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Appendix E Speaker Biographies Eric Alm, Ph.D., is the Doherty Assistant Professor of Ocean Utilization at the Massachusetts Institute of Technology (MIT). His research includes both com- putational/theoretical and experimental approaches to understanding the evolu- tion of microorganisms, emphasizing a “systems-level” perspective. Some areas of special interest include: tools for detecting natural selection in microbes; the evolutionary origin of gene families; mining metagenomic sequence data; experi- mental evolution of microbes; modeling bacterial ecology; gene regulatory net- works in bacteria; and protein structure and design. He enjoys teaching a variety of classes at MIT, spanning his diverse interests in microbiology, computer al- gorithms, and thermodynamics of biomolecules. He is currently looking forward to teaching a new class on microbial evolution and genetics. Dr. Alm has earned the following degrees: B.S., 1995, University of Illinois at Urbana-Champaign; M.S., 1997, University of California, Riverside; Ph.D., 2001, University of Wash- ington, Seattle; and Postdoc, 2005, University of California, Berkeley/Lawrence Berkeley National Laboratory. Bruce Budowle, Ph.D., received a Ph.D. in genetics in 1979 from Virginia Poly- technic Institute and State University. From 1979 to 1982, Dr. Budowle was a postdoctoral fellow at the University of Alabama at Birmingham. Working under a National Cancer Institute fellowship, he carried out research predominately on genetic risk factors for diseases such as insulin-dependent diabetes mellitus, melanoma, and acute lymphocytic leukemia. From 1983 to 2009, Dr. Budowle was employed at the FBI Laboratory Division and carried out research, develop- ment, and validation of methods for forensic biological analyses. Dr. Budowle has worked on laying some of the foundations for the current statistical analyses 395

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396 THE SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS in forensic biology and defining the parameters of relevant population groups. He has published approximately 500 articles, made approximately 600 presentations, and testified in more than 250 criminal cases in the areas of molecular biology, population genetics, statistics, quality assurance, and forensic biology. He has been a chair and member of the Scientific Working Group on DNA Methods, Chair of the DNA Commission of the International Society for Forensic Genetics, and a member of the DNA Advisory Board. He was one of the architects of the CODIS National DNA database, which maintains DNA profiles from convicted felons, from evidence in unsolved cases, and from missing persons. Some of Dr. Budowle’s efforts over the past decade are in counter-terrorism, primarily in identification of victims from mass disasters and in efforts involving microbial forensics and bioterrorism. Dr. Budowle was an advisor to New York State in the effort to identify the victims from the World Trade Center attack. In the area of microbial forensics, Dr. Budowle has been the chair of the Scientific Working Group on Microbial Genetics and Forensics, whose mission was to set quality assurance guidelines, develop criteria for biologic and user databases, set criteria for a National Repository, and develop forensic genomic applications. In 2009 Dr. Budowle became Executive Director of the Institute of Applied Genetics and Professor in the Department of Forensic and Investigative Genetics at the Uni- versity of North Texas Health Science Center at Fort Worth, Texas. His current efforts focus on the areas of human forensic identification, microbial forensics, and emerging infectious disease. Arturo Casadevall, M.D., Ph.D., is Professor and Chair of the Department of Microbiology & Immunology at the Albert Einstein College of Medicine. Dr. Casadevall received both his M.D. and Ph.D. from New York University and completed his internship and residency in internal medicine at Bellevue Hospital in New York, New York. Afterward, he completed subspecialty training in Infec- tious Diseases at the Albert Einstein College of Medicine. Dr. Casadevall’s major research interests are in fungal pathogenesis and the mechanism of antibody action. He has authored more than 540 scientific papers. Dr. Casadevall was elected to membership in the American Society for Clinical Investigation, the American Academy of Physicians, and the American Academy of Microbiology. He is a fellow of the American Association for the Advancement of Science and has received numerous honors including the Solomon A Berson Medical Alumni Achievement Award from New York University, the Maxwell L. Littman Award, the Rhoda Benham Award from Medical Mycology Society of America, and the Kass Lecturership from Infectious Diseases Society of America. He is the Edi- tor in Chief of mBio and serves on numerous editorial boards. Dr. Casadevall served on the National Academy of Sciences committee that reviewed the FBI investigation of the anthrax attacks in 2001. He serves on the National Science Advisory Board for Biosecurity and the National Institute of Allergy and Infec- tious Diseases Board of Scientific Counselors.

