director 100k pathogen genome sequencing …bart c. weimer, professor 1 director 100k pathogen...

BartC.Weimer,Professor

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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.

Co-founder Molecular Food Safety Consortium 2014 – present

I was part of the founding team that 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 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.

Faculty Coordinator Corporate Relations (UC Davis; Office of Research) 2010 – 2015 This position provided leadership for the coordination of all aspects of the campus’s existing and expanding corporate relations outreach and engagement efforts. It was a 50% administrative position that reported 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 was a central administration position that supported a robust, dynamic and successful approach to corporate relations with genomics and metabolomics companies that interacted with UC Davis during this period.

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 facilitated large scale sequencing genomics projects between BGI, the world’s largest genomics company, and UC Davis faculty across the campus. This included oversight of building the facility, installation of the instrumentation, and initiation of genomic services. I initiated a seed

BartC.Weimer,Ph.D.,Professor

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grant program that provided $1 million in funding to expand genomics at UC Davis that funded 45 projects.

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. We use systems microbiology methods to study individual genomes 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 Pathogen Genome 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

• Journal of Breath Research manuscript selected for Highlight Issue 2018 • IBM Shared University Research Award 2015, 2016 • FDA Food Safety Grand Challenge Finalist (1/5 from over 100 applicants) 2015 • Agilent Thought Leader (DNA modification, genome restricted metabolomics) 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


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• Inducted into Empire Who’s Who 2003 • 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 and UC Davis institutional committees • UC Davis CFAH Animal Health/DHH-FS (reviewer, invited) 2016-2017 • UC ANR Strategic Initiative for Sustainable Food Systems (member, invited) 2015-2018 • Committee on Research (member, invited) 2016-2019 • Dean GSM Search Committee (member, invited) 2015-2016 • 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, invited) 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, Chancellor charge) 2011-2012 • School of Veterinary Medicine, International Programs (chair, invited) 2010-2013 • School of Veterinary Medicine, International Programs (member, invited) 2009-2010 • FUTURES committee (invited by Chancellor) 2009-2011 • PHR Departmental Resources (invited) 2009-present • Faculty recruitment committee (chair, invited) 2010-2013 • International development committee (SVM - invited) 2009-2010 • International development committee (SVM - chair) 2010-2012 • SVM curriculum development (co-chair of microbiology) 2009

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

National & International Peer Review Committees • The Japan Prize (invited, nomination committee) 2018-2021 • Polish National Science Center (invited) 2017 • German Research Foundation (DFG) (invited) 2017 • MetaCyc advisor board member (invited) 2004 – present • Genome Canada grant review panel (invited) 2013 – 2015 • 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


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• 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, US Army (Dugway, UT) (invited) 2000–2001 • University of Massachusetts at Amherst, Food Science department 2000 • 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 (FSIS) (ad hoc) 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, Pathogens (member) 2017-present • Editorial board, Virulence (member) 2015-2021 • Series Editor, Elsevier – Microbial Genomics (multiple book series) 2013-2019 • 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 • Reviewer, Microbial Drug Resistance 2017-present • Reviewer, Science 2018-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


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FORC (South Korea) –Use of -omics technologies in food safety January 2018 This meeting was co-organized by the Seoul National University and the 100K Pathogen Genome Project to highlight progress in using WGS and metagenomics in food safety. This included highlights of how the Korean FDA is using NGS and WGS in regulation. Real time sequencing – Oxford Nanopore workshop October 2017 Dr. Weimer initiated and organized the workshop to focus on the use of real genome sequencing in health and foods. The components represented human genome sequencing, plant genome sequencing, microbial genome sequencing, and metagenomics using DNA and RNA. It was conducted by invitation in a roundtable format so that specific opportunities and technology advantages could be discussed. Industrial Metagenomics of the Food Supply May 2016 Dr. Weimer initiated and organized the industrial workshop via ASM-Microbe with IBM, Mars, and Bio-Rad at the national meeting of the American Society for Microbiology. This workshop described the technology, use, implementation, and industrial relevance for metagenomics in foods with 5 international speakers. Genomics 101 – Genomics of the Food Supply June 2016 Dr. Weimer initiated and organized the industrial workshop for Wrigley (Chicago, IL) to train their research division for genomics and metagenomics in the food system. This workshop was held for ~100 people in their R&D division. 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. 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.


