Whole Genome Sequencing Researchers
Below you will find biographies for the CFSAN researchers who are part of FDA’s foods whole genome sequencing program.
Hediye Nese Cinar
Christopher J. Grim
Kelli L. Hiett
Julie Ann Kase
Susan R. Leonard
Lisa Harrison Plemons
Sandra M. Tallent
Gopal R. Gopinath
David W. Lacher
Mark K. Mammel
Anna I. Maounounen-Laasri
Marc Allard, Ph.D.
Research Area Coordinator for Genomics
Marc W. Allard received his Ph.D. in biology in 1990 from Harvard University, Cambridge, MA. Dr. Allard was the Louis Weintraub Associate Professor of Biology (and Genetics) at George Washington University (Washington, DC) for 14 years from 1994 to 2008. He has had appointments to the Visiting Scientists Program both at the Federal Bureau of Investigation’s Counterterrorism and Forensic Science Research Unit (CTFSRU) and in the Chem Bio Sciences Unit (CBSU) for 8 years, where he assisted in the anthrax investigations and human genetics data-basing. Dr. Allard joined FDA's Office of Regulatory Science and the Division of Microbiology in November 2008 and he is using DNA sequence information from the genomes of food borne pathogens to identify unique single nucleotide polymorphisms (SNPs), SAAPs and whole proteins to rapidly identify the various strains of bacteria, particularly Salmonella, E. coli, Shigella and Listeria. Dr. Allard specializes in both phylogenetic analysis and bioinformatics methods, as well as the wet laboratory methods which generate this genetic information.
Uma Babu, Ph.D.
Dr. Uma Babu received her Ph.D. in nutritional sciences from University of Maryland, College Park. She joined CFSAN in 1991 as a Senior Staff Fellow in the Division of Nutrition and became a research biologist in the Division of Science and Applied Technology, Office of Special Nutritionals in 1993. In 1998, she joined the Immunobiology Branch of the Division of Virulence Assessment in the Office of Applied Research and Safety Assessment (OARSA). She is part of a team tasked with developing culture methods for the identification of Campylobacter and Arcobacter species from the farm environment and ready-to-eat produce crops. These bacterial isolates are sequenced by WGS for source attribution and inclusion in the GenomeTrakr database.
Kannan Balan, Ph.D.
Dr. Kannan Balan received his Ph.D. in biology from Howard University. After postdoctoral training at Brown University, he held research appointments at the University of Miami and Case Western Reserve University. Dr. Balan joined FDA in 2009 as a Commissioner’s Fellow, conducting research in the Office of Applied Research and Safety Assessment’s (OARSA) Immunobiology Branch. He is currently developing culture methods for the detection of Campylobacter and Arcobacter species from the farm environment and ready-to-eat produce crops, and performs whole genome sequencing on Campylobacter and Arcobacter isolates from surveillance samples to determine source attribution and for inclusion in the GenomeTrakr database.
Rebecca Bell, Ph.D.
Dr. Rebecca Bell is a research microbiologist in the Molecular Methods and Subtyping Branch, within the Division of Microbiology, at the Food and Drug Administration’s Center for Food Safety and Applied Nutrition. Dr. Bell received her Ph.D. in microbiology from The Ohio State University in 2005. Afterwards, she joined CFSAN in 2006 as a postdoctoral fellow in the Division of Analytical Chemistry where she worked on bacterial protein profiling using liquid chromatography/mass spectrometry. In 2008, Dr. Bell moved to MMSB. She continues to collaborate with the DAC on LC/MS work as well as working on molecular subtyping of Salmonella enterica, the development of rapid screening methods for Salmonella contamination of foods and ecological surveillance of the tomato growing environment for Salmonella.
Rachel Binet, Ph.D.
Dr. Rachel Binet has been with FDA’s Center for Food Safety and Applied Nutrition (CFSAN) since 2009 and currently serves as a research microbiologist in the Microbiological Methods Development Branch, within the Division of Microbiology. Dr. Binet was trained as a microbiologist at the Pasteur Institute in France and received her M.Sc. in microbiology in 1994 and her Ph.D. in microbiology in 1998. She began her career using genetics strategies to explore the physiology of various Gram-negative bacteria, including Escherichia coli, Serratia marcescens, Shigella, and Chlamydia. At FDA her research continues to concentrate on microbial genetics and physiology, with the addition of genomics and metagenomics as tools to differentiate and improve the recovery yield of pathogenic E. coli, Shigella, and Salmonella from contaminated food products. Dr. Binet serves as expert in committees related to laboratory biosafety and security of work involving recombinant DNA molecules, pathogens and toxins at FDA and on microbial methods and pathogens for CFSAN and for the International Organization for Standardization (ISO).
