Posts Tagged ‘jclub’

Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression | eLife

April 21, 2018

Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression https://eLifeSciences.org/articles/25125 More noncoding than coding #allelic activity. Also, finding windows of allelic activity for chromatin

Daniel Andergassen,
Christoph P Dotter,
Daniel Wenzel,
Verena Sigl,
Philipp C Bammer,
Markus Muckenhuber,
Daniela Mayer,
Tomasz M Kulinski,
Hans-Christian Theussl,
Josef M Penninger,
Christoph Bock,
Denise P Barlow ,
Florian M Pauler ,
Quanah J Hudson

Research Center for Molecular Medicine of the Austrian Academy of Sciences, Austria;
Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Austria;
Institute of Molecular Pathology, Austria

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

March 18, 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

February 4, 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

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

January 6, 2018

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in #eQTL Studies http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000770 Early discussion & development of PEER factors

New Haven, CT Electricity Rates | Electricity Local

December 11, 2017

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

Batch Cloud Data Transfer Services – Amazon Snowball Appliance

December 9, 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

November 25, 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

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer | Bioinformatics | Oxford Academic

September 30, 2017

Assembly-based inference of Bcell receptor repertoires from..RNAseq w/
V’DJer https://academic.OUP.com/bioinformatics/article/32/24/3729/2525640/Assembly-based-inference-of-B-cell-receptor Less diversity assoc w/ long survival

Network propagation: a universal amplifier of genetic associations : Nature Reviews Genetics : Nature Research

September 11, 2017

#Network propagation [by Markov walks, heat flow, diffusion, &c]: a universal amplifier of genetic associations
http://www.Nature.com/nrg/journal/v18/n9/abs/nrg.2017.38.html

Lenore Cowen,
Trey Ideker,
Benjamin J. Raphael
& Roded Sharan

http://www.nature.com/nrg/journal/v18/n9/abs/nrg.2017.38.html?foxtrotcallback=true

Protein Structural Memory Influences Ligand Binding Mode(s) and Unbinding Rates – Journal of Chemical Theory and Computation (ACS Publications)

September 4, 2017

Structural Memory Influences Ligand-Binding Mode http://pubs.ACS.org/doi/abs/10.1021/acs.jctc.5b01052 Rearrangement of #solvation layer is ~100x slower than unbinding

J Chem Theory Comput. 2016 Mar 8;12(3):1393-9. doi:
10.1021/acs.jctc.5b01052. Epub 2016 Feb 3.

Xu M, Caflisch A, Hamm P.