

6:25pm February 12th 2018 via Hootsuite

Mattick: Shows '11 Nature Biotech https://t.co/K3G45gvMDw RNA Capture-Seq showing 'deep complexity of the transcriptome' #AGBT18

6:23pm February 12th 2018 via Hootsuite

Mattick: Shows interesting figure from '13 rev https://t.co/HANtm0trw5 of conformational switching of RNAs #AGBT18

6:21pm February 12th 2018 via Hootsuite

Mattick: Shows table 2 from '09 ref https://t.co/WHNkZavASu on functionality of ncRNAs #AGBT18

6:11pm February 12th 2018 via Hootsuite