Colloquium Keith A. Crandall: Computational Approaches for Characterizing Microbiome Diversity
By Keith A. Crandall, PhD, Professor ob Biostatistics & Bioinformatics, Director – Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
Microbiome characterization has become an integral component to the study of a wide variety of disease and health for a diversity of organisms. Through the collection of metagenomic sequence data from DNA and/or RNA samples isolated from host individuals, effective microbiome characterization can identify pathogens, link diversity to disease state, characterize treatment effects, and identify drug resistant variants. I present a computational platform, PathoScope, for metagenomic sequence analysis to characterize microbiome diversity and test hypotheses about diversity associates with disease and diversity dynamics over time. I then describe a second software package, TeleScope, that characterizes transposable elements in genomic data (a part of the microbiome component often ignored), maps those elements back to reference genomes, and identifies active mobile elements and their potential phenotypic impact. I present results from both empirical studies and simulation studies characterizing the utility of our computational approaches with metagenomic data and compare our approach to other leading packages. I then demonstrate our computational tools with applications in endangered species conservation, agriculture, and a variety of aspects of human health. Specifically, I will demonstrate the use of microbiome characterization related to black rhino health, human health related to Konzo disease, and human fecal transplant diversity over time. Finally, I will demonstrate the characterization of human endogenous retroviral elements (HERVs) in relation to head and neck cancer and incorporate this information into risk assessment.
Keith A. Crandall, PhD is the Founding Director of the Computational Biology Institute and Professor in the Department of Biostatistics and Bioinformatics at George Washington University. Professor Crandall studies the computational biology, population genetics, and bioinformatics, developing and testing methods for DNA sequence analysis. He applies such methods to the study of the evolution of both infectious diseases (especially microbiome diversity) and crustaceans (especially Decapod crustaceans). Professor Crandall has published over 300 peer reviewed publications, as well as three books. He has been a Fulbright Visiting Scholar to Oxford University and an Allen Wilson Centre Sabbatical Fellow at the University of Auckland. Professor Crandall has received a number of awards for research and teaching, including the American Naturalist Society Young Investigator Award, an NSF CAREER Award, a PhRMA Foundation Faculty Development Award in Bioinformatics, Honors Professor of the Year award at Brigham Young University, ISI Highly Cited Researcher, and the Edward O. Wilson Naturalist Award. He is an elected Fellow in the American Association for the Advancement of Science (AAAS) and a Fellow of the Linnean Society of London. Professor Crandall earned his BA degree from Kalamazoo College in Biology and Mathematics, an MA degree from Washington University in Statistics, and a PhD from Washington University School of Medicine in Biology and Biomedical Sciences. He also served as a Peace Corps Volunteer in Puyo, Ecuador.
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