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APPENDIX E 397 Claire Fraser, Ph.D., is Director of the Institute for Genome Sciences at the University of Maryland School of Medicine in Baltimore, Maryland. She has joint faculty appointments at the University of Maryland School of Medicine in the Department of Medicine and Microbiology/Immunology. Until 2007, she was President and Director of The Institute for Genomic Research (TIGR) in Rockville, Maryland, and led the teams that sequenced the genomes of several microbial organisms, including important human and animal pathogens. She helped launch the new field of microbial genomics and revolu- tionized the way microbiology has been studied. In a 1995 landmark publication, a group of TIGR investigators reported on the first complete genome sequence of a free-living organism, Haemophilus influenzae. This new approach has, to date, produced DNA sequence data from nearly 1,000 different species across the phylogenetic tree. Her work on the Amerithrax investigation led to the identification of four genetic mutations in the anthrax spores that allowed the FBI to trace the material back to its original source. She is one of the world’s experts in microbial forensics and the growing concern about dual uses—research that can provide knowledge and technologies that could be misapplied. Dr. Fraser has authored more than 200 publications, edited 3 books, and served on the editorial boards of 9 scientific journals. For the past 10 years, she has been the most highly cited investigator in the field of microbiology. Her list of awards includes the E.O. Lawrence Award, the highest honor bestowed on research scientists by the Department of Energy, the Promega Biotechnology Award from the American Society of Microbiology, and the Charles Thom Award from the Society for Industrial Microbiology. She has been selected as one of Maryland’s Top 100 Women Circle of Excellence, and in 2010, was named to the Maryland Women’s Hall of Fame. She has served on many advisory panels for all of the major federal fund- ing agencies, the National Research Council, the Department of Defense, and the intelligence community. In addition, she has contributed her time as a board member for universities, research institutes, and other nonprofit groups because of her commitment to the education of our next generation of scientists. Jennifer Gardy, Ph.D., leads the Genome Research Lab at the British Columbia Centre for Disease Control, where she and her colleagues use emerging genomics technologies as tools for solving problems in public health. Dr. Gardy’s particular interests lie in using next-generation sequencing of pathogen isolates from an out- break situation to understand how outbreaks start, how pathogens transmit from person to person, and community to community, and how to turn this knowledge of transmission dynamics into sustainable and effective public health interven- tions. Her lab published the first genome-based reconstruction of a large tuber- culosis outbreak, a project that also looked at the role of social networks in the spread of disease, and the group is currently working on similar reconstructions

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398 THE SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS for other outbreaks of both bacterial and viral disease. The Genome Research Lab is also exploring the role of metagenomics in public health, investigating its utility in identifying novel microbial markers of disease. Dr. Gardy completed her Ph.D. at Simon Fraser University in 2006 and is currently an Adjunct Professor in Microbiology and Immunology at the University of British Columbia. Elodie Ghedin, Ph.D., is an Associate Professor in the Department of Compu- tational and Systems Biology and a member of the Center for Vaccine Research at the University of Pittsburgh School of Medicine. Her research is aimed at generating critical insights about host-pathogen interaction and pathogen popu- lation structures. She uses functional and comparative genomics, computational and evolutionary biology, and molecular parasitology techniques to focus on the agents that cause diseases endemic to tropical climates, such as lymphatic filaria- sis (elephantiasis), onchocerciasis (River blindness), and leishmaniasis, as well as global diseases such as seasonal and pandemic influenza. Dr. Ghedin came to the University of Pittsburgh in 2006 after spending six years at TIGR where she led the Influenza Genome Project, the first of its kind to characterize large collections of an acute RNA virus, overturning outdated models of influenza evolution that were based on limited genetic data. Using NextGen platforms, she and her team are determining the extent and structure of genetic variation in influenza virus populations sampled within individual hosts, and variant transmission. In 2011, citing the creativity and collaborative nature of her work and her contributions to parasitology and virology, the MacArthur Foundation recognized Dr. Ghedin with its fellowship award. Jack A. Gilbert, Ph.D., earned his Ph.D. from Nottingham University, United Kingdom, in 2002, and received his postdoctoral training in Canada at Queens University. He subsequently returned to the United Kingdom in 2005 and worked for Plymouth Marine Laboratory at a senior scientist until his move to Argonne National Laboratory and the University of Chicago in 2010. Dr. Gilbert is an En- vironmental Microbiologist at Argonne National Laboratory, Adjunct Professor in the Department of Ecology and Evolution at the University of Chicago, and Fellow of the Institute of Genomic and Systems Biology. Dr. Gilbert is currently applying next-generation sequencing technologies to microbial metagenomics and metatranscriptomics to test fundamental hypotheses in microbial ecology. He has authored more than 70 publications and book chapters on metagenomics and approaches to ecosystem ecology. He has focused on analyzing microbial function and diversity, with a specific focus on nitrogen and phosphorus cycling, with an aim of predicting the metabolic output from a community. He is currently working on generating observational and mechanistic models of microbial com- munities associated with aquatic and terrestrial ecosystems. He is on the board of the Genomic Standards Consortium (www.gensc.org), is an editor for PLoS ONE

