Posts Tagged ‘jclub’

JClub papers

February 16, 2017

A #circadian gene-expr atlas in mammals by @jbhclock lab
http://www.PNAS.org/content/111/45/16219.abstract 43% of genes have a daily rhythm in at least 1 tissue [1/2]

.@jbhclock Fewest circadian genes in brain; most in liver. Perhaps this more reflects daily feeding cycle than true light-dark cycle? [2/2]

A circadian gene expression atlas in mammals: Implications for biology and medicine

Ray Zhanga,1,
Nicholas F. Lahensa,1,
Heather I. Ballancea,
Michael E. Hughesb,2, and
John B. Hogenescha,2

* Interestingly brain regions have the fewest circ genes(only ~3%), liver has most

* Diseases assoc with circadian genes correlate with NIH funding

* Genes can have up to a 6-hour phase diff. Between diff. organs (eg Vegfa betw. Heart & fat)

* 56 of the top 100 drugs incl. Top 7, targeted the product of a circadian gene. Related to the half-life of drugs.

* Could the liver genes be more reflective of feeding rhythm rather than true circadian clock.

Jclub Paper

January 28, 2017

#RNA Struc. Determinants of Optimal Codons…by MAGESeq
http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4 Probing effect of synonymous changes; towards a better dN/dS

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4

Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder : Nature Neuroscience : Nature Research

January 28, 2017

Genome-wide…analysis implicates miRNA dysregulation in #ASD http://www.nature.com/neuro/journal/v19/n11/full/nn.4373.html 58 diff. expr. miRNAs incl 17 strongly down in cases

http://www.nature.com/neuro/journal/v19/n11/full/nn.4373.html

QT:{{”
The miRNA expression profiles were very similar between the frontal and temporal cortex, but were distinct in the cerebellum
(Supplementary Fig. 2a–f), consistent with previous observations for mRNAs11, 12. We therefore combined 95 covariate-matched samples (47 samples from 28 ASD cases and 48 samples from 28 controls;
Supplementary Fig. 1c and Supplementary Table 1) from the FC and TC for differential gene expression (DGE) analysis, comparing ASD and CTL using a linear mixed-effects regression framework to control for potential confounders (Online Methods). We identified 58 miRNAs showing significant (false discovery rate (FDR) < 0.05) expression changes between ASD and CTL: 17 were downregulated and 41 were upregulated in ASD cortex (Fig. 1b and Supplementary Table 2). The fold changes for the differentially expressed miRNAs were highly concordant between the FC and TC (Pearson correlation coefficient R = 0.96, P < 2.2 × 10−16; Fig. 1c).
“}}

Jclub paper

January 16, 2017

The impact of #SVs on…gene expression
http://biorxiv.org/content/early/2016/06/09/055962 24k in 147 people in GTEx pilot act as causal variants in 3-7% of ~25k eQTLs

The impact of structural variation on human gene expression

Colby Chiang, Alexandra J Scott, Joe R Davis, Emily
K Tsang, Xin Li, Yungil Kim, Farhan N Damani, Liron Ganel, GTEx Consortium, Stephen B Montgomery, Alexis Battle, Donald F Conrad, Ira M Hall
doi: https://doi.org/10.1101/055962

new CommonMind paper

December 22, 2016

Gene expr. elucidates functional impact of…risk for SCZ
http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4399.html CMC resource contains >2.1M #eQTLs involving ~1.6M SNPs

NATURE NEUROSCIENCE | ARTICLE

Gene expression elucidates functional impact of polygenic risk for schizophrenia

Menachem Fromer,
Panos Roussos,
Solveig K Sieberts,
Jessica S Johnson,
David H Kavanagh,
Thanneer M Perumal,
Douglas M Ruderfer,
….
Eric E Schadt,
Keisuke Hirai,
Kathryn Roeder,
Kristen J Brennand,
Nicholas Katsanis,
Enrico Domenici,
Bernie Devlin
& Pamela Sklar

Gamma frequency entrainment attenuates amyloid load and modifies microglia : Nature : Nature Research

December 19, 2016

Gamma frequency entrainment attenuates amyloid load & modifies microglia http://www.nature.com/nature/journal/v540/n7632/full/nature20587.html Buying a 40 Hz light to fight Alzheimer’s!

Protein-structure-guided discovery of functional mutations across 19 cancer types : Nature Genetics : Nature Research

December 11, 2016

Protein-structure-guided discovery of functional mutations across 19 #cancer types http://www.nature.com/ng/journal/v48/n8/abs/ng.3586.html Cancer3D relates SNVs to drugs

http://www.nature.com/ng/journal/v48/n8/abs/ng.3586.html

A scored human protein-protein interaction network to catalyze genomic interpretation : Nature Methods : Nature Research

December 9, 2016

Scored…PPI #network to catalyze genomic interpretation http://www.Nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4083.html >500k links from lit. mining; up weights small-scale expt

Classification and characterization of microsatellite instability across 18 cancer types : Nature Medicine : Nature Research

December 4, 2016

http://www.nature.com/nm/journal/v22/n11/abs/nm.4191.html

"Classification and characterization of
microsatellite instability across 18 cancer types" by Hause,
Pritchard, Shendure and Salipante from Nature Medicine, 2016

Characterization of microsatellite instability across 18 cancer types http://www.nature.com/nm/journal/v22/n11/abs/nm.4191.html Classifier finds cancer-associated #MSI loci

Frustration in biomolecules | Quarterly Reviews of Biophysics | Cambridge Core

November 1, 2016

#Frustration in biomolecules
https://www.cambridge.org/core/journals/quarterly-reviews-of-biophysics/article/frustration-in-biomolecules/DECEA176849986FC11DB079C1EB4B24A Reviews the field: how large molecules pay a local price to achieve global stability