bart c. weimer, professorweimermicrolab.org/wp-content/uploads/2016/01/weimer-cv-12216.… ·...

Bart C. Weimer, Professor

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Faculty Coordinator Corporate Relations (UC Davis; Office of Research) 2010 – 2015 This position provides leadership for the coordination of all aspects of the campus’s existing and expanding corporate relations outreach and engagement efforts. It is a 50% administrative position that reports to the Vice Chancellor of Research to manage and guide the BGI@UC Davis genome facility, which was highlighted by my role as lead negotiator with BGI to recruit this company to campus and establish a joint sequencing center. This is a central administration position that supports a robust, dynamic and successful approach to corporate relations.

Director BGI@UC Davis Genome Sequencing Center 2011 – 2015

This administrative position reports to the Vice Chancellor of Research to provide strategic direction for the production scale genome sequencing center. As the founding co-director I facilitate large scale sequencing genomics projects between BGI, the world’s largest genomics company, and UC Davis faculty. This includes oversight of building the facility, installation of the instrumentation, and initiation of services. I initiated a seed grant program that provided $1 million in funding to expand genomics at UC Davis.

Co-founder Molecular Food Safety Consortium 2014 – present

Developed this consortium to study the food safety/environment/microbiology interface using genomic tools. This big data/genomics consortium was co-founded by Mars, Co., IBM, and my lab to integrate multi-omics tools that solve complex problems in food safety. The data handling challenges coupled with modeling is being examined to solve this world-wide problem.

Director 100K Pathogen Genome Sequencing Project 2012 – present

I directly oversee the process of sequencing 100,000 zoonotic pathogen genomes commonly found in food, livestock, wildlife, and the environment. An executive committee and steering committee of federal agencies and industrial partners oversee the consortium, which is approaching 20 members from around the world, to guide priorities and funding. Coordination of this consortium is done completely with in my research group in Davis. Expansion to create the 100K-China program was done in 2014 in cooperation with Beijing City.

Director Genomics Integration Core, West Coast Metabolomics Center (Davis) 2012 – 2013

This is an oversight position that reports to NIH-funded center director. The center is focused on creating new methods for metabolomic analysis from complex sample types. I directed integration of multi-omics data for analysis and visualization.

Bart C. Weimer, Ph.D., Professor

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Executive Director Center for Integrated BioSystems (Utah State University) 2002 – 2009 This is an academic leadership position that oversees core biotechnology services, research, and training programs with 25 employees. In this position I manage instructional programs, scheduling and staffing of the core service facility, a diverse research program, provide strategy for developing new training programs, the Center budget, and champion the international development of biotechnology. This also includes management of a university-wide competitive seed grant program focused on graduate and undergraduate student research.

• Increased the Center budget ~550% in 5 years • Initiated a complete research program in life sciences with 15 projects in 2002 that has

since narrowed to natural products discovery and mechanisms of cell biology • Initiated an undergraduate research experience & internship program • Initiated focus on grantsmanship resulting in 24 grant submissions in 2005, 34 in

2006, and 45 in 2007 with a 25-35% success rate in winning grants submitted • Developed a communications strategy that uses a new brochure and redesigned web

site to describe the Center • Initiated an e-commerce program for service laboratory client payment • Doubled revenue in the core services • Tripled the training program offerings – bioinformatics, gene expression, proteomics • Established an Affymetrix core facility • Established core service facilities protein expression and metabolomics for high

through-put data production • Established core service facilities for bioinformatics and metabolomics to support

faculty and high through-put tools • Established an international focus for research & training programs (India, China,

Dominican Republic, Thailand) • Initiated collaborative research agreements in China, Australia, Dominican Republic,

India • Established a biotechnology training program between USU and the Dominican

Ministry of Education • Established a joint biotechnology research center at Xiamen University (China) to

merge life sciences and natural products • Established and signed research agreements between USU and two Chinese

universities to facilitate student and faculty exchange

Co-founder Lactic Acid Bacteria Genome Consortium 2000 This is an academic leadership position that led to sequencing the genome of 12 bacteria associated with food. An additional four organisms are being sequenced.

• Won a competitive award to sequence 12 bacterial genomes (DoE) to coordinate seven US research institutions to complete the genome sequence of each organism

• Collaborated with Affymetrix to produce 7 custom gene expression arrays for bacterial applications

• Co-PI for re-sequencing of Lactococcus with Food Science Australia


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Director Center for Microbe Detection & Physiology (Utah State University) 1998 – 2008 This is an academic leadership position that oversees research designed to exploit microbial physiology for detection and metabolic engineering purposes. Managed staffing of 25 scientists, budget, & technology transfer program resulting from research discoveries in microbial detection.

• 6 patents awarded • Initiated 3 start-up companies • Managed industrial collaborations resulting in ~$1 million in funding • Graduated from the Utah Centers of Excellence program

Professor Population Health & Reproduction (UC Davis) 2008 – present This is an academic position in the School of Veterinary Medicine that encompasses teaching and research. My research program is focused on the response of pathogenic microbes to stress - survival, culturability, and persistence – in food, animals, and the environment. My group uses systems biology of the microbiome (genome structure, gene expression regulation, and plasticity) to define mechanisms of survival and persistence of bacteria that ultimately lead to disease in humans and animals. Molecular mechanisms of bacterial infections are being investigated and determined with the goal of identifying new drug targets to reduce bacterial infection and contamination.

Professor Nutrition & Food Sciences (Utah State University) 1991 – 2008

This was an academic position with focus on graduate student training where I rose through the ranks from assistant to full professor. Microbial genomics and metabolomics were the focus of the labs research program. More than 25 students obtained advanced degrees with Dr. Weimer since 1991 in this program.

• Won & administered >50 grants totaling ~$25 million dollars. • Published more than 65 peer reviewed papers and edited 2 books • Focus is for research to describe the underlying mechanisms of the genetic and

metabolic processes for survival and metabolism of flavor compounds from amino acids during stress

Adjunct Professor School of Life Sciences; Beijing Normal University 2014 – 2019

This affiliation is based on research projects focused on microbial genomes and metagenomics. Student exchanges, advanced methods development, and joint sequencing via the 100K Pathogen Genome Project is the focus for this appointment. This affiliation is part of a larger effort between the Chinese Academy of Science (Institute of Microbiology) and BNU to coordinate microbial genome sequencing with the 100K project.

Adjunct Professor Biology (College of Life Sciences; Xiamen University) 2007 – 2010

This affiliation is based on research projects focused on the parasitic infection process and proving efficacy of bioactive natural products for anti-microbial and anti-cancer activities. Joint students are being advised and exchanged between the institutions.


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Adjunct Professor Horticulture Department (Kasetsart University, Thailand) 2008 – 2012 This is a departmental affiliation that is actively engaged in discovery of natural products. We are providing high throughput array analysis, in vitro screening methods, and mechanism of action studies. This work is focused on use of plants and microbes on plants in Asia for use in biotechnology.

Adjunct Professor Biology Department (College of Science, USU) 2003 – 2008

This departmental affiliation is supportive to the research mission of the department by investigating the fundamental biological processes in microbes and genomic evolution. Participation in teaching advanced graduate student education is expected.

Adjunct Professor Computer Science Department (College of Science, USU) 2006 – 2010

This is a departmental affiliation that is actively engaged in bioinformatics research for use with genomics and high throughput array analysis and metabolomics. This work is focused on visualization, simulation and prediction of metabolic processes, and database integration for a biowarehouse concept.

Adjunct Professor Biological Engineering (College of Engineering, USU) 2003 – 2007

This departmental affiliation is supportive to the teaching mission of the department, as well as research in merging bioengineering of microbes with genomics and metabolomics. Development of biosensors for processes mediated by bacteria in the environment is underway. Participation in teaching advanced graduate courses is expected.