Eric Brown, Ph.D.
Director, Division of Microbiology
Dr. Eric W. Brown currently serves as Director of the Division of Microbiology in the Office of Regulatory Science. He oversees a group of 50 researchers and support scientists engaged in a multi-parameter research program to develop and apply microbiological and molecular genetic strategies for detecting, identifying, and differentiating bacterial foodborne pathogens such as Salmonella and shiga-toxin producing E. coli. His early work on horizontal gene transfer among foodborne pathogens has aided in elucidating the etiologies of several emerging pathogens including many of the group I salmonellae as well as enterohemorrhagic and enteropathogenic E. coli. More recently, his laboratory has been instrumental in adapting next-generation sequencing technologies to augment foodborne outbreak investigations at the FDA. Dr. Brown received his Ph.D. in Microbial genetics from The Genetics Program in the Department of Biological Sciences at The George Washington University. He has conducted research in microbial evolution and microbial ecology as a research fellow in the National Cancer Institute, the U.S. Department of Agriculture, and as a tenure-track Professor of Microbiology at Loyola University of Chicago. Dr. Brown came to the Food and Drug Administration in 1999 and has since carried out numerous experiments relating to the detection, identification, and discrimination of foodborne pathogens. He has been a member of the American Society for Microbiology since 1994 and has co-authored more than 70 publications and book chapters on the molecular differentiation and molecular evolution of bacterial pathogens. His primary research interests are currently to investigate the role of next-generation genome sequencing in the resolution of foodborne outbreaks and to continue to employ a variety of methods that allow for rapid and sensitive identification of enteric pathogens from the food supply.
Laurel Burall, Ph.D.
Dr. Laurel Burall is a research microbiologist in CFSAN’s Office of Applied Research and Safety Assessment. She received her Ph.D. in microbiology and immunology from the Department of Microbiology and Immunology at the University of Maryland in 2004 and joined FDA in 2007, initially as an ORISE Fellow. Her research focuses on aspects of Listeria monocytogenes survival in various environments and food matrices, as well as method development. Dr. Burall uses WGS to evaluate strain persistence of L. monocytogenes in different natural environments, particularly as it pertains to the farm and fresh produce. She uses WGS analysis to examine phylogenetic groups that may be implicated in increased persistence or linked to strains that are more transient. She is also working on a method to rapidly subtype L. monocytogenes into distinct, broad phylogenetic groups, prior to sequencing of an isolate, thus aiding the rapid classification of the organism.
Yi Chen, Ph.D.
Dr. Yi Chen is a research microbiologist and Listeria monocytogenes subject matter expert in CFSAN’s Division of Microbiology. He has developed, compared, and evaluated rapid methods for screening L. monocytogenes in food and environmental matrices, and both led and collaborated on efforts to validate qualitative and quantitative testing methods for the organism. Dr. Chen has studied the behavior of L. monocytogenes in various food matrices to elucidate the relative risk of L. monocytogenes contamination in these foods. He is also an expert on whole genome sequencing analysis of L. monocytogenes, having analyzed strains isolated during regular FDA surveillance and outbreak response. His work has improved understanding of the epidemiology and ecological persistence of this pathogen. He has provided scientific advice on various FDA assignments, outbreak investigations, and laboratory analyses. In addition, Dr. Chen has worked on the method validation and genetic characterization of Cronobacter spp. Dr. Chen received his Ph.D. in Food Science from the Department of Food Science at the Pennsylvania State University in 2007. He currently serves as a member of Microbial Method Validation Subcommittee of FDA, General Referee for AOAC International, Technical Committee member on MicroVal and Editorial Board member for Applied and Environmental Microbiology.
Hediye Nese Cinar, M.D.
Dr. Hediye Nese Cinar is a research biologist on the Parasitology Team, within the Division of Virulence Assessment, at FDA’s Center for Food Safety and Applied Nutrition. Her areas of research specialization include: the study of bacterial virulence mechanisms and immune responses using the model organism Caenorhabditis elegans; heavy metal detection and genome-wide responses to heavy metals in C. elegans; and developmental genetics and neurobiology of nerve regeneration. Since January 2014, Dr. Cinar has led a project investigating the use of whole genome sequencing for epidemiologic investigations of illness outbreaks involving the foodborne parasite Cyclospora cayetanensis.
