bart c. weimer, ph.d., professor · enables fast turnaround times and improved data quality for...

BartC.Weimer,Ph.D.,Professor

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[(a)=refereed, (b)=non-refereed, *=supervising author, (c)=book chapter, (i)=invited] 14. (ai) Gao, S., D–H. Oh, J. Broadbent, M. Johnson, B. Weimer, and J. Steele. 1997. Aromatic

amino acid catabolism by lactococci. Le Lait 77:371. 13. (ai)* Weimer, B. C., C. Brennand, J. Broadbent, J. Jaegi, M. Johnson, F. Milani, J. Steele, and D.

Sisson. 1997. Influence of flavor adjunct bacteria on the flavor and texture of 60% reduced fat Cheddar cheese. Le Lait 77:383.

12. (a)* Blake, M., and B. Weimer. 1997. Rapid and sensitive immunomagnetic detection of Bacillus stearothermophilus spores in food and environmental samples. Appl. Environ. Microbiol. 63:1643.

11. (a)* Broadbent, Jeffery R., Charlotte Brennand, Mark E. Johnson, James L. Steele, Marie Strickland, and Bart C. Weimer. 1997. Contributions by starter and selected adjunct bacteria to flavor development in reduced-fat cheddar cheese. Dairy Industry Int. 62:35–39.

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)=book chapter, (i)=invited] 10. (a)* Strickland, M., B. C. Weimer, and J. R. Broadbent. 1996. Capillary electrophoresis

separates many compounds found in Cheddar cheese. J. Chromatography A 731:305. 9. (a)* M. Blake, R. Koka, B.C. Weimer. 1996. A Semi-Automated Colorimetric Method for the

Determination of Lipase Activity in Milk. J. Dairy Sci. 79:1164.

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)=book chapter, (i)=invited] 8. (a)* B. Dias, B.C. Weimer. 1995. A semi-automated colorimetric method for determination of

peptidases in turbid solutions. J. Rapid Methods and Automation in Microbiol. 3:223.

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)=book chapter, (i)=invited] 7. (a)* M. Blake, B.C. Weimer, D. McMahon, and P. Savello. 1994. Direct steam processing of

extended shelf life milk: sensory and microbial quality. J. Food Prot. 58:1007. 6. (b)* Weimer, B.C., M. Blake. 1994. Lower temperatures for UHT. Aust. Dairy Foods 15:52. 5. (b)* Weimer, B.C., M. Blake. 1994. ESL milk processing and microbiology. Quality Quarterly

Spring (Australia).

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)=book chapter, (i)=invited] 4. (a) Weimer, B. C., M. Blake, A.J. Hillier, and B.E. Davidson. 1993. Studies on factory-

derivation techniques using Lactococcus lactis ssp. cremoris FG2. Australian Journal of Dairy Technology 48:59.

3. (b)* Weimer, B. 1992. Can antibiotic test kits be useful? USU Cooperative Extension leaflet #265.


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2. (a) Oberg, C.J., B. C. Weimer, L.V. Moyes, R.J. Brown, and G.H. Richardson. 1991. Proteolytic characterization of Lactobacillus delbrueckii ssp. bulgaricus strains by amino acid analysis. J. Dairy Sci. 74:398.

Held an industrial position that didn’t allow publication

1. (a) Weimer, B. C., C. J. Oberg, L. V. Moyes, R. J. Brown, and G. H. Richardson. 1989. Comparison of classical ion exchange amino acid analysis and o-phthaldialdhyde methods to characterize proteolysis by Lactobacillus bulgaricus. J. Dairy Sci. 72:2873.

[(a)=invited, (b)=submitted, *=supervising author; **=co-supervising author] 9. (a)** Miller, Bronwen, Beverley van Rooyen, Heather Whitehorn, Piet Jones, Martin Ranik, Eric

van der Walt, Maryke Appel, Nguyet Kong, Carol Huang, Dylan Storey, Bart C. Weimer. 2015, A novel, single-tube enzymatic fragmentation and library construction method enables fast turnaround times and improved data quality for microbial whole-genome sequencing. Kapa Biosystems Application Note (072314 KK1234; DOI: 10.13140/RG.2.1.4534.3440).

8. (a)* Kong, Nguyet, Whitney Ng, and Bart C. Weimer. 2015. Quality Control of Library Construction Pipeline for PacBio SMRTbell 10kb Library Using Agilent 2200 TapeStation. Agilent Technologies application note (5991-6521EN; DOI: 10.13140/RG.2.1.4339.4644)

[(a)=invited, (b)=submitted, *=supervising author; **=co-supervising author] 7. (a)* Kong, Nguyet, Whitney Ng, Lucy Cai, Alvin Leonardo, and Bart C. Weimer. 2014.

Integrating the DNA Integrity Number (DIN) to Assess Genomic DNA (gDNA) Quality Control Using the Agilent 2200 TapeStation System. Agilent Technologies application note (5991-5442EN; DOI: 10.13140/RG.2.1.3616.8409).

6. (a)* Kong, Nguyet, Whitney Ng, Azarene Foutouhi, B. Carol Huang, and Bart C. Weimer. 2014. Quality Control of High-Throughput Library Construction Pipeline for KAPA HTP Library Using an Agilent2200 TapeStation. Agilent Technologies application note (5991-5141EN; DOI: 10.13140/RG.2.1.4927.5604).

5. (a)* Jeannotte, Richard, Eric Lee, Narine Arabyan, Nguyet Kong, Kao Thao, Carol Huang and Bart C. Weimer. 2014. Optimization of Covaris settings for shearing bacterial genomic DNA by focused ultrasonication and analysis using Agilent 2200 TapeStation. Agilent Technologies application note. (5991-5075EN; DOI: 10.13140/RG.2.1.4424.1444).

4. (a)* Jeannotte, Richard, Eric Lee, Nguyet Dao Kong, Whitney Ng, and B. C. Weimer. 2014. High-Throughput Analysis of Foodborne Bacterial Genomic DNA Using Agilent 2200 TapeStation and Genomic DNA ScreenTape System. Agilent Technologies application note. (5991-4003EN; DOI: 10.13140/RG.2.1.3354.6961).

3. (a)* Kong, Nguyet, Kao Thao, Whitney Ng, Kristi Spittle Kim, Jonas Korlach, Luke Hickey, Lenore Kelly, Stephen Lappin, and Bart C. Weimer. 2014. Automation of PacBio


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SMRTbell 10 kb Template Preparation on an Agilent NGS Workstation. Agilent Technologies application note. (5991-4482EN; DOI: 10.13140/RG.2.1.4403.2725).

2. (a)* Kong, Nguyet, Kao Thao, Carol Huang, Maryke Appel, Stephen Lappin, Lisa Knapp, Lenore Kelly, and B. C. Weimer. 2014. 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. Agilent Technologies application note (5991-4296EN; DOI: 10.13140/RG.2.1.2306.1203).

[(a)=invited, (b)=submitted, *=supervising author; **=co-supervising author] 1. (a)* Kong, N., W. Ng, V. Lee, L. Kelly, and B. C. Weimer. 2013. Production and Analysis of

High Molecular Weight Genomic DNA for NGS Pipelines Using Agilent DNA Extraction Kit. Agilent Technologies application note (5991-3722EN; DOI: 10.13140/RG.2.1.2961.4807).

[(a)=invited, (b)=submitted, *=supervising author; **=co-supervising author] ~185 interviews for TV, radio or popular press magazines; including Wired, The New Scientist, The Scientist, New York Times, Wall Street Journal, GenomeWeb, Nature, PNAS, SoAR, and IEEE Spectrum magazines. Press releases for the 100K Pathogen Genome Project are captured on the web site. They are varied and in partnership with multiple companies that participate in the world-wide effort. News for BGI@UC Davis is numerous and captured at the BGI@UCDavis web site. They occur in local news and international science news outlets including GenomeWeb, Nature, JAMA, and The Scientist.

[(a)=invited, (b)=submitted, (k)=keynote, *=supervising author; **=co-supervising author] 337. (a)* Weimer, Bart C. 2018. Unexpected genomic diversity in pathogens: embracing diversity

of the microbial world. IBM lecture series. Almaden, CA 336. (b)** 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. 34th IEEE International Conference on Data Engineering - Context in Analytics: Challenges, Opportunities and Trends. Paris France.

335. (ak)* Weimer, Bart C. 2018. Unexpected genomic diversity in pathogens: implications for food and public safety. Korean FDA Symposium, Seoul S. Korea.

334. (ak)* Weimer, Bart C. 2018. Molecular methods in diagnostics. American Veterinary Medical Association, Denver, CO


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333. (ak)* Weimer, Bart C. B. Huang, N. Kong. 2018. From whole genomes to metagenomes in food safety. Mars, Inc. Techcon. Seattle, WA. Invitation only

332. (b) 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.

[(a)=invited, (b)=submitted, (k)=keynote, *=supervising author; **=co-supervising author] 331. (a)* Weimer, Bart C. B. Huang, N. Kong. 2017. Real time sequencing using the minION for

pure and mixed cultures for food safety. Davis, CA. Invitation only 330. (a)* Weimer, Bart C. 2017. Metagenomic and metabolomics response to toxin addition to

food materials. Mars, Inc., McLean, VA. Invitation only 329. (b)* Chen, Poyin, and Bart C. Weimer. 2017. Molecular effects of prebiotic oligosaccharide

on Listeria monocytogenes infection. Australian Society for Microbiology Annual meeting, Hobart, Tasmania.

328. (a)* Weimer, Bart C. 2017. Genomics in food and predictive microbiology. University of Tasmania, Hobart, Australia.

327. (ak)* Weimer, Bart C. 2017. Metagenomics and genomics in food and health. CSIRO Australian Animal Health Laboratory, Geelong, Australia. Snowdon Oration. Keynote

326. (a)* 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

325. (a)* 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)

324. (b)* 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

323. (ak)* 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

322. (b)* 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)

321. (b)* 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)

320. (a)** Beck, Kristen L., James Kaufman, Stefan Edlund, David Chambliss, Niina Haiminen, Matt Davis, Mark Kunitomi, Robert Prill, Laxmi Parida, Simone Bianco, Bart C.


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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.

319. (a)** 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.

318. (ak)* 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.

317. (a)* Weimer, Bart C. 2017. Metagenomics and whole genome sequencing in food and public health. Oxford Nanopore, Oxford, UK.

316. (b)* Chen, Poyin, and Bart C. Weimer. 2017. Molecular effects of prebiotic oligosaccharides on L. monocytogenes infection. BAMPS XX, San Francisco, CA.

315. (b)* 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.

314. (a)* 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). 3rd Annual Integrative Pathobiology Research Symposium, UC Davis, Davis, CA.