• Black Diamond Genomics Founder & President 2013 – present • BioMatrix Solutions Group Founder & President 2000 – present • High Summit Scientific Founder & President 1995 – present • Citrus & Sage Founder/owner 2005 – 2008 • AuroTech, Inc. Microbiology Group Leader 1989 – 1990 • HyClone Laboratories Microbiology/immunology R&D technician 1986 – 1987 • University Medical Center Microbiology Laboratory technician 1984 – 1986

• Post Doctoral Fellow (Biochemistry/genetics) Univ. of Melbourne 1990 – 1991 • Ph.D. (Nutrition & Food Sciences - Microbiology) Utah State University 1990 • B.S. (Microbiology & Immunology) University of Arizona (Honors) 1986

• FDA Food Safety Grand Challenge Finalist (1/5 from over 100 applicants) 2015 • IBM Shared University Research Award 2015, 2016 • Agilent Thought Leader (DNA modification, genome restricted mass ID) 2010-2013 • HHSInnovate – 100K pathogen genome sequencing project 2012 • Best agronomic paper – Canadian Agronomic Society 2010 • Researcher of the Year – USU, Dept. of Nutrition & Food Sciences 2008 • Inducted into Academic Keys Who's Who in Agriculture Higher Education 2006 • Inducted into Empire Who’s Who 2003


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• Inducted into International Who’s Who Historical Society 2002 • Winder Chair in Food Science – USU, Nutrition and Food Sciences 1996, 2001 to 2004 • Researcher of the Year – USU, College of Family Life 1995, 1999 • President – Institute for Food Technology, Bonneville Section 1995 • B.S. – graduated with Honors 1986

UC Davis institutional committees • Dean GSM Search Committee (member, invited) 2015-present • BGI@UCDavis steering committee (chair; invited) 2012-2015 • Agilent Technologies working group – member (invited) 2010-2015 • Mars, Inc. working group – co-chair (invited) 2010-2015 • N2 Genetics Steering committee member 2013 – 2014 • SVM strategic plan implementation - strategy champion (invited) 2012-2014 • SomaLogic Task Force (invited member; Vice Chancellor charge) 2014 • West Coast Metabolomics Center steering committee (invited) 2012-2013 • Big Data implementation (invited member; Provost charge) 2012-2013 • Lead negotiator for BGI initiative (invited by Chancellor) 2011-2012 • School of Veterinary Medicine, International Programs – Chair 2010-2013 • School of Veterinary Medicine, International Programs - member 2009-2010 • FUTURES committee (invited by Chancellor) 2009-2011 • PHR Departmental Resources 2009-present • Faculty recruitment committee – Chair 2010-2013 • International development committee (SVM - invited) 2009-2010 • International development committee (SVM - chair) 2010-2012 • Curriculum development – co-chair of microbiology (UCD) 2009

21 Utah State Institutional committees, including • USU research council, Scientific research & innovation visioning council 2001 to 2008

National & International Peer Review Committees • Genome Canada grant review panel – invited 2013 – present • MetaCyc advisor board member – invited 2004 – present • Homeland Security, microbe detection program review – invited 2014 • Joint Genome Institute CSP reviewer – invited 2004 – 2014 • visANT advisory board member – invited 2007–2010 • University of Nebraska (Food Science) CSREES review team member 2007 • Technologiestichting STW Technology Foundation (Netherlands) – Invited 2007 • NWO (EU) Council for Earth and Life Sciences – invited 2006 • Utah State University (ADVS) CSREES review team member – invited 2004 • Science Foundation Ireland (SFI) – invited 2003 • USDA/CSREES, Food science and nutrition SBIR program - ad hoc 2001 • Utah Coalition for Food Safety, committee member – invited 2000–2001 • Restoration of Operations (RestOps), Advanced Concept Technology

Demonstration (Dugway, UT) – invited 2000–2001 • University of Massachusetts at Amherst, Food Science department 2000


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• Dairy Management, Inc. 2000 • USDA, Integrated Research, Education, and Extension - Food Safety Initiative 2000 • Pacific Northwest National Laboratory (biowarfare detection program) 1998 • NRI/USDA food safety program national panel (FSIS) – invited 1998, 1999 • FDA food safety program ad hoc (FSIS) 1993–present • FDA food safety program, national panel – invited 1998 • Midwest food consortium (food safety review panel) – invited 1997–1998 • Dairy Research and Development, Inc. (Australia) - ad hoc 1996

Editorial positions & peer review participation • Editorial board, Virulence (member) 2015-2018 • Series Editor, Elsevier – Microbial Genomics (multiple book series) 2013-2018 • Editorial advisory board, Encyclopedia of Food Microbiology – section editor 2012-2013 • Editorial board, American Society for Microbiology (3 consecutive terms) 2004-2013 • Editorial board, Encyclopedia of Biotechnology in Agriculture & Food 2007-2014 • Editor, Woodhead/CRC Press – Metabolomics in food and health 2008-2013 • Editor, Woodhead/CRC Press – Improving the flavor of cheese 2004-2007 • Editor, Journal of Dairy Science, Dairy Foods Microbiology 2000–2001 • Reviewer, Applied & Environmental Microbiology 1991-present • Reviewer, Applied Microbiology 1991-present • Reviewer, Journal of Bacteriology 1995-present • Reviewer, Applied Microbiology and Biotechnology 2010-present • Reviewer, Journal of Dairy Science 2000-present • Reviewer, Food & Function 2015-present

• American Association for the Advancement of Science (AAAS)

• American Society for Microbiology (ASM)

• American Chemical Society (ACS)

• International Food Protection Association (IFPA)

• Institute of Food Technologists (IFT) • Metabolomics Society

Food safety & Next Generation Sequencing August, 2015 Dr. Weimer cooperated with Beijing City Science & Technology to co-host this meeting that focused on molecular food safety. Being held in Beijing the meeting noted the advanced techniques that impact daily use of food safety from the farm to the gut. Dr. Weimer conceived, initiated, and invited speakers as well as planned the sessions. IBM International Genomics Symposium – ‘Sequence the City’ May, 2014 Dr. Weimer cooperated with the IBM genomics research unit at the Almaden Institute and was the chair of the Agriculture section for the organizational committee. This is conference was focused on genomics and the computational long-term needs for the large data sets that are emerging from NGS pipelines.


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ICG-America 2013 September, 2013 Dr. Weimer was the chair of this international conference and executive chair of the organizational committee. This is the initial conference that is co-hosted by BGI and UC Davis to celebrate the BGI@UCDavis sequencing facility and new advances in genomics.

Global Microbial Identifier September, 2013 Dr. Weimer is the host and chair of the conference. This meeting was held by stakeholders interested in molecular epidemiology and food safety. The yearly global meetings are used to coordinate international activities to discuss genomics and foodborne outbreak detection and surveillance. The focus of the meeting in Davis was the 100K Pathogen Genome Project and how it will enable genomics-based outbreak investigation.

Genomics of Food Safety February, 2013 Dr. Weimer was the chair of the conference committee of this invitation only meeting. The conference is focused on how to leverage genomics for food microbiology in the 21st century to meet the expanding demands of bacterial detection.

Food Safety Progress September, 2009 Dr. Weimer initiated and co-organized an industry day on food safety and quality for the UC Davis campus (including profession schools). This activity resulted in a strategic investment by Agilent Technologies in food safety research in the veterinary diagnostic laboratory.

Great Salt Lake Research February 1, 2008 Dr. Weimer initiated this invitation only conference to discuss the research activities in the Great Salt Lake. This is anticipation to an international conference on salt lakes around the world and was based on the monthly GSL brown bag initiated by Dr. Weimer in 2006 for researchers at USU.

The 10th International Conference on Salt Lake Research (ISSLR) May 11-16, 2008 Dr. Weimer was on the organizing committee for the conference. He co-hosted a specific session on bacteria found in hypersaline environments. (http://www.biosystems.usu.edu/ISSLR.pdf)

Intermountain Systems Biology Conference June 2007 Dr. Weimer was a co-founder and member of the organizational committee. This meeting was a collaborative effort with the Inland Northwest Research Alliance.