Christina Ferreira is molecular microbiologist in the Division of Microbiology's Molecular Methods and Subtyping Branch. She graduated in 2008 from Clarion University of Pennsylvania, with a Bachelor of Science degree in molecular biology and biotechnology. At FDA-CFSAN, her work is primarily focused on development of a mass spectrometry-based assay for rapid identification of Salmonella species in food. She is also working on the validation of assembled genomes through comparisons with whole genome (optical) maps, analysis of the evolution of S. enterica Typhimurium over the last 70 years, and an investigation of SNP variations in clinical STEC strains.
Solomon Gebru, Ph.D.
Dr. Solomon Gebru is a staff fellow in the Division of Molecular Biology’s Molecular Genetics Branch within, at CFSAN’s Office of Applied Research and Safety Assessment. Dr. Gebru received his Ph.D. in molecular biology from Howard University in 2006. He joined FDA in 2007 as a contractor molecular biologist, developing rapid Salmonella and E. coli subtyping methods including multi-locus variable tandem repeats (MLVA) approaches and clustered regularly interspaced short palindromic repeats (CRISPR). He collaborates with FDA’s Center of Veterinary Medicine to explore the suitability of pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP), MLVA, and CRISPR typing approaches for resolving closely related foodborne E. coli and Salmonella outbreak strains. Currently he is working on whole genome sequencing analysis of E. coli strains from Penn State University and USDA’s Food Safety and Inspection Service collections, and from fungi found in foods.
Narjol Gonzalez-Escalona, Ph.D.
Dr. Gonzalez-Escalona is a research microbiologist in the Molecular Methods and Subtyping Branch, within the Division of Microbiology, at FDA’s Center for Food Safety and Applied Nutrition. His research interests include the ecology and evolution of marine bacteria, especially those of the genus Vibrio. Other research interests include tracking, subtyping, evolution, comparative genomics, and the identification of novel pathogenicity targets from foodborne pathogens such as E. coli, Clostridium botulinum, and Salmonella using whole genome sequencing approaches. He has developed new methods to detect Salmonella in produce, S. Enteritidis and S. Heidelberg in egg products, and alternative methods for Salmonella subtyping. He is a member of IAFP and ASM and is the curator of the MLST website for V. parahaemolyticus. Dr. Gonzalez-Escalona received his Ph.D. from the University of Chile in 2004 and completed further postdoctoral training at the Gulf Coast Seafood Laboratory (GCSL), FDA, Dauphin Island, AL.
Christopher J. Grim, Ph.D.
Dr. Grim received his B.S. in marine biology from the University of Miami and his Ph.D. in environmental molecular biology from the University of Maryland, College Park. Dr. Grim joined the FDA in 2016. His research is focused on advanced molecular detection strategies, such as whole genome sequencing, pathogen subtyping and comparative genomics, and metagenomic approaches to complex food safety challenges.
Julie Haendiges, M.P.S.
Julie Haendiges is a biologist with the Molecular Methods and Subtyping Branch, in the Division of Microbiology at FDA’s Center for Food Safety and Applied Nutrition (CFSAN). She received her master’s degree from UMBC in biotechnology. She previously was the leader of the core sequencing lab at the Maryland Department of Health where she focused on sequencing foodborne bacterial pathogens and viruses. At CFSAN, her research focuses on functional genomics, preventive controls of Salmonella enterica, and utilizing long-read sequencing technology for transcriptomics.
Kelli L. Hiett, Ph.D.
Director, Division of Virulence Assessment
Dr. Kelli L. Hiett serves as Director of the Division of Virulence Assessment in the Office Applied Research and Safety Assessment (OARSA), CFSAN. Dr. Hiett received her M.S. in molecular genetics, studying operon structure in the fungal model organism, Neurospora crassa, and pathogen, Aspergillus nidulans. She received her Ph.D. in infectious disease from the School of Veterinary Medicine at the University of Georgia, where she investigated molecular mechanisms involved in the colonization of Campylobacter spp. in poultry. Dr. Hiett continued to conduct research on the zoonotic pathogen, Campylobacter spp. as a lead scientist at the U.S. Department of Agriculture’s, Agricultural Research Service. Dr. Hiett came to the FDA in 2017 and has since formed a team to develop culture and molecular methods to recover and detect Campylobacter and Arcobacter species from the farm environment and ready-to-eat produce crops. Campylobacter and Arcobacter isolates from surveillance samples are identified by whole genome sequencing for source attribution and inclusion in the GenomeTrakr database.
