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

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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. 1 2 3 How does the environment contribute to risk? (i.e. how does it influence brain development & function)

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

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Adapted from @BenLangmead

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Adapted from @BenLangmead

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

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Genome (DNA) Mapped reads Adapted from @jtleek

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Adapted from @BenLangmead

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Adapted from @BenLangmead 7

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Adapted from @BenLangmead

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Adapted from @BenLangmead 8

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

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http://bioconductor.org/packages/recount

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http://www.sciserver.org

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

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

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

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

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

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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

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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