• Molecular ecology of Salmonella • Molecular diagnostics development using

lipids, artificial cells, and genomics • Microbiome in health & disease • epigenomics in bacteria • Host/microbe association dynamics

• Bacterial metabolism in host/microbe association and infection

• Natural antibacterial compound discovery • Regulatory networks for integration of

multi-omics data and network modeling • 100K pathogen genome project


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Recent & Active Research Grants:

Agency Title

NIH • Synthesis and screening of bioactive glycolipids. 2009-2012 • Bacterial interactions with glycolipids. 2010-2014 • West Coast Comprehensive Metabolomics Core. 2012-2017

USDA/CSREES Functional genomics in nature. 2006-2010 USDA/AFRI Phylosphere of plants with E. coli O157:H7 introduction. 2010-2014 FDA/CFSAN 100K pathogen sequencing 2012-2014 UC Discovery Milk Oligosaccharides for infant gut development. 2009-2012 Cal Dairy Foundation Inhibition of pathogens with milk fat components. 2010-2011 Western Dairy Center • Ecology of cheese using probiotic microbes. 2008-2010

• Persistence of pathogens in reduced salt cheese. 2011-2013 • Survival of organisms during production of cheese. 2011-2013

DoE - Pacific Northwest National Lab & JGI

• Metaproteomics of the Great Salt Lake. 2010-2012 • Metagenomics of the Great Salt Lake. 2008-2011

DTRA, DoD Photoscrubing to kill bacteria. 2009-2010 Mars, Inc. • Nitrogen fixation in plants. 2011-2014

• 100K Pathogen Genome Project. 2012-2016 • Oral health in dogs. 2011-2013 • Rapid microbe detection. 2014-2016 • MetaRNAseq in foods. 2015-2018 • Fungal toxin removal from complex samples. 2016-2017 • Aflatoxin removal from food samples. 2016-2017

Genome Canada • A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis. 2015-2020

Agilent Technologies • DNA modification. 2010-2013 • Salmonella detection and serotyping. 2010-2014 • 100K pathogen genome sequencing project. 2012-1015

Gojo Industries skin health and metagenomics. 2015-2016 NIH/NCI Helicobacter pylori genomics and epigenome in cancer. 2015 National Marine Mammal Foundation

Respiratory disease in dolphins. 2013-2016

IBM • Molecular food safety. 2014-2016

The MOUs are in place to facilitate joint research projects. In all cases, the agreements involve student and faculty exchange. Topics include natural product discovery, bioinformatics, genome sequencing, and microbial physiology. MOUs between the 100K Pathogen Genome Project and multiple institutions were negotiated to provide a basis to enable strain exchange for genome sequencing. • 100K-China (Chinese Academy of Science, Beijing Normal University) 2014-present • 100K-Korea (Seoul National University) 2015-present • 100K-Canada (McGill University, Laval University) 2016 • 100K-Ireland (UC Dublin) 2016


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Theses in Preparation – 1 Students in Progress – 4 Students Completed - 31 Post-doctoral fellow mentorship – 16 Undergraduate students - 36

Teaching: • VET414 – Food safety for veterinarians (veterinary medicine core curriculum; course leader) • MIB200A – Genomics and microbial physiology (core curriculum for microbiology; course

leader) • PMI201 – Integrative Pathobiology (core curriculum for comparative pathology) • MMI210 - Animal Models of Infectious Disease Seminar

UC Davis Graduate group membership: UC Davis has a graduate student-training program that is based on groups that span departments and colleges. This structure is independent of departmental structure for reporting and student training. Graduate group membership is an application process that is based on area of expertise that entitles the mentor to host students and teach courses within each of the groups.

• Microbiology – course leader for core graduate course; student advisor for group

o Microbiology – founding member, Host/microbe interactions emphasis area

• Comparative Pathology

Preventive Veterinary Medicine • Food Science • Forensics • Biotechnology emphasis area faculty

mentor (NIH funded program) • Masters of Public Veterinary

Medicine (MPVM)

1989–2014 Books edited = 4; publications/chapters = 114; submitted = 23

[(a)=refereed, (b)=non-refereed, *=supervising author/editor, (c)= chapter, (i)=invited, (e)=editor, (k) = book]

(aci)* Ganesan, Balasubramanian and Bart C. Weimer. 2015. Biotechnology of flavor formation in fermented dairy products. In Biotechnology in Flavor Production, 2nd Edition. Edited by Daphna Havkin-Frenkel and Nativ Dudai. Wiley Press, Singapore.

(aieck)* Weimer, B. C. and D. S. Storey. 2015. Food Safety Genomics. Editor. Elsevier/Academic Press, London, England (in production).

(aci)* Weimer, B. C. 2015. Rapid Microbial Detection. Annual Review of Animal Biosciences. Annual Reviews, Palo Alto, CA.

(aci)* Ganesan, B. and Bart C. Weimer. 2014. Amino acid catabolism. In Cheese: Chemistry, Physics, & Microbiology 4th Edition. Edited by P.F. Fox, P.L.H. McSweeney, D.W. Everett and P. Cotter. Academic Press, Oxford (Elsevier group).


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(aci) Marie-Pierre Forquin-Gomez, Bart C. Weimer, Louis Sorieul, Jorn Kalinowski, and Tatiana Vallaeys. 2014. The family Brevibacteriaceae. In The Prokaryotes: Actinobacteria (4th Ed), pp. 141-153. Ed. Eugene Rosenberg, Edward F. DeLong, Dr. Stephen Lory, Prof. Erko Stackebrandt, Fabiano Thompson Prokaryotes. Springer, Singapore. ISBN: 978-3-642-30193-3

(aiek) Batt, C. and M. Tortorello. 2014. Ed.; Bart C. Weimer (section editor). Encyclopedia of Food Microbiology, 2nd Edition. Elsevier, London.

(aci)* Forquin, M-P and Bart C. Weimer. 2013. Brevibacteria. In Encyclopedia of Food Microbiology, 2nd Edition. Ed. C. Batt and M. Tortorello. Elsevier, London.

(aiek)* Weimer, B. C. and C. Slupsky. 2013. Metabolomics for food and health. CRC Press, Boca Raton, FL. & Woodhead Publishing Limited, Cambridge, England. (ISBN1845695127)

(aiek)* Weimer, B. C. 2013. Genomics of fermented foods. CRC Press, Boca Raton, FL. & Woodhead Publishing Limited, Cambridge, England. (In production).

(aci)* Weimer, Bart C. 2011. Stress Responses of Lactic Acid Bacteria. Springer Science & Business Media, LLC, New York.

(aci) Coolbear, Tim, Martin Wilkenson, and Bart C. Weimer. 2011. Lactic acid bacteria: LAB in flavour development. In Encyclopedia of Dairy Science, 2nd Edition, Ed. John W. Fuquay, Pat F. Fox, Paul McSweeney. Elsevier/Academic Press, London, England. ISBN: 9780123744029.

(aci)* Weimer, Bart C. 2011. Lactic acid bacteria: Physiology and stress response. In Encyclopedia of Dairy Science, 2nd Edition, Ed. John W. Fuquay, Pat F. Fox, Paul McSweeney. Elsevier/Academic Press, London, England. ISBN: 9780123744029.

(aci)* Weimer, Bart C., Giovanni Rompato, Jacob Parnell, Reed Gann, Balasubramanian Ganesan, Cristian Navas, Martin Gonzalez, Mario Clavel, Steven Albee-Scott. Microbial biodiversity of Great Salt Lake, Utah. 2009. In Saline lakes around the world: unique systems with unique values. pp.15-22. Eds. Oren, A., D. L. Naftz, and W. A. Wurtsbaugh. S. J. and Jessie E. Quinney Natural Resources Research Library, Utah State University Press, Logan. (http://www.cnr.usu.edu/quinney/htm/publications/nrei).

(aci) Oren, Aharon, Bonnie K. Baxter & Bart C. Weimer. 2009. Microbial communities in salt lakes: Phylogenetic diversity, metabolic diversity, and in situ activities. In Saline lakes around the world: unique systems with unique values. pp. 258-264. Eds. Oren, A., D. L. Naftz, and W. A. Wurtsbaugh. S. J. and Jessie E. Quinney Natural Resources Research Library, Utah State University Press, Logan. (http://www.cnr.usu.edu/quinney/htm/publications/nrei).

(aci)* Desai, P., and Weimer, B. C. 2008. Gene expression in microbial systems to link growth and metabolism. In Handbook of Research on Systems Biology Applications in Medicine, pp. 278-290, Ed. Andriani Daskalaki; IGI Global, Hershey, PA. (ISBN: 978-1-60566-076-9)


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(aeik)* Weimer, B. C. Improving the flavour of cheese. 2007. Woodhead Publishing Limited, Cambridge, England; CRC Press, Boca Raton, FL. (CRC ISBN: 978-0-8493-9158-3; Woodhead ISBN: 978-1-84569-007-6), 600 pages.

(ceai)* Ganesan, B. and B. C. Weimer. 2007. Amino acid metabolism and cheese flavour. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead Publishing Limited, Cambridge, England; CRC Press, Boca Raton, FL.

(ceai)* Ganesan, B., M. Qian, H. Burbank, and B. C. Weimer. 2007. Compounds associated with cheese flavor. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead Publishing Limited, Cambridge, England; CRC Press, Boca Raton, FL.

