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X-WR-CALNAME:UCLA | Bioinformatics
X-ORIGINAL-URL:https://bioinformatics.ucla.edu
X-WR-CALDESC:Events for UCLA | Bioinformatics
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DTSTART:20150101T000000
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DTSTART;TZID=UTC:20160425T110000
DTEND;TZID=UTC:20160425T120000
DTSTAMP:20160420T235528Z
CREATED:20160420T235528Z
LAST-MODIFIED:20160420T235528Z
UID:1783-1461582000-1461585600@bioinformatics.ucla.edu
SUMMARY:Shao-Shan Carol Huang\, Special Seminar
DESCRIPTION:Shao-Shan Carol Huang\, Ph.D. \nGenomic Analysis Laboratory & Plant Biology Laboratory\nThe Salk Institute for Biological Studies\n“Efficient mapping of genome-wide regulatory elements for biological insights” \nWe developed a high-throughput sequencing assay for rapid transcription factor binding site (TFBS) discovery\, DNA affinity purification sequencing (DAP-seq)\, that uses in vitro prepared transcription factors (TFs) to capture native genomic DNA. We applied DAPseq to 1\,812 Arabidopsis thaliana TFs to resolve motifs for 529 factors and genome-wide enrichment maps for 349 factors. Cumulatively\, the ~2.7 million experimentally determined TFBSs captured the Arabidopsis cistrome and predicted thousands of TF target genes enriched for known and novel functions. Base-resolution epicistrome maps were established by comparison of TF-binding to genomic DNA with native cytosinemethylation patterns and genomic DNA that had been synthetically demethylated. This revealed methylcytosine inhibited binding of ~72% of factors and promoted binding of 4.3% of factors. Lastly\, we showed DAP-seq binding sites provided a way to annotate genomic and epigenomic variations in natural populations and interpret results from genome-wide association studies. Overall\, DAP-seq enables rapid development of base-resolution cistrome and epicistrome atlases for a wide-array of applications for eukaryotic genomes.
URL:https://bioinformatics.ucla.edu/event/shao-shan-carol-huang-special-seminar/
LOCATION:158 Hershey Hall
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BEGIN:VEVENT
DTSTART;TZID=UTC:20160425T160000
DTEND;TZID=UTC:20160425T170000
DTSTAMP:20160419T161528Z
CREATED:20160414T211206Z
LAST-MODIFIED:20160419T161528Z
UID:1061-1461600000-1461603600@bioinformatics.ucla.edu
SUMMARY:Sunduz Keles Seminar
DESCRIPTION:Sunduz Keles\, Ph.D. \nProfessor\, Department of Biostatistics & Medical Informatics\, University of Wisconsin \n“Integrative Models of Genomic and Epigenomic Data“ \nConsortium projects such as ENCODE and NIH Roadmap Epigenomics generated a wealth of genomic and epigenomic data. We will present two general modeling frameworks for efficiently utilizing these data in genome-wide inference problems. Specifically\, we will present integrative models to (i) identify protein-DNA and long-range interactions involving repetitive genomic DNA; (ii) integrate functional annotation information into genome-wide association studies. \n  \n 
URL:https://bioinformatics.ucla.edu/event/sunduz-keles-seminar/
LOCATION:Boyer Hall 159
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