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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 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

culture independent methods 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 – an

international collaboration using high through put WGS

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-China (Chinese Academy of Science, Beijing Normal University) 2014-present • 100K-Korea (Seoul National University) 2015-present • 100K-Mexico 2016-present • 100K-Canada (McGill University, Laval University) 2017-present


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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 • Breath analysis for health and infection estimation. 2016-2018 • Effect of arsenic exposure on lung health. 2016-2018

NIH/NCI Helicobacter pylori genomics and epigenome in cancer. 2015 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 2012-2013 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. 2012-2018 • Oral health in dogs. 2011-2013 • Rapid microbe detection. 2014-2017 • MetaRNAseq in foods. 2015-2018 • Fungal toxin removal from complex 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, pathogen sequencing. 2010-2015 Gojo Industries Skin health and metagenomics. 2015-2019 National Marine Mammal Foundation

Respiratory disease in dolphins. 2013-2016

IBM • Molecular food safety. 2014-2019

Theses in Preparation – 0 Students in Progress – 1 Students Completed - 37 Post-doctoral fellow mentorship – 18 Undergraduate students - 42

Didactic 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 • GGG201 – Microbes as model organisms in genetics.


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Graduate Group Student Advisor:

• Forensics • Microbiology

UC Davis Graduate group membership: UC Davis has a graduate student-training program that is based on groups that span departments and colleges. 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

o founding member for Host/microbe interactions emphasis area

• Preventive Veterinary Medicine

• Food Science • Forensics • Biotechnology emphasis area faculty

mentor (NIH funded program) • Masters of Public Veterinary

Medicine (MPVM)

1989–2018 Books edited = 4; peer-reviewed publications/chapters = 156; submitted = 12

[(a)=refereed, (b)=non-refereed, *=supervising author/editor, (c)= chapter, (i)=invited, (e)=editor, (k) = book] (aci)* Kaufman, James H.*, Christopher A. Elkins, Matthew Davis, Allison M. Weis, Bihua C.

Huang, Mark K. Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Judith Douglas, Simone Bianco, Mark Kunitomi, Bart C. Weimer*. 2018. Insular Microbiogeography. In Microbial Ecology: Current advances from genomics, metagenomics and other "omics". Edited by Diana Marco. Caister Academic Press, Poole, UK.

(aci)* Ganesan, Balasubramanian and Bart C. Weimer. 2017. 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 J. Kaufman. 2017. Food Safety Genomics. Editor. Elsevier/Academic Press, London, England (in production).

(aci)* Ganesan, B. and Bart C. Weimer. 2017. Amino Acid Catabolism and Its Relationship to Cheese Flavor Outcomes. 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) (ISBN: 978-0-12-417012-4).

(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.


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(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. Oren, A., D. L. Naftz, and W. A. Wurtsbaugh. Natural Resources and Environmental issues 15 (1):15-22 (http://digitalcommons.usu.edu/nrei/vol15/iss1/3)

(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)

(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.


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(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] 156. (a) Lawton, Samantha, Allison M. Weis, Barbara A. Byrne, Heather Fritz, Conor Taff,

Andrea Townsend, Bart C. Weimer, Asli Mete, Sarah Wheeler, Walter M. Boyce. 2018. Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF, biochemical testing, and sequence analysis. Journal of Veterinary Diagnostic Investigation. In press.

155. (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. 2018. Salmonella enterica ssp enterica serotype Typhimurium Enhances Osteogenic Differentiation in Adipose-Derived Mesenchymal Stem Cells. Stem Cells. In press.