(ceai) Banks, Jean and B. C. Weimer. 2007. Lowfat cheese flavour. In Improving the flavour of cheese. Ed. Bart C. Woodhead Publishing Limited, Cambridge, England; CRC Press, Boca Raton, FL.

(ceai)* Weimer, B. C. 2007. Functional genomics and flavour. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead Publishing Limited, Cambridge, England; CRC Press, Boca Raton, FL.

(aci)* B. C. Weimer and B. Ganesan, S. Rajan. 2007. Biotechnology of flavor production in dairy products. In Biotechnology of Flavor Production, Ed. F. Belanger; Blackwell Publishing Ltd. (Oxford; ISBN: 9781405156493).

(aci)* Weimer, B., Y. Xie, L-S. Chou and A. Cutler. 2004. Gene expression arrays in food. In Microbial Products and Biotransformation, Ed. J.-L. Barredo. Humana Press, Totowa, NJ USA.

(aci)* Weimer, B., and B. Dias. 2004. Volatile Sulfur detection in fermented foods. In Microbial Products and Biotransformation, Ed. J.-L. Barredo. Humana Press, Totowa, NJ USA.

(aci)* Weimer, B. 1999. Brevibacteria. In Encyclopedia of Food Microbiology, Ed. R. K. Robinson et al. Academic Press, London.

(aci) Otte, J., Y. Ardö, B. Weimer, and J. Sørensen. 1998. Capillary electrophoresis used to measure proteolysis in cheese. In Analysis of Milk Proteins. International Dairy Federation Bulletin.

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)= chapter, (i)=invited, (e)=editor, (k) = book]

114. (a)* Weimer, Bart C., Dylan Bobby Storey, Christopher A. Elkins, Robert C. Baker, Peter Markwell, David Chambliss, Stefan Edlund, James H. Kaufman. 2016. Defining the food microbiome for authentication, safety, and process management. IBM Journal of Research & Development. (in press).


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(a) Hu, Yongfei, Xi Yang , Jing Li , Na Lv , Fei Liu , Jun Wu , Ivan Lin , Na Wu , Bart C. Weimer, George Gao , Yulan Liu, Baoli Zhu. 2015. Bacterial phylogeny shapes the horizontal gene transfer network of the mobile resistome under ecological constraint. (submitted).

(a)* Park, Dayoung, Narine Arabyan, Cynthia C. Williams, Ting Song, Bart C. Weimer, and Carlito B. Lebrilla. 2015. Selective Modulation of Glycans on Intestinal Epithelial Cell Surfaces by Salmonella enterica serovar Typhimurium. (submitted).

(a)* Arabyan, N., D. Park, C. Williams, R. Jeannotte, P. Desai, J. Shah, N. Kong, M. L. Yang, C. Lebrilla, and Bart C. Weimer. 2016. Glycan degradation during Salmonella enterica spp. enterica sv Typhimurium infection. (submitted).

(a) Taff, Conor C., Allison M. Weis, Chris Barker, Walter M. Boyce, Mitchell G. Hinton, Melissa Jones, Ryane Logsdon, Woutrina A. Smith, Bart C. Weimer, Sarah Wheeler, and Andrea K. Townsend 2016. Influence of host ecology and behavior on Campylobacter jejuni prevalence and environmental contamination risk in a synanthropic wild bird. (Submitted).

(a) Stevens, John R., Todd R. Jones, Michael Lefevre, Balasubramanian Ganesan, and Bart C. Weimer. 2016. SigTree: identifying and visualizing significantly responsive branches in a phylogenetic tree. (submitted)

(a)* Chen, Poyin, Henk C. den Bakker, Jonas Korlach, Meredith Ashby, Tyson Clarck, Khai Luong, R. J. Roberts, Martin Wiedmann, and Bart C. Weimer. 2016. Large chromosomal rearrangements and epigenome diversity in Listeria monocytogenes. (submitted).

(a)* Foutouhi, Soraya H., Nuradilla Mohamad-Fauzi, Dylan Storey, Azarene A. Foutouhi, Nguyet Kong, Amir Kol, Dori Borjesson, Prerak Desai, Jigna Shah, James D. Murray* and Bart C. Weimer*. 2015. Salmonella enterica ssp enterica serotype Typhimurium Enhances Osteogenic Differentiation in Adipose-Derived Mesenchymal Stem Cells. (submitted).

(a)* Storey, Dylan Bobby, Allison M. Weis, Nguyet Kong, Andrea K. Townsend, Woutrina A. Miller, Barbara A. Byrne, Connor C. Taff, Brent Gilpin, Carl Mason, Colette Fitzgerald, and Bart C. Weimer. 2015. Large-scale release of Campylobacter draft genomes; resources for food safety and public health. (submitted).

(a)* Dhanasekaran, A. Ranjitha and Bart C. Weimer. 2015. DynaFlux: a software tool to estimate the dynamic state flux of a metabolic network and to perform network analyses. (submitted).

(a)* Storey, Dylan Bobby, Narine Arabyan, Whitney Ng, Kao Thao, Poyin Chen, Nguyet Kong, Carol Huang, Soraya Fouthoui, and Bart C. Weimer. 2015 Large scale release of Salmonella draft genomes; resources for food safety and public health. (submitted)

(ai)* Parnell, J. Jacob, Giovanni Rompato, Prerak Desai, Balasubramanian Ganesan, Leigh C. Latta IV, Michael E. Pfrender, Joy D. Van Nostrand, Zhili He, Jizhong Zhou, Bart C.


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Weimer. 2015. Community assembly along salinity gradients in Great Salt Lake, Utah. (submitted)

(a)* Shah, Jigna, Prerak Desai, Darya Mishchuk, Carolyn Slupsky, and Bart C. Weimer. 2015. Dynamics of metabolism during infection of intestinal epithelial cells with cold-stressed S. Typhimurium. (submitted).

(a) Zamora, Pablo, Pierre-Marc Delaux, Don Gibson, Srijak Bhatnagar, Guillaume Jospin, Richard Jeannotte, Mai-Lee Yang, Kevin Schwartz, Jean-Michel Ane, Jonathan Eisen, Bart C. Weimer, Howard Shapiro, Alan B. Bennett. 2015. A functional diazotrophic microbiome associated with an indigenous landrace of corn. (in revision).

(a)* Parnell, J. Jacob, Giovanni Rompato, Prerak Desai, Balasubramanian Ganesan, Leigh C. Latta IV, Michael E. Pfrender, Naftz, Joy D. Van Nostrand, Zhili He, Jizhong Zhou, Bart C. Weimer. 2015. Structure and function of microbial communities along salinity gradients in Great Salt Lake, Utah. (submitted)

(a)* Doherty, Matthew K., Prerak Desai, Leslie Woods, Mai Lee Yang, Janneth Pinzon, Nguyet Dao, and Bart C. Weimer. 2015. Vancomycin and aptamer treatment in vivo are synergistic to inhibit Staphylococcus aureus. (submitted)

(a)* Ganesan, Balasubramanian, Sweta Rhajan, Bart C. Weimer. 2015. Central Role of Glutamate Dehydrogenase in Metabolism and Organic Sulfur Fixation by gdh+ Mutant in Lactococcus lactis. (submitted).

(a)* Desai, P., P. Champine, and B. C. Weimer. 2015. Gene expression profiles to define the mechanism of syrigopeptin 25A inhibition of Listeria monocytogenes. (submitted).

(a) Pate, B.J., B. C. Weimer and K. L. White. 2015. Is a soluble sperm factor involved in bovine oocyte activation? (submitted).

(a)* Dias, B., B. Ganesan, and B. C. Weimer. 2015. Detection of α−keto acids by capillary electrophoresis. (submitted).

(a)* Harrington, E. J., B. C. Weimer, and M. K. Walsh. 2015. Immobilized antibody capture of Salmonella. (submitted).

(a)* Taylor, Bradley J., Yi Xie, Bart C. Weimer, and Marie K. Walsh. 2015. Characterization of immobilized liposomes containing Escherichia coli’s mechanosensitive channel of large conductance using CLSM. (submitted).

(a)* Cheng, Zhe, Dong Chen, Jacob Michaelson, Chong Ti Tang, & Bart C. Weimer. 2015. Induction of host genes during Echinococcus multilocularis infection. (submitted). (a)* Weimer, Bart C., CE Davis, J. Pinzon, I. Pavlovsky. 2015. Substrates patterned with silver nanostructures inactivate bacteria and is enhanced with UV-light treatment.


