Consortium for Sequencing the Food Supply Chain - Selected Publications


Selected Publications:

Kristen L. Beck*, Niina Haiminen*, David Chambliss, Stefan B Edlund, Mark Kunitomi, B. Carol Huang, Nguyet Kong, Balasubramanian Ganesan, Robert Baker, Peter Markwell, Ban Kawas, Matthew Davis, Robert J. Prill, Harsha Krishnareddy, Edward Seabolt, Carl H. Marlowe, Sophie Pierre, Andre Quintanar, Laxmi Parida, Geraud Dubois, James Kaufman, Bart C. Weimer, Consortium for Sequencing the Food Supply Chain, 2021. Monitoring the microbiome for food safety and quality using deep shotgun sequencing. npj Science of Food 5(3), Springer Nature.

Niina Haiminen, Stefan Edlund, David Chambliss, Mark Kunitomi, Bart C. Weimer, Balasubramanian Ganesan, Robert Baker, Peter Markwell, Matthew Davis, B. Carol Huang, Nguyet Kong, Robert J. Prill, Carl H. Marlowe, Andre Quintanar, Sophie Pierre, Geraud Dubois, James H. Kaufman, Laxmi Parida, Kristen L. Beck, Consortium for Sequencing the Food Supply Chain, 2019. Food authentication from shotgun sequencing reads with an application on high protein powders. npj Science of Food 3(24), Springer Nature.
 
Kaufman, J. H., Elkins, C. A.,  Davis, M., A. M. Weis, Huang, B. C., Mammel, M. K., Patel, I. R., Beck, K. L., Edlund, S., Chambliss, D., Douglas, J., Bianco, S., Kunitomi, M., Weimer, B. C., 2018Chapter: Insular microbiogeography in Microbial Ecology: Current advances from genomics, metagenomics and other “omics.
Caister Academic Press, Poole, UK.
Kaufman, J.H., Seabolt, E., Kunitomi, M., Agarwal, A., Beck, K., Krishnareddy, H. and Weimer, B.C., 2018, April. Exploiting Functional Context in Biology: Reconsidering Classification of Bacterial Life. In 2018 IEEE 34th International Conference on Data Engineering Workshops (ICDEW) (pp. 17-20). IEEE.
Weimer, B.C., Storey, D.B., Elkins, C.A., Baker, R.C., Markwell, P., Chambliss, D.D., Edlund, S.B. and Kaufman, J.H., 2016. Defining the food microbiome for authentication, safety, and process management. IBM Journal of Research and Development, 60 (5/6), pp.1-1.
Edlund, S.B., Beck, K.L., Haiminen, N., Parida, L.P., Storey, D.B., Weimer, B.C., Kaufman, J.H. and Chambliss, D.D., 2016. Design of the MCAW compute service for food safety bioinformatics. IBM Journal of Research and Development, 60(5/6), pp.2-1.
Hu, K., Renly, S., Edlund, S., Davis, M. and Kaufman, J., 2016. A modeling framework to accelerate food-borne outbreak investigations. Food Control, 59, pp.53-58.
Kaufman, J., Lessler, J., Harry, A., Edlund, S., Hu, K., Douglas, J., Thoens, C., Appel, B., Käsbohrer, A. and Filter, M., 2014. A likelihood-based approach to identifying contaminated food products using sales data: performance and challenges. PLoS computational biology, 10(7), p.e1003692.
Selected Invited Talks and Presentations: 

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.

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)

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

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.

Kaufman, James and Bart C. Weimer. 2017. Sequencing of the food supply. Pacific Southwest Section -AOAC International 2017 Annual Meeting, Berkeley, CA.

Kaufman, James, and Bart C. Weimer. 2016. Metagenomics of the food supply. Colorado State University, School of Veterinary Medicine, Fort Collins, CO.

J. H. Kaufman, Bart C. Weimer, M. Becker, D. Storey, N. Kong, C. Huang, Haiminen, Niina, Laxmi Parida, D. Chambliss, S. Edlund, R. Prill, S. Bianco, K. Hu, N. Haiminen, Peter Markwell, Bob Baker, 2016. Mapping the Metagenome with an Ever Smaller Ruler. American Society for Microbiology Annual Meeting Special Session, Boston, MA. (Organized by B. C. Weimer)

Weimer, Bart C., J. H. Kaufman, M. Becker, D. Storey, N. Kong, C. Huang, Haiminen, Niina, Laxmi Parida, D. Chambliss, S. Edlund, R. Prill, S. Bianco, K. Hu, N. Haiminen, Peter Markwell, Bob Baker, 2016. Metagenomics: Hazard Detection in the Food Supply. American Society for Microbiology Annual Meeting Special Session, Boston, MA. (Organized by B. C. Weimer)

Weimer, Bart C., R. Torres, M. Becker, D. Storey, N. Kong, A. Foutouhi, C. Huang, Haiminen, Niina, Laxmi Parida, D. Chambliss, S. Edlund, R. Prill, S. Bianco, K. Hu, N. Haiminen, J. H. Kaufman, Peter Markwell, Bob Baker, J. Torres, J. Solnick. 2016. Large-scale genomics in public health and food safety. Colegio Mexicano de Ingenieros Bioquimicos, Veracruz, Mexico. (Keynote speaker)

Haiminen, Niina, Laxmi Parida, D. Chambliss, S. Edlund, R. Prill, S. Bianco, K. Hu, N. Haiminen, and J. H. Kaufman, Dylan Storey, Bart C. Weimer, Peter Markwell, and Bob Baker. 2016. Understanding False Positives in Mapping of Microbiome Sequence Data Using In-silico Simulations. IAFP, St. Louis, MO.

Kaufman, James, R. Baker, N. Limbardi, P. Markwell, D. Storey, C. Huang, B.C. Weimer, D. Chambliss, S. Edlund, R. Prill, S. Bianco, K. Hu, N. Haiminen, and J. H. Kaufman. 2015. Metagenomics For Food Safety: Sequencing the Food Supply Chain. Presented at the bioMérieux Symposium – What is “Big Data” and How Might Metagenomics, Whole Genome Sequences, and other Large Data Sets Change Food Microbiology? IAFP, Portland, OR.

Chambliss, D. S. Edlund, J. H. Kaufman, R. Prill, N. Haiminen, D. Storey, C. Huang, B.C. Weimer, R. Baker, N. Limbardi, P. Markwell. 2015. Metagenomic Applications for Characterizing the Food Microbiome, IAFP, Portland, OR.

Edlund, Stefan, David Chambliss, James Kaufman, Dylan Storey, and Bart C. Weimer. 2015. Estimating genome features. American Public Health Association Annual Meeting, Chicago, IL.