154. (aci)* Kaufman, James H.*, Christopher A. Elkins, Matthew Davis, Allison M. Weis, Bihua C. Huang, Mark K. Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Judith Douglas, Simone Bianco, Mark Kunitomi, Bart C. Weimer*. 2018. Insular Microbiogeography. In Microbial Ecology: Current advances from genomics, metagenomics and other "omics". Edited by Diana Marco. Caister Academic Press, Poole, UK. *co-supervising authors. In press.

153. (a)* Kong, Nguyet, Azarene Foutouhi, B. Carol Huang, Narine Arabyan, Kao Thao, Whitney Ng, Dylan Storey, Lucy Cai, Eric Lee, Richard Jeannotte, Lenore Kelly, Bart C. Weimer. 2018. A Next Generation Sequencing Library Workflow for Foodborne Pathogens with Quality Control Parameters for Quantification and Shearing conditions using the Agilent 2200 TapeStation System. Standards in Genomics. In press.

152. (a) Zamuruyev, Konstantin O, Eva Borras, Dayna R Pettit, Alexander A Aksenov, Jason D Simmons, Bart C. Weimer, Michael Schivo, Nicholas J Kenyon, Jean-Pierre Delplanque, Cristia Davis. 2017. Effect of collection temperature on metabolite content in exhaled breath condensate. Analytica Chimica Acta.1006:49-60 https://doi.org/10.1016/j.aca.2017.12.025

(ai)* Ganesan, B., and Bart C. Weimer. 2018. Methods and applications of metabolomics for discovery and food safety. Separations (submitted) Special Issue

(a) Allen Van Deynze, Pablo Zamora, Pierre-Marc Delaux, Cristobal Heitmann, Dhileepkumar Jayaraman, Shanmugam Rajasekar, Junko Maeda, Srijak Bhatnagar, Guillaume Jospin, Danielle Graham, Richard Jeannotte, Donald Gibson, Aaron Darling,


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Kevin D. Schwartz, Alison M. Berry, Javier Lopez, Bart C. Weimer, Jonathan A. Eisen, Howard-Yana Shapiro, Jean-Michel Ané, and Alan B. Bennett. 2018. The aerial root mucilage associated with a landrace of maize supports a functional diazotrophic microbiota. (submitted)

(a)* Weis, Allison M., Kristin A. Clothier, Bihua C. Huang, Nguyet Kong, Jessica Wasserscheid, Ken Dewar, Bart C. Weimer. 2017. Comparative Genomics of Abortive Campylobacter jejuni Isolates from Multiple Hosts. (submitted)

(a)* Doherty, Matthew K., Prerak T. Desai, Leslie Woods, Mai Lee Yang, Janneth Pinzon, Nguyet Kong, and Bart C. Weimer. 2017. Vancomycin and aptamer treatment in vivo are synergistic to inhibit Staphylococcus aureus. (in revision)

(a)* Chen, Poyin, Prerak T. Desai, Dong Chen, Jigna Shah, and Bart C. Weimer. 2017. Whole cell cross-linking to discover host-microbe protein receptor/ligand pairs. (revision submitted).

(a)* Kaufman, James*, Huang, Mark K Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Simone Bianco, Bart C. Weimer*. 2017. Genomic diversity of microbes. Submitted *co-corresponding author (in revision)

(a)* Kong, Nguyet, Whitney Ng, Vivian Lee, Poyin Chen, Lenore Kelly, and Bart C. Weimer. 2017. Comparing Various DNA Extraction Methods to Obtain High Molecular Weight Genomic DNA in Listeria monocytogenes for Next Generation Sequencing Pipelines. (submitted).

(a)* Kong, Nguyet, Whitney Ng, Lucy Cai, Alvin Leonardo, Patrick Ancheta, B. Carol Huang, Kao Thao, Azarene Foutouhi, Lenore Kelly and Bart C. Weimer. 2017. KAPA Biosystems HTP Library Preparation Kit Using Agilent Electrophoresis Instruments for Quality Control of Library Construction Pipeline. (submitted).

(a)* Dhanasekaran, A. Ranjitha and Bart C. Weimer. 2017. DynaFlux: a software tool to estimate the dynamic state flux of a metabolic network and to perform network analyses. (in revision).