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APPENDIX E 399 and the ISME Journal, and is co-leading the Earth Microbiome Project (www. earthmicrobiome.org). Peter Girguis, Ph.D., is currently a John L. Loeb Associate Professor of Natural Sciences at Harvard University and an Adjunct Research Engineer at the Mon- terey Bay Aquarium Research Institute. His research focuses on the ecological physiology of microbes that live in extreme environments, to better understand the role they play in mediating deep ocean carbon and nitrogen cycling. He is particularly interested in the physiological and biochemical adaptations (adaptive traits) to life in anaerobic environments. His work on microbial fuel cells has furthered our understanding of how microbes generate energy using solid-state minerals as electron acceptors and—in collaboration with colleagues around the world—has led to the development of systems that enable energy to be harnessed and used from the environment. He received his B.Sc. from the University of California, Los Angeles, where he also worked with Drs. David Chapman and William Hamner. He received his Ph.D. from the University of California, Santa Barbara, where he worked with Dr. James Childress on the physiological and biochemical adaptation of deep-sea hydrothermal vent tubeworms and their microbial symbionts to the vent environ- ment. He did his postdoctoral research at the Monterey Bay Aquarium Research Institute with Dr. Edward Delong on the growth and population dynamics of anaerobic methanotrophs. Susan Huse, Ph.D., is an Assistant Research Scientist at Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts. She studies microbial diversities, popu- lation structures, evolution, and bioinformatics. Her research is in the role of the microbiome in human health and disease. She is looking to define what is “nor- mal” in the human mouth and gut within the context of a great level of interper- sonal microbiome variation. Evaluating changes from the “normal healthy” state are critical for understanding health, dysbiosis, and host-microbiome interactions. Her collaborations have included projects describing the progression of pouchitis in inflammatory bowel disease patients, the impacts of antibiotics, and the effects of changing dentition. She has also been active in developing and advancing best practices for the use of 16S ribosomal RNA gene for studying microbial com- munities, starting with her participation in the first paper that used the 454 tag py- rosequencing for studying microbial ecology and the rare biosphere. In addition, she published the first assessment of how to filter low-quality 454 sequence data and developed a new method for assigning taxonomy to these tags (GAST). She also demonstrated that the accepted standard method of clustering 16S rRNA tags for taxonomic-independent methods of evaluating microbial communities was overestimating microbial diversity and underestimating the similarities between

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400 THE SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS communities, and developed the SLP clustering method to more closely estimate the true diversity and inter-community similarities. Paul Keim, Ph.D., holds the Cowden Endowed Chair in Microbiology at North- ern Arizona University (NAU), where he is also a Regents Professor of Biology. In addition, he is now a Professor and Director of the Pathogen Genomics Divi- sion at The Translational Genomics Research Institute (TGen). He is an affiliate researcher at the Los Alamos National Laboratory, where he has been engaged in national security research since 1993. Dr. Keim received his B.S. in biology and chemistry from Northern Arizona University in 1977 and his Ph.D. in botany from the University of Kansas in 1981. His NAU laboratory was heavily involved in analysis of evidentiary material from the 2001 anthrax-letter attacks for the FBI and the Department of Justice. His work has helped lead to the development of a new scientific field known as microbial forensics. He has published extensively on the evolution and population genetics of Bacillus anthracis, Yersinia pestis, Francisella tularensis, Burkholderia pseudomallei, Burkholderia mallei, Brucella spp., and Coxiella burnetii. Recently, these same scientific principles have been applied to other public health and clinically important pathogens such as Vibrio cholerae (cholera in Haiti), S. aureus, and E. coli. Folker Meyer, Ph.D., is a Computational Biologist at Argonne National Labora- tory and a Senior Fellow at the Computation Institute at the University of Chi- cago. He was trained as a computer scientist and with that came his interest in building software systems. He now is interested in building systems that further our understanding of biological data sets. In the past he has been best known for his leadership role in the development of the GenDB genome annotation system and the design and implementation of Bielefeld University’s high-performance computing facility. Currently he is most interested in comparative analysis of large numbers of microbial genomes. Mark Pallen, M.D., Ph.D., is a medically qualified microbiologist (M.D., Ph.D.), educated at Cambridge and in London. Since 2001, he has been Professor of Mi- crobial Genomics at the University of Birmingham. Dr. Pallen’s research interests span bioinformatics, bacterial protein secretion, and bacterial pathogenomics. In recent years, his attention has focused on the application of high-throughput sequencing to medical microbiology, particularly genomic epidemiology, sequence-based approaches to surveying complex microbial communities, and new bench-top sequencing platforms. In the summer of 2011, Dr. Pallen’s group kick-started and guided an open-source genomics programme on the German E. coli outbreak strain, which included innovative crowdsourcing of analysis and culminated in a New England Journal of Medicine paper. More recently, Dr. Pallen has published a performance comparison of bench-top sequencers ap- plied to the German outbreak strain. Dr. Pallen is author of The Rough Guide to

