Events

Talks and events hosted or co-sponsored by the Genome Center

This page lists details of notable talks, seminars, workshops, and other events that happen at the Genome Center, or happen elsewhere at UC Davis but which are organized/co-sponsored by the Genome Center. All of these event details are available in a public Google Calendar which anyone can view or subscribe to by using one of the following links:

  • Genome Center Google Events Calendar: XML ICAL HTML
February  2015
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  • West Coast Metabolomics Center Course: Hands-on LC-MS Data processing and Statistics
    Starts: 12:00 am
    Ends: February 7, 2015 - 12:00 am
    Description: This course will feature hands-on training with real-world metabolomics data covering LC/MS compound identification, data processing, statistical analysis, network mapping and data interpretation. The WCMC will provide laptops for all participants and utilize open source software where possible.

    Registration: https://ucanr.edu/survey/survey.cfm?surveynumber=13398
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  • Dr Alex Nord — Seminar — The Role of Non-Coding DNA in Development and Disease
    Starts: 12:00 pm
    Ends: February 4, 2015 - 1:00 pm
    Location: Medical Education Building room 2222, 4610 X St, Sacramento
    Description: A seminar from the Human Genomics Seminar Series, jointly sponsored by the UC Davis Division of Genomic Medicine and UC Davis Genome Center.

    Web connect: http://uc-d.adobeconnect.com/hu-gen-seminar/
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  • 1st Symposium on International Collaboration "Data-driven Genomics Science towards a NAIST Satellite Office at UC Davis"
    Starts: 12:00 am
    Ends: February 10, 2015 - 12:00 am
    Location: Putah Creek Lodge, UC Davis
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  • Seminar — Dr Kathleen Giacomini — The Metabolic Impact of Drug Transporter Activities
    Starts: 10:00 am
    Ends: February 11, 2015 - 11:00 am
    Location: GBSF Auditorium (room 1005)
    Description: Part of the monthly series of seminars by the West Coast Metabolomics Center
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  • Seminar - Dr. David Doty - DNA origami-seeded self-assembly of DNA single-stranded tile nanotubes
    Starts: 10:00 am
    Ends: February 13, 2015 - 11:00 am
    Location: GBSF Auditorium (room 1005)
    Description: Part of the Genome Center Systems and Synthetic Biology Seminar Series.

    Abstract
    DNA in natural systems such as cells --- and in artificial computational systems such as synthetic genetic transcriptional networks --- typically acts as a read/write memory to store information but is otherwise dormant. DNA nanotechnology uses DNA not only as an passive memory, but also as the primary conductor of assembly/computation. It has transformed our ability to reliably and cheaply engineer nanoscale shapes, structures, machines, circuits, and other devices that autonomously self-assemble according to rules encoded in the DNA sequences that comprise the devices.
    One approach to DNA self-assembly, using DNA "tiles" that each have 4 single-stranded sticky ends that enable them to bind into lattice of tiles, can in theory carry out arbitrarycomputation as the tiles assemble. Thus we call this process algorithmic self-assembly, allowing the structure being grown to act simultaneously as the autonomous machine directing its own growth. Experimentally, the primary challenge in achieving algorithmic self-assembly is enforcing idealized cooperative binding: finding experimental conditions under which a tile can only attach to a lattice of tiles if at least two of its sticky ends are complementary to sticky ends on the lattice.

    In this talk we report on preliminary progress toward this goal, showing how to use a DNA tile motif known as a single-stranded tile to achieve a simple algorithmic task: repeated copying of a binary string encoded into a "seed" structure from which tile growth nucleates. Though apparently a modest goal, to successfully copy bits requires the enforcement of idealized cooperative binding, the key to achieving algorithmic self-assembly.
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  • Seminar — Dr Hao Chen — Allele-specific copy number profiling by next-generation DNA sequencing
    Starts: 9:00 am
    Ends: February 20, 2015 - 10:00 am
    Location: GBSF Room 4202
    Description: Part of the Genome Center Structural and Functional Genomics Seminar Series


    Abstract

    The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in giving a more complete portrait of tumor genomes and the inference of their clonal history. We propose a novel method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normal. Falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. We applied this method in the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allow us to draw detailed conclusions regarding the clonal history of the individual’s colon cancer.
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February 20, 2015
Seminar — Dr Hao Chen — Allele-specific copy number profiling by next-generation DNA sequencing
Starts: 9:00 am
Ends: February 20, 2015 - 10:00 am
Location: GBSF Room 4202
Description: Part of the Genome Center Structural and Functional Genomics Seminar Series


Abstract

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in giving a more complete portrait of tumor genomes and the inference of their clonal history. We propose a novel method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normal. Falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. We applied this method in the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allow us to draw detailed conclusions regarding the clonal history of the individual’s colon cancer.
March 4, 2015
Dr Janine LaSalle — Seminar — Mapping the Placental Methylome at the Interface of Genetics and Environment in Autism Risk
Starts: 12:00 pm
Ends: March 4, 2015 - 1:00 pm
Location: Center for Health and Technology room 1341, 4610 X St Sacramento
Description: Part of the Human Genomic Seminar Series

Upcoming Talks and Events

Events on February 20, 2015
Seminar — Dr Hao Chen — Allele-specific copy number profiling by next-generation DNA sequencing
Starts: 9:00 am
Ends: February 20, 2015 - 10:00 am
Location: GBSF Room 4202
Description: Part of the Genome Center Structural and Functional Genomics Seminar Series


Abstract

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in giving a more complete portrait of tumor genomes and the inference of their clonal history. We propose a novel method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normal. Falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. We applied this method in the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allow us to draw detailed conclusions regarding the clonal history of the individual’s colon cancer.
Events on March 4, 2015
Dr Janine LaSalle — Seminar — Mapping the Placental Methylome at the Interface of Genetics and Environment in Autism Risk
Starts: 12:00 pm
Ends: March 4, 2015 - 1:00 pm
Location: Center for Health and Technology room 1341, 4610 X St Sacramento
Description: Part of the Human Genomic Seminar Series

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