Phone: (352) 374-5930

1600-1700 SW 23rd Drive
Gainesville, FL 32608

Research Group Site

Google Scholar Citations

Ph.D. Biological Oceanography, Massachusetts Institute of Technology/ Woods Hole Oceanographic Institution, 2009

B.A. Biology/Chemistry, New College of Florida, 2001

My research focuses on developing new software and computational methods to advance agriculture by understanding and controlling microbial communities and applying artificial intelligence and machine learning to agricultural data.

Research areas

• Applying machine learning to agricultural data (sequence, image, and chemometric data)
• Engineering and optimizing microbial consortia
• Developing software (e.g. Itsxpress, Guidemaker) for bioinformatics
• Applying volatiles mass spectrometry and machine learning to agricultural challenges
• Viral metagenomics

Service areas

• Design and sequencing of amplicon, metagenome, and metatranscriptome experiments
• The development of training courses for ARS, like our 2019 UF/ARS Machine learning Workshop
• Guiding SCINet ARS’s scientific computing initiative as Chair of the SCINet Advisory Committee
• Establishing the ARS AI Center of Excellence in collaboration with our Associate Administrator and Chief Scientific information officer
• Editorial board for the journal ACS Agriculture Science and Technology

• Projects

  Integrative Applied Agricultural ‘Omics and Bioinformatics Research In-House Appropriated (D)   Accession Number:444279

  Developing a Cyberinformatic Platform for the Rapid Identification of Salmonella Outbreak Strains Using Population Metagenomics and Machine Learning Interagency Reimbursable Agreement (I)   Accession Number:436487

  Bioinformatics and Application Development Non-Assistance Cooperative Agreement (S)   Accession Number:438896

  USDA ARS Research Apprenticeship Program at University of Texas at Arlington Non-Assistance Cooperative Agreement (S)   Accession Number:442862

  Xenosurveillance of Flies in Wet Markets to Monitor for the Emergence and Spillover Potential of Viral, Bacterial, and Parasitic Pathogens Non-Assistance Cooperative Agreement (S)   Accession Number:442865

  Biologically-inspired Odor Olfactory Detection Guided Machine Learning (BIODOG-ML): Odor Detection from Canines to Instrumentation Non-Assistance Cooperative Agreement (S)   Accession Number:442872

  The Development of Novel RNA Dependent RNA Polymerases, Nucleases, and Transposases by Metagenomics and Protein Engineering Non-Assistance Cooperative Agreement (S)   Accession Number:443104

  Research Training for the Geospatial and Environmental Epidemiology of Plant and Animal Disease Non-Assistance Cooperative Agreement (S)   Accession Number:444083

  Developing Detection and Modeling Tools for the Geospatial and Environmental Epidemiology of Animal Disease Non-Assistance Cooperative Agreement (S)   Accession Number:444979

• Publications

  • (Clicking on the reprint icon will take you to the publication reprint.)
  • Annotated whole-genome sequences of fermentative and spoilage associated Bacilli and Proteobacteria autochthonous to commercial cucumber fermentation -(Peer Reviewed Journal)
    Page, C.A., Simpson, S.A., Perez Diaz, I.M., Rivers, A.R. 2024. Annotated whole-genome sequences of fermentative and spoilage associated Bacilli and Proteobacteria autochthonous to commercial cucumber fermentation. Microbiology Resource Announcements. 13:e00926-23. https://doi.org/10.1128/mra.00926-23.
    
  • Effect of dietary phytase on water and fecal prokaryotic and eukaryotic microbiomes in a hybrid tilapia (Oreochromis aureus x O. niloticus) mixotrophic biofloc production system -(Peer Reviewed Journal)
    Ray, C.L., Abernathy, J.W., Green, B.W., Rivers, A.R., Schrader, K., Rawles, S.D., McEntire, M.E., Lange, M.D., Webster, C.D. 2024. Effect of dietary phytase on water and fecal prokaryotic and eukaryotic microbiomes in a hybrid tilapia (Oreochromis aureus x O. niloticus) mixotrophic biofloc production system. Aquaculture. 581. Article 740433. https://doi.org/10.1016/j.aquaculture.2023.740433.
    