313. (a)* Weimer, Bart C. 2017. Metagenomics and genomics of Campylobacter to diagnose outbreaks in animals. Utah’s Hogle Zoo, Salt Lake City, UT.

312. (a)* Weimer, Bart C. 2017. WGS for pathogen detection and trace back. Mars Chocolate, Slough, UK.

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

310. (a)* 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.

[(a)=invited, (b)=submitted, (k)=keynote, *=supervising author; **=co-supervising author] 309. (a)* Weimer, Bart C. 2016. Metagenomics in food safety and links to WGS. BioRad, Inc.,

Paris, France. 308. (a)* Weimer, Bart C., and Ning Chin. 2016. Metagenomics in food safety: uses and forensic

options to identify hazards. Uncommon collaborations and the future of food safety science. Beijing, PRC.

307. (a)* Weimer, Bart C. 2016. Metagenomics in food safety: real time sequencing options. Oxford Nanopore, Oxford, UK.

306. (a)** Chew, Stephanie, Ning Chin, Carol B. Huang, Bart C. Weimer, and Elizabeth A. Maga. 2016. Metagenomic Analysis of Intestinal Microbiota in Malnourished Pigs Supplemented with Lysozyme-Rich Transgenic Goat Milk. UC Davis Animal Science Symposium, Davis, CA.


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

304. (ak)* Weimer, Bart C. 2016. Food Safety and the Role of Genomics for the Future. Korean Society of Food Science and Technology (KFoST) annual meeting. Daegu, Korea.

303. (a)* Weimer, Bart C. 2016. Linking food safety with metagenomics: sequencing the supply chain. Mars Plant Science and Genetics working group. Davis, CA.

302. (a)* Fouthoui, Azarene, Allison M. Weis, Marina Becker, Carol Huang, Bart C. Weimer. 2016. How the microbiome structure changes between mom and baby orientation of the placeneta. Signature Research Program Symposium. Davis, CA.

301. (a)* Weis, Allison M., Bart C. Weimer, Azarene Fouthoui, Marina Becker, Carol Huang. 2016. Defining the placental microbiome using metagenomics. Signature Research Program Symposium. Davis, CA. (2nd place award)

300. (ak)* Weimer, Bart C. 2016. Rapid detection and its link to genomics and food safety. Biodefense World Summit 2016. Rapid Detection for Food Safety. Baltimore, MD.

299. (ak)* Weimer, Bart C. 2016. Genomics and food safety. Wrigley Innovation Center, Chicago, IL.

298. (a)* 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)

297. (ak)* 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)

296. (b)* Weis, Allison M., Dylan B. Storey, Conor C. Taff, Kristen Clothier, Nugget Kong, Woutrina A. Smith, Barbara A. Byrne, Walter M. Boyce, Andrea K. Townsend, Bart C. Weimer. 2016. Genomic Comparisons and Zoonotic Potential of Campylobacter isolates around Davis, California. American Society for Microbiology Annual Meeting, Boston, MA.

295. (b)* Chen, Poyin, Nguyet Kong, and Bart C. Weimer. 2016. Inhibitory Effects of Oligosaccharides on Enteric Pathogens. Association with the Gastrointestinal Barrier. American Society for Microbiology Annual Meeting, Boston, MA. (DOI: 10.13140/RG.2.2.22748.59522)

294. (b)* Arabyan, N., D. Park, H. Yu, S. Foutouhi, C. C. Williams, P. Desai, J. Shah, R. Jeannotte, N. Kong, X. Chen, C. B. Lebrilla, and Bart C. Weimer. 2016. Host Glycan Remodeling - Sweet Cross Talk between the Host and the Microbe. Association with the Gastrointestinal Barrier. American Society for Microbiology Annual Meeting, Boston, MA.

293. (a)* Weimer, Bart C. 2016. Genomics and public health. Vice President Glenda Humiston – Agriculture and Natural Resources, UC. Davis, CA.

292. (b)* Weis, Allison M., Dylan B. Storey, Connor C. Taff, Kristen Clothier, Andrea Townsend, Bart C. Weimer. 2016. Genomic comparisons and zoonotic potential of Campylobacter isolates. BAMPS, San Francisco, CA.

291. (b)* Weis, Allison M., Dylan B. Storey, Connor C. Taff, Kristen Clothier, Andrea Townsend, Bart C. Weimer. 2016. Genomic comparisons and zoonotic potential of Campylobacter


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isolates. Interdisciplinary Graduate and Professional Student Symposium, Davis. CA. (won Dean’s Prize for Best Oral Presentation in Medicine and People’s Choice award).

290. (a)** Torres, Roberto Francisco Aviles, Alfonso Mendez, Margarita Camorlinga, Marina Becker, Dylan Storey, Allison Weis, Carol Huang, Nguyet Kong, Bart C. Weimer; Javier Torres. 2016. Relationship of gastric cancer development with the different vacA alleles, the number of cagA-EPIYA motifs and the presence of the dupA gene in Helicobacter pylori. IX International Congress, XX National Congress on Biochemical Engineering and the XIV Biomedicine and Molecular Biotechnology Scientific Meetings, Boca del Rio, Veracruz, Mexico. (won 1st place for the poster competition for the entire joint conference).

289. (b)** Taff, Conor C., Allison M. Weis, Bart C. Weimer, and Andrea K. 2016. Townsend Influence of host ecology and behavior on Campylobacter jejuni prevalence and environmental contamination risk in a synanthropic wild bird. Ecology & Evolution of Infectious Diseases Conference, Ithica, NY.

288. (ak)* 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)

287. (b)** 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.

286. (b)* Arabyan, N., D. Park, H. Yu, S. Foutouhi, C. C. Williams, P. Desai, J. Shah, R. Jeannotte, N. Kong, X. Chen, C. B. Lebrilla and Bart C. Weimer. 2016. Host glycan remodeling - sweet cross talk between the host and the microbe. ASM-Microbe, Boston, MA

285. (a)* Weimer, Bart C., A. Foutouhi, N. Kong, M. Becker, D. Storey. 2016. Rapid bacterial detection – capture/concentration to remove growth before detection. Mars Global Food Safety Conference, Davis, CA.

284. (b)* Chen, Poyin, Nguyet Kong, and Bart C. Weimer. 2016. Inhibitory effects of oligosaccharides on enteric pathogen association with the gastrointestinal barrier. ASM-Microbe, Boston, MA

283. (b)* Weis, Allison M., Dylan B. Storey, Conor C. Taff, Kristen Clothier, Nugget Kong, Woutrina A. Smith, Barbara A. Byrne, Walter M. Boyce, Andrea K. Townsend, Bart C. Weimer. 2016. Genomic comparisons and zoonotic potential of Campylobacter isolates around Davis, California. ASM-Microbe, Boston, MA

282. (a)* Weimer, Bart C. 2016. Rapid bacterial detection – increasing speed with genomics and capture. Mars Global Science Conference, Davis, CA.

281. (a)* Weimer, Bart C. 2016. Genomics – the basics for food and health. Mars Global Science Conference. Davis, CA.

280. (a)* Weimer, Bart C. 2016. Genomics and culture independent methods in food safety. Food Safety 2016.

279. (a)* Weimer, Bart C. 2016. The intersection of big data, genomics, microbiology in molecular food safety. Uncommon collaborations and the future of food safety science. Beijing China.

278. (a)* Weimer, Bart C. 2016. The skin microbiome and metabolome – integration to understand community structure and function. GoJo Industries, Akron, OH.


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277. (b)** Camargo, M. Constanza, Javier Torres, Jay Solnick, Castle Raley, Dylan Storey, Marina Becker, Roberto Torres, Xiongfong Chen, Bao Tran, Bart C. Weimer, Charles S. Rabkin. 2016. DNA Methylation Profiles of Helicobacter pylori Strains from Patients with Gastric Cancer and Gastris. American Association for Cancer Research annual meeting, New Orleans.

[(a)=invited, (b)=submitted, (k)=keynote, *=supervising author; **=co-supervising author] 276. (a)* Weimer, Bart C. 2015. Use of genomics in health and food safety, Kinsella Symposium,

UC Dublin. Dublin, Ireland 275. (a)* Weimer, Bart C. 2015. The genomes of nitrogen fixation bacteria in the corn

microbiome. Corn Summit, Davis, CA. 274. (a)* Weimer, Bart C., A. Foutouhi, D. Storey, R. Baker, P. Markwell. 2015. Culture

independent detection using capture concentration. USDA/FSIS monthly webinar. 273. (a)* Weimer, Bart C. 2015. Big data in agriculture, UC Dublin Foods for Health and

Agriculture. Dublin, Ireland 272. (a)* Zamora, Pablo, Jonathan A. Eisen, Bart C. Weimer, Jean-Michel Ané, Howard-Yana

Shapiro, Alan B. Bennett. 2015. The aerial root mucilage associated with an indigenous landrace of maize supports a diazotrophic microbiota. BioStimulants. Florence, Italy.

271. (a)* Weis, Allison, Dylan Story, and Weimer, Bart C. 2015. Genomic comparisons and pathogenic potential of Campylobacter Isolates. CHRO, Rotorua, New Zealand.

270. (a)* Storey, Dylan, Allison Weis, Bart C. Weimer. 2015. Genomics in food safety outbreak detection. ASM Conference for NGS in Food Safety, Washington DC.

269. (a)* Weimer, Bart C. 2015. Nitrogen fixation in diazotrophic microbiome members associated with maize. Corn Summit, Davis, CA

268. (a)* Weimer, Bart C. 2015. Big Data in food safety. LARTA, St. Louis, MO. 267. (a)* Weimer, Bart C. 2015. Genomics and risk in governance of genomic information.

Governance of Human Genetic Information & Development of Precision Medicine. 266. (a)* Weimer, Bart C. 2015. Large scale genomics and the future of food safety. The 8th

International Biotechnology and Agriculture Summit. Beijing, China. 265. (a)* Weimer, Bart C. 2015. 100K Pathogens: From genomes to diagnostics. Chinese

Academy of Microbiology, Beijing, China. 264. (a)* Weimer, Bart C. 2015. Host/microbe interactions using large scale genomics and

biosecurity. Bridging science and security for biological research: Personnel Security Programs. Washington, D.C., Invited meeting hosted by AAAS, FBI, and Gryphon Scientific.

263. (a)* Weimer, Bart C., A. Foutouhi, D. Storey, R. Baker, P. Markwell. 2015. Rapid detection of bacteria from food by eliminating enrichment. Mars Pathogen Management Meeting, McLean, VA (invitation only)

262. (a)** 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 in 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.

261. (a)** 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.


