Favorite Tweets from BOG '17 & GP-Write (i0gpwrite, i0bog17, #BOG17, #GPWrite)

  1. Last talk: deep learning on microscopy images- from yeast to GTeX, correlating images with molecular traits @LeopoldParts #BoG17
  2. LP: understanding the individual layers in the dnn and classification per layer #bog17 https://t.co/3WKf7jjIOO
    LP: understanding the individual layers in the dnn and classification per layer #bog17 pic.twitter.com/3WKf7jjIOO
  3. Anchor talk, to close off, Leopold Parts @LeopoldParts “Classification of cells & tissues from hi throughput micros. images using DL” #BoG17
  4. Looking at all questions at #bog17 (including mods) in order. See all those "streaks" of 1 color? Not seen in random permutations. https://t.co/9P2ZLiFzic
    Looking at all questions at #bog17 (including mods) in order. See all those "streaks" of 1 color? Not seen in random permutations. pic.twitter.com/9P2ZLiFzic
  5. Not discussed so far, but I'm curious to see if single cell/nuclei transcriptome would be even more powerful; and what about CAGE? #BoG17
  6. Yongjin Park, one more talk about association of transcriptome studies with genetic traits, as a notable trend from this meeting #BoG17
  7. Yongjin Park showing pretty cool tensor factorizations to find hidden confounders #BoG17
  8. Unequal distribution of samples per tissue in affects analysis! Not enough brain 😊, says Park #BoG17
  9. Essential genes expression is less divergent than other genes, even less divergent in the important tissue. It makes sense. #BoG17
  10. JC: Having established expectation of gene expression evolution, can now look at deviations to #BoG17
  11. Gene expression for 17 mammal across 7 tissues. Modelling for neutral (few tissue) vs stabilizing selection (most tissue) #BoG17
  12. JC: Rate of expression evolution is not linear and depends on the actual tissue #BoG17
  13. JC: PCA of RNA-seq from 17 species in 7 tissues clusters by tissue [tick] and then by species within each cluster [tick] #BoG17
  14. JC: Unfort, we are lacking a null model of the evolution of gene expression (~neutral evolution but for transcriptomics) #BoG17
  15. Chen showing that the rate of expression evolution is not a linear relationship #BoG17
  16. Jenny Chen, gene expression evolution, is this a major driver of diversity in mammalian? #BoG17
  17. @emo_davenport : Connectivity and centrality though different in asthma vs control were not consistent in other disease comparisons #bog17
  18. MODISCO learns >70 non redundant novel transcription factor motifs. This has been a difficult task at least in FANTOM5. Validations? #BoG17
  19. Last anchor session at #BoG17 is the Computational Genomics Session 11 @cshlmeetings
  20. @markgerstein @mason_lab Thank you! I was pleasantly startled when I discovered that this handle was still available.
  21. @kanzure "comments" on code may be a great use of the noncoding space #gpwrite
  22. .@cshperspectives discuss decoupling various aspects of journal publication: reproducibility, discovery, discussion & certification #GPwrite
  23. Great to Richard Sever from @biorxivpreprint here at #gpwrite - our lab is a big fan of preprints.
  24. #GPWrite "The only interesting Standards are the ones that get used; and the ones that get used make data sharing less painful." -Marc Salit
  25. "What I cannot create I cannot understand." Historic #GPwrite goal to build large genomes— thank you @andrewhessel!  http://theatln.tc/2pxGyvh 
  26. Gerstein: Kryder’s Law (summed S-curves) not Moore’s Law governs cost of DNA sequencing #gpwrite @markgerstein https://t.co/JtXR3B9MR1
    Gerstein: Kryder’s Law (summed S-curves) not Moore’s Law governs cost of DNA sequencing #gpwrite @markgerstein pic.twitter.com/JtXR3B9MR1
  27. Our next session kicks off with @markgerstein, who is discussing how to scale computation to keep pace with data generation. #GPwrite https://t.co/Skt2dxEiHV
    Our next session kicks off with @markgerstein, who is discussing how to scale computation to keep pace with data generation. #GPwrite pic.twitter.com/Skt2dxEiHV
  28. After #gpwrite lunch, I'll be discussing @Sagebio's experience engaging distributed groups of researchers & building supporting technologies
  29. Jay Konieczka of enEvolv discusses biologically inspired engineering of microorganisms. #GPwrite https://t.co/JPiCbScE5O
    Jay Konieczka of enEvolv discusses biologically inspired engineering of microorganisms. #GPwrite pic.twitter.com/JPiCbScE5O
  30. Leslie Mitchell is back to tell us about the Genome Foundry @ ISG and their work in designing, assembling and verifying 'big DNA.' #GPwrite
  31. Today we are attending #GPwrite meeting - excited to be part of this ambitious collaboration @RosserLab @caiyizhi @EdinGenFoundry
  32. Enjoying watching #BoG17 coverage. Unfortunate that #GPwrite, another NY-area genomics meeting, was scheduled in an overlapping time frame.
