Beckman Symposium 2018 - Technology Innovation and Human Genomics

February 12, 2018 | Berg Hall - Li Ka Shing Center

Schedule

TIME	TOPIC	SPEAKERS
8:45 – 9:00	Introductory Remarks	Lucy Shapiro, Director of the Beckman Center, Stanford University
9:00 – 9:45	The Impact of Technology on How We See Biology	Deanna Church, 10x Genomics
9:50 – 10:35	Computing Cancer’s Playbook: The Need for Theory and Big Data	Christina Curtis, Stanford University
10:35 – 10:50	BREAK
10:50 – 11:35	Twelve Petabases and Counting…the Increasing Scale and Resolution of DNA Sequencing in Human Genetics and Cancer Genomics	Stacey Gabriel, MIT Broad Institute
11:40 – 12:25	Generating Effective Therapeutic Hypotheses from Human Genetic Data Linked to Health Records	Manuel Rivas, Stanford University
12:30 – 1:30	LUNCH
1:30 – 2:15	Who's Afraid of Lossy Compression of Genomic Data?	Tsachy Weissman, Stanford University
2:20 – 3:05	Accuracy in Precision Medicine	Euan Ashley, Stanford University
3:05 – 3:20	BREAK
3:20 – 4:05	Statistics for Solving Problems, and Creating New Ones	Daniela Witten, University of Washington
4:10 – 4:55	Using Omics to Understand Drug Response	Russ Altman, Stanford University
5:00 – 5:15	Closing Remarks

Speaker Profiles

Russ Biagio Altman, M.D., Ph.D. is Professor of Bioengineering, Genetics, Medicine, and Biomedical Data Science (and of Computer Science, by courtesy) and past Chairman of the Bioengineering Department at Stanford University. His primary research interests are in the application of computing and informatics technologies to problems relevant to medicine. He is particularly interested in methods for understanding drug action at molecular, cellular, organism and population levels. His lab studies how human genetic variation impacts drug response (e.g., http://www.pharmgkb.org/). Other work focuses on the analysis of biological molecules to understand the actions, interactions and adverse events of drugs (e.g., http://feature.stanford.edu/). He helps lead an FDA-supported Center of Excellence in Regulatory Science & Innovation. He currently serves on the NIH Director’s Advisory Committee, and is co-chair of the IOM Drug Forum. He is an organizer of the annual Pacific Symposium on Biocomputing, and a founder of Personalis, Inc.

Euan Ashley, M.D., Ph.D. is Professor of Medicine, Genetics and Data Science at Stanford University. His lab is focused on the science of precision medicine. In 2010, he led the team that carried out the first clinical interpretation of a human genome. This study, the focus of over 300 news stories, became one of the most cited articles in clinical medicine that year and was later featured in the Genome Exhibition at the Smithsonian in D.C. Today, Dr. Ashley directs the Clinical Genomics Program at Stanford hospitals and is founding director of the Center for Inherited Cardiovascular Disease. In 2013, he was recognized by the Obama White House for his contributions to personalized medicine. He is recipient of the National Innovation Award from the American Heart Association, as well as an NIH Director’s New Innovator Award. He is principal investigator of the MyHeart Counts Cardiovascular Health Study, launched in collaboration with Apple in 2015. In 2016, he was part of the winning team of the $75m One Brave Idea competition funded by Google, the AHA, and Astra Zeneca. He is founder of two companies: Personalis, Inc. and DeepCell, Inc.

Deanna Church, Ph.D. is the Senior Director of Applications at 10x Genomics, a company dedicated to accelerating genomics and high-throughput single cell transcriptomics discovery. Her group focuses on demonstrating the power of the Chromium™ System in a wide variety of research areas, including genomic health, immunology, and cancer. Of particular interest is investigating how the integration of multiple genomics approaches improves our understanding of biological problems. Prior to joining 10x Genomics, Dr. Church was a senior director of genomics and content at Personalis, Inc. where she developed bioinformatics tools and approaches to significantly improve genome analysis. Before Personalis, Inc., she worked for the National Center for Biotechnology (NCBI) for 14 years. While there, Dr. Church headed the Genome Reference Consortium team and led the effort to build truly high quality, maximally informative reference genomes.

Christina Curtis, Ph.D., M.Sc. is Assistant Professor of Medicine and Genetics in the School of Medicine at Stanford University and is Co-Director of the Molecular Tumor Board at the Stanford Cancer Institute. Dr. Curtis’s laboratory couples innovative experimental approaches, high-throughput molecular profiling, statistical inference and computational modeling to interrogate the evolutionary dynamics of tumor progression and therapeutic resistance to improve the diagnosis and treatment of cancer. She and her team have employed these tools to measure clinically relevant patient-specific parameters and to delineate mechanisms of tumor progression, resulting in their recent description of a Big Bang model of colorectal tumor growth, which has resulted in a new paradigm in understanding clonal evolution. Her research also aims to develop a systematic interpretation of genotype/phenotype associations in cancer by leveraging state-of-the-art technologies and robust data integration techniques. For example, using integrative statistical approaches to mine multiple data types, she lead a seminal study that redefined the molecular map of breast cancer revealing novel subgroups with distinct clinical outcomes. Dr. Curtis has been the recipient of several young investigator awards, including the 2012 V Foundation for Cancer Research V Scholar Award, the 2012 STOP Cancer Research Career Development Award, an American Cancer Society Seed Grant in 2013, and an AACR Career Development Award in 2016, and is a 2016 Kavli Foundation Scholar of the National Academy of Sciences.