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260. (b) Pramod K Pandey, Sagor Biswas, Mark Lejeune, Daniel Morash, Bart Weimer, Glenn Young. 2015. Assessing Pathogen Challenge in Foodwaste Biofertilizers. American Society of Agricultural and Biological Engineers (ASABE).

259. (b)** Pinho, R.M., C. Huang, B.C. Weimer, E.A. Maga. 2015. Library construction using the KAPA mRNA strand kit for RNA-sequencing of pig intestinal tissues after consumption of milk from lysozyme transgenic goats. X Transgenic Animal Research Conference, Lake Tahoe, CA.

258. (a)* Weimer, Bart C., A. Foutouhi, D. Storey, R. Baker, P. Markwell. 2015. Culture independent detection using capture concentration. FDA Food Safety Grand Challenge Finals. Washington, DC. (1 of 5 finalists selected by judges from FDA, CDC, USDA, and food safety industry for the national competition in food safety).

257. (a)* Weimer, Bart C. 2015. Host/microbe interactions using large scale genomics. Food+IT conference, San Francisco, CA.

256. (a)* Foutouhi, Soraya and Bart C. Weimer. 2015. RNASeq Analysis of Mesenchymal Stem Cells Following Salmonella Infection. Fluidigm User Meeting, San Francisco, CA.

255. (b)* Agulto, Reginaw, Nguyet Kong, Whitney Ng, Lucy Cai, Alvin Leonardo, Lenore Kelly and Bart C. Weimer. 2015. Integrating the DNA Integrity Number (DIN) to Assess Genomic DNA (gDNA) Quality Control Using the Agilent 2200 TapeStation System. UC Davis Undergraduate Research Conference, Davis, CA. wUndergraduate.

254. (b)* Ancheta, Patrickw, Nguyet Kong, Whitney Ng, Azarene Foutouhi, B. Carol Huang, Lenore Kelly and Bart C. Weimer. 2015. Quality Control of High-Throughput Library Construction Pipeline for KAPA HTP Library Using an Agilent 2200 TapeStation. UC Davis Undergraduate Research Conference, Davis, CA. wUndergraduate.

253. (b)* Liu, Kendraw, Narine Arabyan, Nguyet Kong, Marie-Pierre Forquin Gomez, and Bart C. Weimer. 2015. Development of an assay to quantify and detect the physiological state of the cells. UC Davis Undergraduate Research Conference, Davis, CA. wUndergraduate.

252. (b)* Storey, Dylan, Carol Huang, Whitney Ng, Kao Thao, Nguyet Kong, Alli Weis, Poyin Chen, Narine Arabyan, Richard Jeannotte, Soraya Foutouhi, Azarene Foutouhi, Lois Soreiul, Bart C. Weimer. 2015. 100K Pathogen Genomes Project: Progress, Expansion, and Interrogation. Sequencing, Finishing, and Analysis in the Future; Santa Fe, NM.

251. (a)* Arabyan, Narine, Dayoung Park, Soraya Foutouhi, Cynthia C. Williams, Prerak Desai, Jigna Shah, Richard Jeannotte, Nguyet Kong, Carlito B. Lebrilla, and Bart C. Weimer. 2015. Salmonella Degrades the Host Glycocalyx Leading to Altered Infection and Glycan Remodeling. 115th Annual American Society for Microbiology, Young Investigator Oral Presentation.

250. (a)* Arabyan, Narine, Dayoung Park, Carlito Lebrilla, and Bart C. Weimer. 2015. Salmonella Degrades the Host Glycocalyx Leading to Altered Infection and Glycan Remodeling. Gordon Research Conference, Como, Italy.

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

248. (b)* Agulto, Regina, Nguyet Kong, Whitney Ng, Lucy Cai, Alvin Leonardo, and Bart C. Weimer. 2015. Integrating the DNA Integrity Number (DIN) to Assess Genomic DNA (gDNA) Quality Control Using the Agilent 2200 TapeStation System. Undergraduate Research, Scholarship & Creative Activities Conference, UC Davis, Davis, CA.

247. (b)* Ancheta, Patrick, Nguyet Kong, Whitney Ng, Azarene Foutouhi, B. Carol Huang, Lenore Kelly, and Bart C. Weimer. 2015. Quality Control of High-Throughput Library Construction Pipeline for KAPA HTP Library Using an Agilent 2200 Tapestation.


35

Undergraduate Research, Scholarship & Creative Activities Conference, UC Davis, Davis, CA.

246. (a)* Folster, Jason P., Davina Campbell, Heather Carleton, Maria Sjӧlund-Karlsson, Jared Reynolds, Allison M. Weis, Dylan Storey, Nguyet Kong, Bart C. Weimer, Yuansha Chen, Cong Li, Shaohua Zhao, Patrick McDermott, and Jean M. Whichard. 2015. Using Whole Genome Sequencing to Predict Antimicrobial Resistance in Salmonella. American Society for Microbiology Annual Meeting.

245. (a)* Weimer, Bart C. and Soraya Foutouhi. 2015. Host/microbe interactions using large scale genomics. Plant and Animal Genomes Conference, San Diego, CA

[(a)=invited, (b)=submitted, (k)=keynote, *=supervising author; **=co-supervising author] 244. (a)* Weimer, Bart C. 2014. Genomics in global food safety. USDA office of the

Undersecretary. Washington, DC. 243. (a)* Weimer, Bart C. 2014. 100K Pathogen Genome Sequencing Project – progress and

process. NIST-DHS Standards for Pathogen Identification via Next-Generation Sequencing (SPIN) Workshop, Gaithersburg, MD

242. (a)* Weimer, Bart C. 2014. NGS, food safety, and society. School of Veterinary Medicine Dean’s Advisory Council. Davis, CA.

241. (b)* Weimer, Bart C., Nguyet Kong, Carol Huang, Whitney Ng, Dylan Storey, Paul Frere, Nicolas Lin, Christina Siebert, Jeremy Lambert, Bronwen Miller, Victoria van Kets, Eric van der Walt, Paul McEwan, and Maryke Appel. 2014. A novel, robust library construction workflow for the rapid and large-scale production of draft bacterial genome sequences. The 16th Annual Advances in Genome Biology and Technology (AGBT) Meeting, San Marco Islands, FL.

240. (a)* Foutouhi, Soraya and Bart C. Weimer. 2014. Harnessing the 100K Genome Project for culture collection characterization. US Culture Collection Network, Fall meeting, University of California, Davis.

239. (ak)* Weimer, Bart C. 2014. Rapid Serotyping of Salmonella in Food and standards associated with genomics in food safety. Microbiologics, Inc., St. Cloud, MN.

238. (a)* Weis, Allison, and Bart C. Weimer. 2014. Harnessing the 100K Genome Project to identify genomic clues to primate diarrhea in Campylobacter isolates. California National Primate Research Center, Primate Medicine GI Day. Davis, CA.

237. (a)* Weimer, Bart C. 2014. Rapid Serotyping of Salmonella in Food by Microfluidic Capillary Electrophoresis. IFSH-UW Symposium - Rapid Methods for Food Safety Microbiology, Chicago, IL.

236. (ak)* Weimer, Bart C. 2014. Genomics, food safety and translation to food and agriculture. Seoul National University, South Korea.

235. (ak)* Weimer, Bart C. 2014. Genomics in food safety and food science. 81st Annual Meeting and International Conference of Korean Society of Food Science and Technology (KoSFoST), Gwangju, Republic of Korea.

234. (a)* Weimer, Bart C. 2014. Implementation of NGS is food safety. Centro Operativo Veterinario per l'Epidemiologia, Programmazione, Informazione e Analisi del Rischio (COVEPI) National Reference Center for Veterinary Epidemiology, Istituto Zooprofilattico Sperimentale, dell'Abruzzo e del Molise "G. Caporale" Teramo, Italy.

233. (a)* Weimer, Bart C. 2014. Genomics in food safety. European Food Safety Authority NGS implementation workshop, Parma, Italy.


36

232. (a)* Weimer, Bart C. 2014. Genomics, food safety and translation to food and agriculture. China Animal Health & Epidemiology Center - Department for Safety supervision of animal products (Ministry of Agriculture), China.

231. (ak)* Weimer, Bart C. 2014. Translating large-scale genomics to Knowledge. Beijing Normal University, School of Life Sciences, Beijing, China.

230. (ak)* Weimer, Bart C. 2014. Molecular food safety: 100K pathogen genomes and beyond. Sinogenomax Co., Ltd. Conference and partnering announcement, Beijing, China.

229. (ak)* Weimer, Bart C. 2014. Molecular methods and the future of food security: 100K genomes as the basis. 3rd Annual Food Microbiology Symposium, St. Cloud, MN. (Conference keynote speaker)

228. (ak)* Weimer, Bart C. 2014. Molecular methods and the future of food security. Almaden Institute – Sequence the city, IBM International Genomics Symposium, San Jose, CA. (Agriculture keynote)

227. (b) Stevens, John R., Balasubramanian Ganesan, Michael Lefevre, and Bart C. Weimer. 2014. SigTree: Identifying and Visualizing Significantly Responsive Branches in a Phylogenetic Tree. Western Dairy Center annual meeting, Logan, UT.

226. (a)* Weimer, Bart C. 2014. Molecular methods and the future of food security for produce. Center for Produce Safety, Davis, CA.

225. (a)* Weimer, Bart C. 2014. Genomics and the microbiome in health and disease. South Australian Health and Medical Research Institute, Adelaide, Australia.

224. (a)* Weimer, Bart C. and Richard Jeannottee. 2014. Nitrogen fixing bacteria from plants. Corn Summit. Davis, CA

223. (a)* Arabyan, Narine, Dayoung Park, Cynthia Williams, Ting Song, Carlito Lebrilla, and Bart C. Weimer. 2014. Cell surface glycan changes during Salmonella infection. 17th Annual Bay Area Microbial Pathogenesis Symposium (BAMPS), San Francisco, CA.

222. (a)* Arabyan, N., D. Park, C. Williams, R. Jeannotte, P. Desai, J. Shah, N, Kong, M.L. Yang, C. Lebrilla, and B. C. Weimer. Host glycan degradation during Salmonella enterica spp. enterica sv Typhimurium infection. UC Davis College of Biological Sciences - Microbiology & Molecular Genetics Department. Davis, CA

221. (a)* Arabyan, N., D. Park, C. Williams, R. Jeannotte, P. Desai, J. Shah, N, Kong, M.L. Yang, C. Lebrilla, and B.C. Weimer. Glycan digestion during Salmonella enterica spp. enterica sv Typhimurium infection. Microbiology Graduate Student Annual Symposium, UC Davis. Davis, CA

220. (a)* Weimer, Bart C. 2014. Genomics and the food industry. Center for Produce Safety. Davis, CA.

