Posts Tagged ‘brainspan’

Thoughts on the PsychENCODE workshop & Psychiatric Genomics in the Era of Team Science – 2 recent DC meetings on Neurogenomics

July 10, 2017

https://linkstream2.gerstein.info/tag/i0pec17/

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

Single Cell Analysis paper

June 30, 2017

http://genome-tech.ucsd.edu/public/Lake_Science_2016/
https://twitter.com/mikejg84/status/880240608144531456

16 Neuronal subtypes & [inter-regional] diversity revealed by [#singlecell]-nucleus RNAseq of…the brain
http://science.sciencemag.org/content/352/6293/1586.long

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain.
Lake BB, Ai R, Kaeser GE, Salathia NS, Yung YC, Liu R, Wildberg A, Gao D, Fung HL, Chen S, Vijayaraghavan R, Wong J, Chen A, Sheng X, Kaper F, Shen R, Ronaghi M, Fan JB, Wang W, Chun J, Zhang K.
Science. 2016 Jun 24;352(6293):1586-90. doi: 10.1126/science.aaf1204.

A comprehensive transcriptional map of primate brain development

June 19, 2017

A…transcriptional map of primate (macaque) #brain development http://www.Nature.com/nature/journal/vaop/ncurrent/full/nature18637.html Gene expression changes more rapidly before birth
Nature (2016) doi:10.1038/nature18637

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors : Nature Genetics : Nature Research

May 6, 2017

http://www.nature.com/ng/journal/v49/n5/full/ng.3818.html

Ref component analysis..of transcriptomes, by @Robson_Paul &co http://www.Nature.com/ng/journal/v49/n5/full/ng.3818.html Clustering similarity of samples to tissue references

You’re an Adult. Your Brain, Not So Much.

December 26, 2016

Your 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.”
“}}

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

BrainSpan genotypes

December 9, 2016

There are BrainSpan genotypes available through dbGAP:
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000406.v1.p1

Spatiotemporal 16p11.2 Protein Network Implicates Cortical Late Mid-Fetal Brain Development and KCTD13-Cul3-RhoA Pathway in Psychiatric Diseases

November 15, 2016

Spatiotemporal…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,

http://dx.doi.org/10.1016/j.neuron.2015.01.010

miRNA atlas

November 1, 2016

Distribution 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

https://ccb-web.cs.uni-saarland.de/tissueatlas/