Archive for the 'SciLit' Category

Post-transcriptional regulation across human tissues

July 16, 2017

Post-transcriptional reg…across…tissues [v genes], by @SlavovLab http://journals.PLoS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005535 Simpson’s paradox! Diff in protein-mRNA corr.

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

July 10, 2017

https://www.researchgate.net/publication/291391911_The_Cellular_and_Molecular_Landscapes_of_the_Developing_Human_Central_Nervous_System

good dev fig?

Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. – PubMed – NCBI

July 10, 2017

https://www.ncbi.nlm.nih.gov/pubmed/24267887

Cell. 2013 Nov 21;155(5):1008-21. doi: 10.1016/j.cell.2013.10.031.

Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism.

Parikshak NN1, Luo R, Zhang A, Won H, Lowe JK, Chandran V, Horvath S, Geschwind DH.

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies : Nature Genetics : Nature Research

July 10, 2017

http://www.nature.com/ng/journal/v47/n3/full/ng.3211.html

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. – PubMed – NCBI

July 10, 2017

https://www.ncbi.nlm.nih.gov/pubmed/24267886

Cell. 2013 Nov 21;155(5):997-1007. doi: 10.1016/j.cell.2013.10.020.

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.

Willsey AJ1, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW.

Using brainspan to see where ASD genes are enriched in certain developmental times

Integrated Model of De Novo and Inherited Genetic Variants Yields Greater Power to Identify Risk Genes

July 10, 2017

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003671

TADA tool, integrates evidence

Integrated Model of De Novo and Inherited Genetic Variants Yields Greater Power to Identify Risk Genes
Xin He,
Stephan J. Sanders,
Li Liu,
Silvia De Rubeis,
Elaine T. Lim,
James S. Sutcliffe,
Gerard D. Schellenberg,
Richard A. Gibbs,
Mark J. Daly,
Joseph D. Buxbaum,
Matthew W. State,
Bernie Devlin,
Kathryn Roeder

logo.plos.95.png

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways : Nature Neuroscience : Nature Research

July 10, 2017

https://www.nature.com/neuro/journal/v18/n2/full/nn.3922.html
older stats approach

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways : Nature Neuroscience : Nature Research

A comprehensive review of genetic association studies. – PubMed – NCBI

July 10, 2017

https://www.ncbi.nlm.nih.gov/pubmed/11882781

QT:{{"
We find that over 600 positive associations between common gene variants and disease have been reported; these associations, if correct, would have tremendous importance for the prevention, prediction, and treatment of most common diseases. However, most reported associations are not robust: of the 166 putative associations which have been studied three or more times, only 6 have been consistently replicated.

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Searching for missing heritability: Designing rare variant association studies

July 10, 2017

http://www.pnas.org/content/111/4/E455.abstract

Genetic architectures of psychiatric disorders: the emerging picture and its implications. – PubMed – NCBI

July 10, 2017

https://www.ncbi.nlm.nih.gov/pubmed/22777127
has a nice plot showing heritability of these conditions