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APPENDIX E 401 Evolution, a wide-ranging introduction to this topic, and is currently writing a book titled The Last Days of Smallpox. Julian Parkhill, Ph.D., is a Professor in pathogen genomics at the Sanger In- stitute. Since joining the Sanger Institute in 1997, he has been involved in the genomic analysis of a large number of bacteria from a wide diversity of genera, including Bordetella, Burkholderia, Campylobacter, Chlamydia, Clostridium, Corynebacterium, Escherichia, Haemophilus, Mycobacterium, Neisseria, Salmo- nella, Staphylococcus, Streptococcus, Yersinia, and many others. His current research uses very high-throughput sequencing and phenotyping technologies to understand the evolution of bacterial pathogens on short and long time scales, how they transmit between hosts on a local and global scale, how they adapt to different hosts, and how they respond to natural and human-induced selective pressures. Dr. Parkhill gained his Ph.D. in 1991 from the University of Bristol through work on bacterial transcriptional regulation. He subsequently pursued post- doctoral research at the University of Birmingham, first on bacterial transcrip- tional regulation, and then on the transforming proteins of adenoviruses. David Rasko, Ph.D., is an Assistant Professor in the Department of Microbiol- ogy and Immunology and a member of the Institute for Genome Sciences. Dur- ing his career he has developed expertise in comparative microbial genomics, bioinformatics, and functional genomics. Dr. Rasko has led comparative genome sequencing and analysis projects for important human diarrheal pathogens, fo- cusing on Escherichia coli and Shigella species as well as Bacillus cereus group isolates including Bacillus anthracis. He has developed comparative bioinformat- ics tools designed to characterize the genetic diversity in closely related bacterial isolates. Dr. Rasko was the first to publish a comparative genomic study that in- cluded a genome reference from a true commensal, each of the six diarrheagenic E. coli pathogenic variants (pathovars) as well as representatives of the urinary tract and avian derived E. coli. Recent comparative genomic studies have focused on the development of genomic epidemiology tools for study of hundreds of enterotoxigenic E. coli and Shigella species isolates. These comparative works provide the framework for the continued functional study of the evolution of these pathogens, as well as functional studies of identified unique and conserved gene features as vaccine and therapeutic targets. Kim Ritchie, Ph.D., is Senior Scientist and Manager of the Marine Microbiol- ogy program at Mote Marine Laboratory, Florida. She is a molecular biologist investigating the microbial community structure of Florida coral reefs and its role in disease resistance. She received her Ph.D. in the laboratory of Thomas Petes studying telomere length regulation in 2000 followed by postdoctoral work at the Smithsonian’s Tropical Research Laboratory in Panama. Past work