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

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

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

(a)* Ganesan, Balasubramanian, Sweta Rhajan, Bart C. Weimer. 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. Gene expression profiles to define the mechanism of syrigopeptin 25A inhibition of Listeria monocytogenes. (submitted).

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)= chapter, (i)=invited, (e)=editor, (k) = book] 151. (ai)* Chen, Poyin, Taylor Reiter, Bihua Huang, Nguyet Kong, and Bart C. Weimer. 2017.

Prebiotic oligosaccharides potentiate host protective responses against Listeria


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monocytogenes infection. Pathogens 6:68 (invited contribution in - Special issue on Listeria monocytogenes and host interactions; Feature Article). (DOI:10.3390/pathogens6040068; PMID: 29257110)

150. (ai)* Weis, Allison M. and Bart C. Weimer. 2017. The journey of Campylobacter: a genomic analysis of a successful zoonotic pathogen. Atlas of Science (http://atlasofscience.org/the-journey-of-campylobacter-a-genomic-analysis-of-a-successful-zoonotic-pathogen/#more-22426).

149. (a) Borras, Eva; Aksenov, Alexander; Baird, Mark; Novick, Brittany; Schivo, Michael; Zamuruyev, Konstantin; Pasamontes, Alberto; Parry, Celeste; Foutouhi, Soraya; Venn-Watson, Stephanie; Weimer, Bart C.; Davis, Cristina. 2017. Exhaled breath metabolomic longitudinal study for an early prediction of health alterations in dolphins. Analytical and Bioanalytical Chemistry. 409(28):6523-6536. (highlight paper for issue) (PMID: 29063162)

148. (a) Stevens, John R., Todd R. Jones, Michael Lefevre, Balasubramanian Ganesan, and Bart C. Weimer. 2017. SigTree: identifying and visualizing significantly responsive branches in a phylogenetic tree. Computational and Structural Biology Journal 15:372-376. (PMID:28748045)

147. (a)* Arabyan, Narine, Bihua C. Huang and Bart C. Weimer. 2017. Draft genomes of Salmonella enterica sv Typhimurium LT2 with deleted chitinases that are emerging virulence factors. Genome Announcements 5:e00659-17 (PMID:28774970).

146. (ai)* Weimer, Bart C. 2017. 100K Pathogen Genome Project. Genome Announcements 5:e00594-17 (invited commentary) (PMID: 28705971)

145. (a)* Kong, Nguyet, Narine Arabyan, Kao Thao, Whitney Ng, Bihua C. Huang, Dylan Bobby Storey, Poyin Chen, Allison M. Weis, Soraya Foutouhi, Azarene Foutouhi, Yi Xie, and Bart C. Weimer. 2017. Draft genome sequences of 1183 Salmonella from the 100K Pathogen Genome Project. Genome Announcements 5:e00518-17. (PMID: 28705963).

144. (a)* Arabyan, Narine, Bihua C. Huang and Bart C. Weimer. 2017. Draft Genomes of Salmonella lysozyme knockouts. Genome Announcements 5:e00519-17. (PMID: 28596411).

143. (ai) Rheault, Jean-Guillaume Emond, Julie Jeukens, Luca Freschi, Irena Kukavica-Ibrulj, Brian Boyle, Marie-Josée Dupont, Anna Colavecchio, Virginie Barrere, Brigitte Cadieux, Maud Kerhoas, Alanna Crouse, Lei Zhu, Line Larivière, Ana Victoria Pilar, Camille Cavestri, Travis K. Chapin, Denise Tremblay, Caroline Vincent, Eric Fournier, Khadija Youfsi, Ida Ngueng-Feze, Lingqiao Song, Valentine Usongo, Florence Doualla-Bell, Chrystal Berry, Aleisha R. Reimer, Nguyet Kong, Carol B. Huang, Karen Fong, Emily D. Wilson, Kakali Mukhopadhyay, Walid Mottawea, Dele Ogunremi, Hongsheng Huang, Gitanjali Arya, Ann Perets, Catherine Yoshida, James Robertson, Joel Weadge, Michelle D. Danyluk, John Rohde, Rafael Garduno, Siyun Wang, Céline Nadon, Paul Thomassin,Yann Joly, Ismail Fliss, Gisèle Lapointe, Linda Harris, Roger Stephan, Elton Burnett, Sylvain Moineau, Sandeep Tamber, Sadjia Bekal, France Daigle, Samantha Gruenheid, Danielle Malo, Thomas Wittum, Pascal Delaquis, Alexander Gill, Kenneth E. Sanderson, Martin Wiedmann, Eelco Franz, Lucas Wijnands, Bart C. Weimer, Lawrence Goodridge, and Roger C. Levesque. 2017. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis. Frontiers in Microbiology 8:996. (PMID: 28626454) Special issue on food safety