Maria Hoffmann, Ph.D.
Dr. Hoffmann's thesis research was, performed at the U.S. Food and Drug Administration in College Park, Maryland, under Dr. Eric Brown, focused on the molecular evolution and speciation of the genus Vibrio. She completed her Ph.D. work in July 2012 at the University of Hamburg. Currently she is performing analyses to acquire data for differentiation and characterization of pathogens, particularly outbreak isolates from non-outbreak isolates and closely-related antibiotic-resistant Salmonella species using whole genome sequencing (WGS) and comparative genomic analyses. Further using the Pacific Biosciences (PacBio) RS sequencer and their hierarchical genome assembly process (HGAP) we are sequencing different pathogens to completly close reference genomes which will support the pilot studies of testing the applicability of WGS in public health surveillance activities.
Hyein Jang, Ph.D.
Dr. Jang is an ORISE fellow in the Virulence Mechanisms Branch within the Division of Virulence Assessment at CFSAN. She earned a Ph.D. in food science from Rutgers, the State University of New Jersey in 2017, where she studied the microbial safety of fresh produce, particularly molecular interactions and survival of pathogenic E. coli on plants and leafy vegetables. Since joining FDA that same year, she has performed whole genome sequencing to investigate genotypic and phenotypic features of Cronobacter and Salmonella to better understand their virulence traits, genomic diversity, and phylogenetic relatedness, as a part of GenomeTrakr. Dr. Jang currently performs transcriptomic analysis of Cronobacter persister cells grown under stress and developing an isolation and detection method for Cronobacter foods of plant-origin.
Julie Ann Kase, Ph.D.
Julie Ann Kase is a research microbiologist in the Microbial Methods Development Branch within the Division of Microbiology at FDA’s Center for Food Safety and Applied Nutrition. Dr. Kase joined FDA in 2008 and quickly established herself as an agency subject matter expert for Shiga toxin-producing E. coli (STEC) and Brucella spp. She has spent over 25 years at the lab bench encompassing work as a pharmaceutical chemist, public health scientist, and food microbiologist and has authored dozens of peer-reviewed publications and book chapters. Her research activities have touched upon the transmission and detection of infectious agents in the environment, the microbiocidal efficacy of chemical disinfectants, and methods to culture and identify pathogenic STEC and Brucella spp. from various matrices. Much of her current work utilizes the power of nucleic acid sequencing for either a more specific characterization of STEC or the refinement of classical bacteriological culture methods. Dr. Kase has served on numerous committees including the National Advisory Committee on Microbiological Criteria for Foods (NACMCF), the FDA Bacteriological Analytical Manual (BAM) Council, the ILSI North America Committee on Food Microbiology, and currently serves as Chair of the FDA STEC Advisory Council.
Susan R. Leonard, Ph.D.
Dr. Susan Leonard is a research biologist in the Division of Molecular Biology, at CFSAN’s Office of Applied Research and Safety Assessment. Her research interests include utilizing shotgun metagenomic sequencing for the detection and genomic characterization of Shiga toxin-producing Escherichia coli (STEC) in food samples, the characterization of E. coli populations in environmental samples, and for assessing factors that impact STEC contamination or survival during fresh produce production and storage. In addition, her projects include whole genome sequence comparative analyses of STEC isolates as well as other foodborne pathogens. She received her Ph.D. in molecular microbiology and immunology from the University of Maryland, Baltimore.
Sara Lomonaco, Ph.D.
Dumitru Macarisin, Ph.D.
Dumitru Macarisin is a research microbiologist in the Division of Microbiology at FDA’s Center for Food Safety and Applied. He is subject matter expert for Listeria monocytogenes and leads FDA’s development and implementation of research projects related to microbial safety of fresh fruits and vegetables. Dumitru earned his Ph.D. in plant physiology and biochemistry in 2003 and pursued further postdoctoral research in the Agricultural Research Organization at the Volcani Center in Israel. He followed this with an 8-year research tenure at the United States Department of Agriculture’s Agricultural Research Service, where conducted extensive research in postharvest pathology and biocontrol, plant stress response, produce safety, microbiology, parasitology and public health. Dumitru came to FDA in 2013, where his current research focuses on understanding the routes/mechanisms of fresh produce contamination and environmental reservoirs of foodborne pathogens and developing mitigation strategies to improve good agricultural practices in the prevention of produce recalls and foodborne outbreaks. He has represented FDA nationally and internationally on critical food safety issues, providing recommendations on preventive controls, environmental monitoring, and quality control improvements to government agencies and the food industry.
