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Adam R. Rivers, PhD - PI (SY)

PhD Massachusetts Institute of Technology / Woods Hole Oceanographic Institution, 2009

I am a microbial ecologist turned computational biologist. I began my career woking on nutrient limitation in marine phytoplankton and became involved in metagenomics early. During the Deepwater Horizon oil spill I applied metatranscriptomics to understand the fate of oil and gas released. In 2014 A became a research scientist at the Joint Genome Institute, a part of Lawrence Berkeley National Laboratory. I was the head of the Metagenome Program at JGI until 2017. In January of 2017 I joined the Agricultural Research Service to start the Agricultural Microbiomes Group.

Agriculture is an exciting field to apply microbiome methods. A key question in microbiome research is how the genetics of the host and the ecology of the microbial community interact. Plant breeders have extensive pedigree and genotypic information that enables us to start unraveling the interaction experimentally. Microbiome analyses is poised to upend conventional methods for food safety allowing us to track and eliminate pathogens, develop agricultural systems that limit their impact through environmental manipulation. Agriculture in an area where microbiome science will have a tremendous impact.

At the USDA Agricultural Research Service I hold a career scientist position as a Computational Biologist in the Genomics and Bioinformatics Research Unit.

I have a courtesy faculty appointment in the Department of Microbiology and Cell science at the University of Florida.

Academic CV
Google Scholar profile

Postdoctoral Associates

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Alicia Foxx, PhD

PhD Northwestern University, 2020

Dr. Foxx is the USDA/ORISE Postdoctoral Fellow for the USDA SCINet Scientific computing initiative. She has experience in plant ecology and will be working on dataset shift in machine learning and Seed microbiomes.

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Karla Franco Melendez, PhD

PhD Arizona State University, 2020

Dr. Franco Melendez graduated in June 2020 from the Microbiology doctoral program Arizona State University. Her PhD dissertation centered in characterizing the effect of physiologically relevant fluid shear levels on the human enteric pathogen Salmonella Typhimurium. Specifically, she studied the effect of fluid shear on pathogenesis-related stress responses and changes in gene expression across different phases of growth. In July 2020, Dr. Franco Melendez joined the USDA-ARS as a post-doctoral fellow in bioinformatics, under the supervision of Dr. Adam Rivers. Her current position focuses on engineering soil microbial consortia with inhibitory phenotypes against the phytopathogen Ralstonia solanacearum using new Bayesian optimization algorithms and deep learning methods. Additionally, she is currently performing a comparative analysis on the intestinal microbial community composition and antimicrobial profile of poultry specimens from the pre- and post-antibiotic eras.

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Ravin Poudel, PhD

PhD University of Florida, 2018

Dr. Poudel is an ARS funded post-doctoral researcher and the Department of Microbiology and Cell Science at the University of Florida who works in the group. He interested in the ecology of microbial communities, mostly microbial assemblies, diversities, interactions, and their community level functions, in the natural as well as in the agricultural systems. He is developing software and statistical methods to analyze data for high-throughput fitness-profiling experiments in the model organism E. coli, with the aim to scale it up to other microbes in the future. He is also working on methods to model microbial communities using amplicon sequencing, metabolomics, and Bayesian networks in order to identify key microbial structures and functional signatures to support the selection of candidate taxa or microbial-consortia for microbiome-based crop productions. More on his research is here.

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Jeremy Winders, PhD

PhD, Mississippi State University, 2019

Dr. Winders is working on a project to determine the sex of chicken eggs when they are laid by applying high-throughput Proton transfer reaction mass spectrometry (PTR-MS) and machine learning.

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Chris Gaby, PhD

PhD, University of Tennessee

Dr. Gaby is working on Large scale-comparative genomics in Salmonella and the application of Machine learning methods for genotype and phenotype prediction in Salmonella. He is also developing methods for investigating nitrogen fixation in sugar cane. More in his research is here

Staff

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Ryo (Leo) Iwata

BS University of Florida, 2018

Leo is a Python based analyst that is creating bioinformatic workflows for machine learning and data processing. While assisting others with programming and high-performance computing in a research setting.

Former members

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Anushka Swarup, MS

PhD Candidate, University of Florida

Anushka is a PhD student with Dr. Damon Woodard in the Electrical & Computer Engineering Department at the University of Florida. Her primary area of research lies in the domain of Image Analysis wherein she has developed applications for fields ranging from agricultural monitoring to biometrics.

For the Agricultural Microbiomes group, she is developed a web application for designing CRISPR-Cas guide RNAs