PLoS Genetics

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Outline Background Transcriptional Regulation, ENCODE, ChIP-Seq Selected Projects from my PhD work Understanding the technical aspects of ChIP-Seq scoring and how choice of reference sample matters Using high-throughput sequencing to gain a genome-wide view of chromatin remodeling (SWI/SNF complex) Understanding the effects of long-range interactions and genome folding on transcription CAPE: a tool to classify features by RNAPII binding and gene expression 2
g DNA folding Transcriptional Regulation: A Cartoon View TF combinations DNA folding Site-specific binding Holstege and Young, PNAS, 1999 Histone modifications Chromatin remodeling 3 Credit: Adam Steinberg
Page 1: Elucidating Transcriptional Regulat
Page 5 and 6: ChIP-Seq 5
Page 7 and 8: Highlights from Key Papers Nature B
Page 9 and 10: Origin of Input DNA from Nuclear Ly
Page 11 and 12: Reference Types We Examined Input D
Page 13 and 14: Aggregation Plot Expressed Genes (T
Page 15 and 16: Regions Associated with Transcripti
Page 17 and 18: Summary and Bioinformatics Contribu
Page 19 and 20: Considerations with Early Peak Call
Page 21 and 22: Chromatin Remodeling: Why You Shoul
Page 23 and 24: Role in Cancer SWI/SNF subunit Canc
Page 25 and 26: Project Overview Analysis Questions
Page 27 and 28: How to Combine Data 27
Page 29 and 30: SWI/SNF Co-occurrences CTCF, Pol II
Page 31 and 32: Pathway Analysis Euskirchen and Aue
Page 33 and 34: Summary and Bioinformatics Contribu
Page 35 and 36: Exploring Transcription, DNA Foldin
Page 37 and 38: So How Does ChIA-PET Work (Cliffs N
Page 39 and 40: The Textbook Version 39
Page 41 and 42: Second Goal - Formation of Protein
Page 43 and 44: Gene Expression Characteristics Li,
Page 45 and 46: IRS1 and T2D: Long Range Interactio
Page 47 and 48: Bioinformatics Contributions Integr
Page 49 and 50: Combining RNAPII ChIP-Seq with RNA-
Page 51 and 52: CAPE: Coupled Analysis of Polymeras
Page 53 and 54:
Sample CAPE-compare Output (raw) 53
Page 55 and 56:
Sample CAPE-compare Output (Venn) 5
Page 57 and 58:
Other Work While at Yale Co-author
Page 59:
Questions 59
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