219. (a)* Weimer, Bart C. 2014. Genomics and pathogens: molecular methods for the future in food security. Mars Scientific Advisory Board, Davis, CA.

218. (b)** Park, Dayoung; Narine Arabyan; Cynthia Williams; Ting Song; Bart Weimer; Carlito Lebrilla Determination of changes in cell surface glycosylation with cellular transformations. 2014. American Society for Mass Spectrometry, Baltimore, MD.

217. (b)** Crawford, Elizabeth; Domizio, Paola; Musselman, Brian D.; Joseph, C. M. Lucy; Bisson, Linda F., Weimer, Bart C., and Jeannotte, Richard. 2014. Preventing Wine Spoilage: Rapid Screen & Quantification of Off-flavor Phenolics using Ambient Ionization coupled with High Resolution MS/MS. The 47th Annual German Society for Mass Spectrometry (DGMS), Frankfurt.


37

[(a)=invited, (b)=submitted, *=supervising author; **=co-supervising author] 216. (a)* Weimer, Bart C. 2013. Genomics and pathogens: molecular serotyping methods.

FDA/CFSAN, Washington, DC. 215. (a)* Weimer, Bart C. 2013. Genomics and pathogens: large scale sequencing and

computational needs. IBM, Davis, CA. 214. (a)* Weimer, Bart C. 2013. Microbial ecology and pathogens in animal waste streams. UC

Davis Animal Waste Workshop, Davis, CA. 213. (a)* Weimer, Bart C. 2013. Sequencing 100K genomes for population microbiology in food

safety and security. China Center for Disease Control, Microbiology Division, Beijing, PRC.

212. (a)* Weimer, Bart C. 2013. Sequencing 100K genomes for population microbiology in food safety and security. Chinese Academy of Science. Microbial Genome Research Center & Key Lab of Pathogenic Microbiology and Immunology, Institute of Microbiology, Beijing, PRC.

211. (a)* Weimer, Bart C. 2013. Sequencing 100K genomes for population microbiology in food safety and security. AgStart Showcase, SARTA, Sacramento, CA. (keynote)

210. (a)* Weimer, Bart C. 2013. Sequencing 100K genomes for population microbiology in food safety and security. ANSES, Paris, France.

209. (b)* Arabyan, Narine, Dayoung Park, Nguyet Kong, Cynthia Williams, Carlito Lebrilla, and Bart C. Weimer. 2013. Glycan digestion during Salmonella enterica spp. enterica sv Typhimurium infection. Salmonella, ASM meeting, Boston, MA.

208. (b)* Chen, Poyin, Nguyet Kong, and Bart C. Weimer. 2013. Inhibitory Effects of Lipids on Salmonella Association with the Gastrointestinal Barrier. Salmonella, ASM meeting, Boston, MA.

207. (a)* Weimer, Bart C. 2013. Sequencing 100K genomes for population microbiology in food safety and security. Nestle, Lausanne, Switzerland.

206. (a)* Weimer, Bart C. 2013. Microbiomes, microbe and epigenomes in sulfur metabolism. Agilent Technologies, Santa Clara, CA.

205. (a)* Weimer, Bart C. 2013. Microbiomes and microbe databases for plant breeding. Seed Central, Davis, CA.

204. (a)* Weimer, Bart C. and Qiaoning Guan. 2013. The success of BGI@UCDavis. SARTA, MedStart mixer, Sacramento, CA. (invited keynote)

203. (a)* Weimer, Bart C. 2013. Sequencing 100K genomes for population microbiology. Pacific Biosciences user meeting. Palo Alto, CA. (invited keynote)

202. (a)* Chen, Poyin, Nguyet Kong, Richard Jeannotte, Hamza Fakhri, Tyson Clark, Ellen Paxinos, Meredith Ashby, Jonas Korlach, Luke Hickey, Cheryl Tarr, and Bart C. Weimer. 2013. Application of Next Generation Sequencing for the Identification of Listeria monocytogenes Predictive Genome Features and the Epigenome. ICGAmerica 2013, Sacramento, CA.

201. (a)* Thao, Kao Nguyet Kong, Carol Huang, Whitney Ng, Soraya Foutouhi, Poyin Chen, Yi Xie, Narine Arabyan, and Bart C. Weimer. 2013. Food Safety and Security: The 100K Pathogen Genome Project. ICGAmerica 2013, Sacramento, CA.

200. (a)* Arabyan, Narine and Bart C. Weimer. 2013. Insights into evolution and diversity of sialidases. ICGAmerica 2013, Sacramento, CA.

199. (a)* Weimer, Bart C. 2013. Sequencing 100K genomes for public health. GMI6. Davis, CA. (invited keynote)

198. (a)* Weimer, Bart C. 2013. 100K Foodborne Pathogen Genome Project and food safety. International Association for Food Protection, Charlotte, SC. (invited keynote)


38

197. (b)* Kelly, Lenore, Paul Zavitsanos and Bart C. Weimer. 2013. 100K Foodborne Pathogen Genome Project and food safety. International Association for Food Protection, Charlotte, SC.

196. (b)* Richard Jeannotte and Bart C. Weimer. 2013. Bioactive characterization of the microbiome associated with crops. N2 Genetics, Napa Valley, CA.

195. (a)* Weimer, Bart C. 2013. Molecular genomics and food safety: the 100K genome project. 8th Annual Sequencing, finishing, analysis in future. Santa Fe, NM

194. (b) Desai, Prerak T., Steffen Porwollik, Fred Long, Pui Cheng, Sandra W. Clifton, Aye Wollam, George M. Weinstock, Michael McClelland, Jonathan Frye, Mathew Mikoleit, Bart C. Weimer, Donald Guiney, Ohad Gal-Mor, Wolfgang Rabsch, Jean Guard, Patricia Fields. 2013. Taxonomic structure of Salmonella enterica subspecies enterica. American Society for Microbiology annual meeting. Denver, CO.

193. (a)* Weimer, Bart C. 2013. Epigenomics in microbial genomes and pathogenicity. American Society for Microbiology, Microbial genomics workshop sponsored by Pacific Biosciences, American Society for Microbiology annual meeting, Denver, CO. (keynote)

192. (a)* Weimer, Bart C. 2013. Optical mapping in pathogen genomes. American Society for Microbiology, Microbial genomics workshop sponsored by OpGen, Inc. at American Society for Microbiology annual meeting, Denver, CO. (keynote)

191. (a)* Weimer, Bart C. 2013. Using microbial genomes in molecular food safety. American Society for Microbiology annual meeting, Denver, CO.

190. (a)* Doherty, Matthew K., Prerak Desai, Leslie Woods, Mai Lee Yang, Janneth Pinzon, Nguyet Dao, and Bart C. Weimer. 2013. Vancomycin and aptamer to Staphylococcus aureus are synergistic in vivo. American Society for Microbiology annual meeting. Denver, CO.

189. (a)* Weimer, Bart C. 2013. Genomics in molecular food safety: The 100K pathogen genome project. Genomics in Agriculture and Food, Davis, CA (invitation only meeting).

188. (a)* Weimer, Bart C. 2013. Increasing research and graduate education connections. School of Veterinary Medicine, UC Davis, CA.

187. (a)* Weimer, Bart C. 2013. Using microbial genomics in rapid bacterial detection. Gojo International, Akron, OH.

186. (a)* Weimer, Bart C. 2013. Microbial genomics in molecular food safety. Sigma-Aldrich Corp. St. Louis, MO.

185. (a)* Weimer, Bart C. 2013. Molecular food safety in outbreak detection. National Livestock Association, Louisville, KY.

184. (a)* Weimer, Bart C. 2013. Microbial genomics in molecular food safety: the 100K genome project. Pittcon, Philadelphia, PA. (keynote)

183. (a)* Weimer, Bart C. 2013. Molecular food safety – the 100K pathogen genome project. University of Georgia, Food safety consortium, Atlanta, GA. (keynote)

182. (b)* Weimer, Bart C., Kao Thao, Winnie Ng, Nyuet Dao. 2013. Large-scale bacterial genomics – the 100K pathogen genome project and its implications for pathogenomics. NCGR annual conference, Santa Fe, NM.

181. (a)** Kelly, Lenore, Paul Zavitsanos and Bart C. Weimer. 2013. 100K Foodborne Pathogen Genome Project and food safety. Agilent Labs Annual Research Conference, Santa Clara, CA.

180. (a)* Weimer, Bart C. 2013. Molecular food safety in outbreak detection in poultry products. Pacific Egg and Poultry Association, Monterey, CA.

179. (a)** Korlach, Jonas, Marc Allard, Bart C. Weimer. 2013. Automated, Non-Hybrid De Novo Genome Assemblies and Epigenomes of Bacterial Pathogen. Advances in Genome Biology & Technology. Marco Island, FL.


39

178. (a)* Weimer, Bart C. 2013. Genomics to empower pathogen detection in food. Mars, Inc. Rapid Bacterial Detection Symposium, Davis, CA (invitation only meeting).

177. (a)* Weimer, Bart C. 2013. Rapid capture and concentration of large-scale complex matrices for pathogen detection. Mars Rapid Bacterial Detection Symposium, Davis, CA (invitation only meeting). (keynote)

176. (a)* Weimer, Bart C. 2013. Molecular food safety: The 100K pathogen genome project. USDA/ARS/FSIS annual conference. Washington, DC (invitation only meeting).

[(a)=invited, (b)=submitted, *=supervising author; **=co-supervising author] 175. (a)* Weimer, Bart C. 2012. Microbial genomics – can you have too many genomes? NIH

training grant in biotechnology, UC Davis Biotechnology Program. 174. (a)* Weimer, Bart C. 2012. Molecular food safety and international trade. University of Jinin

delegation to UC Davis. 173. (a)* Weimer, Bart C. 2012. Molecular food safety: The 100K genome project. ICMSF – China

International Conference on Food Safety, Xiamen, China 172. (a)* Weimer, Bart C. 2012. Rapid detection of pathogens in the food supply during outbreaks.

