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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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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
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) * **** **** ** * ** * * * ** ** * * **
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!
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
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
genome assembly chicken genome annotation Thomas et al., 2014 PLoS One
variant analysis placental virulence-associated-variation in Listeria monocytogenes Holly Morrison Anna Bakardjiev
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
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
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
identifying regulators of stem cell fate Paige et al., 2013 Cell
identifying direct targets of Brg1 chromatin remodeling (critical for heart development) Benoit Bruneau
epigenetic characterization of a post-translational RNA pol II modifications
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
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
programmed changes in long range chromatin interactions during stem cell differentiation
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