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402 THE SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS includes identification and characterization of coral disease pathogens. Her cur- rent studies include characterizations of symbiotic microfauna in multiple coral species (mountainous star coral, sea fan corals, threatened Elkhorn and staghorn corals) as well as culture-based studies on the production of anti-microbial and anti-fungal compounds produced by bacterial symbionts. Dr. Ritchie is also interested in dinoflagellate-bacterial interactions including the relationship be- tween symbiotic bacteria and the coral dinoflagellate, Symbiodinium sp, and vital interactions between bacterial symbionts and the red tide causing dinoflagellate, Karenia brevis. Erica Bree Rosenblum, Ph.D., is currently an Assistant Professor at University of California (UC), Berkeley, in the Department of Environmental Science Policy and Management. Research in the Rosenblum lab focuses on the evolutionary processes of speciation and extinction in changing environments. One current emphasis is on the impact of emerging infectious diseases on wildlife. To address questions across spatial and temporal scales, Dr. Rosenblum’s research uses in- tegrative methods, and she is involved in a number of interdisciplinary initiatives including the Berkeley Initiative for Global Change Biology and the NSF Bio/ computational Evolution in Action CONsortium Center (BEACON). The Rosen- blum lab is also highly invested in scientific outreach and facilitates a number of activities to improve public understanding of science including a “Save the Frogs Day” for pre-school students and a “Lizard Camp” for middle school students. Her research has been featured broadly in the popular press including in the New York Times, Science magazine, the Discovery Channel, National Public Radio, and Ranger Rick magazine. Dr. Rosenblum conducted her Ph.D. research at UC Berkeley in the De- partment of Integrative Biology and her postdoctoral research at the Lawrence Berkeley National Lab in the Department of Genomics. Tim Stearns, Ph.D., is a Professor in the Stanford University Department of Biology, the Stanford University Medical School Department of Genetics, and the Cancer Biology Program. Dr. Stearns received his Ph.D. at the Massachusetts Institute of Technology, was a postdoctoral fellow at University of California, San Francisco, and joined the Stanford faculty in 1993. Research in Dr. Stearns’ lab is focused on the centrosome and cilium, microtubule-based structures that are at the center of cell signaling and cell division, and on using simple microbial models to assess human genetic variation. Dr. Stearns is the recipient of a How- ard Hughes Medical Institute Professor award and the Stanford Dean’s Award for Distinguished Teaching. In addition to undergraduate and graduate teaching at Stanford, he has taught laboratory courses at Cold Spring Harbor Laboratory, Woods Hole, and internationally in Chile, South Africa, Ghana, and Tanzania, and is a member of the International Affairs Committee of the American Society for Cell Biology. Dr. Stearns is a member of JASON, a panel that advises the U.S.

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APPENDIX E 403 government on defense and technology issues, and he is on the scientific advisory board of the Temasek Life Sciences Laboratory in Singapore. He currently holds the Frank Lee and Carol Professorship at Stanford University. David Wang, Ph.D., is currently an Associate Professor at Washington Univer- sity in St. Louis. He earned a B.S. degree in chemistry from Stanford University in 1992 and a Ph.D. in biological chemistry from the Massachusetts Institute of Technology in 1998. Following postdoctoral training at University of California, San Francisco, he started his own research laboratory at Washington University in St. Louis in 2004. Research in the Wang laboratory focuses upon the iden- tification and characterization of novel viruses. Dr. Wang has pioneered novel genomic approaches for viral discovery, including pan-viral DNA microarray and high–throughput sequencing–based strategies. Application of these methods to unexplained cases of acute respiratory disease and diarrheal disease in humans has lead to the discoveries of many novel viruses, such as WU polyomavirus, As- troviruses VA1, VA2, VA3, MLB1, and MLB2, human klassevirus 1, and human cosavirus E1. Characterization efforts have focused on defining the epidemiology and seroepidemiology as well as the basic virology of these viruses. In addition, his laboratory has analyzed a diverse array of non-human specimens including marine mammals, insect vectors, and environmental samples (e.g., raw sewage). Most recently, his laboratory discovered the first viruses capable of infecting the nematode C. elegans and established an infection system for studying host-virus interactions in this genetically robust model organism. George Weinstock, Ph.D., is currently Professor of Genetics and of Microbiol- ogy and Associate Director of The Genome Institute at Washington University in St. Louis, where he leads a number of projects in human genetics and microbial genomics including projects in the Human Microbiome Project and other metage- nomic studies of humans, monkeys, and mice. Previously he was Co-Director of the Human Genome Sequencing Center at Baylor College of Medicine, where he was a leader of the Human Genome Project and a number of other genome projects. He has had a long-term interest in genetics, genomics, and bioinformat- ics, particularly as bioinformatics couples technological advances to new biol- ogy through increases in the size and quality of data sets as well as explaining phenotypes through characterization of genotypes.

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