142. (a)* Arabyan, Narine, Allison M. Weis, Bihua C. Huang and Bart C. Weimer. 2017. Implications of sialidases in diseases: Genome release of Salmonella sialidase knockout strains. Genome Announcements 5:e00341-17. (PMID: 28495784)


15

141. (a)* Arabyan, Narine, Bihua C. Huang and Bart C. Weimer. 2017. Amylases and their importance during glycan degradation: Genome sequence release of Salmonella amylase knockout strains. Genome Announcements 5:e00355-17. (PMID: 28522713)

140. (a)* Kaufman, James H., Christopher A. Elkins, Matthew Davis, Allison M Weis, Bihua C. Huang, Mark K Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Simone Bianco, Mark Kunitomi, Bart C. Weimer*. 2017. Microbiogeography and microbial genome evolution. arXiv:1703.07454 [q-bio.GN]. *co-corresponding author

139. (a)* Weis, Allison M., Brent Gilpin, Bihua C. Huang, Nguyet Kong, Poyin Chen, and Bart C. Weimer. 2017. Shigella draft genomes: resources for food safety and public health. Genome Announcements 5:e00176-17. (PMID: 28428292)

138. (a)* Weis, Allison M., Kristen A. Clothier, Bihua C. Huang, Nguyet Kong, and Bart C. Weimer. 2017. Multidrug resistant abortive Campylobacter jejuni draft genome from Northern California. Genome Announcements 5:e00171-17. (PMID: 28408683)

137. (a) Draper, Jenny L., Lori M. Hansen, David Bernick, Samar Abedrabbo, Jason G. Underword, Nguyet Kong, Carol B. Huang, Allison M. Weis, Bart C. Weimer, Arnoud Van Vliet, Nader Pourmand, Jay V. Solnick, Kevin Karplus, Karen M. Ottemann. 2017. Fallacy of the unique genome: Sequence diversity within single Helicobacter pylori strains. mBio 8:e02321-16. (PMID: 28223462).

136. (a)* Chen, Poyin, Nguyet Kong, Bihua Huang, Kao Thao, Whitney Ng, Dylan Bobby Storey, Narine Arabyan, Azarene Foutouhi, Soraya Foutouhi, and Bart C. Weimer. 100K Pathogen Genome Project: 306 Listeria draft genomes for food safety and public health. 2017. Genome Announcements 5:e00967-16. (PMID: 28183778).

135. (a)* Aksenov, Alexander, Konstantin Zamuruyev, Alberto Pasamontes, Joshua Brown, Michael Schivo, Soraya Foutouhi, Bart C. Weimer, Nicholas Kenyon, and Cristina Davis. 2017. Analytical methodologies for broad metabolic coverage of exhaled breath condensate. J. Chrom B. 1061-1062:17-25. (PMID: 28697414)

134. (a)* Kong, Nguyet, Whitney Ng, Kao Thao, Regina Agulto, Allison Weis, Kristi Spittle, and Bart C. Weimer. 2017. Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing. Standards in Genomics. 12:27-37 (PMID: 28344744). (highly accessed notation by journal)

133. (a)* Weis, Allison M., Bihua C. Huang, Dylan B. Storey, Nguyet Kong, Poyin Chen, Narine Arabyan, Brent Gilpin, Carl Mason, Andrea K. Townsend, Woutrina A. Miller, Barbara A. Byrne, Conor C. Taff, and Bart C. Weimer. 2017. Large-scale release of Campylobacter draft genomes; resources for food safety and public health from the 100K Pathogen Genome Project. Genome Announcements 5(1):e00925-16. (PMID: 28057746).