23


113. (a) Pandey, Pramod, Mark Lejeune, Sagor Biswas, Daniel Morash, Bart C. Weimer, Glenn Young. 2015. A new method for converting foodwaste into pathogen free soil amendment for enhancing agricultural sustainability. Journal of Cleaner Production. (in press; online Sept 25, 2015).

112. (aci)* Ganesan, Balasubramanian and Bart C. Weimer. 2015. Biotechnology of flavor formation in fermented dairy products. In Biotechnology in Flavor Production, 2nd Edition. Edited by Daphna Havkin-Frenkel and Nativ Dudai. Wiley Press, Singapore. (in press)

111. (a) Lüdeke, Catharina H.M., Nguyet Kong, Bart C. Weimer, Markus Fischer, Jessica L. Jones. 2015. Complete genome sequences of a clinical and an environmental Vibrio parahaemolyticus isolate. Genome Announcements. 3(2):e00216-15. DOI: 10.1128/genomeA.00216-15. (PMID: 25814612)

110. (a)* Dhanasekaran, A. Ranjitha, Jon L. Pearson, Balasubramanian Ganesan, and Bart C. Weimer. 2015. Metabolome Searcher: A high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and metabolites. BMC Bioinformatics 16:62 (DOI: 10.1186/s12859-015-0462-y). (PMID: 25887958)

109. (a)* Desai, Prerak T., Jigna Shah, Dong Chen & Bart C. Weimer. 2015. Whole cell cross-linking to discover host-microbe protein receptor/ligand pairs. PLoSOne (in press).

108. (a) Wende, Adam R., Brian T. O'Neill, Heiko Bugger, Joseph Tuinei, Jonathan Buchanan, Pilar Caro-Martin, Aili Guo, Crystal Sloan, Bum Jun Kim, Xiaohui Wang, Renata O. Pereira, Tetsuo Shioi, Bart C. Weimer, and E. Dale Abel. 2015. Enhanced cardiac Akt/protein kinase B signaling contributes to pathological cardiac hypertrophy in part by impairing mitochondrial function via transcriptional repression of mitochondrion-targeted nuclear genes. Mol Cell Bio 35:831-46. (PMID: 25535334).

107. Worden, Natasha, Thomas E. Wilkop, Victor Esteva Esteve, Richard Jeannotte, Rahul Lathe, Samantha Vernhettes, Bart C. Weimer, Glenn Hicks, Jose Alonso, John Labavitch, Staffan Persson, David Ehrhardt, Georgia Drakakaki. 2015. CESTRIN, inhibits cellulose deposition and interferes with the trafficking of cellulose synthase complexes and their associated proteins KORRIGAN1 and POM2/CSI1. Plant Physiology 167: 381-93. (PMID: 25535279)


24


106. (a) Bua-In, S., Paisooksantivatana, Y., Weimer, B.C., Chowpongpang, S. 2014. Molecular cloning and expression levels of the monoterpene synthase gene (ZMM1) in cassumunar ginger (Zingiber montanum (Koenig) Link ex Dietr.). Archives of Biological Sciences 66:1321-1331.

105. (aci) Marie-Pierre Forquin-Gomez, Bart C. Weimer, Louis Sorieul, Jorn Kalinowski, and Tatiana Vallaeys. 2014. The family Brevibacteriaceae. In The Prokaryotes: Actinobacteria (4th Ed), pp. 141-153. Ed. Eugene Rosenberg, Edward F. DeLong, Dr. Stephen Lory, Prof. Erko Stackebrandt, Fabiano Thompson Prokaryotes. Springer, Singapore. ISBN: 978-3-642-30193-3

104. (a) Ferreyra, Jessica, Katherine Wu, Donna Bouley, Bart C. Weimer, and Justin L. Sonnenburg. 2014. Gut microbiota-produced succinate promotes Clostridum difficile infection after antibiotics or motility disturbance. Cell Host Microbe. 16(6):770-7. (PMID: 25498344).

103. (a)* Ganesan, B. and Bart C. Weimer. 2014. Amino acid catabolism. In Cheese: Chemistry, Physics & Microbiology 4th Edition. Edited by P.F. Fox, P.L.H. McSweeney, D.W. Everett and P. Cotter. Academic Press, Oxford (Elsevier group).

102. (a)* Shah, Jigna, Prerak T. Desai, & Bart C. Weimer. 2014. Genetic mechanisms underlying pathogenicity of cold-stressed Salmonella Typhimurium in cultured intestinal epithelial cells. Appl. Environ. Microbiol. 80:6943-53. (PMID: 25192993)

101. (a)* Kol, A., S. Foutouhi, N.J. Walker, N.T. Kong, B.C. Weimer*, and D.L. Borjesson*. 2014. Gastrointestinal microbes interact with canine adipose derived mesenchymal stem cells in vitro and enhance immunomodulatory functions. Stem Cells and Development 23:1831-43 (PMID: 24803072). *co-corresponding authors.

100. (ai)* Chen, Poyin, Richard Jeannotte, and Bart C. Weimer. 2014. Exploring Bacterial Epigenomics in the NGS Era—A New Approach for an Emerging Frontier. Trends in Microbiology 22:292–300. (Invited reviewed submission for -omics special issue). (PMID: 24725482)

99. (a) Deng, Xiangyu, Prerak T. Desai, Henk C. den Bakker, Matthew Mikoleit, Beth Tolar, Eija Trees, Rene S. Hendriksen, Jonathan Frye, Steffen Porwollik, Bart C. Weimer, Martin Wiedmann, George M. Weinstock, Michael McClelland, Patricia I. Fields. 2014. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. Emerging and Infectious Diseases. 20:1481-9. (PMID: 25147968)

98. (a)* Ganesan, Balasubramanian, Bart C. Weimer, Nguyet Dao, Janneth Pinzon, Giovanni Rompato, Carl Brothersen, and Donald J. McMahon. 2014. Probiotic bacteria survive in Cheddar cheese and modify populations of other lactic acid bacteria. J. Appl. Microbiol. 116:1642–1656. (co-first authorship) (PMID: 24905221).


25

[(a)=refereed, (b)=non-refereed, *=co- or supervising author, (c)= chapter, (i)=invited, (e)=editor, (k) = book]

97. (a)* He, Xuan, Darya O. Mishchuk, Jigna Shah, Bart C. Weimer, Carolyn M. Slupsky. 2013. Cross-talk between two E. coli strains and a human colorectal adenocarcinoma-derived cell line. Scientific Reports 3:3416-3426. (PMCID: PMC3849634)

96. (a)* Shah, J., Prerak Desai, Dong Chen, John Stevens, and Bart C. Weimer. 2013. Proteomics of cold stress in Salmonella enterica sv Typhimurium LT2. Appl. Environ. Microbiol. 79:7281-7289. (PMID: 24056458) (1 of 6 manuscripts selected for special highlight in this issue).95. (a) Riehle, Christian, Adam R. Wende, Sandra Sena, Karla Maria Pires, Renata Pereira-Alambert, Yi Zhu, Heiko Bugger, Deborah Frank, Jack Bevins, Dong Chen, Cynthia N. Perry-Garza, Xiaocheng Dong, Steven Valdez, Xiaoming Sheng, Bart C. Weimer, Roberta A. Gottlieb, Morris F. White and E. Dale Abel. 2013. Insulin Receptor Substrates are Required for Suppressing Neonatal Autophagy in the Heart. Journal of Clinical Investigation 123:5319-33 (PMID: 24177427).

94. (a) Ng, Katharine M., Jessica Ferreyra, Steven Higginbottom, Jonathan B. Lynch, Smita Gopinath, Natasha Naidu, Biswa Choudhury, Bart C. Weimer, Denise Monack, and Justin L. Sonnenburg. 2013. Microbiota-liberated mucosal sugars facilitate enteric pathogen post-antibiotic emergence. Nature 502:96–99. (PMID: 23995682).

93. (aiek) Batt, C. and M. Tortorello. 2013. Ed.; Bart C. Weimer section editor. Encyclopedia of Food Microbiology, 2nd Edition. Elsevier, London.

92. (aci)* Forquin, M-P and Bart C. Weimer. 2013. Brevibacteria. In Encyclopedia of Food Microbiology, 2nd Edition. Ed. C. Batt and M. Tortorello. Elsevier, London.

