Archive for August, 2014

PLOS Computational Biology: Target Essentiality and Centrality Characterize Drug Side Effects

Thursday, August 7th, 2014

Target Essentiality… Characterizes Drug Side Effects – much more so than the total number of targets for a #drug
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.100311

Dissecting Disease Inheritance Modes in a Three-Dimensional Protein Network Challenges the “Guilt-by-Asso ciation” Principle

Thursday, August 7th, 2014

Inheritance Modes in… #Network Challenges… Guilt-by-Association http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710751 #Diseases of recessive interface SNVs predictable

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710751/

surprisingly, no positional effects on LOF mutations … significant proportion of truncation alleles give rise to functional products

“guilt by assoc works”

signif. number dom mut give rise to func products

Activating Mutations Cluster in the “Molecular Brake” Regions of Protein Kinases and Do Not Associate w ith Conserved or Catalytic Residues

Thursday, August 7th, 2014

Activating Mutations Cluster in… Regions of… #Kinases & Do Not Associate with Conserved or Catalytic Residues
http://onlinelibrary.wiley.com/doi/10.1002/humu.22493/abstract

related to Kin-Driver – a database of driver mutations, which can be used as a gold std in driver predictions

The Skyscraper Boom That’s Going To Make American Cities Way Taller

Monday, August 4th, 2014

http://gizmodo.com/why-so-many-american-cities-are-suddenly-getting-taller-1614693798?utm_campaign=socialflow_gizmodo_twitter&utm_source=gizmodo_twitter&utm_medium=socialflow

Oncotator

Monday, August 4th, 2014

http://www.broadinstitute.org/oncotator
https://github.com/broadinstitute/oncotator

Useful listing of data sources, viz:

QT:{{”

Protein Annotations

Site-specific protein annotations from UniProt.
Druggable target data from DrugBank.
Functional impact predictions from PolyPhen-2.

Cancer Annotations

Observed cancer mutation frequency annotations from COSMIC.
Cancer gene and mutation annotations from the Cancer Gene Census. Significant amplification/deletion region annotations from Tumorscape and theTCGA Copy Number Portal.
Overlapping Oncomap mutations from the Cancer Cell Line Encyclopedia. Significantly mutated gene annotations aggregated from published MutSiganalyses. Cancer gene annotations from the Familial Cancer Database.
Human DNA Repair Gene annotations from Wood et al.

“}}

Uses bamboo testing software
https://www.atlassian.com/software/bamboo

Somatic mosaicism

Sunday, August 3rd, 2014

http://www.nytimes.com/2014/07/31/science/having-more-than-one-set-of-dna-carries-legacy-of-risk.html?partner=rss&emc=rss&_r=0

Is Sleep Essential?

Sunday, August 3rd, 2014

Is Sleep Essential?
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060216 Amusing evidence from varied animals, eg 1-hemisphere dolphin #sleep & dying sleep-deprived rats

Flurrish – Times Table

Sunday, August 3rd, 2014

Jason H. Moore, Ph.D @moorejh · Jul 5
MT @randal_olson #visualization of the hardest parts of the
multiplication table #math #edchat
http://www.flurrished.co.uk/blog/2013/07/03#the_hardest_times%20table

MT @moorejh @randal_olson #viz of hardest parts of the times table; note, difficulty of 10*11
http://www.flurrished.co.uk/blog/2013/07/03#the_hardest_times%20table http://pic.twitter.com/hAeVd49XZX

http://www.flurrished.co.uk/blog/2013/07/03#the_hardest_times%20table

Notes from NHGRI planning mtg. on Future Opportunities for Genome Sequencing and Beyond

Sunday, August 3rd, 2014

Took lots of notes at the NHGRI planning meeting,

http://www.genome.gov/27558232

http://new.livestream.com/accounts/2556895/events/3137731

(session I was in
http://new.livestream.com/accounts/2556895/events/3137731/videos/57826515)

Saved “public” versions of these as a storified tweet-stream, viz:

https://storify.com/markgerstein/tweets-related-to-nhgri-planning-meeting-gspfuture

Also tagged lots of sites & papers that I discovered at the meeting, viz: http://linkstream2.gerstein.info/tag/i0gspplan

My (very brief) talk from the meeting:
http://lectures.gersteinlab.org/summary/NHGRI-Breakout-Session-func-n-variants-summary-MG-1030p

Some of my “private” notes (need passwords) are:

https://mail.google.com/mail/u/0/#search/i0gspplan

http://archive.gersteinlab.org/meetings/s/2014/08.03/i0gspplan

How to Install Screen Protector on Tablet

Sunday, August 3rd, 2014

http://www.armorsuit.com/screen-protector-tablet