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July 2019

Inferring Genetic Co-dependencies to Identify New Vulnerabilities in Cancer

July 2 @ 3:00 pm - 5:00 pm PDT
PSB, Room 305

Thomas J. Matthew Dissertation Defense Abstract:  Translation of cancer genomic data into cancer therapies and companion diagnostics remains a primary challenge in personalized medicine. Much of this challenge is due to the difficulty of identifying genetic co-dependencies that lead to clinically actionable drug targets. Targeting many of the known essential gene products are not always selectively efficacious because these targets may be common to both malignant and benign cells. However, essential genes that are associated with particular genomic alterations in cancer…

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A Guide to Using the UCSC Genome Browser

July 12 @ 9:30 am - 11:30 am PDT
E2 Room 599

Presenter: Robert Kuhn, PhDAssociate Director, UCSC Genome Browser The UCSC Genome Browser provides visualization tools for a large genomic database spanning more than 100 animals. In addition to providing a viewer for a large number of annotation datasets including mRNA alignments, gene predictions, epigenetic marker mapping and expression data, new features include a tool to analyze sequence variant data, and a new capability for users to host a fully functional Browser on organisms not part of the UC Santa Cruz…

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Dissertation Defense: Classifying Cancer Genomic Alterations Using Machine Learning and Multi-Omic Data

July 30 @ 1:30 pm - 4:00 pm PDT
PSB, Room 305

David Haan, PhD Candidate  Systems Biology, Stuart Lab Abstract In 2018, an estimated 1,762,450 new cases of cancer will be diagnosed in the United States and 606,880 people will die from these diseases. Cancer is a group of diseases characterized by the overgrowth of abnormal cells as the result of genomic mutations. Mutations that initiate tumorigenesis are called driver mutations whereas those which can not are called passenger mutations. Driver mutations define a tumor's sub-type and can be used as…

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August 2019

Dissertation Defense: Enabling comparative genomics at the scale of hundreds of species

August 1 @ 11:00 am - 12:15 pm PDT
E2 Room 599

Dissertation Defense Joel Armstrong, Graduate Student Researcher, BiomolecularEngineerings AbstractComparing related (homologous) subsequences between genomes from different species gives insight into the function and evolution of the genome. This information is captured in “genome alignments,'' which are essential for many comparative genomics analyses. However, most existing methods to create a genome alignment suffer from reference-bias (where only one genome is fully aligned to all others), or ignore duplication events. Though the Cactus genome aligner avoided these restrictions, it could not align…

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Cell type-specific patterns of activity in an in vitro model of a reticulospinal circuit

August 5 @ 11:15 am - 12:15 pm PDT

Postdoc candidate talk Adele Bubnys, Ph.D; Biomedical sciencesThe Rockefeller University, New York, NY AbstractAs the capacity to isolate distinct neuronal cell types has advanced over the past several decades, new two- and three-dimensional in vitro models of the interactions between differentbrain regions have expanded our understanding of human neurobiology and origins of disease.These cultures develop distinctive patterns of activity, but the extent that these patterns aredetermined by the molecular identity of individual cell types versus the specific pattern of network…

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