Presentations

This reflects the past 5 years

2021

  • Bandoy, DJ Darwin R. and Bart C. Weimer. 2021. Whole genome sequencing in Salmonella Dublin to determine antimicrobial resistance. USDA, FSIS ORISE student review (online).
  • Schlesener, Cory, Sarah Depenbrock, and Bart C. Weimer. 2021. Discordance between identified genes and MIC Determination of AMR in bovine respiratory pathogens. NIAMMRE Student Scientist Research Showcase.
  • Weimer, Bart C., and DJ Darwin R Bandoy. 2021. Using whole genome sequencing of COVID-19 to track epidemiological outbreaks. UC Davis Townhall with global attendance
  • Bandoy DJ Darwin R., and Bart C. Weimer. 2021.Epidemiology of COVID-19 in the Philippines – A Veterinary Perspective (Keynote Speech). 88th Philippine Veterinary Medical Association  Annual Convention & Scientific Conference (virtual)
  • Crook Erika K., Nancy A. Carpenter, DJ Darwin R Bandoy, Bihua C. Huang and
    Bart C. Weimer. 2021. Whole genome sequencing to diagnose and guide treatment of Campylobacter in zoo housed orangutans (Pongo pygmaeus pygmaeus) and gorillas (Gorilla gorilla gorilla). American Association of Zoo Veterinarians Annual meeting (Lexington, KY).
  • Schlesener, Cory and Bart C. Weimer. 2021. Use of Machine Learning to Parse the Dense Genomic Diversity of Helicobacter pylori Populations to Find Genetic Elements Predictive of Gastric Cancer. ASM/FEMS Annual meeting
  • Schlesener, Cory and Bart C. Weimer. 2021. Representative global distribution of AMR genes in Helicobacter pyloriby time and space. NIAMRRE Annual conference. (3rdplace in student presentation competition)
  • Bandoy, DJ Darwin R. and Bart C. Weimer. 2021. Deconvolution of clonal interference mutations in Sars-CoV-2 using Monte Carlo and epidemic modeling. GGIP student symposium, Davis, CA (3rdplace in student competition)
  • Weimer, Bart C. 2021. COVID genome variation and emergence of variants. UC Davis LIVE, virtual webinar (zoom).

2020

  • Weimer, Bart C.2020. Metagenomics & Biogas: Optimizing biogas production from the bacterial community. 2nd Renewable Natural Gas Summit (virtual) – 12/3/2020
  • Bandoy, DJ Darwin R. and Bart C. Weimer. 2020. SAR-CoV2 evolution predicts outbreak shifts. COVID-19 Townhall, UC Davis, (virtual) – 11/20/2020
  • Bandoy, DJ Darwin R. and Bart C. Weimer. 2020. Deconvolution of clonal interference by D614G mutation in Sars-CoV-2 using Monte Carlo and epidemic modeling. Cold Spring Harbor Laboratory, Biological Data Science Symposium (virtual)
  • Bart C. Weimerand DJ Darwin R. Bandoy. 2020. Clonal interference of D614G mutation in Sars-Cov-2 using a Monte Carlo and Epidemic Modelling. 9th Workshop on Computational Advances in Molecular Epidemiology, 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) (SIGBio), September 21, 2020 (virtual).
  • Bandoy, DJ Darwin R. and Bart C. Weimer. 2020. Pandemic genomics of COVID-19. 40th PAASE Anniversary & 2020 APAMS Annual Meeting (virtual) – Philippines
  • Bandoy, DJ Darwin R. andBart C. Weimer *COVID-19 Superspreading Inference using Large Scale Pathogen Genomic Data. Genome Informatics, Wellcome Trust, Hixton, UK (virtual) Sept. 14-16
  • Weimer, Bart C. 100K Pathogen Genome Project: Merging Population Genomics and Machine Learning. RECOM – Network of -omic sciences. Universidade Federal deMinas Gerais, Belo Horizonte Brazil (virtual). July 9, 2020
  • Erika K. Crook, Nancy A. Carpenter, DJ Darwin R Bandoy, Bihua C. Huang, and Bart C. Weimer. 2020.Whole-genome sequencing to diagnose Campylobacter outbreak in zoo housed Gorillas (Gorilla gorilla gorilla) and Orangutans (Pongo pygmaeus pygmaeus). American Association of Zoo Veterinarians, Nashville, TN.
  • Sebastian, Peter J., Barbara A. Byrne, Bart C. Weimer, Melissa Miller, Francesca Batac, Woutrina Smith, Michael Murray, Joseph Tomoleoni, Carrie Goertz, Kathy Burek Huntington, Christine K Johnson. 2020. Investigation of antimicrobial resistance gene patterns among Vibrio spp. in sea otters. Southern Sea Otter Research Conference
  • Bandoy, DJ Darwin R., Carol Huang, Bart C. Weimer. 2020. Diagnostic Metatranscriptomics for Precision Medicine. ASM Microbe, Chicago, IL. (virtual)
  • Bandoy, DJ Darwin R., Carol Huang, Bart C. Weimer. 2020. Antimicrobial Resistance Forecasting using Longitudinal Whole Genome Sequencing of Salmonella.
    ASM Microbe, Chicago, IL. (virtual)
  • Bandoy, DJ Darwin R., Carol Huang, Bart C. Weimer. 2020. Machine Learning combined with Reverse Ecology reveals Ecological Diversification in Campylobacter.
    ASM Microbe, Chicago, IL. (virtual)