Stacey Gabriel, Ph.D. leads the Genomics Platform of the Broad Institute of the MIT and Harvard, one of the largest producers of human genomic data in the world. Under Dr. Gabriel’s guidance, the Genomics Platform is responsible for exploring, validating, optimizing, and implementing new technologies, methods, and analysis tools to meet the scientific needs of the Broad community and beyond. In addition to her activities with the Genomics Platform, Dr. Gabriel’s research interests lie in using genomic techniques to understand the genetic components of common disease. She has represented the Institute in many large national projects, including providing foundational research for the International HapMap Project; serving on the steering committee for the 1000 Genomes Project; serving on the steering committee for The Cancer Genome Atlas; serving as principal investigator on the National Heart, Lung and Blood Institute’s Exome Sequencing Project and TransOMIC for Precision Medicine Project; and co-principal investigator of the National Human Genome Research Institute’s large-scale sequencing center. She has also served as principal investigator on numerous NIH grants and contracts related to large-scale genotyping, sequence production, and analysis. Dr. Gabriel has been ranked #1 in Thomson Reuters' list of "The World's Most Influential Scientific Minds” in 2014 and 2105 based on citation of research articles. Dr. Gabriel joined the Whitehead Institute/MIT Center for Genome Research in 1998.

Manuel Rivas, Ph.D. is Assistant Professor of Biomedical Data Science. His laboratory focuses on population analytics using genomic and phenotype data. Rivas' lab develops statistical models, algorithms, and computational tools for the analysis of millions of samples. Scientific themes that the lab will focus on: 1) generating effective therapeutic and preventative hypotheses for human diseases from human genetic, imaging, wearable sensor, and environmental data; 2) developing technologies for integrated learning healthcare systems with a particular focus on underserved communities and developing regions of the world; 3) genetic epidemiology where the aim is to understand the global distribution of common and rare disease predisposition genes; and 4) high dimensional methods development and optimization. His team is responsible for the discovery of genetic variants that protect individuals from Crohn’s disease and ulcerative colitis. They have developed Global Biobank Engine, an inference platform for population-scale genetic studies of human diseases.

Tsachy Weissman, Ph.D. is Professor of Electrical Engineering at Stanford University. He spends most of his time researching information theory, digital communications, statistical signal processing, the interplay between them, and their applications. In recent years, he has been dabbling in applying knowledge and techniques from these areas to genomic data compression and processing. He is the inventor of several patents and involved in a number of companies as researcher or member of the technical board. Honors include an NSF CAREER award, several best paper awards, the Horev Fellowship for Leaders in Science and Technology, the Henry Taub Prize for Excellence in Research, incumbent of the STMicroelectronics Chair in the School of Engineering, and IEEE Fellow. He is founding director of the Stanford Compression Forum.

Daniela Witten, Ph.D. is an Associate Professor of Statistics and Biostatistics at the University of Washington, and an Affiliate Investigator at the Fred Hutchinson Cancer Research Center. Her research focuses on the development of statistically- and computationally-efficient statistical machine learning methods for the analysis of high-dimensional data, with applications to genomics, neuroscience, and other fields. Given that contemporary data sets are often collected with the goal of hypothesis generation rather than hypothesis testing, she is particularly interested in unsupervised learning methods that can be used for hypothesis generation. These include methods for graphical modeling, matrix factorization, and clustering. She is the recipient of a number of honors, including an NIH Director's Early Independence Award, a Sloan Research Fellowship, and an NSF CAREER Award.

About Beckman Center

Lucy Shapiro, Ph.D., Beckman Center Director, is the Virginia and D.K. Ludwig Professor of Cancer Research in the Department of Developmental Biology at the Stanford University School of Medicine. She is a microbial geneticist whose research has resulted in major advances in understanding cell differentiation. Her innovative use of the bacterium Caulobacter crescentus has yielded fundamental insights for understanding the bacterial cell as a paradigm for an integrated system in which the transcriptional circuitry is interwoven with the three-dimensional deployment of key regulatory and morphological proteins. Dr. Shapiro showed for the first time that bacterial DNA replication occurred in a spacially organized way, and that the act of replication and the subsequent segregation of the DNA to opposite ends of the cell dictates the cellular position and time of function of the cell division machinery. She has won numerous awards and distinctions for her contributions to the field of microbial genetics including the 2005 Selman Waksman Award, the 2009 Canada Gairdner International Award, the 2012 Louisa Horwitz Prize, the 2012 National Medal of Science, and the 2014 Pearl Meister Greengard Prize awarded by Rockefeller University to celebrate the achievements of outstanding women in science.

The Beckman Center for Molecular and Genetic Medicine was established in 1989 to promote exchange across diverse scientific disciplines throughout the schools of Stanford University. Founded on the principle that innovation transcends traditional boundaries, the Beckman Center fosters the integration of basic science with clinical medicine by supporting programs in translational research, shared resource facilities, technological innovation, scientific discourse, scholarly concentrations, and faculty recruitment. Learn more about Beckman Center

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