91. (aiek)* Weimer, B. C. and C. Slupsky. 2013. Metabolomics for food and health. CRC Press, Boca Raton, FL. & Woodhead Publishing Limited, Cambridge, England. ISBN1845695127


90. (a) Barboza, Mariana, John W. Froehlich, Janneth Pinzon, Isabelle Moeller, Bo Lonnerdal, J. Bruce German, Bart C. Weimer, and Carlito B. Lebrilla. 2012. Glycosylation of human milk lactoferrin exhibits dynamic changes during early lactation enhancing its role in pathogenic bacteria-host interactions. Molecular and Cellular Proteomics. 11(6):M111.015248. (PMID: 22261723).

89. (a) Bugger, Heiko, Christian Riehle, Adam R. Wende, Dong Chen, Jamie Soto, Karla M Pires, Sihem Boudina, Heather A. Theobald, Ivan Luptak, Benjamin Wayment, Xiaohui Wang, Sheldon E. Litwin, Bart C. Weimer, and E. Dale Abel. 2012. Genetic Loss of Insulin


26

Receptors Worsens Cardiac Efficiency in Diabetes. Journal of Molecular and Cellular Cardiology. 52:1019-26. (PMID: 22342406).

88. (a) Heithoff, Douglas M. William R. Shimp, John K. House, Yi Xie, Bart C. Weimer, Robert L. Sinsheimer, and Michael J. Mahan. 2012. Intraspecies variation in the emergence of hyperinfectious bacterial strains in nature. PLoS Pathogen 8(4):e1002647 (PMID: 22511871).

87. (a) Maga, Elizabeth, Prerak Desai, Bart C. Weimer, Nguyet Dao, Dietmar Küeltz, and James Murray. 2012. Consumption of lysozyme-rich milk can alter microbial fecal populations. App. Environ. Microbiol. 78:6153-60. (PMID: 22752159).

86. (ai) Maga, Elizabeth A., Bart C. Weimer, and James D. Murray. 2012. Lysozyme-rich milk can modulate gut microbiota much like human milk. Gut Microbes (Enteric Pathogens Special Issue) 12:4(2). (PMID: 23235404).


85. (a) Latta, L.C. IV, M. Baker, T. Crowl, J.J. Parnell, B. Weimer, D. DeWald, M.E. Pfrender. 2011. Species and genotype diversity drive community and ecosystem properties in experimental microcosms. Evolutionary Ecology 25:1107-1125. DOI 10.1007/s10682-010-9457-3

84. (a) Marcobal A., Barboza M., Sonnenburg E.D., Martens E., Desai P., Lebrilla C., Weimer B.C., Mills D.A., German B., Sonnenburg J.L. 2011. Bacteroides in the Infant Gut Consume Milk Oligosaccharides via Mucus-Utilization Pathways. Cell Host Microbe. 10:507-14. (PMID: 22036470)

83. (a) Parnell, John, Giovanni Rompato, Todd Crowl, Bart C. Weimer, and Michael Pfrender. 2011. The effect of disturbance on phylogenetic diversity in microbial communities. Aquatic Microbial Ecology 64:267–273.

82. (ai)* Shah, J., P. T. Desai, R. Gann, and B. C. Weimer. 2011. Environmental stress and feed additives regulates Salmonella survival and host association. Proceedings of the Western Poultry Federation.

81. (aci)* Coolbear, Tim, Martin Wilkenson, and Bart C. Weimer. 2011. Lactic acid bacteria: LAB in flavour development. In Encyclopedia of Dairy Science, 2nd Edition, Ed. John W. Fuquay, Pat F. Fox, Paul McSweeney. In production. Elsevier/Academic Press, London, England.

80. (aci)* Weimer, Bart C. 2011. Lactic acid bacteria: Physiology and stress response. In Encyclopedia of Dairy Science, 2nd Edition, Ed. John W. Fuquay, Pat F. Fox, Paul McSweeney. In production. Elsevier/Academic Press, London, England.


27

79. (aci)* Weimer, Bart C. 2011. Stress Responses of Lactic Acid Bacteria. Springer Science & Business Media, LLC, New York.


78. (a) Bugger, H., M. Schwarzer, D. Chen, A. Schrepper, P.A. Amorim, M. Schoepe, T.D. Nguyen, F.W. Mohr, O. Khalimonchuk, B. C. Weimer, T. Doenst. 2010. Proteomic remodeling of mitochondrial oxidative pathways in pressure overload-induced heart failure. Cardiovascular Research. 85:376-84. (PMID: 19843514).

77. (a)* Parnell, John, Giovanni Rompato, Leigh Latta IV, Michael Pfrender, Joy Van Nostrand, Zhili He, Jizhong Zhou, Gary Andersen, Patti Champine, Balasubramanian Ganesan, and Bart C. Weimer. 2010. Functional biogeography as evidence of gene transfer in hypersaline microbial communities. PLoS One 5(9):e12919. (PMID: 20957119).

76. (a)* Wang, Jifeng, Baobing Zhao, Wei Zhang, Xuan Wu, Ruoyu Wang, Yaojian Huang, Dong Chen, Kum Park, Bart C. Weimer, and Yuemao Shen. 2010. Mycoepoxydiene, a fungal polyketide, induces apoptosis and cell cycle arrest at the G2/M phase in HeLa Cells. Bioorganic & Medicinal Chemistry Letters 20:7054-8 (PMID: 20970330).

75. (a)* LoCascio, Riccardo G., Prerak Desai, David A. Sela, Bart C. Weimer, and David A. Mills. 2010. Comparative genomic hybridization of Bifidobacterium longum strains reveals broad conservation of milk utilization genes in subsp. infantis. J. Bacteriology 76:7373-81. (PMID: 20802066)


74. (a) Boudina, Sihem, Heiko Bugger, Sandra Sena, Brian T. O’Neill, Vlad G. Zaha, Olesya Ilkun, Jordan J. Wright, Pradip K. Mazumder, Eric Palfreyman, Heather Theobald, Oleh Khalimonchuk, Benjamin Wayment, Kenneth J. Rodnick, Ryan Centini, Dong Chen, Sheldon E. Litwin, Bart C. Weimer, E. Dale Abel. 2009. Contribution of impaired myocardial insulin signaling to mitochondrial dysfunction and oxidative stress in the heart. Circulation. 119:1272-83.

73. (a) Bugger, Heiko Dong Chen, Christian Riehle, Jamie Soto, Heather A. Theobald, Xiao X. Hu, Balasubramanian Ganesan, Bart C. Weimer, and E. Dale Abe. 2009. Tissue-Specific Remodeling of the Mitochondrial Proteome in Type 1 Diabetic Akita Mice. Diabetes. 58:1986-97.

72. (a) Parnell, J. Jacob, Todd A. Crowl, Bart C. Weimer, and Michael E. Pfrender. 2009. Biodiversity in microbial communities: system scale patterns and mechanisms. Molecular Ecology 18:1455–1462.


28

71. (aci)* Weimer, Bart C., Giovanni Rompato, Jacob Parnell, Reed Gann, Balasubramanian Ganesan, Cristian Navas, Martin Gonzalez, Mario Clavel, Steven Albee-Scott. 2009. Microbial biodiversity of Great Salt Lake, Utah. In Saline lakes around the world: unique systems with unique values. Eds. Oren, A., D. L. Naftz, and W. A. Wurtsbaugh. S. J. and Jessie E. Quinney Natural Resources Research Library, Utah State University Press, Logan.

70. (aci) Oren, Aharon, Bonnie K. Baxter & Bart C. Weimer. 2009. Microbial communities in salt lakes: Phylogenetic diversity, metabolic diversity, and in situ activities. In Saline lakes around the world: unique systems with unique values. Eds. Oren, A., D. L. Naftz, and W. A. Wurtsbaugh. S. J. and Jessie E. Quinney Natural Resources Research Library, Utah State University Press, Logan.

69. (a) Chen, Dong, Michael D. Peel, Kenneth C. Olson, Bart C. Weimer and Daryll B. DeWald. 2009. Differential Ruminal Degradation of Alfalfa Proteins. Canadian Journal of Plant Science 89:1065-1074. (Voted best paper of the year by Canadian Agronomy Society)

68. (a) Tang, Chong-Ti, Yue Guo, Ming-Ke Lu, Yi-Nan Wang, Mi Jiang, Jin-Yong Peng, Wei-Bao Wu, Wen-Hong Li, Bart C. Weimer, and Dong Chen. 2009. Development of larval Schistosoma japonicum was blocked in Oncomelania hupensis by pre-infection with larval Exorchis. J. Parasitology. 10:1-6.