ICMSF – China International Conference on Food Safety, Xiamen, China 171. (a)* Weimer, Bart C. 2012. BGI@UCDavis - Genomic partnerships. Departmental seminar,

Biochemistry & Molecular Biology, UC Davis School of Medicine. 170. (a)* Weimer, Bart C. 2012. Integration of multi-omics data sets. West Coast Metabolomics

Center Opening Symposium, Davis, CA. 169. (a)* Weimer, Bart C. 2012. Molecular food safety: The 100K genome project. National Center

for Food Protection and Defense, Webinar. 168. (a)* Weimer, Bart C. 2012. Bacterial Epigenetics. Thought Leader Invitational Lecture. Agilent

Technologies, Inc. Santa Clara, CA. (invited keynote) 167. (a)* Weimer, Bart C. 2012. Progress in the 100K pathogen genome project. Global Workshop

to Build a Genomic Molecular Epidemiology Network. Washington DC. Invitation attendance only. (invited keynote)

166. (a)* Weimer, Bart C. 2012. The 100K pathogen genome project. Mars, Inc. 165. (a)* Weimer, Bart C. 2012. Microbiome and biosecurity. DARPA site visit, Davis, CA. 164. (a)* Kelly, Lenore, Paul Zavitsanos and Bart C. Weimer. 2012. 100K Foodborne Pathogen

Genome Project. Agilent Labs Annual Research Conference. 163. (a)* Weimer, Bart C. 2012. BGI@UCDavis - Genomic partnerships. Departmental seminar,

Medical Microbiology, UC Davis. 162. (a)* Weimer, Bart C. 2012. BGI@UCDavis - Genomic partnerships. STAR invited keynote

speaker 161. (a)* Weimer, Bart C. 2012. BGI@UCDavis - Genomic partnerships. CSUPERB Faculty

Consensus Group, Long Beach, CA 160. (a)* Weimer, Bart C. 2012. BGI@UCDavis - Genomic partnerships. UC Technology

Innovation Roundtable, Burlingame, CA. 159. (a)* Weimer, Bart C. 2012. BGI@UCDavis Progress. UC Davis campus (Davis and

Sacramento). 158. (a)* Weimer, Bart C. 2012. 100K Pathogen Genome Project – foodborne viruses are welcome.

Netherlands National Virology Reference Laboratory, Bilthoven, Netherlands. 157. (a)* Weimer, Bart C. 2012. Bacterial detection in the ‘-omics’ era. Technical University of

Denmark (DTU), Lyngby, Denmark.


40

156. (a)* Weimer, Bart C. 2012. Foodborne pathogen genomics and detection. Delaware BIO Association, Wilmington, DE. (invited keynote)

155. (a)* Weimer, Bart C. 2012. 100K Pathogen Genome Project, CDC – Zoonotic disease and public health branch. Washington, DC. (invited keynote)

154. (a)* Weimer, Bart C. 2012. 100K Pathogen Genome Project – Expansion is welcome. FDA (CFSAN) - invitation only meeting, Washington DC. (invited keynote)

153. (a)* Forquin-Gomez, Marie-Pierre, Richard Jeannotte, Nguyet Dao, Yi Xie, Bart C. Weimer. 2012. Stress response of Brevibacterium aurantiacum. American Society for Microbiology annual meeting, San Francisco, CA.

152. (a) Heithoff, Douglas M., William R. Shimp, John K. House, Yi Xie, Bart C. Weimer, Robert L. Sinsheimer, and Michael J. Mahan. 2012. In vivo screen for hypervirulent Salmonella strains. American Society for Microbiology annual meeting, San Francisco, CA.

151. (a)* Xie, Yi, Mai lee Yang, and Bart C. Weimer. 2012. Salmonella serotyping using multiplex PCR and nanofluidic electrophoresis. IAFP European International Conference, Warsaw, Poland.

150. (b)* Xie, Yi and Bart C. Weimer. 2012. 100K Pathogen Genome Project. IAFP European International Conference, Warsaw, Poland.

149. (a)* Xie, Yi and Bart C. Weimer. 2012. Salmonella serotyping using multiplex PCR. Food borne pathogen genomics, FDA invitation only, Washington DC.

148. (a)* Xie, Yi and Bart C. Weimer. 2012. 100K Pathogen Genome Project. Food borne pathogen genomics, FDA invitation only, Washington DC.

147. (a)* Weimer, Bart C. 2012. Pathogen detection in the genomics era. Biotechnology Breakfast, Little Falls, DE. (invited keynote)

[(a)=invited, (b)=submitted, *=supervising author; **=co-supervising author] 146. (a) Shao, M., L. B. Corbeil, B. C. Weimer, and L. J. Gershwin. 2011. Genome-wide analysis of

gene expression profile change in response to BRSV and H. somni in bovine respiratory epithelial cells. Conference of Research Workers in Animal Disease. Chicago IL.

145. (a)* Weimer, B. C. 2011. Genomics of foodborne pathogens. Agilent/FDA conference on foodborne pathogens, Davis, CA. (invited keynote)

144. (a) Ferreyra, Jessica, Bart. C. Weimer, Justin L. Sonnenburg. 2011. Mechanisms of Clostridium difficile emergence in the intestinal ecosystem. Stanford Microbiology retreat, Palo Alto, CA.

143. (a)* Forquin-Gomez, Marie-Pierre, Richard Jeannotte, Marek A. Domin, Bart C. Weimer. 2011. Metabolomics of salt stress. Western Microbial Physiology Association, Monterey, CA.

142. (a)* Weimer, B. C. 2011. The metabolic role of lactococci. 8th Cheese Symposium. Cork, Ireland. (invited keynote).

141. (a)* Weimer, B. C. 2011. Food safety and the changing world. UCOP President’s council. Oakland, CA.

140. (a)* Weimer, B. C., Shah J. D., P. T. Desai. 2011. Salmonella carriage and mitigation strategies at the farm. Poultry Federation Annual Meeting (Sacramento, CA). (invited keynote)

139. (a)* Forquin, M.-P. and B. C. Weimer. 2011. Sulfur metabolism in brevibacteria. Waltham Pet Center, Melton-Marberry, England

138. (a)* Weimer, B. C., Shah J. D., P. T. Desai, R. Gann. 2011. Abiotic stress increases host association of Salmonella enterica sv Typhimurium LT2. University of Minnesota, Minneapolis


41

137. (a)* Weimer, B. C., Shah J. D., P. T. Desai. 2011. Practical solutions to reduce Salmonella enterica Typhimurium carriage in poultry. Minnesota Turkey Growers Association, Buffalo, MN.

[(a)=invited, (b)=submitted, *=supervising author; **=co-supervising author] 136. (a)* Weimer, Bart C. 2010. Mechanisms of bacterial host association. Microbiology group,

Tahoe, CA. 135. (a)* Weimer, Bart C. 2010. Bacterial deflection and mechanisms of host association.

AgraQuest, Davis, CA. 134. (b)** Barboza, Mariana, Janneth Pinzon, J Bruce German, Bart C Weimer, Carlito B Lebrilla.

2010. N-glycans from human milk lactoferrin reduce adhesion and/or invasion of Caco-2 cells by enteropathogenic bacteria. Annual Conference of the Society for Glycobiology, St. Pete Beach, FL.

132. (a)* Weimer, Bart C. 2010. Using food grade bacteria to product flavorants. Mars, Inc., UC Davis, Davis, CA.

131. (b)** Barboza, Mariana, Janneth Pinzon, J Bruce German, Bart C Weimer, Carlito B Lebrilla. 2010. N-glycans from human milk lactoferrin reduce adhesion and/or invasion of Caco-2 cells by enteropathogenic bacteria. Glyco2010, Salt Lake City, UT.

130. (b)* Desai, Prerak, Elizabeth Maga, James Murray, Bart. C. Weimer. 2010. Effect of transgenic goat milk expressing human lysozyme on the gut ecology of pigs. Beneficial Microbes, Miami, FL.

129. (b)** Zapka, Carrie, Brad Ramsay, Elze Rackaityte, Chris Lauber, Bart Weimer, Prerak Desai, Noah Fierer, David Macinga, and Matthew W. Fields. 2010. Comparison of Methods to Evaluate Bacterial Communities of Human Hands After Alcohol-Washing. Beneficial Microbes, Miami, FL.

128. (a)* Weimer, Bart C. 2010. Functional oligosaccharides to deflect bacteria from the skin and gut. Gojo Industries, Akron, OH.

127. (a)* Weimer, Bart C. 2010. Food systems to improve gut health. Centre for Advanced Food Studies, Copenhagen, Denmark

126. (b)* Shah J. D., P. T. Desai, R. Gann, B. C. Weimer. 2010. Abiotic stress increases host association of Salmonella enterica sv Typhimurium LT2. American Society for Microbiology annual meeting, San Diego, CA.

125. (b)* Parnell, J. J., G. Rompato, J. Zhou, B.C. Weimer. 2010. Functional biogeography as evidence of gene transfer in the Great Salt Lake. American Society for Microbiology annual meeting, San Diego, CA.

124. (b)* Desai, Prerak T., Dong Chen, B. C. Weimer. 2010. Characterization of a novel Salmonella adhesin and its cognate receptor. American Society for Microbiology annual meeting, San Diego, CA.

123. (b)* Desai, Prerak T., Dong Chen, B. C. Weimer. 2010. Covalent cross-linking of whole cells to identify host-microbe receptors. American Society for Microbiology annual meeting, San Diego, CA.

122. (a)* Weimer, Bart C. 2010. Gut health and food systems. Danone Foods. UC Davis, CA. 121. (b)* Parnell, J. J., G. Rompato, P. Desai, S. Callister, D. Naftz, G. Andersen, B.C. Weimer.

2010. Diversity of lithifying microbial communities in the Great Salt Lake, Utah. ISME 2010, Seattle, WA.


42

120. (b)* Desai, Prerak T., Dong Chen, B. C. Weimer. 2010. Covalent cross-linking approach to identify host-microbe receptors. Bay Area Microbial Pathogenesis (BAMPS XIII), UC San Francisco, CA.

119. (b)* Shah J. D., P. T. Desai, R. Gann, B. C. Weimer. 2010. Abiotic stress increases host association of Salmonella enterica Typhimurium LT2. Bay Area Microbial Pathogenesis (BAMPS XIII), UC San Francisco, CA.

118. (a)* Ganesan, Balasubramanian, Bart C. Weimer, Giovanni Rompato, Janneth Pinzon, Prerak Desai, Carl Brothersen, and Donald J. McMahon. 2010. Addition of probiotic bacteria modifies the biodiversity of other lactic acid bacteria in Cheddar cheese. American Dairy Science Association annual meeting, Denver, CO.

117. (b)* Weimer. B. C., Prerak T. Desai, Dong Chen. 2010. Covalent cross-linking of whole cells to identify host-microbe receptors. American Society for Microbiology Annual meeting, San Diego, CA.

116. (b)* Desai, Prerak T., Dong Chen, B. C. Weimer. 2010. Characterization of a novel Salmonella adhesin and its cognate host receptors. American Society for Microbiology Annual meeting, San Diego, CA.

115. (b)* Shah, JD, P. Desai, R. Gann, B. C. Weimer. 2010. Abiotic stress increases survival and host association of Salmonella enterica Typhimurium LT2. American Society for Microbiology Annual meeting, San Diego, CA.

