Archive for the 'SciLit' Category

The Cancer Genome Atlas: Creating Lasting Value beyond Its Data

June 15, 2018

Commentary
The Cancer Genome Atlas: Creating Lasting Value beyond Its Data Carolyn Hutter + Jean Claude Zenklusen

https://www.sciencedirect.com/science/article/pii/S009286741830374X

Papers for Journal Club

June 7, 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

Potential role for microglia in Alzheimer’s

June 2, 2018

http://www.sciencemag.org/news/2016/03/alzheimer-s-may-be-caused-haywire-immune-system-eating-brain-connections

Alzheimer’s may be caused by haywire immune system eating brain connections Study targets new mechanism in fight against cognitive decline

Computationally-designed synthetic protein assemblies that evolve like viruses | Nature Research Microbiology Community

May 22, 2018

Evolution of a designed protein assembly encapsulating its own RNA genome https://www.Nature.com/articles/nature25157 The opposite, in a sense, of #BioInspired. Computational design of man-made virus capsid

ALSO:

Computationally-designed synthetic protein assemblies that evolve like viruses | Nature Research Microbiology Community

https://naturemicrobiologycommunity.nature.com/users/75986-gabriel-butterfield/posts/29055-computationally-designed-synthetic-protein-assemblies-that-evolve-like-viruses

Paper for Journal Club Tomorrow

May 22, 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

Multi-day rhythms modulate seizure risk in epilepsy | Nature Communications

May 1, 2018

https://www.nature.com/articles/s41467-017-02577-y

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

April 28, 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

Cryo-EM structure of substrate-bound human telomerase holoenzyme | Nature

April 28, 2018

#CryoEM structure of substrate-bound human telomerase holoenzyme https://www.Nature.com/articles/s41586-018-0062-x Quote: “2 flexibly RNA-tethered lobes: the catalytic core (w/ #TERT & conserved motifs of telomerase RNA) & an H/ACA RNP”

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

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