2019

  • Weimer, Bart C. 2019. Microbial population (meta)genomics: a new era of computation for health and disease. X-Meeting 2019, São Paulo (Campos do Jordão), Brazil.
  • Bandoy, DJ Darwin R., Carol Huang, Bart C. Weimer. 2019. Machine learning approach for microbial genomics: Bacterial genome-wide association in abortive
    Campylobacter jejuni. N. California Computational Biology Symposium. Davis, CA
  • Bandoy, D., E. Crook, N. Kong, C. Huang, and B.C. Weimer. 2019. Chronic Campylobacteriosis Outbreak Investigation in Great Apes Using Next-Generation Sequencing. ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatics Pipeline 2019. San Francisco, CA (DOI:10.13140/RG.2.2.15220.09601)
  • Bandoy, DJ Darwin, Sofia Carolina Egana-Labrin, Rodrigo A. Gallardo,
    Bart C. Weimer. 2019. Viral Pangenomics: A novel framework of viral whole-genome analysis in avian reovirus. Annual Bay Area Symposium on Viruses, University of California, Berkeley, CA June 7, 2019 (DOI: 10.13140/RG.2.2.31997.3120)
  • Weimer, Bart C. 2019. Pathogens in sewage – the genomics gap. 1stAnnual Scientific Summit on Dairy Methane Management Research. UC Davis, Davis, CA June 11, 2019
  • Bandoy, DJ Darwin R. and Bart C. Weimer. 2019. Emerging Disease Diagnostics using Whole Genome Sequencing. 3rd Pan Asian One Health International Conference (OHIC 2019), University of the Philippines Diliman Quezon City, Philippines
  • Weimer, Bart C. 2019. Phylogenomics: impact of genome diversity in pathogen relationships? California Department of Public Health, (CDPH), Richmond, CA
  • Bandoy, DJ Darwin R., B. Carol Huang, Erika Crook,
    Bart C. Weimer. 2019. Application of whole-genome sequencing with an emerging pathogen Campylobacter hyointestinalis. CHRO 2019, Belfast, Ireland
  • Bandoy, DJ Darwin R., Carol Huang, Bart C. Weimer. 2019. Machine learning approach for microbial genomics: Bacterial genome-wide association in abortive
    Campylobacter jejuni. CHRO 2019, Belfast, Ireland
  • Bandoy, DJ Darwin R., Nguyet Kong, B. Carol Huang, Bart C. Weimer. 2019. Pangenome Wide Association Study identifies novel allelic variants linked to livestock abortion from Campylobacter jejuni using machine Learning. BAMPS, San Francisco, CA
  • Weimer, Bart C. 2019. Population genomics and metagenomics: diagnostics to therapy. UC Davis Symposium on Metagenomics, Sacramento, CA
  • Bandoy, D., A. Weiss, N. Kong, C. Huang, andB.C. Weimer. 2019. Pangenome Wide Association Study Identifies Novel Allelic Variants Linked to Livestock Abortion from
    Campylobacter jejuniUsing Machine Learning Abortive and non-abortive
    Campylobacter jejuniin ruminants. ASM Microbe 2019, San Francisco, CA.
  • Higdon, Shawn M., Tania Pozzo, Nugget Kong, Mai Lee Yang, Eva Borras, Colleen Chiu, Pablo Zamora, Richard Jeannotte, Alan B. Bennett, Bart C. Weimer. 2019.
    Functional Genomic Characterization of Diazotrophs from the Aerial Root Microbiota of an Isolated Maize Landrace.American Society for Microbiology, San Francisco, CA
  • Bandoy, DJ Darwin R., Nguyet Kong, B. Carol Huang, Erika Crook, Bart C. Weimer. 2019. Diarrheal Disease Diagnostics using Whole Genome Sequencing. GGIP Symposium, UC Davis, Davis, CA
  • Weimer, Bart C.2019. Genomics of Listeria: population genomics and implications for disease association. Quadram Institute, Norwich, UK

