Posts Tagged ‘fromjclub’

Today: Jason Moore, Computational Biology and Bioinformatics speaker, 6-6-18 in BML Auditorium at 4 pm

Friday, June 8th, 2018

https://linkstream2.gerstein.info/tag/talk20180606/
https://twitter.com/MarkGerstein/status/1004566413036617728

Papers for Journal Club

Thursday, June 7th, 2018

Alternative evolutionary histories in the sequence space of an ancient protein https://www.Nature.com/articles/nature23902 Great viz of different potential but not necessarily realized evolutionary trajectories. Quite relevant for molecular #evolution & #pseudogenes

Paper for Journal Club Tomorrow

Tuesday, May 22nd, 2018

Susceptibility of brain atrophy to TRIB3 in #Alzheimer’s disease, evidence from functional prioritization in imaging genetics
http://www.PNAS.org/content/115/12/3162.long Nice connection of developing phenotypes from #imaging, combined w. simple polygenic scores from genotypes

ADNI Website

Sunday, May 20th, 2018

http://adni.loni.usc.edu/

Genome-Scale Signatures of Gene Interaction from Compound Screens Predict Clinical Efficacy of Targeted Cancer Therapies – ScienceDirect

Sunday, April 29th, 2018

Genome-Scale Signatures of Gene Interaction from #CompoundScreens Predict…Efficacy of Targeted Cancer Therapies
https://www.ScienceDirect.com/science/article/pii/S2405471218300097 How to find drug combos: Find expression response profiles associated w/ a drug target. A synergistic drug might change profiles similarly

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data | Nature Genetics

Monday, March 19th, 2018

Fast, scalable prediction of deleterious #noncoding variants from functional & population genomic data
https://www.Nature.com/articles/ng.3810 LINSIGHT, by @ASiepel et al., combines DNAse & conservation information

Yi-Fei Huang, Brad Gulko & Adam Siepel
Nature Genetics 49, 618–624 (2017)
doi:10.1038/ng.3810
Published online:
13 March 2017

JClub by BW on “3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets”, Genome Medicine

Monday, February 5th, 2018

3D clusters of somatic mutations…reveal numerous rare mutations as functional targets
https://GenomeMedicine.BiomedCentral.com/articles/10.1186/s13073-016-0393-x Introduces 3DHotSpots, which is one of a number of recent approaches (incl. CLUMPS, Hotspot3D, Mutation3D & HotMAPS) for finding groupings of somatic SNVs via structure

New Haven, CT Electricity Rates | Electricity Local

Tuesday, December 12th, 2017

Useful
https://www.electricitylocal.com/states/connecticut/new-haven/

Batch Cloud Data Transfer Services – Amazon Snowball Appliance

Saturday, December 9th, 2017

Batch Cloud Data Transfer for @AWScloud
https://AWS.amazon.com/snowball & https://AWS.amazon.com/snowmobile Snail mail trumps email for really large data. Interesting to calculate effective transfer rates as compared “Ethernet.” Surprised that I couldn’t find even crude estimates.

Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins

Sunday, November 26th, 2017

Accurate Prediction of Contact Numbers for Multi-Spanning Helical #MembraneProteins – via #NeuralNetwork w/ dropout
http://pubs.ACS.org/doi/abs/10.1021/acs.jcim.5b00517 In turn, this can enable accurate prediction of the rotation of TM helices & then the 3D #StructurePrediction of the whole protein