114. (a)** Barboza, Mariana, John W. Froehlich, Janneth Pinzon, Isabelle Moeller, J. Bruce German, B. C. Weimer, Carlito Lebrilla. 2010. Monitoring quantitative changes in protein specific glycosylation during lactation using MALDI-FTICR MS and its effect on interactions with pathogenic bacteria. 58th ASMS Conference on Mass Spectrometry.

113. (a)* Weimer. B. C. 2010. Food safety and microbe detection. Agilent Technologies. (Santa Clara, CA).

112. (a)* Weimer. B. C., P. Desai, J. Shah, R. Gann, J. Pinzon. 2010. Salmonella interactions vary with cellular stress and probiotic microbes. UC Davis, Food Science seminar series. (Davis, CA).

111. (a)* Weimer. B. C., P. Desai, J. Shah, R. Gann, J. Pinzon. 2010. Host microbe interactions modulated by cellular stress and probiotic microbes. Alltech, Inc. (Lexington, KY).

[(a)=invited, (b)=submitted, *=supervising author] 110. (b) Wende, A., B. O’Neill, H. Bugger, D. Chen, B.C. Weimer, E.D. Abel. 2009. Akt impairs

myocardial mitochondrial function by FOXO1 mediated regulation of OXPHOS. American Heart Association Annual Meeting (Orlando, FL. USA).

109. (a)* Weimer. B. C., C. Lebrilla, and B. German. 2009. Systems biology in health and infection. Agilent Technologies, Santa Clara, CA.

108. (a)* Weimer. B. C. 2009. Microbes and the new egg rule – detecting microbes in poultry. Poultry Health Symposium. Ontario, CA.

107. (a)* Weimer. B. C. 2009. Microbes and the new egg rule – detecting microbes in poultry. Poultry Health Symposium. Modesto, CA.

106. (a)* Shah, J. and B. C. Weimer. 2009. Abiotic stress increases survival and adherence of Salmonella enterica sv. Typhimurium. Microbiology Retreat, UC Davis.

105. (b)* Desai, P., D. Chen, and B. C. Weimer. 2009. Validation of chemical cross-linking to identify host-microbe receptors. Microbiology Retreat, UC Davis.

104. (a)* Weimer. B. C. Microbe and host interactions. Center for Comparative Medicine. UC Davis.


43

103. (a)* Weimer. B. C. Salmonella on the horizon – What’s new. Poultry Health Symposium. Ontario, CA.

102. (b)* Parnell, J. J., G. Rompato, B. Ganesan, L. Latta, M.E. Pfrender, D. Naftz, G. Andersen, J. VanNostrand, Z. He, J. Zhou, B.C. Weimer. Phylogenetic and Functional Diversity across an Extreme Salinity Gradient. American Society for Microbiology Annual Meeting, Philadelphia.

[(a)=invited, (b)=submitted, *=supervising author] 101. (b) Sela, D., L. Lerno, R. G. LoCascio, P. Desai, D. Garrido, J. Kim, J. Chapman, J. B. German,

D. S. Rokhsar, P. M. Richarson, B. C. Weimer, C. B. Lebrilla, D. A. Mills. 2008. Human milk oligosaccharides mediate interactions between the commensal Bifidobacterium longum spp. infantis and it’s infant host. ASM Beneficial Microbes (San Diego, CA.)

100. (a)* Weimer, Bart C., P. Desai, M. Walsh B. Taylor, and G. Rompato. 2008. Real time detection of microbes to improve food safety. International Food Safety Conference, Beijing, China.

99. (a)* Weimer, Bart C. 2008. Biotechnology in China. Utah State University Board of Trustees (Logan).

98. (b)* Rajan, Sweta, Balasubramanian Ganesan, and Bart C. Weimer. 2008. Metabolic influence inserting synthetic glutamate dehydrogenase (gdh) gene into Lactococcus lactis ssp. cremoris SK11. LAB9 (The Netherlands).

97. (b)* Ganesan, Balasubramanian, Jon L. Pearson, Jake Michaelson, and Bart C. Weimer. 2008. CIBCyc: Metabolic reconstructions and orthologs of lactic acid bacteria. LAB9 (The Netherlands).

96. (b)* Ganesan, Balasubramanian, Prerak Desai, Tomas Garcia-Cayuela, and Bart C. Weimer. 2008. Gene expression and comparative genomics of lactococci reveal extensive diversity between sub-species. LAB9 (The Netherlands).

95. (b)* Rompato, Giovanni, Supriyo Ghosh, Luca Pignatti, Sweta Rajan, Balasubramanian Ganesan, and Bart C. Weimer. 2008. Inorganic sulfur fixation by Brevibacterium linens. LAB9 (The Netherlands).

94. (b)* Ganesan, Balasubramanian, Supriyo Ghosh, Luca Pignatti, Sweta Rajan, Giovanni Rompato, and Bart C. Weimer. 2008. Inorganic sulfur fixation by Lactococcus lactis. LAB9 (The Netherlands)

93. (b) Bugger, Heiko, Dong Chen, Bart C. Weimer, and E. Dale Abel. 2008. Differential regulation of the cardiac mitochondrial proteome by PI3 Kinase and Akt. American Heart Association Annual Meeting (New Orleans, LA, USA).

92. (a)* Rompato, G., and B. C. Weimer. 2008. qRT-PCR detection of probiotic bacteria in cheese. Western Dairy Center Annual meeting (Logan, UT).

91. (a)* Weimer, B. C. 2008. Biotechnology in drought and pathogen survival. Northwest Agricultural and Forestry University, Xi’an China. (visiting delegation to USU).

90. (b)* Rompato, G., J. Parnell, and B. Ganesan, and B. Weimer. 2008. Microbial diversity and functional ecology of the Great Salt Lake. International Society for Microbial Ecology (Cairns, Australia).

89. (b)* Parnell, J., G. Rompato, J. Norton, and B. Weimer. 2008. Ammonia-oxidizing microorganisms in the Great Salt Lake, Utah. International Society for Microbial Ecology (Cairns, Australia).


44

88. (a)* Parnell, J., B. Ganesan, G. Rompato, and B. Weimer. 2008. Surveying the metabolic diversity of the Great Salt Lake. 2008. International Conference on Salt Lake Research, International Society for Salt Lake Research (Salt Lake City, UT, USA).

87. (a)* Rompato, G., J. Parnell, and B. Ganesan, and B. Weimer. 2008. Microbial diversity and functional ecology of the Great Salt Lake. International Conference on Salt Lake Research, International Society for Salt Lake Research (Salt Lake City, UT, USA).

86. (a)* Weimer, B. Parnell, J., G. Rompato, and B. Ganesan, and. 2008. Mercury and sulfur cycling in the Great Salt Lake. International Conference on Salt Lake Research, International Society for Salt Lake Research (Salt Lake City, UT, USA).

85. (a)* Parnell, J., G. Rompato, B. Ganesan, and B. Weimer. 2008. Evidence of autotrophic ammonia oxidation in the hypersaline North Arm of the Great Salt Lake. International Conference on Salt Lake Research, International Society for Salt Lake Research (Salt Lake City, UT, USA).

84. (b)* Parnell, J. , G. Rompato, J. Van Nostrand, Z. He, M. Pfrender, J. Zhou, B. Weimer. 2008. Microbial assessment of mercury and methylmercury toxicity in the Great Salt Lake. Annual American Society for Microbiology (Boston, MA, USA).

83. (b)* Rompato, G., J. Parnell, B. Ganesan, and B. Weimer. 2008. Microbial diversity and functional ecology of the Great Salt Lake. Annual American Society for Microbiology (Boston, MA, USA).

82. (b)* Shah, J. D., D. Chen, J. R. Stevens, B. C. Weimer. 2008. Proteomics of Salmonella typhimurium LT2 in response to cold stress. Annual American Society for Microbiology (Boston, MA, USA).

81. (b) Stevens, John R., Bala Ganesan, Sweta Rao, and Bart C. Weimer. 2008. Statistical Issues in the Normalization of Multi-Species Microarray Data. Kansas State University Conference on Applied Statistics in Agriculture (Norman, KS, USA).

80. (a)* Weimer. B. C. 2008. Natural products as antimicrobial agents. Xiamen University, College of Life Sciences (Xiamen, Fujian, PRC).

79. (a)* Weimer. B. C. 2008. Internationalization of life sciences. Kaasetsart University, College of Life Sciences. (Bangkok, Thailand).

78. (a)* Weimer. B. C. 2008. Internationalization of life sciences. Hanoi University, College of Life Sciences. (Hanoi, Vietnam).

77. (a)* Weimer. B. C. 2008. Pathogen survival in extreme environments. TessArae, LLC. (Washington, DC).

[(a)=invited, (b)=submitted, *=supervising author] 76. (a)* Weimer, B. C. 2007. Genomics of food safety. University of California, Davis. School of

Veterinary Medicine. 75. (a)* Weimer, B. C. and B. Ganesan. 2007. Bacterial starvation and non-culturability. University

of California, San Diego. 74. (a)* Weimer, B. C. and P. Deasi. 2007. Natural products as antimicrobial agents. Danisco

Company, St. Louis, MO., USA 73. (a)* Weimer, B. C. 2007. Food defense strategies. University of Maryland, JFSAN Center.

College Park, Maryland. 72. (a)* Weimer, B. C. and B. Ganesan. 2007. Homeland security of food and the environment.

Homeland Security and Defense Education Western Conference. Utah Valley State University, Provo, UT.


45

71. (a)* Desai, P., M.K. Walsh, and B. C. Weimer. 2007. Bacterial adhesion to ECM components. Gordon Research Conference - Microbial Adhesion and Signal Transduction, Newport, RI.

70. (a)* Weimer, B. C. 2007. Impact of functional genomics in food safety and security – an overview of the “–omics” tools and their application. International Association for Food Protection Annual meeting. Orlando, FL.

69. (a)* Weimer, B. C. and Bala Ganesan. 2007. Nutrient starvation and nonculturability in bacteria. 1st Intermountain Systems Biology Symposium. Logan, UT.

68. (b)* P. Desai, M.K. Walsh, B. C. Weimer. 2007. Capture and detection of bacteria using gangliosides and real time PCR. 1st Intermountain Systems Biology Symposium. Logan, UT.

67. (b)* P. Desai, Patricia Champine, B. C. Weimer. 2007. Antimicrobial activity and transcriptional profile of Listeria monocytogenes in response to inhibition by syringopeptin 25A and rhamnolipids. 1st Intermountain Systems Biology Symposium, Logan, UT.

