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Sean Thomas

Who is this guy and why is he talking to me?. Sean Thomas. BA Architecture, BS Biology 2000. PhD Molecular Biology, 2006. currently: Staff Research Scientist, Gladstone Institutes Adjunct Assistant Professor, UCSF Biostatistics Lead Bioinformatics Consultant, CTSI. Hedgehog. Fox.

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Sean Thomas

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  1. Who is this guy and why is he talking to me? Sean Thomas BA Architecture, BS Biology 2000 PhD Molecular Biology, 2006 currently: Staff Research Scientist, Gladstone Institutes Adjunct Assistant Professor, UCSF Biostatistics Lead Bioinformatics Consultant, CTSI

  2. Hedgehog Fox

  3. Productive collaborations (last 5 years) Principle Investigators and Companies Study Focus Publications Anna Bakardjiev Mark Biggin Benoit Bruneau Laura Buttitta Scott Hansen Daniel Hart Peter Myler Melanie Ott Pacific Biosciences Deepak Srivastava John Stamatoyannopoulos Chuck Murry Ken Poss bacterial pathogenesis embryonic development cardiac development cell cycle control DNA replication timing small-sample genomics parasite gene expression RNA polymerase II post-translational modifications long-read sequencing stem cell fate epigenomics and chromatin biology stem cell fate cardiac regeneration methods development (monkey, rank expectation) * **** **** ** * ** * * * ** ** * * **

  4. Who is this guy and why is he talking to me? CTSI wants to help you get the resources you need to do excellent science!

  5. common data sources sequencing genome assembly variant discovery gene expression microarrays RNA-seq (mRNA, total RNA, miRNAs) methylation analysis microarrays bisulfite sequencing nucleic-acid-binding DNA ChIP-seq (transcription factors, epigenetic marks) ChIP-exo RNA RIP-seq RIP-exo chromatin accessibility DNaseI ATAC-seq long-range chromatin interactions HiC 5C 4C

  6. common data sources sequencing genome assembly variant discovery gene expression microarrays RNA-seq (mRNA, total RNA, miRNAs) methylation analysis microarrays bisulfite sequencing nucleic-acid-binding DNA ChIP-seq (transcription factors, epigenetic marks) ChIP-exo RNA RIP-seq RIP-exo chromatin accessibility DNaseI ATAC-seq long-range chromatin interactions HiC 5C 4C

  7. genome assembly chicken genome annotation Thomas et al., 2014 PLoS One

  8. variant analysis placental virulence-associated-variation in Listeria monocytogenes Holly Morrison Anna Bakardjiev

  9. common data sources sequencing genome assembly variant discovery gene expression microarrays RNA-seq (mRNA, total RNA, miRNAs) methylation analysis microarrays bisulfite sequencing nucleic-acid-binding DNA ChIP-seq (transcription factors, epigenetic marks) ChIP-exo RNA RIP-seq RIP-exo chromatin accessibility DNaseI ATAC-seq long-range chromatin interactions HiC 5C 4C

  10. gene expression analyses…

  11. common data sources sequencing genome assembly variant discovery gene expression microarrays RNA-seq (mRNA, total RNA, miRNAs) methylation analysis microarrays bisulfite sequencing nucleic-acid-binding DNA ChIP-seq (transcription factors, epigenetic marks) ChIP-exo RNA RIP-seq RIP-exo chromatin accessibility DNaseI ATAC-seq long-range chromatin interactions HiC 5C 4C Deepak Srivastava

  12. common data sources sequencing genome assembly variant discovery gene expression microarrays RNA-seq (mRNA, total RNA, miRNAs) methylation analysis microarrays bisulfite sequencing nucleic-acid-binding DNA ChIP-seq (transcription factors, epigenetic marks) ChIP-exo RNA RIP-seq RIP-exo chromatin accessibility DNaseI ATAC-seq long-range chromatin interactions HiC 5C 4C

  13. identifying regulators of stem cell fate Paige et al., 2013 Cell

  14. identifying direct targets of Brg1 chromatin remodeling (critical for heart development) Benoit Bruneau

  15. epigenetic characterization of a post-translational RNA pol II modifications

  16. common data sources sequencing genome assembly variant discovery gene expression microarrays RNA-seq (mRNA, total RNA, miRNAs) methylation analysis microarrays bisulfite sequencing nucleic-acid-binding DNA ChIP-seq (transcription factors, epigenetic marks) ChIP-exo RNA RIP-seq RIP-exo chromatin accessibility DNaseI ATAC-seq long-range chromatin interactions HiC 5C 4C

  17. identifying footprints of DNA-binding proteins

  18. common data sources sequencing genome assembly variant discovery gene expression microarrays RNA-seq (mRNA, total RNA, miRNAs) methylation analysis microarrays bisulfite sequencing nucleic-acid-binding DNA ChIP-seq (transcription factors, epigenetic marks) ChIP-exo RNA RIP-seq RIP-exo chromatin accessibility DNaseI ATAC-seq long-range chromatin interactions HiC 5C 4C

  19. programmed changes in long range chromatin interactions during stem cell differentiation

  20. http://accelerate.ucsf.edu/research/bi-consult sequencing genome assembly variant discovery gene expression microarrays RNA-seq (mRNA, total RNA, miRNAs) methylation analysis microarrays bisulfite sequencing nucleic-acid-binding DNA ChIP-seq (transcription factors, epigenetic marks) ChIP-exo RNA RIP-seq RIP-exo chromatin accessibility DNaseI ATAC-seq long-range chromatin interactions HiC 5C 4C

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