132. (a)* Chen, Poyin, Henk C. den Bakker, Jonas Korlach, Meredith Ashby, Tyson Clark, Khai Luong, R. J. Roberts, Martin Wiedmann, and Bart C. Weimer. 2017. Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes. App. Environ. Microbiol. 83:e02091-16. (PMID: 27836852).

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)= chapter, (i)=invited, (e)=editor, (k) = book] 131. (a) Zamuruyev, Konstantin, Alexander Aksenov, Alberto Pasamontes, Josh Brown, Dayna

Pettit, Soraya Foutouhi, Bart C. Weimer, Michael Schivo, Nicholas Kenyon, Jean-Pierre Delplanque, Cristina Davis. 2016. Human breath metabolomics using an optimized non-invasive respiratory sampler for health diagnostics. Journal of Breath Research


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11(1):016001. (PMID: 27689905) Selected for special 2017 highlight issue (http://iopscience.iop.org/article/10.1088/1752-7163/11/1/016001)

130. (a)* Weis, Allison M., Kristin A. Clothier, Bihua C. Huang, Nguyet T. Kong, and Bart C. Weimer. 2016. Campylobacter jejuni that cause abortion in livestock. Genome Announcements 4(6):e01324-16. (PMID: 27908990).

129. (a)* Park, Dayoung, Narine Arabyan, Cynthia C. Williams, Ting Song, Anupam Mitra, Bart C. Weimer, Emanual Maverakis, and Carlito B. Lebrilla. 2016. Salmonella Typhimurium enzymatically landscapes the host intestinal epithelial cell surface glycome to increase invasion. Molecular and Cellular Proteomics 15(12):3653-3664 (PMID: 27754876)

128. (a)* Weis, Allison M., Dylan B. Storey, Conor C. Taff, Andrea K. Townsend, Bihua C. Huang, Nguyet T. Kong, Kristin A. Clothier, Abigail Spinner, Barbara A. Byrne, Bart C. Weimer. 2016. Genomic comparison of Campylobacter spp. and their potential for zoonotic transmission between birds, primates, and livestock. App. Environ. Microbiol. 82: 7165-7175. (PMID: 27736787)

127. (a) Zamuruyev, Konstantin; Alexander Aksenov; Mark Baird; Alberto Pasamontes; Celeste Parry; Soraya Foutouhi; Stephanie Venn-Watson; Bart C. Weimer; Jean-Pierre Delplanque; Cristina Davis. 2016. Enhanced non-invasive respiratory sampling from bottlenose dolphins for optimum breath metabolomics measurements. Journal of Breath Research 10(4):046005. (PMID: 27689905)

126. (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. 2016. The transfer network of bacterial mobile resistome connecting animal and human microbiome. App. Environ. Microbiol. 82:6672-6681 (PMID: 27613679)

125. (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. App. Environ. Microbiol. 82:4811-4820. (PMID: 27260356)

124. (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. Sci. Rep. 6:29525 (doi: 10.1038/srep29525). (PMID:27389966)123. (ai)* Edlund, Stefan, Kristen L. Beck, Niina Haiminen, Laxmi Parida, Dylan Bobby Storey, Bart C. Weimer, James H. Kaufman, David Chambliss. 2016. Design of the MCAW Compute Service for Food Safety Bioinformatics. IBM Journal of Research and Development, 60 (5/6):2.1-2.12 (DOI: 10.1147/JRD.2016.2584798).

122. (ai)* 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 and Development, 60 (5/6):1.1-1.13. (DOI: 10.1147/JRD.2016.2582598).

121. (a) Pandey, Pramod, Mark Lejeune, Sagor Biswas, Daniel Morash, Bart C. Weimer, Glenn Young. 2016. A new method for converting foodwaste into pathogen free soil amendment for enhancing agricultural sustainability. Journal of Cleaner Production 112:205-213. (DOI: 10.1016/j.jclepro.2015.09.045).


