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Next Steps for Functional Genomics: Proceedings of a Workshop (2020)

Chapter: Appendix C: Planning Committee Biographies

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Suggested Citation:"Appendix C: Planning Committee Biographies." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
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Page 126
Suggested Citation:"Appendix C: Planning Committee Biographies." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
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Page 127
Suggested Citation:"Appendix C: Planning Committee Biographies." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
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Page 128

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  Appendix C Planning Committee Biographies Gene E. Robinson (NAS, NAM), Ph.D. (Chair), is the director of the Carl R. Woese Institute for Genomic Biology. He holds a Swanlund Chair at the University of Illinois at Urbana- Champaign, where he has been since 1989 with a primary appointment in the Department of Entomology. He also holds affiliate appointments in the Department of Cell & Developmental Biology, the Program in Ecology, Evolution and Conservation Biology, and the Beckman Institute of Science and Technology. Dr. Robinson’s research group uses genomics and systems biology to study the mechanisms and evolution of social life, using the western honeybee, Apis mellifera, as the principal model system along with other species of bees. The research is integrative, involving perspectives from evolutionary biology, behavior, neuroscience, molecular biology, and genomics. The goal is to explain the function and evolution of behavioral mechanisms that integrate the activity of individuals in a society, neural and neuroendocrine mechanisms that regulate behavior within the brain of the individual, and the genes that influence social behavior. Research focuses on division of labor, aggression, and the famous dance language, a system of symbolic communication. Dr. Robinson received his Ph.D. from Cornell University and was a National Science Foundation postdoctoral fellow at The Ohio State University.   Philip N. Benfey (NAS), Ph.D., graduated from the University of Paris and received his Ph.D. in cell and developmental biology from Harvard University under the guidance of Dr. Philip Leder. He did postdoctoral research at The Rockefeller University in the field of plant molecular biology with Dr. Nam-Hai Chua and was appointed assistant professor there in 1990. In 1991, he moved to New York University, where he became an associate professor in 1996 and full professor in 2001. He was the founding director of the Center for Comparative Functional Genomics at New York University. In 2002, he was named professor and chair of the Biology Department at Duke University and in 2003 was named a distinguished professor. Dr. Benfey is the recipient of a Natiional Science Foundation predoctoral fellowship and a Helen Hay Whitney postdoctoral fellowship. He was named a fellow of American Association for the Advancement of Science in 2004 and was elected to the National Academy of Sciences in 2010. In 2011, the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation named Dr. Benfey an investigator under an initiative to support fundamental plant science research. He currently serves on the editorial boards of Proceedings of the National Academy of Sciences of the United States of America, Science, Developmental Cell, and BMC Plant Biology. Dr. Benfey is also a pioneer in the cutting-edge technology of plant biology. His lab invented a device called the RootArray, which allows scientists to grow 60 to 120 seedlings at a time. With this device, it also is possible to observe the response of plants and tagged genes. In 2007, he formed a start-up company, GrassRoots Biotechnology, based on this technology that used systems biology approaches to develop new crop traits for the bioenergy, food, and industrial markets. The company was sold in 2013, after which he founded a second company, Hi Fidelity Genetics, which has developed a predictive breeding platform and invented a device, the RootTracker, 126 Prepublication Copy

Appendix C  which is able to monitor root growth in the field over time. The company is breeding plants with enhanced root systems with the goal of producing resiliant crops in the face of climate change. Charles Danko, Ph.D., is the Robert N. Noyce Assistant Professor at Cornell University. His primary research interest is to understand how DNA sequence encodes complex programs of gene expression. Dr. Danko uses genetic differences affecting various steps in the RNA polymerase II transcription cycle to understand the molecular basis of phenotypic changes between species. Much of his work is done using molecular and computational tools developed in the Danko lab. Dr. Danko has a longstanding interest in using nascent transcription as a rich source of information about multiple layers of mammalian genome function. He played a vital role in developing assays that map the location of RNA polymerase (PRO-seq, ChRO-seq), and has led to the development of computational tools that leverage this information to identify active functional elements (dREG). Emma Farley, Ph.D., is an assistant professor at the University of California (UC), San Diego, in the Division on Biological Sciences and School of Medicine. She employs high-throughput functional approaches within developing embryos to decipher how the instructions for successful development are encoded in our genomes. She studies enhancers, which encode these instructions and act as genetic switches to control the timing and location of gene activity. Dr. Farley received a master’s degree in biochemistry from Oxford University and a Ph.D. in developmental biology from the MRC London Institute of Medical Science. She worked as a postdoctoral researcher at UC Berkeley and Princeton University, where she exploited the sea squirt Ciona intestinalis as a model organism for functional genomics. She developed cost- effective and scalable methods to create and functionally test millions of enhancer variants in every cell of a developing embryo. Her research enabled the first high-throughput dissection of an enhancer within whole developing embryos and revealed the unexpected property that enhancer features and organization must be suboptimized to produce tissue-specific patterns of gene activity. Her lab at UC San Diego continues to investigate how enhancers encode the instructions for successful development and how mistakes in these instructions lead to disease. Trudy F. C. Mackay (NAS), Ph.D., is the director of Clemson University’s Center for Human Genetics located on the campus of the Greenwood (South Carolina) Genetic Center. She is recognized as one of the world’s leading authorities on the genetics of complex traits. Dr. Mackay is also the Self Family Chair in Human Genetics and Professor of Genetics and Biochemistry at Clemson University and a member of the National Academy of Sciences (2010). Dr. Mackay received a bachelor of science degree in 1974 and master of science degree in 1976 in biology from Dalhousie University. She completed postgraduate study at the University of Edinburgh with a Ph.D. in genetics awarded in 1979 for research supervised by Alan Robertson. Dr. Mackay’s research investigates the environmental and genetic factors that influence quantitative traits. These phenotypic traits include height or weight and are represented by continuous, rather than discrete, values. Her work is undertaken by studying the impact of natural variants and mutations on many behavioral, morphological, physiological, and life history traits in fruit flies, which she uses as a model organism. Prepublication Copy 127

