http://www.cs-114.org/wp-content/uploads/2015/01/Elements_of_Information_Theory_Elements.pdf
local copy at
http://meetings.gersteinlab.org/2018/04.05/Cover%20Thomas%202006_-_Elements_of_Information_Theory_2nd_Ed.pdf
Posts Tagged ‘from_gg’
info theory book by Cover&Thomas
April 5, 2018DNA Tattoos Are the Final Frontier of Love
December 18, 2017DNA Tattoos Are the Final Frontier of Love
https://www.NYTimes.com/2017/12/09/style/dna-tattoos.html Putting some DNA into tattoo ink via @Everence_Life. But what of putting tattoos into non-functional DNA with CRISPR? Maybe next? HT @gamzeandgursoy
QT:{{
Four years, a handful of dedicated colleagues and nearly a dozen patents later, Mr. Duffy has brought the idea to life with Everence, a product he and his partners hope will deepen bonds — in the most literal and physical way — between family, friends and loved ones. It is about as biologically intimate as one can get. Everence is a powdery substance synthesized from a sample of DNA, something as simple as a few thousand cells from a swab of a person’s inner cheek, or from cremated ashes. A small vial of Everence can be brought to a tattoo artist and added to any type of inks.
The result: A tattoo imbued with the DNA of another human being — or, if you prefer, a dog, cat or other furry friend.
In so doing, Mr. Duffy and Endeavor Life Sciences, his company, join the ranks of a winding list of biohackers, artists and technologists dabbling in the world of biogenic tattoo artistry. Many have mixed ash, hair or other material with inks to include organics in tattooing for years.
“}}
google released variant calling with deep learning
December 16, 2017$GOOG Is Giving Away AI That Can Build Your Genome Seq. https://Research.GoogleBlog.com/2017/12/deepvariant-highly-accurate-genomes.html + https://www.Wired.com/story/google-is-giving-away-ai-that-can-build-your-genome-sequence GATK creators now doing a tensor-flow version. Release sounded a bit like IBM unveiling Deep Blue decades ago: “Today, we announce…DeepVariant, a #DeepLearning tech…"
Steven Salzberg’s response to deep variant:
https://www.forbes.com/sites/stevensalzberg/2017/12/11/no-googles-new-ai-cant-build-your-genome-sequence/#5953db7b5774
QT:{{"On Monday, Google released a tool called DeepVariant that uses deep learning—the machine learning technique that now dominates AI—to identify all the mutations that an individual inherits from their parents.1 Modeled loosely on the networks of neurons in the human brain, these massive mathematical models have learned how to do things like identify faces posted to your Facebook news feed, transcribe your inane requests to Siri, and even fight internet trolls. And now, engineers at Google Brain and Verily (Alphabet’s life sciences spin-off) have taught one to take raw sequencing data and line up the billions of As, Ts, Cs, and Gs that make you you.”
"}}
Google Is Giving Away AI That Can Build Your Genome Sequence
https://www.wired.com/story/google-is-giving-away-ai-that-can-build-your-genome-sequence/
differential privacy
November 29, 2017”
Box 1 of the following paper has a nice definition for differential privacy in genomics sense (phenotypic differential privacy): http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30121-1 “
link to nasa+starry night t-shirt
August 22, 2017Here is the link:
https://teechip.com/nasa-yy#id=0&c=131313&sid=fruit-of-the-loom-cotton-t&s=front
There is this one too :
Finally, they also made an eclipse one :
https://pro.teechip.com/sc-ns-ec
link to nasa+starry night t-shirt
May 6, 2017whole genome assembly from Hi-C data
April 2, 2017De novo assembly of the A aegypti genome using #HiC, by @erezaterez et al http://science.ScienceMag.org/content/early/2017/03/22/science.aal3327.full Works on human too, w. promise for #SVs
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
Olga Dudchenko1,2,3,4,
Sanjit S. Batra1,2,3,*,
Arina D. Omer1,2,3,*,
Sarah K. Nyquist1,3,
Marie Hoeger1,3,
Neva C. Durand1,2,3,
Muhammad S. Shamim1,2,3,
Ido Machol1,2,3,
Eric S. Lander5,6,7,
Aviva Presser Aiden1,2,8,9,
Erez Lieberman Aiden1,2,3,4,5,†
Science 23 Mar 2017:
eaal3327
DOI: 10.1126/science.aal3327
on whole genome assembly from Hi-C reads. There is also some info on chromosomal rearrangement from Hi-C.
Classification and characterization of microsatellite instability across 18 cancer types : Nature Medicine : Nature Research
December 4, 2016http://www.nature.com/nm/journal/v22/n11/abs/nm.4191.html
"Classification and characterization of
microsatellite instability across 18 cancer types" by Hause,
Pritchard, Shendure and Salipante from Nature Medicine, 2016
Characterization of microsatellite instability across 18 cancer types http://www.nature.com/nm/journal/v22/n11/abs/nm.4191.html Classifier finds cancer-associated #MSI loci
linkstream2 microblog 