PEC package preprints

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This is the page gives an overview of the Yale contribution to Dec. '18 PsychENCODE rollout. (This is a "private page" to those who have the link.)
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This is the page gives an overview of the Yale contribution to Dec. '18 PsychENCODE rollout.  
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(This is a '''"private page"''' to those who have the link. Please do NOT redistribute material on this page without explicit permission.)
== PsychENCODE introduction ==
== PsychENCODE introduction ==
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*[http://files.gersteinlab.org/public-docs/2018/11.29/aaw0544_ArticleContent-further-suggestions-28nov18.notrk.docx  ''Introduction (draft as of 28-Nov.)'']
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*[http://files.gersteinlab.org/public-docs/2018/11.29/aaw0544_ArticleContent-further-suggestions-28nov18.notrk.docx  Draft of introduction as of 28-Nov.]
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== Capstone papers from Yale==
== Capstone papers from Yale==
*Developmental Capstone - [http://files.gersteinlab.org/public-docs/2018/11.19/Li_S18_aat7615_Combined.pdf '''Integrative Functional Genomic Analysis of Human Brain Development and Neuropsychiatric Risk''']
*Developmental Capstone - [http://files.gersteinlab.org/public-docs/2018/11.19/Li_S18_aat7615_Combined.pdf '''Integrative Functional Genomic Analysis of Human Brain Development and Neuropsychiatric Risk''']
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*Adult Capstone - [http://files.gersteinlab.org/public-docs/2018/11.20/Wang_S18_aat8464_Combined_nofig.pdf '''Comprehensive functional genomic resource and integrative model for the human brain''']
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**[http://development.psychencode.org/ Development.psychencode.org] & [http://brainspan.org/ BrainSpan.org]
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**[http://files.gersteinlab.org/public-docs/2018/11.20/Wang_S18_aat8464_Combined_fig.pdf '''Figures''']
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*Adult Capstone - [http://files.gersteinlab.org/public-docs/2018/11.20/Wang_S18_aat8464_Combined_nofig.pdf '''Comprehensive functional genomic resource and integrative model for the human brain''']  
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**[http://files.gersteinlab.org/public-docs/2018/11.20/capstone4-summary-text.pdf '''One page summary'''] (Summary [http://files.gersteinlab.org/public-docs/2018/12.05/capstone4-summary-graphic-Screenshot.png Figure])
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**Main text: [https://www.dropbox.com/s/pm08ztoffxvg603/aat8464_galley_revised.pdf?dl=0 '''Proofs'''], [http://files.gersteinlab.org/public-docs/2018/12.05/Wang_S18_aat8464_Combined_fig_resized2.pdf Figures]
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**'''One page summary''': [https://www.dropbox.com/s/z3rotgy5nx5hrg7/aat8464_summary_revised.pdf?dl=0 '''Proofs'''], [http://files.gersteinlab.org/public-docs/2018/11.20/capstone4-summary-text.pdf Text], [http://files.gersteinlab.org/public-docs/2018/12.05/capstone4-summary-graphic-Screenshot.png Figure]
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**Fun pics of  cell-type specfic regulatory networks, based on single-cell data ([https://www.dropbox.com/s/ttnoefsjmux79kn/celltype_GRN_forpress.jpg?dl=0 Big JPEG Wheel]) ([http://files.gersteinlab.org/public-docs/2018/12.05/CellType_Rasterized.pdf PDF blow-ups])
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**Lectures on the Adult Capstone: [http://lectures.gersteinlab.org/summary/Using-population-scale-functional-genomics-mental-disease-n-exploiting-data-exhaust-20181025-i0sigma/ i0sigma], [http://lectures.gersteinlab.org/summary/Pop-scale-genomics-for-mental-disease-n-privacy-risks--20180921-i0mssm18/ i0mssm18]
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**[http://resource.psychencode.org/ '''Resource'''.psychencode.org]
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== Other main Yale papers ==
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== Other Yale papers ==
*[http://files.gersteinlab.org/public-docs/2018/11.20/Amiri_S18_aat6720_CombinedPDF.pdf '''Transcriptome and epigenome landscape of human cortical development modeled in brain organoids''']
*[http://files.gersteinlab.org/public-docs/2018/11.20/Amiri_S18_aat6720_CombinedPDF.pdf '''Transcriptome and epigenome landscape of human cortical development modeled in brain organoids''']
**[http://files.gersteinlab.org/public-docs/2018/11.20/Amiri_S18_aat6720_OnePageSummary.pdf '''One page summary''']
**[http://files.gersteinlab.org/public-docs/2018/11.20/Amiri_S18_aat6720_OnePageSummary.pdf '''One page summary''']
*[http://files.gersteinlab.org/public-docs/2018/11.19/Zhu_S18_aat8077_CombinedPDF_v6.pdf '''Spatiotemporal transcriptomic divergence across human and macaque brain development''']
