Presentations

This reflects the past 5 years

2023

  • Shaw, Claire, Matthias Hess,  Bart C. Weimer. 2023. Salmonella enhances osteogenic differentiation in adipose-derived mesenchymal stem cells. FEMS, Hamburg.
  • Lee, Katie Y, Edward R Atwill, Xunde Li, Hillary R Feldmann, Deniece R Williams,
    Bart C. Weimer, Sharif S Aly. 2023. Zinc supplementation and phenotypic antimicrobial resistance of fecal commensal bacteria from pre-weaned dairy calves. Northern California ASM chapter. 2nd place student award
  • Avalos, Angel, Shawn M. Higdon, Cory L. Schlesener, Rodrigo Profeta, Alan Bennett,
    Bart C. Weimer.2023. Microbial gene expression in Sierra Mixe aerial root mucilage. Nitrogen fixation, Naples, IT
  • Lee, Katie Y, Edward R Atwill, Xunde Li, Hillary R Feldmann, Deniece R Williams,
    Bart C. Weimer, Sharif S Aly. 2023. Impact of zinc supplementation on phenotypic antimicrobial resistance of fecal commensal bacteria from pre-weaned dairy calves. National Institute of Antimicrobial Resistance Research & Education (NIAMRRE), Gainesville, FL. 1st place student award
  • Lee, Katie Y., Cory Schlesener, Sharif S Aly, Hillary R Feldmann, Carol Huang, Xunde Li, Edward R Atwill, Bart C. Weimer. 2023. Whole genome-based insights on diarrhea-associated fecal Escherichia coli from pre-weaned dairy calves. 16th International Conference on Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases (MEEGID XVI).Dresden, Germany
  • Sebastian, Peter J., Cory Schlesener, Barbara A. Byrne, Melissa Miller, Woutrina Smith, Francesca Batac, Kathy Burek-Huntington, Caroline E.C. Goertz, Natalie Rouse, Natalie Hunter, Bart C. Weimer, Christine K. Johnson. 2023. Virulent Vibrio
    parahaemolyticus in humans and sea otters. Wildlife Disease Association, Seattle, WA
  • Schlesener, Cory, Depenbrock, Sarah, Bart C. Weimer. 2023. Meta-transcriptomes of a Cattle Population under Healthy and Bovine Respiratory Disease Conditions. MGG student presentations
  • Schlesener, Cory, Depenbrock, Sarah, Bart C. Weimer. 2023. Pathogen-Microbiome Dynamics in the Nasopharyngeal Meta-transcriptomes of a Cattle Population under Healthy and Bovine Respiratory Disease Conditions. Cell Symposia: Infection biology in the age of the microbiome, Paris, FR
  • Sebastian, Peter J., Cory Schlesener, Barbara A. Byrne, Melissa Miller, Woutrina Smith, Francesca Batac, Kathy Burek-Huntington, Caroline E.C. Goertz, Natalie Rouse, Natalie Hunter, Bart C. Weimer, Christine K. Johnson. 2023. Virulent
    Vibrio parahaemolyticus in humans and sea otters. BAMPS, San Francisco, CA.
  • Sebastian, Peter J., Cory Schlesener, Barbara A. Byrne, Melissa Miller, Woutrina Smith, Francesca Batac, Kathy Burek-Huntington, Caroline E.C. Goertz, Natalie Rouse, Natalie Hunter, Bart C. Weimer, Christine K. Johnson. 2023. Clonal expansion of virulent Vibrio parahaemolyticus in humans and sea otters. Wildlife Disease Association, Seattle, WA.
  • van Heule, M., H. El-Sheikh Ali, C. Schlesener, K. Scoggin, B. Ball, P. Daels, B. Weimer, P. Dini. 2023. The placental microbiome during nocardioform placentitis. International Symposium on Equine Reproduction (ISER), Foz do Iguaçu, Brazil.
  • Depenbrock, Sarah, Cory Schlesener, Bart C. Weimer. 2023. Presence and expression of antimicrobial resistance genes in respiratory bacterial isolates from weaned dairy heifers. Conference of Research Workers in Animal Diseases (CRWAD), Chicago, IL.
  • Lee, M., M. Questa, B.C. Weimer, A. Avalos, B. Mclaughlin, A. Buono, J.S. Suchodolski, S. Marsilio. 2023. Safety profile and effects of fecal microbiota transplantation on the peripheral immune response in healthy dogs. Digestive Disease Week 2023, Chicago, IL