Next Steps for Functional Genomics Terry Magnuson (NAM), Ph.D., is the Sarah Graham Kenan Professor of Genetics and vice chancellor for research at the University of North Carolina at Chapel Hill. He was the founding chair of the Department of Genetics and the director of the Genome Science Center. He leads the Cancer Genetics Program in the Lineberger Comprehensive Cancer Center. Dr. Magnuson was appointed vice dean for research in the School of Medicine and then vice chancellor for research for the university. Dr. Magnuson served as the chair of the Jackson Laboratory Board of Scientific Overseers, a member of the Board of Directors for the Society for Developmental Biology and for the Genetics Society of America (GSA). He is currently the president of GSA. He was appointed by the National Academies to establish guidelines for human embryonic stem cells. He served as vice chair of an Institute of Medicine (IOM) committee that evaluated the California Institute for Regenerative Medicine, and as a member of the IOM committee reviewing the charge of the National Institutes of Health (NIH) Recombinant DNA Advisory Committee. Dr. Magnuson is a member of the NIH Council of Councils. He has been elected to the American Academy of Arts and Science and to the National Academy of Medicine and is a fellow of the American Association for the Advancement of Science. Dr. Magnuson’s research focuses on the genome-wide dynamics of chromatin remodeling complexes. Dr. Magnuson received his Ph.D. from Cornell University and he was a postdoctoral fellow at the University of California, San Francisco. Lauren O’Connell, Ph.D., is an assistant professor of biology at Stanford University. She received her Ph.D. in cellular and molecular biology from The University of Texas at Austin and her B.S. in biology, neurobiology, and behavior concentration at Cornell University. She holds interests in understanding how animals come up with new ways to face challenges and opportunities in their environment. She believes these evolutionary innovations in physiology and behavior can teach basic organismal biology, evolutionary mechanisms of adaptation, and how flexible organisms are to changing environments. Dr. O’Connell’s lab uses amphibians as a model system for understanding the molecular and genomic contributions to biological diversity because they display tremendous variation in behavior and physiology. Members of her lab work on a variety of topics, but most of their work centers on investigating behavior and toxicity in poison frogs and they have worked to develop gene editing technologies in “non-model” amphibians to test these questions in the field and laboratory. Andrea Sweigart, Ph.D., is an associate professor in the Department of Genetics at the University of Georgia. She received her Ph.D. from Duke University in 2006 with prime focus on genetics and evolutionary biology. Dr. Sweigart believes that a fundamental goal of evolutionary biology is to explain how populations become reproductively isolated species. Her research pursues this goal using Mimulus (monkeyflowers), a genus of closely related, ecologically diverse wildflowers that exhibit tremendous variation in reproductive isolation between populations and species. She uses a range of approaches—from field and greenhouse experiments to genetic mapping and bioinformatics—to investigate the genetic mechanisms and evolutionary dynamics of speciation. 128 Prepublication Copy

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One of the holy grails in biology is the ability to predict functional characteristics from an organism’s genetic sequence. Despite decades of research since the first sequencing of an organism in 1995, scientists still do not understand exactly how the information in genes is converted into an organism’s phenotype, its physical characteristics. Functional genomics attempts to make use of the vast wealth of data from “-omics” screens and projects to describe gene and protein functions and interactions. A February 2020 workshop was held to determine research needs to advance the field of functional genomics over the next 10-20 years. Speakers and participants discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications that would benefit society. This publication summarizes the presentations and discussions from the workshop.

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