66. (b)* S. Rajan, B. Ganesan, and B. C. Weimer. 2007. Metabolic influences of inserting synthetic glutamate dehydrogenase (gdh) gene into Lactococcus lactis spp. cremoris SK11. 1st Intermountain Systems Biology Symposium. Logan, UT.

65. (b)* Dhanasekaran, R., J. L. Pearson, B. Ganesan, and B. C. Weimer. 2007. From masses to pathways: CIB-USU Metabolome Searcher. 1st Intermountain Systems Biology Symposium, Logan, UT.

64. (b)* Ganesan, B., M. Signs, T.J. Sorenson, J. J. Michaelson, D. Chen, and B. C. Weimer. 2007. Alternate pathways for metabolism of n-butanol to n-butyric acid by Saccharomyces cerevisiae. 1st Intermountain Systems Biology Symposium, Logan, UT.

63. (b)* Ganesan, B., J. L. Pearson, J. J. Michaelson, D. Chen, R. Dhanasekaran, and B. C. Weimer. Metabolic reconstruction plug-ins to build pathways and networks from the Lactococcus lactis ssp. cremoris SK11 genome using Pathway Tools. 1st Intermountain Systems Biology Symposium, Logan, UT.

62. (a)* Weimer, B. C. 2007. Gene expression in microbial systems to link growth and metabolism. Affymetrix Webinar, March 8, 48 participates world-wide.

61. (a)* Dubai, A., R. Gann, G. Rompato, B. C. Weimer. 2007. Microbial diversity in the Great Salt Lake. Utah Conference on Undergraduate Research, Salt Lake City.

60. (a)* Dubai, A., R. Gann, G. Rompato, B. C. Weimer. 2007. Microbial diversity in the Great Salt Lake. Posters on the Hill, Salt Lake City.

59. (a)* Weimer, B. C. 2007. Bacterial response to carbohydrate starvation. Biotechnology seminar series, Utah State University, Logan.

58. (a)* Weimer, Bart, Dong Chen, and Bala Ganesan. 2007. Functional genomics – an integrated approach. Northwest Agricultural and Forestry University, Xi’an China.

57. (b)* Gann, R., A. Dubey, G. Rompato, Bart Weimer. 2007. Microbial biodiversity of Great Salt Lake. INRA Bioremediation and Bioinformatics Conference, Logan, UT.

56. (b)* Chen, Dong, Bart Weimer, Lan-Szu Chou, Yi Xie, Bala Ganesan. 2007. Proteomic shift to arginine metabolism during carbon starvation in Lactococcus lactis. American Society for Mass Spectrometry Annual Conference.

55.(b)* Desai, Prerak, Patti Champine and Bart C. Weimer. 2007. Antimicrobial activity and transcriptional profile of Listeria monocytogenes in response to inhibition by syringopeptin 25A and rhamnolipids. American Society for Microbiology Annual Conference.

54. (b)* Ganesan, Bala, Mark Signs, Tony Sorenson, Jake Michaelson, Dong Chen & Bart C. Weimer 2007. Adaptation mechanisms during persistent alkaline stress in Saccharomyces cerevisiae. 2nd American Society for Microbiology Conference on Integrating Metabolism and Genomics (IMAGE2), Montreal, CA.


46

53. (b)* Rajan, Sweta, Bala Ganesan, & Bart C. Weimer. 2007. Metabolic influence inserting synthetic glutamate dehydrogenase (gdh) gene into Lactococcus lactis ssp. cremoris SK11. 2nd American Society for Microbiology Conference on Integrating Metabolism and Genomics (IMAGE2), Montreal, CA.

52. (b)* Ganesan, Bala, Jon L. Pearson, Jake Michaelson, Dong Chen, Ranjitha Dhanasekaran & Bart C. Weimer. 2007. Metabolic reconstruction plug-ins to build pathways and networks from the Lactococcus lactis ssp. cremoris SK11 genome using Pathway Tools. 2nd American Society for Microbiology Conference on Integrating Metabolism and Genomics (IMAGE2), Montreal, CA.

51. (b)* Ganesan, Bala, Mark Signs, Tony Sorenson, Jake Michaelson, Dong Chen, and Bart C. Weimer. 2007. Alternate pathways for metabolism of n-butanol to n-butyric acid by Saccharomyces cerevisiae. 2nd American Society for Microbiology Conference on Integrating Metabolism and Genomics (IMAGE2), Montreal, CA.

50. (b)* Ganesan, Bala, Mark R. Stuart and Bart C. Weimer. 2007. Carbohydrate starvation causes a metabolically active, but nonculturable cells in Lactococcus lactis. 2nd American Society for Microbiology Conference on Integrating Metabolism and Genomics (IMAGE2), Montreal, CA.

[(a)=invited, (b)=submitted, *=supervising author] 49. (a)* Weimer, B. C. 2006. Merging bioinformatics with laboratory tools for metabolic discovery.

University of Pune (Pune, India). 48. (a)* Weimer, B. C. 2006. Attracting the best and brightest to Utah. Nanotech 2006 (University

of Utah, Salt Lake City). 47. (a) Differential Ruminal Degradation of Alfalfa Proteins. Michael D. Peel, Dong Chen, Daryll

B. DeWald, Kenneth C. Olson, and Bart Weimer. 2006. Alfalfa improvement conference. 46. (a)* Shenai, K., and B. C. Weimer. 2006. Biotechnology and nanotechnology research and

education in Utah. vSpring Capital (Salt Lake City, UT) 45. (a)* Weimer, B. C. 2006. Genomics in the food and dairy industry. 17th Biennial Cheese

Conference, Sun Valley, ID. 44. (a)* Weimer, B. C. 2006. Gene expression and metabolic predictions. Gene Expression and

Microarray Analysis, Logan, UT. 43. (a)* Weimer, B. C. 2006. Microbial genome sequencing and gene expression. Gene Expression

and Microarray Analysis, Logan, UT. 42. (b) Bensaci, M., P. Desai, B. C. Weimer, J. Takemoto. 2006. Antibacterial Activities,

Mechanisms of Action, and Toxicity Studies of Syringopeptin SP25A Produced by Pseudomonas Syringae. International Conference on Antimicrobial Agents and Chemotherapy, San Francisco, CA.

41. (a)* Weimer, B. C. 2006. Agricultural biotechnology and the food supply – biosafety concerns. Utah Film Institute. Salt Lake City, UT.

40. (a)* Weimer, B. C., B. Ganesan, J. Pederson, J. Mickelson, D. Chen. 2006. Mapping the metabolome on to Pathway Tools databases. SRI International, Menlo Park, CA.

39. (a)* Weimer. B. C. 2006. Use of genomics in biosafety. 1st Annual Biosafety conference. Instituto de Innovaction en Biotechnolgia e Industria (IIBI), Santo Domingo, Dominican Republic.

38. (a)* Weimer. B. C. 2006. Understanding cellular metabolism with functional genomics. Xiamen University, College of Life Sciences, Xiamen, PRC.


47

37. (a)* Weimer. B. C. 2006. Use of genomics and metabolomics to understand cellular metabolism. Chinese Academy of Science, Soil Institute, Nanjing, PRC.

36. (a)* Weimer. B. C., Mickelson, J., J. Pearson, D. Chen, B. Ganesan. 2006. Metabolomic plug-ins for Pathway Tools. SRI International, Pathway Tools User Group, Palo Alto, CA.

35. (b)* Ganesan, B., M. Signs, C. Brothersen D. Chen, and B. C. Weimer. 2006. Functional genomics of redox potential-mediated growth of Lactococcus lactis ssp. cremoris SK11. FoodMicro 2006, Bologna, Italy.

34. (b)* Ganesan, B., M. Signs, C. Brothersen D. Chen, and B. C. Weimer. 2006. Alternate pathways for metabolism of n-butanol to n-butyric acid by Saccharomyces cerevisiae. FoodMicro 2006, Bologna, Italy.

33. (b)* Ganesan, B. and B. C. Weimer. 2006. Catabolism of branched chain amino acids to branched chain fatty acids in Lactococcus lactis is initiated in sugar starvation and persists in nonculturability. FoodMicro 2006, Bologna, Italy.

32. (b)* Ganesan, B. M. Stuart, and B. C. Weimer. 2006. Carbohydrate starvation leads to a nonculturable but metabolically active state in Lactococcus lactis. FoodMicro 2006, Bologna, Italy.

31. (b)* Ganesan, B. and B. C. Weimer. 2006. Gene expression of biosynthetic pathways during carbohydrate starvation and nonculturability in Lactococcus lactis ssp. lactis IL1403. FoodMicro 2006, Bologna, Italy.

30. (b)* Roa, S., S. Ghosh, D. Chen, L. Pignatti, B. Ganesan, B. C. Weimer. 2006. Metabolomics of sulfur amino acids in Lactococcus lactis and Brevibacterium linens. FoodMicro 2006, Bologna, Italy.

29. (b)* Desai, P. and B. C. Weimer. 2006. Syringopeptin 25A inhibits Listeria monocytogenes by 29. gene repression. American Society for Microbiology Intermountain Section, Provo, UT.

28. (b)* Mickelson, J., J. Pearson, D. Chen, B. Ganesan, A. Cutler, B. C. Weimer. 2006. Use of statistical analysis to integrate gene expression analysis and metabolism. Utah Undergraduate Research Posters on the Hill, State Capital, Salt Lake City.

27. (b)* Mickelson, J., J. Pearson, D. Chen, B. Ganesan, A. Cutler, B. C. Weimer. 2006. Use of statistical analysis to integrate gene expression analysis and metabolism. Utah State University Undergraduate Research Conference, Logan.

[(a)=invited, (b)=submitted, *=supervising author] 26. (b) Lili Ma, YangQuan Chen, Dong Chen and Bart Weimer. 2005. Automatic Addressing for

DNA Microarray Images, JCIS/CSI, Salt Lake City, Utah, USA. 25. (a) Pate, B.J., White, K.L., Chen, D., Aston, K.I., Sessions, B.R. and B. C. Weimer. 2005. A

Novel Approach to Identify Bovine Sperm Membrane Proteins that Interact with Receptors on the Vitelline Membrane of Bovine Oocytes. Mole. Biol. Cell 16:519.

24. (a)* Chen, D., J. Mickelson, J., Desai, P., Pearson, B. Ganesan, B. C. Weimer. 2005. Development of a Proteome Database from a Genome Sequence or ESTs for Protein Identification and in silico Predictions. ROCKY 2005, Aspen, CO.

23. (b)* Mickelson, J., J. Pearson, D. Chen, B. Ganesan, B. C. Weimer. 2005. Integrating statistical analysis of gene expression data onto metabolic pathways facilitates understanding of gene expression in the metabolic context. ROCKY 2005, Aspen, CO.