Andrea Ottesen, Ph.D.
Research Area Coordinator for Metagenomics
Dr. Andrea Ottesen is the Research Area Coordinator (RAC) for Metagenomics at FDA's Center for Food Safety and Applied Nutrition (CFSAN) in the Molecular Methods and Subtyping Branch (MMSB) of the Division of Microbiology. She received her Ph.D. in 2000 from the University of Maryland. Ottesen works to provide target and non target metagenomic data to describe ecologies associated with high risk crops. Her ecological data are used to complement and improve Salmonella detection methods and provide data to improve recommendations for Good Agricultural Practices (GAPs).
Isha Patel is a research biologist in CFSAN’s Office of Applied Research and Safety Assessment. Her research focuses on the use of next-generation sequencing methods for detection and characterization of commensal bacteria as well as foodborne pathogens. She has a M.Sc. degree in microbiology from India and pursued further graduate studies at University of Maryland where she earned an M.S. degree in microbiology.
Lisa Harrison Plemons, Ph.D.
Dr. Lisa Plemons received her Ph.D. in medical sciences from the Medical Microbiology and Immunology Department at Texas A&M University in 2004. Following postdoctoral training at the University of Maryland, Baltimore (2004-2009), she joined the Immunobiology Branch of the Division of Virulence Assessment in the Office of Applied Research and Safety Assessment as a Staff Fellow. Currently, Dr. Plemons is a research microbiologist in the Immunobiology Branch and works with a team to develop culture methods to detect Campylobacter and Arcobacter species from the farm environment and ready-to-eat produce crops. Campylobacter and Arcobacter isolates from surveillance samples are identified by whole genome sequencing for source attribution and inclusion in the GenomeTrakr database.
Shashi Sharma, Ph.D.
Ben Tall, Ph.D.
Acting Branch Chief, Virulence Mechanisms Branch
Dr. Ben Tall currently serves as Acting Branch Chief of the Virulence Mechanisms Branch, in the Office of Applied Research and Safety Assessment’s Division of Virulence Assessment. He oversees a group of researchers and support scientists engaged in a research program focused on the development of microbiological and molecular genetic approaches for detecting, identifying, and differentiating bacterial foodborne pathogens such as Salmonella, Cronobacter, Bacillus cereus, marine Vibrios, and Listeria spp. His early work on development of vaccines for Vibrio cholerae, Salmonella typhi, Shigella spp., and enteropathogenic E. coli was performed at the Center for Vaccine Development, University of Maryland School of Medicine. More recently, his laboratory has been instrumental in adapting next-generation sequencing technologies to augment FDA foodborne illness outbreak investigations involving Cronobacter and several serovars of Salmonella enteritidis. Dr. Tall received his Ph.D. in microbiology from the Department of Microbiology, University of Maryland Dental School in 1988. Dr. Tall came to FDA in 1990 and has since carried out numerous studies relating to the detection, identification, and characterization of foodborne pathogens. He has been a member of the American Society for Microbiology since 1977 and has co-authored more than 130 publications and book chapters on the molecular detection, identification, and characterization of foodborne bacterial pathogens. His primary research interests currently are investigating the application of next-generation genome sequencing to characterization of foodborne pathogens and employing a variety of methods that allow for rapid and sensitive identification of enteric foodborne pathogens, which is a prerequisite towards development of future countermeasures against these pathogens.
Sandra M. Tallent, Ph.D.
Chief, Molecular Methods and Subtyping Branch
Sandra Tallent serves as Chief of the Molecular Methods and Subtyping Branch, within the Division of Microbiology, at FDA’s Center for Food Safety and Applied Nutrition. Dr. Tallent began her career as a clinical microbiologist, but the continued challenges of antimicrobial resistance prompted her to alter her career focus to public health research. She earned her Ph.D. from the Medical College of Virginia in Richmond prior to selection as a CDC Emerging Infectious Disease Research Fellow with Virginia’s Division of Consolidated Laboratory Services. Dr. Tallent accepted an appointment with FDA in 2008, where her research continues to concentrate on virulence and pathogenicity of Staphylococcus aureus, but also includes numerous experiments on Bacillus cereus. As a research microbiologist, Dr. Tallent has validated new protocols in an effort to update the FDA’s Bacteriological Analytical Manual. She is currently developing new methods that are based on genomic sequence information.
