Slides - UCSF Department of Epidemiology & Biostatistics

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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
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
Study Focus
Publications
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
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methods development (monkey, rank expectation)
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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
DNase I
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
DNase I
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
DNase I
ATAC-seq
long-range chromatin interactions
HiC
5C
4C
gene expression analyses…
common data sources
sequencing
genome assembly
variant discovery
gene expression
microarrays
RNA-seq (mRNA, total RNA, miRNAs)
methylation analysis
microarrays
bisulfite sequencing
Deepak Srivastava
nucleic-acid-binding
DNA
ChIP-seq (transcription factors, epigenetic marks)
ChIP-exo
RNA
RIP-seq
RIP-exo
chromatin accessibility
DNase I
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
DNase I
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 posttranslational 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
DNase I
ATAC-seq
long-range chromatin interactions
HiC
5C
4C
identifying footprints of DNA-binding proteins
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
DNase I
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
DNase I
ATAC-seq
long-range chromatin interactions
HiC
5C
4C

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