Posts Tagged ‘jclub’

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

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


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 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.

Whole-genome landscapes of major melanoma subtypes : Nature : Nature Research

September 4, 2017

Hayward, Nicholas K., et al. "Whole-genome landscapes of major melanoma subtypes." Nature 545.7653 (2017): 175-180.

Whole-genome landscapes of…#melanoma subtypes Sun-exposed cutaneous w. many C>T SNVs v acral/mucosal w. many SVs

Genome sequence-independent identification of RNA editing sites : Nature Methods : Nature Research

August 27, 2017

Genome seq–independent Identification of #RNAediting Accurate sites from uncorrelated SNV pair, spanned by reads

Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells

August 14, 2017

Naldi, A. et al. Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells. PLOS Computational Biology 13, e1005432 (2017).

Reconstruction & signal propagation analysis of the Syk signaling #network Inferring potential targets of the kinase

Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information

August 8, 2017

#mHealth: Tracking Physiomes & Activity w/ Wearable Biosensors, by @SnyderShot et al >250K/day data pts on 43 people

Evaluation Of Chromatin Accessibility In Prefrontal Cortex Of Schizophrenia Cases And Controls | bioRxiv

July 31, 2017

Eval of Chromatin Accessibility [via #ATACSeq] in DLPFC of SCZ Cases/Ctrls, by @JulienBryois et al. List of cQTLs

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak — NEJM

July 22, 2017

WGS & Social-#Network Analysis of a TB Outbreak Nice tech combo but not sure transmission & phylogeny are consistent

Zika virus evolution and spread in the Americas : Nature : Nature Research

June 25, 2017

#Zika virus evolution & spread in the Americas, by @sabeti_lab #Phylogeny reconstruction of 110 new + 64 known seqs.

Journal Club Paper

June 18, 2017

Zhou, J. and Troyanskaya, O.G. (2015). Predicting effects of noncoding variants with deep learning–based sequence model. Nature Methods, 12, 931–934.

Predicting (& prioritizing) effects of noncoding variants w. [DeepSEA] #DeepLearning…model Trained w #ENCODE data