Carmen Tartera, Ph.D.
Dr. Carmen Tartera received her Ph.D. in microbiology from the University of Barcelona, Spain. In 2009, she joined the Division of Molecular Biology at the Center of Food Safety and Applied Nutrition. Currently, she is leading a study to examine foods supplemented with live microbes. The objective of this research program is to identify adulteration in these products sold in the U.S., using WGS analysis through metagenomics.
Ruth Timme, Ph.D.
Ruth Timme is a research microbiologist at the FDA’s Office of Regulatory Science. She received her Ph.D. in 2006 in Plant Biology at The University of Texas at Austin. Her research background is focused mainly on utilizing comparative genomics and phylogenetics methods to answer evolutionary questions. Although her training is in botany, her published research spans a diversity of organisms, including sunflowers (Helianthus), Dinoflagellates, Charophyte green algae, and Salmonella. At the FDA she is implementing phylogenomic methods for tracking foodborne pathogens through the US food supply.
Zhihui Yang, M.D.
Dr. Yang joined CFSAN in 2012 and is currently a research biologist on the Molecular Virology Team, within the Office of Applied Research and Safety Assessment’s Division of Molecular Biology. Her research mainly focuses on the application of genomic-scale molecular biology techniques (next-generation sequencing) for the detection and further identification/genotyping of epidemiologically important foodborne viruses, including but not limited to, norovirus hepatitis A, and newly emergent viral species. Her research interests also include: development of novel sequencing methodologies for virus detection and analysis, and application of these methodologies to issues of virus carriage in foods, clinical and environmental samples, and exploration of the virome through a metagenomics approach.
Jie Zheng, Ph.D.
Dr. Jie Zheng currently serves as a staff microbiologist of the Molecular Methods and Subtyping Branch within the Division of Microbiology. Dr. Zheng finished her Ph.D. in Food Science from University of Maryland at College Park, MD in 2006 and her dissertation is on "Campylobacter jejni/coli – Host Intestinal Epithelial Cell Interaction". Dr. Zheng joined the laboratories at the Center for Food Safety and Applied Nutrition (CFSAN) in July of 2008 after her two-year post-doctoral training at UM. She is interested in development of SNP-based detection, identification and subtyping methods for various phyletic and pathovar divisions of pathogenic Salmonella. She is also engaged in reducing carriage of Salmonella Newport on tomato plants with bio-control intervention method.
Phillip Curry, Ph.D.
Research Microbiologist, PulseNet Team
Research Microbiologist, PulseNet Team
Eric Stevens, Ph.D.
Statistics and Bioinformatics
Jayanthi Gangiredla is a biologist in FDA’s Office of Applied Research and Safety Assessment and has been working its Division of Molecular Biology’s Molecular Genetics Branch since 2008. With an M.S. degree in biochemistry and an M.S. in bioinformatics, she uses bioinformatics to compare the genomics of foodborne pathogens. She is involved with several metagenomics and metatranscriptomics projects that require extensive analysis of microbial populations from both the gut and the environment and conducts functional profiling of microbes in community-wide studies. She provides key bioinformatic analyses for the beneficial microbiome project, analyzing whole genome sequences of Gram positive, commensal, food, and probiotic bacteria associated with dietary supplements.
Gopal R. Gopinath, Ph.D.
Dr. Gopal Gopinath is a geneticist in CFSAN’s Office of Applied Research and Safety Assessment. His research focuses on genomics and bioinformatics of foodborne parasites like Cyclospora cayetanensis, and bacterial pathogens including Cronobacter spp., Salmonella spp., and Bacillus cereus. Dr. Gopinath was one of the earliest members of GenomeTrakr team at OARSA. As part of the Parasitology Team, Dr. Gopinath is working on consolidating parasite genomics efforts as part of CycloTrakr, a component BioProject of GenomeTrakr, dedicated for foodborne parasites. As part of this project, he has started to implement bioinformatic workflows developed for the Parasitology Team on CFSAN’s GalaxyTrakr platform. Dr. Gopinath graduated with a doctorate in biotechnology from the Center for Biotechnology, Anna University, Chennai, India in 1999. After completing postdoctoral fellowships at Brandeis University and the University of California, Berkeley (2001), he left laboratory research for a career in bioinformatics and biological databases, first at the Medical College of Wisconsin and later at the Cold Spring Harbor Laboratory in New York. His primary research interests are in comparative genomics, bioinformatics, data mining, and the use of next generation sequencing technology to obtain an “-omic” perspective of research questions in food safety.
