Kandahar University training introduction

Introduction about my work for Kandahar University MPH training

Transcript

1. 11
   recount
   A large-scale resource of analysis-ready RNA-
   seq expression data
   Leonardo Collado-Torres
   @fellgernon
   

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2. ABOUT LIEBER
   WHAT ARE THE BIG QUESTIONS IN BRAIN
   RESEARCHTODAY?
   How do genes contribute to risk for psychiatric illness?
   (i.e. how do they influence brain development & function)
   How will new targets for the next generation of therapies
   be discovered andtested?
   LIBD was founded in 2010 to put under one roof a world-class team of
   scientists that could translate genetic insights into breakthrough treatments
   and bring them to market as quickly as possible.
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   How does the environment contribute to risk?
   (i.e. how does it influence brain development & function)
   

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3. Working at the intersection of environment, brain development and behavior, and
   genetic and epigenetic science.
   BASIC SCIENCES
   iPSC Models
   Model Cell Systems
   Developmental
   Electrophysiology
   Genome Informatics
   Neuropathology
   DRUG
   DISCOVERY
   Medicinal Chemistry
   Assay Development
   In vivo Behavioral
   Models
   CLINICAL
   Cognitive Neuroscience
   + Imaging Genetics
   Clinical Pharmacology
   + Pharmacogenetics
   Genetics, Epigenetics
   + Bioinformatics
   NOVEL
   TREATMENTS
   THE SCIENTIFIC FRONTIER
   LIBD’S MODEL CAPITALIZES ON SCIENTIFIC ADVANCES
   A non-profit biotech with end-to-end translational capabilities under one roof
   

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4. Research theme
   - annotation-agnostic
   - reproducible analyses
   - easily accessible data
   - statistical tools for the genomics community
   

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5. Adapted from @BenLangmead
   

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6. Adapted from @BenLangmead
   

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7. RNA-seq
   reads
   Genome
   (DNA)
   RNA transcripts
   (many possible
   variants)
   Measuring gene expression: RNA-seq
   Adapted from @jtleek
   

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8. Genome
   (DNA)
   Mapped reads
   Adapted from @jtleek
   

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9. Adapted from @BenLangmead
   

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10. Adapted from @BenLangmead
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11. Adapted from @BenLangmead
    

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12. Adapted from @BenLangmead
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13. recount: from the web
    https://jhubiostatistics.shinyapps.io/recount/
    

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14. http://bioconductor.org/packages/recount
    

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15. http://www.sciserver.org
    

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21. github.com/leekgroup/recount-website/blob/master/sciserver_demo
    

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22. github.com/leekgroup/recount-website/blob/master/sciserver_demo
    

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23. github.com/leekgroup/recount-website/blob/master/sciserver_demo
    

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24. github.com/leekgroup/recount-website/blob/master/sciserver_demo
    

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25. github.com/leekgroup/recount-website/blob/master/sciserver_demo
    

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27. ACKNOWLEDGEMENTS
    Authors
    Abhinav Nellore
    Kai Kammers
    Shannon Ellis
    Margaret Taub
    Kasper Hansen
    Andrew Jaffe
    Ben Langmead
    Jeffrey Leek
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    Collaborators
    Chris Wilks
    SciServer
    Funding
    NIH
    LIBD
    

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28. REFERENCES + SOFTWARE + CODE
    • Collado-Torres and Nellore, et al. bioRxiv (2016)
    • doi: 10.1101/068478
    • http://bioconductor.org/packages/recount
    • https://jhubiostatistics.shinyapps.io/recount
    • Nellore, Collado-Torres, et al. Bioinformatics (2016)
    • doi:10.1093/bioinformatics/btw575
    • rail.bio
    • Nellore, et al. bioRxiv (2016)
    • doi:10.1101/038224
    • intropolis.rail.bio
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