Building a Brain in the Lab
https://www.ScientificAmerican.com/article/building-a-brain-in-the-lab/ Nice summary of the development of organoids & their promise for personalized treatments
Posts Tagged ‘psychencode’
Building a Brain in the Lab – Scientific American
January 30, 2017Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder : Nature Neuroscience : Nature Research
January 28, 2017Genome-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).
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Jclub paper
January 16, 2017The 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
You’re an Adult. Your Brain, Not So Much.
December 26, 2016Your an adult. Your brain, not so much by @CarlZimmer
http://www.nytimes.com/2016/12/21/science/youre-an-adult-your-brain-not-so-much.html Non-obvious ethical implications of developmental neuroscience
QT:{{”
“The human brain reaches its adult volume by age 10, but the neurons that make it up continue to change for years after that. The connections between neighboring neurons get pruned back, as new links emerge between more widely separated areas of the brain.
Eventually this reshaping slows, a sign that the brain is maturing. But it happens at different rates in different parts of the brain.
The pruning in the occipital lobe, at the back of the brain, tapers off by age 20. In the frontal lobe, in the front of the brain, new links are still forming at age 30, if not beyond.
“It challenges the notion of what ‘done’ really means,” Dr. Somerville said.
As the anatomy of the brain changes, its activity changes as well. In a child’s brain, neighboring regions tend to work together. By adulthood, distant regions start acting in concert. Neuroscientists have speculated that this long-distance harmony lets the adult brain work more efficiently and process more information.”
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new CommonMind paper
December 22, 2016Gene 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
BrainSpan genotypes
December 9, 2016There are BrainSpan genotypes available through dbGAP:
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000406.v1.p1
Vernon Mountcastle, ‘father of neuroscience’ and longtime member of Johns Hopkins faculty, dies at 96 | Hub
December 9, 2016Spatiotemporal 16p11.2 Protein Network Implicates Cortical Late Mid-Fetal Brain Development and KCTD13-Cul3-RhoA Pathway in Psychiatric Diseases
November 15, 2016Spatiotemporal…Protein Network Implicates Cortical…Fetal Brain Development & KCTD13…RhoA Pathway in…Diseases
http://www.sciencedirect.com/science/article/pii/S0896627315000367
dyanamic PPI w brainspan data
Spatiotemporal 16p11.2 Protein Network Implicates Cortical Late Mid-Fetal Brain Development and KCTD13-Cul3-RhoA Pathway in
Psychiatric Diseases
Guan Ning Lin1, 5,
Roser Corominas1, 5,
Irma Lemmens2,
Xinping Yang3,
Jan Tavernier2,
David E. Hill3,
Marc Vidal3,
Jonathan Sebat1, 4,
Lilia M. Iakoucheva1,
R package: variancePartition
November 13, 2016https://bioconductor.org/packages/release/bioc/html/variancePartition.html
new tool in psychencode meeting
miRNA atlas
November 1, 2016Distribution of #miRNA expression across human tissues
http://nar.oxfordjournals.org/content/44/8/3865 Atlas of ~1400 RNAs in at least 1 of 61 tissues; 143 in all
linkstream2 microblog 