  • IgE and IgG4 epitopes of the peanut allergens shift following oral immunotherapy -(Peer Reviewed Journal)
    Rambo, I., Kronfel, C.M., Rivers, A.R., Swientoniewski, L., Mcbride, J.K., Cheng, H., Simon, R.J., Ryan, R., Tilles, S., Nesbit, J.B., Kulis, M.D., Hurlburt, B.K., Maleki, S.J. 2023. IgE and IgG4 epitopes of the peanut allergens shift following oral immunotherapy. Frontiers in Allergy. 4: Article 1279290. https://doi.org/10.3389/falgy.2023.1279290.
    
  • RNA virus discoveries in the electric ant, Wasmannia auropunctata -(Peer Reviewed Journal)
    Valles, S.M., Zhao, C., Rivers, A.R., Iwata, R.L., Oi, D.H., Cha, D.H., Collignon, R., Cox, N.A., Morton, G.J., Calcaterra, L.A. 2023. RNA virus discoveries in the electric ant, Wasmannia auropunctata. Virus Genes. 59:276–289. https://doi.org/10.1007/s11262-023-01969-1.
    
  • Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon -(Peer Reviewed Journal)
    Vaughn, J.N., Branham, S.E., Abernathy, B.L., Hulse-Kemp, A.M., Rivers, A.R., Levi, A., Wechter, W.P. 2022. Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon. Nature Genetics. https://doi.org/10.1038/s41467-022-35621-7.
    
  • Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti -(Peer Reviewed Journal)
    Coatsworth, H., Bozic, J., Carillo, J., Buckner, E., Rivers, A.R., Dinglasan, R., Mathias, D. 2022. Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti. Molecular Ecology. 31(9):2545-2561. https://doi.org/10.1111/mec.16412.
    
  • Gross morphology of diseased tissues in Nezara viridula (Hemiptera: Pentatomidae) and molecular characterization of an associated microsporidian -(Peer Reviewed Journal)
    Rivers, A.R., Grodowitz, M.J., Miles, G.P., Allen, M.L., Elliott, B., Weaver, M.A., Bon, M., Rojas, M.G., Morales Ramos, J.A. 2022. Gross morphology of diseased tissues in Nezara viridula (Hemiptera: Pentatomidae) and molecular characterization of an associated microsporidian. Journal of Insect Science. 22(2):4. https://doi.org/10.1093/jisesa/ieac013.
    
  • GuideMaker: software to design CRISPR-Cas guide RNA pools in non-model genomes -(Peer Reviewed Journal)
    Poudel, R., Trujillo-Rodriguez, L., Reisch, C., Rivers, A.R. 2022. GuideMaker: software to design CRISPR-Cas guide RNA pools in non-model genomes. Gigascience. 11. Article giac007. https://doi.org/10.1093/gigascience/giac007.
    
  • AT homopolymer strings in salmonella enterica subspecies I contribute to speciation and serovar diversity -(Peer Reviewed Journal)
    Guard, J.Y., Rivers, A.R., Vaughn, J.N., Rothrock Jr, M.J., Oladeinde, A.A., Shah, D. 2021. AT homopolymer strings in salmonella enterica subspecies I contribute to speciation and serovar diversity. Microorganisms. 9(10):2075. https://doi.org/10.3390/microorganisms9102075.
    
  • Advancing equity and inclusion in microbiome research and training -(Peer Reviewed Journal)
    Foxx, A., Franco Melendez, K.P., Hariharan, J., Kozik, A., Wattenburger, C., Godoy-Vitorino, F., Rivers, A.R. 2021. Advancing equity and inclusion in microbiome research and training. mSystems. 6(5):e01151-21. https://doi.org/10.1128/mSystems.01151-21.
    