2018

  • Weimer, Bart C. 2018. Functional -omics in food and public health. Pepsico, Inc.; Davis, CA
  • Weimer, Bart C. 2018. Molecular methods in diagnostics. American Veterinary Medical Association, Denver, CO
  • Weimer, Bart C.2018. From whole genomes to metagenomes in food and health. Mars, Inc. Davis, CA. Invitation only
  • Weimer, Bart C. 2018. Integrated -omics in food and health. Merek, Inc.; Davis, CA
  • Bandoy, DJ Darwin R., Erika Crook, Carol Huang, Nguyet Kong, Bart C. Weimer.2018. Chronic Campylobacteriosis Outbreak Investigation in Great Apes using Next-Generation Sequencing. ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines, Washington DC
  • Falcon, Alexandria K., Mei Yamaguchi, Nguyet Kong, Mitchell M. McCartney, Eva Borras, Nicholas J. Kenyon, Bart C. Weimer, Cristina E. Davis. 2018. Infectious Bacteria Isolated from Cetacean Species Emit Volatile Compounds That May Serve as Biomarkers for Early Health Diagnosis. Lung Day 2018-Interstitial Lung Disease: Toward a Personalized Future. Davis, CA – Invitation only
  • Weimer, Bart C. 2018. Microbes in the health – a robust population. Wexler Medical School, Ohio State University, Columbus, OH.
  • Luu, Bao K, Nguyet Kong, Whitney ng, Lenore Kelly, and Bart C. Weimer. 2018. Improving quality of DNA fragments for next generation sequencing with Agilent 2200 Tapestation.  UC Davis Undergrad Research Conference, UC Davis, Davis, CA
  • Lew, Megan, Nguyet Kong, Kao Thao, Carol Huang, Maryke Appel, Stephen Lappin, Lisa Knapp, Lenore Kelly, and Bart C. Weimer. 2018. Automated library construction using KAPA library preparation kits on the Agilent NGS workstation yields high-quality libraries for whole-genome sequencing on the Illumina platform. UC Davis Undergrad Research Conference, UC Davis, Davis, CA
  • Weimer, Bart C. 2018. Metabolomics in food and health. Foods for Health Discovery, Ohio State University, Columbus, OH
  • Weimer, Bart C. 2018. From Genomes to Metagenomes: food safety and public health. Department of Food Science and Technology, Ohio State University, Columbus, OH
  • Weimer, Bart C. 2018. From Genomes to Metagenomes: food safety and public health. Department of Food Science, UC Davis, Davis, CA
  • Weimer, Bart C., and B. Huang. 2018. The need for speed: is it time for real time detection of Salmonella? Oxford Nanopore Day, San Francisco, CA
  • Weimer, Bart C. 2018. Unexpected genomic diversity in pathogens: embracing diversity of the microbial world. Accelerated Discovery Forum – IBM Research. Almaden, CA
  • Miller, John J., Catharina H. M. Lüdeke, Bart C. Weimer, and Jessica L. Jones. 2018. population genetics, biogeography, and phylogenetics of Vibrio parahaemolyticus from North America using whole genome sequence data. National Shellfisheries Association, Seattle, WA.
  • Weimer, Bart C. 2018. Genomics of food safety organisms: emerging genotypes and disease. Quadram Institute, Norwich, UK.
  • Weimer, Bart C. 2018. Unexpected genomic diversity in pathogens: implications for food and public safety. Korean FDA Symposium, Seoul S. Korea.
  • Kaufman, James, Ed Seabolt, Mark Kunitomi, Akshay Agarwal, Kristen Beck, Harsha Krishnareddy and Bart C. Weimer. 2018. Exploiting Functional Context in Biology: Reconsidering Classification of Bacterial Life. 34thIEEE International Conference on Data Engineering – Context in Analytics: Challenges, Opportunities and Trends. Paris France.

