Posts Tagged ‘gg’

scientists on twitter: preaching to the choir or singing from the rooftops?

July 11, 2018

http://www.facetsjournal.com/doi/full/10.1139/facets-2018-0002#.WzmasWXTsqo.twitter

Leonardo Da Vinci’s DNA

July 1, 2018

original announcement here:
https://www.eurekalert.org/pub_releases/2016-05/tca-ldv050316.php Rumors that they will make his DNA public very soon.

DNA by numbers

June 26, 2018

https://www.forensicmag.com/article/2015/10/dna-numbers)
work related to DNA leakage in daily life

mammalian tissue expression database

June 1, 2018

curated tissue expression database for mammalians: human, mouse, rat, pig

web: https://tissues.jensenlab.org/
paper: https://academic.oup.com/database/article/doi/10.1093/database/bay003/4851151 a relevant figure:
https://academic.oup.com/view-large/figure/112879298/bay003f2.tif

Augmented reality for macromolecule viewing

April 22, 2018

Incredible Android app for AR viewing of macromolecules http://CIRC.Rutgers.edu/new-dimension-poster-presentation Especially neat when pointed at another phone or tablet. Shows the molecule literally coming out of the screen HT @gamzeandgursoy

an app that might be interesting: When you look at the molecule pictures that are called triggers through this
app, it shows them three dimensional in different angles. You can even
create movie type augmented realities.

systematic comparison of dnase-seq & atac-seq

April 21, 2018

Reproducible inference of TF footprints in #ATACseq & DNase-seq…via protocol-specific bias modeling
https://www.BiorXiv.org/content/early/2018/03/19/284364 Systematic comparison of the 2 assay HT @gamzeandgursoy

info theory book by Cover&Thomas

April 5, 2018

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

DNA Tattoos Are the Final Frontier of Love

December 18, 2017

DNA 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 “