67. (aci)* Desai, P. and B. C. Weimer. 2008. Gene expression in microbial systems to link growth and metabolism. In Handbook of Research on Systems Biology Applications in Medicine, pp. 278-290, Ed. Andriani Daskalaki; IGI Global, Hershey, PA. (ISBN: 978-1-60566-076-9)

66. (a) Zhan, Y., X. Du, Q. Xu, G. Li, M. Zhang, J. Liu, D. Huang, B. Zhao, B. C. Weimer, D. Chen, Z. Cheng, L. Zhang, Q. Li, S. Li, Z. Zheng, S. Song, Y. Huang, Z. Ye, W. Su, S-C Lin, Y. Shen, Q. Wu. 2008. An anticancer and blood glucose-increasing endophytical fungal octaketide as ligand for nuclear orphan receptor Nur77. Nature Chemical Biology 4:548-56.

65. (a)* Desai, P., M. K. Walsh, and B. C. Weimer. 2008. Solid phase capture of bacteria using gangliosides and detection by real time PCR. Appl. Environ. Microbiol. 74:2254-2258.

64. (a) Chen, Dong, Ming-Xiang Liang, Daryll DeWald, Bart Weimer, Michael D. Peel, Bruce Bugbee, Jacob Michaelson, Elizabeth Davis, Yajun Wu. 2008. Identification of drought response genes from two alfalfa cultivars using Medicago truncatula microarrays. Acta Physiologiae Plantarum 30:183-199.

63. (a) Pate, B. J., K.L. White, D. Chen, K.I. Aston, B. R. Sessions, T.D. Bunch, and B. C. Weimer. 2008. A novel approach to identify bovine sperm membrane proteins that interact with receptors on the vitelline membrane of bovine oocytes. Mol. Reprod. Dev. 75:641-9.


29

62. (a) Lee, J-H., V.N. Karamychev, S.A. Kozyavkin, D. Mills, A.R. Pavlov, N.V. Pavlov, N.N. Polouchine, P.M. Richardson, V.V. Shakhova, A.I. Slesarev, B. Weimer, D.J. O’Sullivan. 2008. Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 9:247-265. (PMID: 18505588)

61. (ai) Stevens, John R., Balasubramanian Ganesan, Prerak Desai, Sweta Rao, and Bart C. Weimer. 2008. Statistical issues for normalization of multi-species microarray data. Proceedings of the Nineteenth Annual Kansas State University Conference on Applied Statistics in Agriculture, p 47–62.

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)= chapter, (i)=invited, (e)=editor, (k) = book] 60. (a) Pate B.J., K. L. White, Q. A. Winger, L.F. Rickords, K.I. Aston, B.R. Sessons, G.P. Li,

K.D. Campbell, B. Weimer, T.D. Bunch. 2007. Specific integrin subunits in bovine oocytes, including novel sequences for alpha 6 and beta 3 subunits. Mol. Reprod. Dev. 74:600-7.

59. (a)* Ganesan, B., M. Stuart, and Bart C. Weimer. 2007. Carbohydrate starvation causes a metabolically active but nonculturable state in Lactococcus lactis. Appl. Environ. Microbiol. 73:2498-2512.

58. (aeik)* Weimer, B. C. Improving the flavour of cheese. 2007. Woodhead Publishing Limited, Cambridge, England & CRC Press, Boca Raton, FL.

57. (acei)* Ganesan, B. and B. C. Weimer. 2007. Amino acid metabolism and cheese flavour. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead Publishing Limited, Cambridge, England; CRC Press, Boca Raton, FL.

56. (acei)* Ganesan, B., M. Qian, H. Burbank, and B. C. Weimer. 2007. Compounds associated with cheese flavor. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead Publishing Limited, Cambridge, England; CRC Press, Boca Raton, FL.

55. (acei)* Banks, Jean and B. C. Weimer. 2007. Lowfat cheese flavour. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead Publishing Limited, Cambridge, England; CRC Press, Boca Raton, FL.

54. (caei)* Weimer, B. C. 2007. Functional genomics and flavour. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead Publishing Limited, Cambridge, England; CRC Press, Boca Raton, FL.

53. (aci)* Weimer, B. C., S. Rajan, and B. Ganesan. 2007. Biotechnology of flavor production in dairy products. In Biotechnology in Flavor Production, Ed. F. Belanger; Blackwell Publishing Ltd. (Oxford).


30

52. (a) Champine, P., J. Michaelson, B. Weimer, D. R. Welsh, and D. B. DeWald. 2007. Microarray analysis reveals potential mechanisms of BRMS1-mediated metastasis suppression. Clinical & Experimental Metastasis. 24:551-65.

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)=book chapter, (i)=invited, (e)=editor]

51. (a)* Makarova, K., A. Slesarev, Y. Wolf, A. Sorokin, B. Mirkin, E. Koonin*, A. Pavlov, N. Pavlova, V. Karamychev, N. Polouchine, V. Shakhova, I. Grigoriev, Y. Lou, D. Rohksar, S. Lucas, K. Huang, D. M. Goodstein, T. Hawkins, V. Plengvidhya, D. Welker, J. Hughes, Y. Goh, A. Benson, K. Baldwin, J. H. Lee, I. Diaz-Muniz, B. Dosti, V. Smeianov, W. Wechter, R. Barabote, G. Lorca, E. Altermann, R. Barrangou, B. Ganesan, Y. Xie, H. Rawsthorne, D. Tamir, C. Parker, F. Breidt, J. Broadbent, R. Hutkins, D. O'Sullivan, J. Steele, G. Unlu, M. Saier, T. Klaenhammer*, P. Richardson, S. Kozyavkin, B. C. Weimer*, and D. A. Mills*. 2006. Comparative genomics of the lactic acid bacteria. Proc. Natl. Acad. Sci. USA 103:15611-6. *Co-corresponding authors.

50. (a) Liang, Y., D. R. Gardner, C. D. Miller, D. Chen, A. J. Anderson, B. C. Weimer, R. C. Sims. 2006. Biochemical pathway and enzymatic study of pyrene degradation by Mycobacterium sp. KMS. Appl. Environ. Microbiol. 72:7821-7828.

49. (a)* Ganesan, B., P. Dobrowolski, and B. C. Weimer. 2006. Identification of the Leucine-to-2-Methylbutyric Acid Catabolic Pathway of Lactococcus lactis. Appl. Environ. Microbiol. 72:4264-73.

48. (ai)* Rashid, K., and B. C. Weimer. 2006. Academia’s response to the growing biopharma’s workforce needs. Biotrends 3:1-3. (biotrends.org/from_the_street/from_the_street_Developing_Workforce.htm)

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)=book chapter, (i)=invited, (e)=editor]

47. (bi) Rashid, K., and B. Weimer. 2005. The role of academia in biotechnology workforce development. BioProcess International. 3:16-22.

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)=book chapter, (i)=invited]

46. (a)* Ganesan, B,. K. Seefeldt, R. Koka, B. Dias, and B. Weimer. 2004. Monocarboxylic acid production by lactococci and lactobacilli. Int. Dairy J. 14:2135-41.


31

45. (a)* Ganesan, B., and B. Weimer. 2004. The role of the aminotransferase IlvE in production of branched chain fatty acids by Lactococcus lactis subsp. lactis. Appl. Environ. Microbiol. 70:638-641.

44. (a)* Ganesan, B,. K. Seefeldt, and B. Weimer. 2004. Fatty acid production by Brevibacterium linens via amino acid utilization. Appl. Environ. Microbiol. 70:6385-6393.

43. (a)* Xie, Y., L-S Chou, A. Cutler, and B. Weimer. 2004. Expression profile of Lactococcus lactis ssp. lactis IL1403 during environmental stress with a DNA macroarray. Appl. Environ. Microbiol. 70:6738-6747.

42. (aci)* Weimer, B., Y. Xie, L-S. Chou and A. Cutler. 2004. Gene expression arrays in food. Ed. J.-L. Barredo. Microbial Products and Biotransformation. Humana Press, Totowa, NJ USA.

41. (aci)* Weimer, B., and B. Dias. 2004. Volatile Sulfur detection in fermented foods. Ed. J.-L. Barredo. Microbial Products and Biotransformation. Humana Press, Totowa, NJ USA.