*[http://files.gersteinlab.org/public-docs/2018/11.19/Zhu_S18_aat8077_CombinedPDF_v6.pdf '''Spatiotemporal transcriptomic divergence across human and macaque brain development''']
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**[http://evolution.psychencode.org/ Evolution.psychencode.org]
==Listing of all the Papers in Science==
==Listing of all the Papers in Science==
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1.    Li et al, aat7615, Integrative Functional Genomic Analysis of Human Brain Development and Neuropsychiatric Risk. This is one of the 3 capstone papers. Topic: It’s the only one that talks about all main topics of the consortium: development, adult and disorders. Also the intro is broad and serves as a good intro to the whole consortium.
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*Capstones
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# Li et al, aat7615, Integrative Functional Genomic Analysis of Human Brain Development and Neuropsychiatric Risk.  
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2.    Gandal et al, aat8127, Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder This is one of the 3 capstone papers. Topic: Disease brains.
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# Gandal et al, aat8127, Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder
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# Wang et al, aat8464, Comprehensive functional genomic resource and integrative model for the human brain.
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3.    Wang et al, aat8464, Comprehensive functional genomic resource and integrative model for the human brain. This is one of the 3 capstone papers. Topic: Integrated analysis of all data from adult brains.
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*Other Papers
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# Zhu et al, aat8077, Spatiotemporal transcriptomic divergence across human and macaque brain development.  
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4.    Zhu et al, aat8077, Spatiotemporal transcriptomic divergence across human and macaque brain development. Topic: This paper on the evolution of human brain development (human vs macaque comparison) and the data is extensively used by Amiri aat6720.  
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# Amiri et al, aat6720, Transcriptome and epigenome landscape of human cortical development modeled in brain organoids.  
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# Rajarajan et al, aat4311, Neuron-specific Signatures in the Chromosomal Connectome Associated with Schizophrenia Risk.  
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5.    Amiri et al, aat6720, Transcriptome and epigenome landscape of human cortical development modeled in brain organoids. Topic: Human brain development in vitro, evolutionary comparisons and relevance to developmental diseases.
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# An et al, aat6576, Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder.
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6.    Rajarajan et al, aat4311, Neuron-specific Signatures in the Chromosomal Connectome Associated with Schizophrenia Risk. Topic: New schizophrenia and in vitro development data as well as integrated analyses including data from the 3 capstone papers.
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7.    An et al, aat6576, Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Topic: Autism WGS data and integrated analysis with mainly data from Li aat7615 and Wang aat8464.
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Latest revision as of 15:43, 9 December 2018

This is the page gives an overview of the Yale contribution to Dec. '18 PsychENCODE rollout.

(This is a "private page" to those who have the link. Please do NOT redistribute material on this page without explicit permission.)

Contents

PsychENCODE introduction

Capstone papers from Yale

Other Yale papers

Listing of all the Papers in Science

  • Capstones
  1. Li et al, aat7615, Integrative Functional Genomic Analysis of Human Brain Development and Neuropsychiatric Risk.
  2. Gandal et al, aat8127, Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder
  3. Wang et al, aat8464, Comprehensive functional genomic resource and integrative model for the human brain.
  • Other Papers
  1. Zhu et al, aat8077, Spatiotemporal transcriptomic divergence across human and macaque brain development.
  2. Amiri et al, aat6720, Transcriptome and epigenome landscape of human cortical development modeled in brain organoids.
  3. Rajarajan et al, aat4311, Neuron-specific Signatures in the Chromosomal Connectome Associated with Schizophrenia Risk.
  4. An et al, aat6576, Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder.
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