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Kandahar University training introduction

Kandahar University training introduction

Introduction about my work for Kandahar University MPH training


Leonardo Collado-Torres

December 26, 2016

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  1. 11 recount A large-scale resource of analysis-ready RNA- seq expression

    data Leonardo Collado-Torres @fellgernon

    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. 1 2 3 How does the environment contribute to risk? (i.e. how does it influence brain development & function)
  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
  4. Research theme - annotation-agnostic - reproducible analyses - easily accessible

    data - statistical tools for the genomics community
  5. Adapted from @BenLangmead

  6. Adapted from @BenLangmead

  7. RNA-seq reads Genome (DNA) RNA transcripts (many possible variants) Measuring

    gene expression: RNA-seq Adapted from @jtleek
  8. Genome (DNA) Mapped reads Adapted from @jtleek

  9. Adapted from @BenLangmead

  10. Adapted from @BenLangmead 7

  11. Adapted from @BenLangmead

  12. Adapted from @BenLangmead 8

  13. recount: from the web https://jhubiostatistics.shinyapps.io/recount/

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

  15. http://www.sciserver.org

  16. None
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  21. github.com/leekgroup/recount-website/blob/master/sciserver_demo

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

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

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

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

  26. None
  27. ACKNOWLEDGEMENTS Authors Abhinav Nellore Kai Kammers Shannon Ellis Margaret Taub

    Kasper Hansen Andrew Jaffe Ben Langmead Jeffrey Leek 27 Collaborators Chris Wilks SciServer Funding NIH LIBD
  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 28