David W. Lacher, Ph.D.
Dr. Lacher is a research microbiologist in the Division of Molecular Biology, within CFSAN’s Office of Applied Research and Safety Assessment. His research interests include the evolutionary genetics of virulence and the molecular subtyping of bacterial pathogens. He is currently examining the genetic diversity present within Escherichia coli and Shigella spp. through the use of whole genome sequence analyses.
Mark K. Mammel
Mark Mammel is a research microbiologist in CFSAN’s Office of Applied Research and Safety Assessment. With an M.S. degree in microbiology and an M.S. in computer science, he uses bioinformatics for comparative genomics of foodborne pathogens. He develops methods for analyzing whole genome shotgun sequencing of metagenomic samples to identify the microbial composition and detect pathogens in food or environmental samples.
James B. Pettengill, Ph.D.
Dr. Pettengill uses metagenomic approaches (i.e., the sequencing of DNA contained in an environmental sample) to investigate important agricultural and food safety questions. Specifically, he and other scientists at the FDA have employed metagenomics to describe the effects of different bacterial enrichment procedures and how they might impact our ability to detect specific pathogens. They are also evaluating how different pesticides alter microbial diversity and the prevalence of certain pathogens within the ecosystem.
Hugh Rand, Ph.D.
Supervisory Mathematical Statistician
Hugh Rand is a Team Leader in the Biostatistics Branch at the FDA’s Center for Food Safety and Applied Nutrition. He received his Ph.D. in 1995 in applied mathematics at the University of Washington. His research interests focus on the application of mathematical and statistical tools to the analysis of biological problems, primarily in the area of human health. Much of his early work involved the applications of bioinformatics in drug discovery within inflamation and oncology. Currently, a major focus of his efforts at the FDA are in the use of genomic sequencing for aiding in tracking foodborne pathogens through the U.S. food supply.
Tammy Barnaba uses the Illumina MiSeq and NextSeq platforms to sequence metagenomic and single colony isolate samples from dietary supplements. She has completed shotgun sequencing of several E. coli isolates for upload to GenomeTrakr.
George Kastanis is part of the genomics team working under the supervision of Dr. Marc Allard. His primary function is to run the MiSeq personal sequencing of various isolates that come through the pipeline.
Anna I. Maounounen-Laasri
Anna I. Maounounen-Laasri received her M.Sc. in biology and chemistry in 1994 from State Pedagogical University, in Saint Petersburg, Russia. Mrs. Maounounen-Laasri served as a teacher and practical adviser for biology, chemistry, and ecology at the Kaskolovka School, in Kingisepp, Russia from 1994 to 2001. In 2010, she joined FDA’s Center for Biologics Evaluation and Research as a volunteer researcher in the Laboratory of Method Development, within the Office of Vaccine Research and Review, where she developed molecular methods for evaluation and identification of viral vaccine strains. In November 2010, she came to FDA’s Center for Food Safety and Applied Nutrition as an ORISE fellow, working in its Division of Microbiology. Mrs. Maounounen-Laasri is currently a biologist in the division, conducting research focused on improvement, validation, and evaluation of culture-based and molecular methods for the detection, typing, and isolation of Salmonella, Escherichia coli O157:H7, non-O157 Shiga toxin-producing E. coli (STEC), and Listeria monocytogenes in food products and environment. She also serves as a microbial strain curator and sample custodian for the division.
Tim Muruvanda collects and analyzes NGS data from the Pacific Biosciences RS II sequencers. He is primarily focused on generating closed microbial reference genomes to support the applicability of WGS in public health.
Justin Payne is an integration and bioinformatics developer and the author of "Bootsie", a statistical tool for RFLP analysis. He graduated in 2011 from the University of Nebraska, Lincoln with a Bachelor of Science degree in biochemistry. At FDA-CFSAN, his work is primarily focused on database development, high-throughput assembly of NGS data, and transparent integration with NCBI data stores.
Strain Curator for the Division of Microbiology