40. (a) Xie, Yi, A. Cutler, B. Weimer, A. Parfionovas. 2003. Statistical methods for spot detection with macroarray data. Proceedings of the 35th Symposium on the Interface.

39. (ai) Newsome, R. et al. 2003. Dormant microbes: Research Needs. Food Technology 57:38-42. [Expert panel report and overview]


38. (ai)* Weimer, B., and D. Mills. 2002. Enhancing foods with Functional Genomics. Food Technology 56:184–188.

37. (a)* Ummadi, M. and B. C. Weimer. 2002. Use of capillary electrophoresis-laser induced fluorescence detection to monitor bacterial growth and amino acid utilization. J. Chrom. A 964: 243-253.

36. (ai) Klaenhammer, T. Eric Altermann, Fabrizio Arigoni, Alexander Bolotin, Fred Breidt, Jeffrey Broadbent, Raul Cano, Stephane Chaillou, Josef Deutscher, Mike Gasson, Maarten van de Guchte, Jean Guzzo, Trevor Hawkins, Pascal Hols, Robert Hutkins, Michiel Kleerebezem, Jan Kok, Oscar Kuipers, Mark Lubbers, Emmanuelle Maguin, Larry McKay, David Mills, Arjen Nauta, Ross Overbeek, Herman Pel, David Pridmore, Milton Saier, Douwe van Sinderen, Alexei Sorokin, James Steele, Daniel O’Sullivan, Willem de Vos, Bart Weimer, Monique Zagorec, and Roland Siezen. 2002. Discovering lactic acid bacteria by genomics. Antonie van Leeuwenhoek 82:29-58. (note: authorship is alphabetical).


32


35. (a)* Koka, R., and B. C. Weimer. 2001. Influence of growth condition on phospholipase production in Pseudomonas. J. Dairy Research 68:109–116.

34. (a)* Walsh, Marie K., Xinwen Wang and Bart C. Weimer. 2001. Optimizing the immobilization of single-stranded DNA onto glass beads. J. Biochem. Biophys. Methods. 47:175-185.

33. (a)* Weimer, B., M. Walsh, C. Beer, X. Wang, and R. Koka. 2001. Solid-phase capture of proteins, spores, and bacteria. Appl. Environ. Microbiol. 67:1300–1307.

32. (a)* Ummadi, M. and B. C. Weimer. 2001. Tryptophan metabolism in Brevibacterium linens BL2. J. Dairy Sci 84:1773–1782.

31. (a)* Chou, L.–S., B. Weimer. 2001. Interaction between glucose and arginine on the acid production in Lactococcus lactis ssp. lactis. Int. Dairy J. 11:253-258.


30. (a)* Koka, R., and B. C. Weimer. 2000. Isolation and characterization of a protease from Pseudomonas fluorescens RO98. J. Appl. Microbiol. 89:280-288.

29. (a)* Weimer, B., M. Walsh, and X. Wang. 2000. Influence of a polyethylene glycol spacer on antigen capture by immobilized antibodies. J. Biochem. Biophys. Methods. 43:107-117.

28. (a)* Koka, R., and B. C. Weimer. 2000. Investigation of the ability of a purified protease from Pseudomonas fluorescens RO98 to de–bitter cheese. Int. Dairy J. 10:75-79.

27. (a)* Seefeldt, K. and B. C. Weimer. 2000. Diversity of sulfur compounds in lactic acid bacteria J. Dairy Sci. 83: 2740-2746.


26. (aci)* Weimer, B. 1999. Brevibacteria. In Encyclopedia of Food Microbiology, R. K. Robinson et al. (Ed.), Academic Press, London.

25. (a)* Chou, L.–S., and Bart Weimer. 1999. Isolation and biochemical characterization of acid and bile tolerant Lactobacillus acidophilus. J. Dairy Sci. 82:23–31.


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24. (a) Pederson, J. A., G. J. Mileski, B. C. Weimer, J. L. Steele. 1999. Genetic Characterization of a Cell Envelope-Associated Proteinase from Lactobacillus helveticus CNRZ32. J. Bact. 181:4592–4597.

23. (a)* Dias, B., and B. C. Weimer. 1999. Production of volatile sulfur compounds in Cheddar cheese slurries. International Dairy Journal 9:605–611.

22. (ai)* Weimer, B., K. Seefeldt, and B. Dias. 1999. Sulfur metabolism in bacteria associated with cheese. Antonie van Leeuwenhoek 76:247–261.


21. (aci) Otte, J., Y. Ardö, B. Weimer, and J. Sørensen. 1998. Capillary electrophoresis used to measure proteolysis in cheese – Chapter 3. Bulletin of the International Dairy Federation, Analysis of Milk Proteins.

20. (ai) Steele, J.L., M.E. Johnson, J.R. Broadbent, and B.C. Weimer. 1998. Starter culture attributes which affect cheese flavor development, pp. 157-170. In, Proc. LACTIC '97 conference, Which strains? For which products?

19. (ai) Johnson, M. E., J. L. Steele, J. Broadbent, and B. C. Weimer. 1998. Manufacture of gouda and flavour development in reduced–fat cheddar cheese. Aust. J. Dairy Tech. 53:67.

18. (a)* Stuart, M., L.–S. Chou, and B. C. Weimer. 1998. Influence of carbohydrate starvation on the culturability and amino acid utilization of Lactococcus lactis ssp. lactis. Appl. Environ. Microbiol 65:665–673.

17. (a)* Dias, B., and Bart Weimer. 1998. Conversion of methionine to thiols by lactococci, lactobacilli, and brevibacteria. Appl. Environ. Microbiol. 64:3320–3326.

16. (a)* Dias, B., and Bart Weimer. 1998. Purification and characterization of methionine γ–lyase from Brevibacterium linens BL2. Appl. Environ. Microbiol. 64:33273331.

15. (a) Broadbent, J.R., M. Strickland, B. Weimer, M.E. Johnson, and J.L. Steele. 1998. Peptide accumulation and bitterness in Cheddar cheese made using single-strain Lactococcus lactis starters with distinct proteinase specificities. J. Dairy Sci. 81:327.


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.


34

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.


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.


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).


35


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.

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)


36


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


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).


37

[(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 and IEEE Spectrum magazines. Press releases for the 100K 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. 100K-China Pathogen Genome Project – in 2014 multiple media interviews were conducted in China announcing the consortium in Beijing that has begun to sequence 10% of the 100K Pathogen Genome Project founded in Dr. Weimer’s lab. 100K-Canada Pathogen Genome Project – founded in 2015 with funding from Genome Canada and partnerships with McGill University and Laval University. 100K-Korea Pathogen Genome Project – founded in 2015 with funding the Korean government and partnerships with Seoul National University.

[(a)=invited, (b)=submitted, (k)=keynote, *=supervising author; **=co-supervising author]

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.

277. (b)** M. Constanza Camargo, 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.


38


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.

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


39

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.

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, Regina!, 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. !Undergraduate.

254. (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. UC Davis Undergraduate Research Conference, Davis, CA. !Undergraduate.

253. (b)* Liu, Kendra!, 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. !Undergraduate.

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.


40

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. 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


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.


41

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.

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.


42

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


43

with High Resolution MS/MS. The 47th Annual German Society for Mass Spectrometry (DGMS), Frankfurt.


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.


44

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)

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)


45

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.

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)


46

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


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


47

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.

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)


48


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

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.


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.


49

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.


50

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).


51

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.

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.


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).


52

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).

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).


53

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).


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.


54

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.


55

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.

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.


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).


56

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.

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.


57

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.


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.


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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.


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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 α-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.

• Team coordinator for corporate strategy - School of Veterinary Medicine • 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


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• 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.

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.

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.

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

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

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

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

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

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.

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.


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

Weimer, B. 2003. Real time bacterial detection. New Zealand Patent WO 99/508172.

Weimer, B. 2003. Ligand-DNA composition for capture and detection of contaminants on a solid surface. U.S. Patent 6,531,278.

Weimer, B. 2002. Real time bacterial detection. Australian Patent 754,077.

Weimer, B. 2002. Real time bacterial detection. U.S. Patent 6,399,317.

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

• ImmunoDNA® – 2000

• TissueTag® – 2000


1

• BioMatrix Solutions, LLC

• AffySphere, LLC

High Summit Scientifics, LLC

Citrus & Sage, LLC

BioMatrix Sciences Group, LLC

Black Diamond Genomics, LLC

Supplied as requested

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