2017

  • Weimer, Bart C. B. Huang, N. Kong. 2017. Real-time sequencing using the minION for pure and mixed cultures forfood safety. Davis, CA. Invitation only
  • Weimer, Bart C. 2017. Metagenomic and metabolomics response to toxin addition to food materials. Mars, Inc., McLean, VA. Invitation only
  • Chen, Poyin, and Bart C. Weimer. 2017. Molecular effects of prebiotic oligosaccharide on Listeria monocytogenes infection. Australian Society for Microbiology Annual meeting, Hobart, Tasmania.
  • Weimer, Bart C. 2017. Genomics in food and predictive microbiology. Universityof Tasmania, Hobart, Australia.
  • Weimer, Bart C. 2017. Metagenomics and genomics in food and health. CSIRO Australian Animal Health Laboratory, Geelong, Australia. Snowdon Oration. Keynote
  • Chen, Poyin, and Bart C. Weimer. 2017. Molecular effects of prebiotic oligosaccharide on Listeria monocytogenes infection. Mini-Symposium: Microbiome and Immunity at the Skin and Gut Interfaces in Health and Disease, Davis, CA
  •  Weimer, Bart C. B. Huang, N. Kong, N. Chin, J. Kaufman, M. Davis, K. Beck, N. Haiminen, R. Prill, S. Edlund, D. Chambliss. 2017. Genomics to Metagenomics in food and public health. IFSH Whole Genome Sequencing (WGS) for the Food Industry: Current Procedures, Advances, Obstacles and Solutions, Burr Ridge, IL. (Mars Special Speaker)
  • Chin, Ning, Dylan B. Storey, Bihua C. Huang, Maggie Butler, Russell Griggs, Jessica Tittl, Elizabeth DeNardo, Sarah Edmonds-Wilson, Carrie A. Zapka, Bart C. Weimer. 2017. Using Shotgun Metagenomics to Examine the Use of Hand Microbiome as a Forensic Tool. Mini-Symposium: Microbiome and Immunity at the Skin and Gut Interfaces in Health and Disease, Davis, CA
  • Weimer, Bart C., B. Huang, N. Kong, N. Chin, J. Kaufman, M. Davis, K. Beck, N. Haiminen, R. Prill, S. Edlund, D. Chambliss. 2017. Genomics to Metagenomics in food and public health. American Society for Microbiology annual meeting, New Orleans, LA. Invited Keynote in food metagenomics section
  • Weis, Allison M., Kristin A. Clothier, Bihua C. Huang, Nguyet Kong, Ken Dewar, Bart C. Weimer. 2017. Identifying virulence factors that lead to abortion from zoonotic transmission and whole genome sequencing. CHRO 2017, Nantes, France. (Plenary session)
  • Arabyan, Narine, Prerak Desai, Jigna Shah, Reed N. Gann, Hai Yu, Nguyet Kong, Mai Lee Yang, Janneth Pinzon, Xi Chen, and Bart C. Weimer.2017. Salmonella wins the war with prebiotics and probiotics during infection. American Society for Microbiology annual meeting, New Orleans, LA. (DOI: 10.13140/RG.2.2.23708.28808)
  • Beck, Kristen L., James Kaufman, Stefan Edlund, David Chambliss, Niina Haiminen, Matt Davis, Mark Kunitomi, Robert Prill, Laxmi Parida, Simone Bianco, Bart C. Weimer, Carol Huang, Nguyet Kong, Robert Baker, Peter Markwell. 2017. A big tech approach to a “small” problem: microbiome characterization of raw food ingredients to improve food safety. National Academy of Sciences, Washington, DC. #authors listed by organization.
  • Beck, Kristen L., James Kaufman, Stefan Edlund, David Chambliss, Niina Haiminen, Matt Davis, Mark Kunitomi, Robert Prill, Laxmi Parida, Simone Bianco, Bart C. Weimer, Carol Huang, Nguyet Kong, Robert Baker, Peter Markwell. 2017. A big tech approach to a “small” problem: microbiome characterization of raw food ingredients to improve food safety. Functional Foods Conference, San Diego, CA. #authors listed by organization.
  • Weimer, Bart C. 2017. Metagenomics and genomics in food and health. Australian Society for Microbiology annual meeting, Hobart, Tasmania, AU. Invited Keynote lecture – Snowdon Oration.
  • Weimer, Bart C. 2017. Metagenomics and whole genome sequencing in food and public health. Oxford Nanopore, Oxford, UK.
  • Chen, Poyin, and Bart C. Weimer. 2017. Molecular effects of prebiotic oligosaccharides on L. monocytogenesinfection. BAMPS XX, San Francisco, CA.
  • Arabyan, Narine, and Bart C. Weimer. 2017. Salmonella requires two enzymes to degrade the host glycocalyx that leads to altered infection and host cell glycan remodeling. BAMPS XX, San Francisco, CA.
  • Fouthoui, Azarene, Carol Huang, Kristen Beck, Allison M. Weis, Amir Ardeshir, Rachael Reader, Bart C. Weimer. 2017. Placental Microbiome of Healthy Pregnancies Exhibits Complex Microbial Interactions. (DOI:10.13140/RG.2.2.11322.39366). 3rdAnnual Integrative Pathobiology Research Symposium, UC Davis, Davis, CA.
  • Weimer, Bart C. 2017. Metagenomics and genomics of Campylobacter to diagnose outbreaks in animals. Utah’s Hogle Zoo, Salt Lake City, UT.
  • Weimer, Bart C.2017. WGS for pathogen detection and trace back. Mars Chocolate, Slough, UK.
  • Kaufman, James, and Bart C. Weimer. 2017. Sequencing of the food supply. Pacific Southwest Section -AOAC International 2017 Annual Meeting, Berkeley, CA.
  • Weimer, Bart C., Allison M. Weis, Azarene Fouthoui, and B. Carol Huang. 2017. Metagenomics and genomics of Campylobacter. National Center for Primate Research, Davis, CA.