One of biology’s greatest mysteries—predicting an organism’s characteristics from what we know about its genetics—remains unsolved. Functional genomics uses broad genome-wide approaches to understand how DNA defines an organism’s phenome, which determines physical and functional characteristics. However, the work to understand how genotypes translate into phenotypes is just beginning. The National Academies of Sciences, Engineering, and Medicine (NASEM) will organize and convene a workshop to be held in early 2020 (date TBD) to explore the scientific advancements needed to utilize functional genomics to solve societal problems in area such as conservation, evolutionary studies, agriculture, energy, defense, human health, and other sectors. The workshop will delineate the current state of the science, what lessons have been learned thus far, what current impediments there are to further progress, and areas where additional investments could help move the field forward.
Next Steps for Functional Genomics: A Workshop
February 10-12, 2020
Please review our workshop via the videos linked below. The 45 videos are in chronological order of the presentations, discussions and sessions over the course of the three days.
Please stay tuned for information on the proceedings of the workshop.
– Case studies of success and failure in functional genomics research on a variety of intensively studied model organisms, such as E. coli and C. elegans. What are the results of these projects? What obstacles did the investigators encounter and could they or could they not surmount them? What tools did the investigators use that produced high quality results and what tools did they need that were not yet developed and readily available for use?
– Whether there are universal “rules of life” behind resilience, adaptation, and other emerging properties to guide the development of key baseline and comparative questions for research across the realms of microbes, animals, and plants.
– Ideas for short- and medium-term research and knowledge goals and potential strategies, pathways, and needs to achieve these goals.
– Research strategies to examine the interplay of genetic, epigenetic, and environmental factors to determine which factors or combinations of factors may be most influential for determining phenotype.
– Key considerations for selecting experimental systems (model organisms, “non-model” organisms, in vitro versus in vivo methods, computational models, etc.) and research approaches (e.g., convergence and research networks) to leverage the full range of disciplines that could contribute to research in future studies of functional genomics.
– The advantages and limitations of available research tools and databases, the potential for using emerging tools and databases that are not yet widely available, and the need for the development and dissemination of these new tools to the research community.
– The training needs for future genotype-to-phenotype research and how to attract the best research talent into the effort.
Gene E. Robinson 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 honey bee, 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 an NSF Postdoctoral Fellow at Ohio State University.
Philip N. Benfey 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 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. Philip is the recipient of an NSF predoctoral fellowship and a Helen Hay Whitney postdoctoral fellowship. He was named a fellow of AAAS 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 Philip an investigator under an initiative to support fundamental plant science research. He currently serves on the editorial boards of Science, Developmental Cell, and BMC Plant Biology. Philip is also a pioneer in the cutting-edge technology of plant biology. His lab invented a device called 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 uses systems biology approaches to develop new crop traits for the bioenergy, food, and industrial markets.
Charles Danko is a Robert N. Noyce Assistant Professor in Life Sciences and Technology at the Baker Institute and the College of Veterinary Medicine, Cornell University. His research focuses on understanding gene regulation using methods from molecular biology and genetics, computer science, statistics, and machine learning. He received his Ph.D. from SUNY Upstate Medical University, with his dissertation title being Bioinformatic Identification of Putative Regulatory Motifs, and his B.S. in biomedical engineering from John Hopkins University. Dr. Danko is interested in how DNA, the basic blueprints for all living things, is interpreted by cells to produce living, breathing organisms. He also explores how diseases like cancer change these interpretations and impact health.
Emma Farley is an assistant professor at the University of California, 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. Farley received a master’s 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 sub-optimized 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. MacKay
Trudy F. C. Mackay is the director of Clemson University’s Center for Human Genetics located on the campus of the Greenwood (S.C.) Genetic Center. She is recognized as one of the world’s leading authorities on the genetics of complex traits. 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). 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. 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.
Terry Magnuson, Sarah Graham Kenan Professor and founding chair of the University of North Carolina (UNC) Department of Genetics, became UNC’s vice chancellor for research on July 1, 2016. In this role, he leads a campus-wide research program that attracted nearly $1 billion in contract and grant funding in fiscal 2014; connects academic units across campus with university priorities; and manages research support offices as well as 14 centers and institutes. Magnuson, a geneticist who studies chromatin and gene expression in various diseases, joined the UNC School of Medicine in 2000 to create its $245 million-backed genetics and genomics program. He also directed the pan-campus Carolina Center for Genome Sciences, developed the Cancer Genetics Program within the Lineberger Comprehensive Cancer Center, and in 2010 was named vice dean for research in the School of Medicine. He is a member of both the American Academy of Arts and Sciences and the National Academy of Medicine. In 2014, he was appointed to the National Institutes of Health Council of Councils, an exclusive group of the top minds in the nation charged with guiding research projects that transcend the National Institute of Health’s centers and institutes. He is also a founding member of the International Mammalian Genome Society, and has served on the board of directors for both the Society for Developmental Biology and the Genetics Society of America.
Lauren O’Connell is assistant professor of biology at Stanford University. She received her Ph.D. in cellular and molecular biology from 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 biotic and abiotic environments. Dr. O’Connell’s lab uses amphibians as a model system for understanding the molecular and genomic contributions to biological diversity, as 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. Her own projects in the lab involve studying the neural basis of tadpole social behavior and the physiology of toxicity in poison frogs.
Andrea Sweigart is associate professor in the department of genetics at University of Georgia. She received her Ph.D. from Duke Univeristy in 2006 with prime focuses on molecular genetics and evolutionary biology. Dr. Sweigart believes a fundamental goal of evolutionary biology is to explain how populations become reproductively isolated species. Her research at Sweigart Lab tackles these questions in an emerging model system: the Mimulus guttatus species complex, a group 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.