  • Genetic variation in methane emissions in rice alters seasonal profiles of methanogenic microbial communities in anaerobic soils-(Abstract Only)
    Barnaby, J.Y., Fernandez-Baca, C.P., McClung, A.M. 2021. Genetic variation in methane emissions in rice alters seasonal profiles of methanogenic microbial communities in anaerobic soils. Food and Drug Administration (FDA) Science Forum. https://jam-2021.virtualpostersession.org/
    
  • Exploring adaptation to changing environments (E) and mitigation strategies through genetics (G) and management (M) for crop improvement-(Abstract Only)
    Barnaby, J.Y., Fernandez-Baca, C.P., McClung, A.M., Edwards, J., Huggins, T.D., Rivers, A.R., Fleisher, D.H. 2021. Exploring adaptation to changing environments (E) and mitigation strategies through genetics (G) and management (M) for crop improvement. Korean Women in Science Symposium. https://www.kwise.org/blog/kwse-kwise-joint-web-seminar/
    
  • Changes in rhizosphere soil microbial communities across plant developmental stages of high and low methane emitting rice genotypes -(Peer Reviewed Journal)
    Fernandez-Baca, C.P., Rivers, A.R., Kim, W., McClung, A.M., Roberts, D.P., Reddy, V., Barnaby, J.Y. 2021. Changes in rhizosphere soil microbial communities across plant developmental stages of high and low methane emitting rice genotypes. Soil Biology and Biochemistry. http://doi.org/10.1016/j.soilbio.2021.108233.
    
  • Rice plant-soil microbiome interactions driven by root and shoot biomass -(Peer Reviewed Journal)
    Fernandez-Baca, C.P., Rivers, A.R., Maul, J.E., Kim, W., McClung, A.M., Roberts, D.P., Reddy, V., Barnaby, J.Y. 2021. Rice plant-soil microbiome interactions driven by root and shoot biomass. Diversity. https://doi.org/10.3390/d13030125.
    
  • Harnessing AI to transform agriculture and inform agricultural research -(Peer Reviewed Journal)
    Peters, D.C., Rivers, A.R., Hatfield, J.L., Lemay, D.G., Liu, S.Y., Basso, B. 2020. Harnessing AI to transform agriculture and inform agricultural research. IEEE IT Professional. 22(3):16-21. https://doi.org/10.1109/MITP.2020.2986124.
    
  • Under-the-radar dengue virus infections in natural populations of aedes aegypti mosquitoes -(Peer Reviewed Journal)
    Boyles, S., Mavian, C., Finol, E., Ukhanova, M., Stephenson, C., Hamerlinck, G., Kang, S., Baumgartner, C., Geesey, M., Rivers, A.R. 2020. Under-the-radar dengue virus infections in natural populations of aedes aegypti mosquitoes. mSphere. 5(2):e00316-20. https://doi.org/10.1128/mSphere.00316-20.
    
  • AI down on the farm -(Peer Reviewed Journal)
    Sudduth, K.A., Woodward Greene, M.J., Penning, B., Locke, M.A., Rivers, A.R., Veum, K.S. 2020. AI down on the farm. IEEE IT Professional. 22(3):22-26. https://doi.org/10.1109/MITP.2020.2986104.
    
  • Rice plant biomass traits influencing rhizosphere soil microbial community composition-(Proceedings)
    Fernandez-Baca, C., Rivers, A.R., Maul, J.E., Kim, W., McClung, A.M., Roberts, D.P., Barnaby, J.Y. 2020. Rice plant biomass traits influencing rhizosphere soil microbial community composition. Proceedings of Rice Technical Working Group Meeting, February 24-27, 2020, Orange Beach, Alabama. p 65. Electronic Publication.
    
  • Genomic signatures for sedimentary microbial utilization of phytoplankton detritus in a fast-flowing estuary -(Peer Reviewed Journal)
    Smith, M.W., Herfort, L., Rivers, A.R., Simon, H.M. 2019. Genomic signatures for sedimentary microbial utilization of phytoplankton detritus in a fast-flowing estuary. Frontiers in Microbiology. Volume 10, Article 2475. https://doi.org/10.3389/fmicb.2019.02475.
    
  • QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science -(Peer Reviewed Journal)
    Bolyen, E., Rideout, J., Dillon, M., Bokulich, N., Abnet, C., Al-Ghalith, G., Alexander, H., Alm, E., Arumugam, M., Asnicar, F., Rivers, A.R. 2019. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. Nature Biotechnology. https://doi.org/10.1038/s41587-019-0209-9.
    
  • Rice soil microbiome interactions with plant growth characteristics and methane emissions-(Abstract Only)
    Fernandez-Baca, C.P., Rivers, A.R., Maul, J.E., Kim, W., Yarwood, S.A., Roberts, D.P., McClung, A.M., Barnaby, J.Y. 2019. Rice soil microbiome interactions with plant growth characteristics and methane emissions. American Society for Microbiology.
    
  • Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range -(Peer Reviewed Journal)
    Valles, S.M., Rivers, A.R. 2019. Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range. Virus Genes. 55:368-380. https://doi.org/10.1007/s11262-019-01652-4.
    
  • ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis -(Peer Reviewed Journal)
    Rivers, A.R., Weber, K.C., Gardner, T.G., Liu, S., Armstrong, S. 2018. ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Research. 7:1418. https://doi.org/10.12688/f1000research.15704.1.
    
  • A metagenomics study of the corn kernel and silk microbiome following infection with aflatoxigenic and non-aflatoxigenic Aspergillus flavus strains-(Abstract Only)
    
    
  • Profiles of rhizosphere soil microbial composition affecting methane emissions-(Abstract Only)
    Barnaby, J.Y., Kim, W., Rivers, A.R., McClung, A.M., Maul, J.E. 2018. Profiles of rhizosphere soil microbial composition affecting methane emissions. 5th International Rice Conference Abstract. Available: http://ricecongress2018.irri.org/sites/default/files/Profiles%20of%20Rhizosphere%20soil%20microbial%20composition%20affecting%20methane%20emmissions.pdf.
    
  • Understanding the physiological and molecular mechanisms of rice-microbial interactions that produce methane-(Abstract Only)
    Woojae, K., Liem, B., Chun, J., McClung, A.M., Adviento-Borbe, A.A., Rivers, A.R., Pinson, S.R., Maul, J.E., Reddy, V., Barnaby, J.Y. 2018. Understanding the physiological and molecular mechanisms of rice-microbial interactions that produce methane. 29th Annual Beltsville Poster Day Book, pg 33.
    
  • Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea -(Peer Reviewed Journal)
    Bowers, R.M., Kyrpides, N.C., Stepanauskas, R., Harmon-Smith, M., Schulz, F., Doud, D., Reddy, T.K., Jarett, J., Rivers, A.R., Eloe-Fadrosh, E.A., Tringe, S.G., Ivanova, N., Copeland, A., Clum, A., Becraft, E.D., Malmstrom, R.R., Birren, B., Schriml, L., Podar, M., Bork, P., Weinstock, G.W., Banfield, .F., Garrity, G.M., Hugenholtz, P., Parks, D.H., Tyson, G.W., Rinke, C., Dodsworth, J.A., Yooseph, S., Sutton, G., Yilmaz, P., Glöckner, F.O., Meyer, F., Gilbert, J.A., Nelson, W.C., Hallam, S.J., Jungbluth, S.P., Ettema, T.J., Tighe, S., Konstantinidis, K.T., Liu, W., Baker, B.J., Rattei, T., Eisen, J.A., Hedlund, B., Mcmahon, K.D., Fierer, N., Knight, R., Finn, R., Karsch-Mizrachi, I., Eren, A.M., Woyke, T. 2017. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 35, 725–731. doi:10.1038/nbt.3893.
    
  • Patterns and drivers of fungal community depth stratification in Sphagnum peat -(Peer Reviewed Journal)
    Lamit, L.J., Romanowicz, K.J., Potvin, L.R., Rivers, A.R., Singh, K., Lennon, J.T., Tringe, S., Kane, E.S., Lilleskov, E.A. 2017. Patterns and drivers of fungal community depth stratification in Sphagnum peat. FEMS Microbiology Ecology. https://doi: 10.1093/femsec/fix082.
    

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