2022

  • Monterio, Hugo, Bart C. Weimer, and Fabio Lima. 2022. Effect of diet on the rumen microbiome and feed efficiency in dairy cattle. Microbiome in Veterinary Medicine, UC Davis, Davis, CA.
  • Lee, M., M. Questa, B.C. Weimer, A. Avalos, B. Mclaughlin, A. Buono, J.S. Suchodolski, S. Marsilio. 2023. Effect of fecal microbiota transplantation on the peripheral immune response in healthy dogs. Microbiome in Veterinary Medicine, UC Davis, Davis, CA.
  • Depenbrock, Sarah, Cory Schlesener, Bart C. Weimer. 2022. antimicrobial resistance genes in respiratory bacterial isolates from weaned dairy heifers. Microbiome in Veterinary Medicine, UC Davis, Davis, CA.
  • Weimer, Bart C.,Cory Schlesener. 2022. WGS informed microbiome analysis. Microbiome in Veterinary Medicine, UC Davis, Davis, CA
  • Lee, Mary Ann; Sini Marsilo; Bart C. Weimer. 2022. Metagenomics of fecal transplant engraftment. STAR, UC Davis, Davis, CA. poster session
  • Flores, Ashleigh, Cory Schlesener, Carol Huang, and Bart C. Weimer. The role of bacteria in the formation of the struvite equine enterolith. 2022. STARs in Science Student Poster, UC Davis School of Veterinary Medicine, Davis, CA. Poster session
  • Weimer, Bart C. 2022. Analytical considerations for genomics and metagenomics. AOAC Pacific Northwest Section annual meeting, Davis, CA (keynote)
  • Flores, Ashleigh and Bart C. Weimer. The role of bacteria in the formation of the struvite equine enterolith. 2022. STAR, UC Davis, Davis, CA. Oral symposium.
  • Lee, Mary Ann; Sini Marsilo; Bart C. Weimer. 2022. Metagenomics of fecal transplant engraftment. STAR, UC Davis, Davis, CA. Oral symposium.
  • Chomel, Bruno; Jonathan Gonçalves-Oliveira; Ricardo Gutierrez; Bart C. Weimer; David Jaffe; Alvaro Auguilar-Setien; Henri-Jean Boulouis; Yaarit Natchum-Biala; Shimon Harrus. 2022. Three new novel strains of Bartonella in rodents and bats from Mexico. 10th International Conference on Bartonellaas Emerging Pathogens, Lima, Peru.
  • Weimer, Bart C., and DJ Darwin R Bandoy. 2022. Infectious disease & population genomics: WGS Diversity, function, & machine learning. UC Davis, CA
  • Shaw, Claire, Matthias Hess, and Bart C. Weimer. 2022. Structurally diverse prebiotic oligosaccharides differentially alter Salmonella-Caco2 interactions in an in-vitro gut model. ISME, Lausanne Switzerland.
  • Avalos, A., L. D. Rodgers, S. M. Higdon, A. B. Bennett, B. C. Weimer. 2022. Oxygen Depletion by Maize Aerial Root Diazotrophs. The 25th North American Symbiotic Nitrogen Fixation Conference, Madison, WI.
  • Monteiro H. F., R. S. Bisinotto, C. C. Figueiredo, J. E. P. Santos, F. Penagaricano, E. S. Ribeiro, F. Schenkel, M. Marcondes, B. C. Weimer, and F. S. Lima. 2022. Characterizing ruminal microbiome contribution to residual feed intake and milk production efficiency in a large cohort of lactating dairy cows. American Dairy Science Association; J. Dairy Sci. Vol. 105, (Suppl. 1): 8
  • Monteiro H. F., R. S. Bisinotto, C. C. Figueiredo, J. E. P. Santos, F. Penagaricano, E. S. Ribeiro, F. Schenkel, M. Marcondes, B. C. Weimer, and F. S. Lima. 2022. Rumen microbiome contributions to dry matter intake modulation in lactating dairy cows. American Dairy Science Association; J. Dairy Sci. Vol. 105, (Suppl. 1):7
  • Schlesener, Cory, Sarah Depenbrock, and Bart C. Weimer. 2022. Population genomics of the pathogens that cause bovine respiratory disease. BAMPS, San Francisco, CA.
  • van Heule, Machteld, Cory Schlesener, Kirsten Scoggin, Hossam El-Sheikh Ali, Barry Ball, Peter Daels, Bart Weimer, Pouya Dini. 2022.Characterizing the equine placental microbiome in healthy pregnancies using metatranscriptomics analysis. Society for the Study of Reproduction annual meeting, Spokane, WA.
  • Monteiro, H. F., R. S. Bisinotto, C. C. Figueiredo, J. E. P. Santos, F. Penagaricano, E. S. Ribeiro, F. Schenkel, M. I. Marcondes, B. C. Weimer, and F. S. Lima. 2022. Characterizing ruminal microbiome contribution to residual feed intake and milk production efficiency in a large cohort of lactating dairy cows. American Dairy Science Association annual meeting.
  • Monteiro, H. F., R. S. Bisinotto, C. C. Figueiredo, J. E. P. Santos, F. Penagaricano, E. S. Ribeiro, F. Schenkel, M. I. Marcondes, B. C. Weimer, and F. S. Lima. 2022. Rumen microbiome contributions to dry matter intake modulation in lactating dairy cows. American Dairy Science Association annual meeting.
  • Schlesener, Cory, Sarah Depenbrock, and Bart C. Weimer. 2022. Population genomics of bovine respiratory disease pathogens. UC Davis, Microbiology Graduate Group.

2021

  • Brahmaver Dharmaveer Shetty, Noha Amaly, Bart C. Weimer, and Pramod Pandey. 2021. Using Machine Learning Models to Predict Coliform Risk in Alternate Dairy Effluent Management Plants with Gravitational or Mechanical Solid Separation of Manure. 3rd Renewable Natural Gas Summit, AIChE – Society of Chemical Engineers.
  • 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.