22. (a)* Weimer, B. C. 2005. Functional genomics of bacteria. Universidad Autónoma de Santo Domingo (Dominican Republic). College of Science.

21. (a)* Weimer, B. C. 2005. Lactococcal genomics for flavor production in fermented dairy products. Kraft Foods, Glenview, IL.


48

20. (a)* Weimer, B. C. B. Ganesan, D. Chen. 2005. Genomics and cheese flavor development. 8th Symposium on Lactic Acid Bacteria, The Netherlands.

19. (b) Automatic Addressing for DNA Microarray Images. 2005. Lili Ma, YangQuan Chen, Dong Chen and Bart Weimer, Joint Conference on Information Sciences, Salt Lake City, UT.

18. (a)* Weimer, B. C. 2005. Lactococcal genomics and flavor production. University of Minnesota, Microbial and Plant Genomics Center.

17. (a)* Weimer, B. C., D. DeWald, D. Chen. 2005. Functional genomics in agriculture. USDA/CSREES; Washington, DC.

16. (a)* Weimer, B. C., D. DeWald, D. Chen. 2005. Agricultural biotechnology. Xiamen University, Xiamen, China.

15. (a)* Weimer, B. C., D. DeWald, D. Chen. 2005. Functional genomics of alfalfa. Northwest Agricultural & Forestry University, Xi’an, China.

14. (a)* Weimer, B. C., D. DeWald, D. Chen. 2005. Functional Genomics in Agricultural biotechnology. Hong Kong University of Science and Technology.

13. (a)* Weimer, B. C., D. DeWald, D. Chen. 2005. Agricultural biotechnology. Ministry of Science and Technology, Beijing, China.

12. (a)* Weimer, B. C., D. DeWald, D. Chen. 2005. Agricultural biotechnology. Ministry of Agriculture, Beijing, China.

11. (a)* Weimer, B. C., D. DeWald, D. Chen. 2005. Functional Genomics in Agricultural biotechnology. Nanjing Normal University. Nanjing, China.

10. (b)* Weimer, B. C., D. Chen, B. Ganesan, and Y. Xie. 2005. The proteomics of arginine utilization. 8th Symposium on Lactic Acid Bacteria, The Netherlands.

9. (b)* Weimer, B. C., L. McKay, K. Baldwin, B. Ganesan, Y. Xie, and D. Chen. 2005. The genome of Lactococcus lactis ssp. cremoris SK11. 8th Symposium on Lactic Acid Bacteria, The Netherlands.

8. (b)* Weimer, B. C., Y. Xie, B. Ganesan, and D. Chen. 2005. The genome of Brevibacterium linens ATCC 9174. 8th Symposium on Lactic Acid Bacteria, The Netherlands.

7. (b)* Weimer, B. C., and Y. Xie. 2005. Gene expression during nitrogen starvation in Lactococcus lactis ssp. lactis IL1403. 8th Symposium on Lactic Acid Bacteria, The Netherlands.

6. (b)* Weimer, B. C., S. Ghosh, D. Chen, and L. Pignatti. 2005. Metabolomics of sulfur amino acids in Lactococcus lactis and Brevibacterium linens. 8th Symposium on Lactic Acid Bacteria, The Netherlands.

5. (b)* Weimer, B. C., and B. Ganesan. 2005. Gene expression of biosynthetic pathways during carbohydrate starvation and non-culturability in Lactococcus lactis ssp. lactis IL1403. 8th Symposium on Lactic Acid Bacteria, The Netherlands.

4. (b)* Weimer, B. C., and B. Ganesan. 2005. Gene expression during the catabolism of branched chain amino acids and a-keto acids to branched chain fatty acids in Lactococcus lactis. 8th Symposium on Lactic Acid Bacteria, The Netherlands.

3. (b)* Weimer, B. C., and B. Ganesan. 2005. Catabolism of leucine to 2-methylbutyric acid by Lactococcus lactis: a possible pathway and its gene expression profile. 8th Symposium on Lactic Acid Bacteria, The Netherlands.

2. (b)* Weimer, B. C., B. Ganesan, and M. Stuart. 2005. Carbohydrate starvation leads to non-culturable but metabolically active state in Lactococcus lactis. 8th Symposium on Lactic Acid Bacteria, The Netherlands.

1. (b)* Weimer, B. C., and B. Ganesan. 2005. Comparative genomic hybridization of starter and adjunct bacteria using an oligonucleotide macroarray designed for Lactococcus lactis ssp. lactis IL1403. 8th Symposium on Lactic Acid Bacteria, The Netherlands.


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• Team coordinator for corporate strategy - School of Veterinary Medicine (2015) • UC Davis faculty lead for Agilent Technologies, Inc. – 2 gifts in 2010 • SVM co-leader for Mars relationship – 3 research grants in 2010 • Director of BGI@UCDavis • Co-organizer of ICG America conference (2013) • Co-organizer of IBM systems biology conference (2014)

• Corporate research interactions:

• Danisco, Inc. • DSM • Agilent Technologies • Loxbridge, LLC • Agilent Technologies

• Mars, Inc. • Alltech • Gojo Industries • Kraft Foods, Inc. • Perkin Elmer

• Pacific Biosciences • Illumina, Inc. • cBio, LLC • Kapa Biosystems • DuPont, Inc.

• Metabosearcher – published and implemented method to conduct genome restricted mass identification from metabolomics data

• NGS pipeline for automated data processing from raw sequence deposit into the SRA at NCBI within the 100K bioproject

• Barcode tracking system for tracking 100K genome project NGS data • CIB R-GUI for Apple Cluster (http://cib-xcluster.biotec.usu.edu/). • ProCyc - metabolic reconstruction mapping for microbes based on the genome sequencing.

The interactive tool is located at http://www.usu.edu/westcent/procyc. • Custom Affymentrix Genechips (seven chips where each chip contains multiple genomes) • MS-RMA (multi-species normalization methods) used to normalize hybridization intensities

for custom gene chips with >1 genome. • Protocols for analysis of probe-level intensity normalization that for comparative genomic

hybridization.

18. Kaufman, James, Matthew A. Davis, Bart C. Weimer, Geraud Dubois. 2017. A new taxonomy. US provisional application.

17. Weimer, Bart C., and James Kaufman. 2017. A Method to Estimate Food Safety Risk based on Community Response. US provisional application.

16. Kaufman, James, Matthew A. Davis, Bart C. Weimer, Geraud Dubois. 2017. A Method and Means to Create and Maintain Accurate Databases for Pathogen Identification. US provisional application.

15. Bennett, Alan, Pablo Zamora, Bart C. Weimer, Jonathan Eisen, Richard Jeannotte, MaiLee Yang. 2015. Bacterial isolates with plant growth-promoting characteristics and uses thereof. US provisional application No. 62/237,353.


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14. Weimer, Bart C., Richard Jeannotte, Pablo Zamora, Jonathon Eisen, MaiLee Yang, Alan Bennett, Howard Shapiro. 2014. Bacterial isolates with plant growth-promoting characteristics and uses thereof. U.S. Provisional Application. Docket No. 61/951,466.

13. Bennett, Alan, Pablo Zamora, Bart C. Weimer, Jonathan Eisen. 2012. Nitrogen Fixing Corn. U.S. Patent Application No. 13/750,643.

12. Bennett, Alan, Pablo Zamora, Bart C. Weimer, Jonathan Eisen. 2012. Nitrogen Fixing Corn. U.S. Provisional Patent Application No. 61/734,658.

11. Bennett, Alan, Pablo Zamora, Bart C. Weimer, Jonathan Eisen. 2012. Nitrogen Fixing Corn. U.S. Provisional Patent Application No. 61/734,651.

10. Bennett, Alan, Bart C. Weimer, Jonathan Eisen. 2012. Nitrogen Fixing Corn. U.S. Patent Provisional Application No. 61/648,913.

9. Bennett, Alan, Bart C. Weimer, Jonathan Eisen. 2012. Nitrogen fixing corn. U.S. Patent Provisional Application No. 61/591,121.

8. Weimer, B., and P. Desai. 2010. Compositions and methods for use syringopeptin 25A and rhamnolipids. U.S. Patent pending (Application No. 20080261891). Office action approving some claims issued 01/10, but abandoned by USU.

7. Pate, B. J., K. L. White, D. Chen, and B. C. Weimer. 2007. Bovine Sperm Membrane Proteins for fertilization. U.S. Patent abandoned by USU.

6. Weimer, B., and Marie Walsh. 2007. Real time detection of bacterial antigens. U.S. Patent 7,220,596.

5. Weimer, B. 2003. Real time bacterial detection. New Zealand Patent WO 99/508172. 4. Weimer, B. 2003. Ligand-DNA composition for capture and detection of contaminants on a

solid surface. U.S. Patent 6,531,278. 3. Weimer, B. 2002. Real time bacterial detection. Australian Patent 754,077. 2. Weimer, B. 2002. Real time bacterial detection. U.S. Patent 6,399,317. 1. Weimer, B. 1999. Reconditioning antibiotic adulterated food products. U.S. Patent 5,998,222.

[(o)=Option agreement; (a)=License agreement] (a) Bennett, Alan, Bart C. Weimer, Jonathan Eisen. 2013. Nitrogen fixation in corn. N2 Genetics,

LLC (McClean, VA). (a) Weimer, B, and M. Walsh. 2000. Rapid bacterial detection. Stellar Technologies, LLC (Boise,

ID). (a) Weimer, B, and M. Walsh. 1999. Rapid bacterial detection in industrial waste. MesoSystems,

Inc. (Richland, WA). (a) Weimer, B. 1996. Rapid detection of bacteria from food. Cultor Food Science (Ardsley, NY). (a) Weimer, B, J. Broadbent, J. Steele, M. Johnson. 1994. Addition of live adjunct bacteria to

enhance cheese flavor. Invention disclosure submitted. DSM Foods/GB (Delft, The Netherlands).

(a) Weimer, B. and M. LeFevre. 1994. Maxum 2000 fermentation control software. High Summit Scientifics (Logan, UT). Used for industrial fermentation and production by 2 multi-national companies.

Weimer, B, and M. LeFevre. 1993. Maxum 2000 - software for computer controlled fermentation. Licensed to High Summit Scientifics, Logan, UT.

• ImmunoFlow™ – 2000 • GlycoBind® – 2000


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• ImmunoDNA® – 2000 • TissueTag® – 2000

• BioMatrix Solutions, LLC • AffySphere, LLC High Summit Scientifics, LLC

Citrus & Sage, LLC BioMatrix Sciences Group, LLC Black Diamond Genomics, LLC

Supplied as requested

bart c. weimer, ph.d., professor · enables fast turnaround times and improved data quality for...

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