  33. @kanzure @markgerstein Could always use ultraconserved elements? Apparently evolutionarily optimized.  http://ultraconserved.org/  #GPwrite
  34. Favorite part of genome meetings: speaker asks who's been sequenced. In audience of experts/enthusiasts, 1 in 10 say yes. #GPwrite @GP_write
  35. @kanzure Good point. But perhaps strategies could be employed similar to those that have been used to make DNA a pot. data storage medium #GPwrite
  36. @sudogene @mason_lab Good comment. @sudogene: I really like your handle as I like both #pseudogenes & being root !
  37. Zuchner: suggests that unique & registered DNA signatures could be used to comment on genome engineering "code" #GPWrite
  38. #GPwrite: Should we include "comments" in synthetic DNA like we do for computer programming code? Might inform downstream users, programmers
  39. Beal: advocates  http://SBOLStandard.org  for the #GPWrite world. It supports expressing deferred choices beyond simple seq. representations …
  40. #GPwrite Great summary of ways to engineer new types of cells that are ultra-safe for manufacturing and therapy, thx @geochurch & @JefBoeke https://t.co/SQbPkcj4jt
    #GPwrite Great summary of ways to engineer new types of cells that are ultra-safe for manufacturing and therapy, thx @geochurch & @JefBoeke pic.twitter.com/SQbPkcj4jt
  41. Getting ready for a group discussion lead by our scientific executive committee: @JefBoeke, @geochurch, Pam Silver & Farren Isaacs! #GPwrite https://t.co/8hxN4XATcV
    Getting ready for a group discussion lead by our scientific executive committee: @JefBoeke, @geochurch, Pam Silver & Farren Isaacs! #GPwrite pic.twitter.com/8hxN4XATcV
  42. They figured out how to turn on double spacing for #GPwrite. Just use haploid cells ;)
  43. Oh: goal is to characterize the skin metagenome & then use a mathematical model to design probiotics, eg microbial hypercolonizers #GPwrite
  44. The Jackson Laboratory’s @jjss0 discusses the human skin microbiome, from metagenomes to therapeutics. #GPwrite https://t.co/qAKO84q8Vm
    The Jackson Laboratory’s @jjss0 discusses the human skin microbiome, from metagenomes to therapeutics. #GPwrite pic.twitter.com/qAKO84q8Vm
  45. Columbia University’s Harris Wang discusses engineering the microbiome and mammalian genome with enhanced metabolic functions. #GPwrite https://t.co/gYMltaCxPK
    Columbia University’s Harris Wang discusses engineering the microbiome and mammalian genome with enhanced metabolic functions. #GPwrite pic.twitter.com/gYMltaCxPK
  46. At #GPwrite just saw a 1955 @sciencemagazine paper cited - looked like a recipe for minimal media
  47. Way: Recode Salmonella (removing 2 codons), making an attenuated, live bacterial vaccine. Q: Is this "firewalled" against E coli? #GPwrite
  48. @mnitabach Actually, @geochurch explicitly argued NO, based on the scale of the necessary simultaneous change #GPwrite
  49. Using genome synthesis to explore fundamental questions of yeast gene function and genome structure. Nice! @caiyizhi #GPwrite
  50. The plasmid is called pBUCA...pronounced pBoeke.
#GPwrite Synthetic Regulatory Genomics (SyRGe) https://t.co/pw9Jwn5kGX
    The plasmid is called pBUCA...pronounced pBoeke. #GPwrite Synthetic Regulatory Genomics (SyRGe) pic.twitter.com/pw9Jwn5kGX
  51. Maurano: synthetic approach allowing flexible incorporation of of alt. functional modules in noncoding DNA #GPwrite
  52. Pilot Project: @ggronvall shares insights on understanding and anticipating governance systems. #GPwrite https://t.co/fBr3ueYL7Y
    Pilot Project: @ggronvall shares insights on understanding and anticipating governance systems. #GPwrite pic.twitter.com/fBr3ueYL7Y
  53. @geochurch it's not fair for viruses to miss seeing our genome recoding exps. Recoded cells will be safe ! #GPwrite
  54. Ostrov: recoded "safe," cell lines that are virus resistant. But could a virus co-evolve? #GPwrite
  55. From phage-resistant Re.Coli to ultra-safe cell-lines - 1st GP-write pilot project from Church lab being presented by Nili Ostrov #GPwrite
  56. .@nancyjkelley introducing #GPWrite meeting @nygenome with reminder of how much NYGC has brought to NYC and genomics over past few years.
  57. So far, more than 220 scientists, industry leaders, ethicists, and policy makers from 10 countries will gather next week to plan #GPwrite https://t.co/IocGqb8ipY
    So far, more than 220 scientists, industry leaders, ethicists, and policy makers from 10 countries will gather next week to plan #GPwrite pic.twitter.com/IocGqb8ipY