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[(a)=refereed, (b)=non-refereed, *=supervising author, (c)= chapter, (i)=invited, (e)=editor, (k) = book] 120. (ai)** 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).

119. (ai)* 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)

118. (aci)* Ganesan, Balasubramanian and Bart C. Weimer. 2015. Biotechnology of flavor formation in fermented dairy products. In Biotechnology in Flavor Production, 2nd Edition. pp. 133-158. Edited by Daphna Havkin-Frenkel and Nativ Dudai. Wiley Press, Singapore. ISBN 978-1-118-35406-3

117. (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. (PMID: 25814612)

116. (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)

115. (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).

114. (a) 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)

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)= chapter, (i)=invited, (e)=editor, (k) = book] 113. (ai)* 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).

112. (ai)* 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).


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111. (ai)* 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).

110. (ai)* 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).

109. (ai)* Kong, Nguyet, Kao Thao, Whitney Ng, Kristi Spittle Kim, Jonas Korlach, Luke Hickey, Lenore Kelly, Stephen Lappin, and Bart C. Weimer. 2014. Automation of PacBio SMRTbell 10 kb Template Preparation on an Agilent NGS Workstation. Agilent Technologies application note. (5991-4482EN; DOI: 10.13140/RG.2.1.4403.2725).

108. (ai)* 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).

107. (a) Bua-In, S., Y. Paisooksantivatana, B. C. Weimer, S. Chowpongpang. 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.

106. (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. Springer, Berlin Heidelberg. ISBN: 978-3-642-30193-3

105. (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).

104. (a)* Ganesan, B. and Bart C. Weimer. 2014. Amino acid catabolism. In Cheese: Chemistry, Physics & Microbiology. Volume 1, 4th Edition. Edited by P.F. Fox, P.L.H. McSweeney, D.W. Everett and P. Cotter. Elsevier, Oxford.

103. (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)

102. (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.

101. (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)

100. (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


19

epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. Emerging and Infectious Diseases. 20:1481-9. (PMID: 25147968)

99. (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).

[(a)=refereed, (b)=non-refereed, *=co- or supervising author, (c)= chapter, (i)=invited, (e)=editor, (k) = book] 98. (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).

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. 2013. Ed.; Bart C. Weimer section editor. Encyclopedia of Food Microbiology, 2nd Edition. Elsevier, London. ISBN 978-0-12-384733-1

92. (aci)* Forquin, M-P and Bart C. Weimer. 2013. Brevibacterium. In Encyclopedia of Food Microbiology, 2nd Edition. Ed. C. Batt. pp. 324–330. Elsevier, London. ISBN 978-0-12-384733-1

91. (aiek)* Weimer, B. C. and C. Slupsky. 2013. Metabolomics for food and health. CRC Press, Boca Raton, FL. & Woodhead Publishing Limited, Cambridge, England. (ISBN: 1845695127)

90. (ai) Maga, Elizabeth A., Bart C. Weimer, and James D. Murray. 2013. Lysozyme-rich milk can modulate gut microbiota much like human milk. Gut Microbes 4(3):136-139. (invited for Enteric Pathogens Special Issue) (PMID: 23235404).

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)= chapter, (i)=invited, (e)=editor, (k) = book] 89. (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).


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

87. (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).

86. (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).

[(a)=refereed, (b)=non-refereed, *=supervising author, (c)= chapter, (i)=invited, (e)=editor, (k) = book] 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. 60th Proceedings of the Western Poultry Federation 60:16.

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. ISBN 9780123744074

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. ISBN 9780123744074

79. (aci)* Weimer, Bart C. 2011. Responses of Lactic Acid Bacteria to Starvation. In Stress Responses of Lactic Acid Bacteria. Springer, New York. Pp. 129-144. DOI: 10.1007/978-0-387-92771-8_7

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


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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)

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

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. Natural Resources and Environmental Issues 15:15-22. Special Issue: 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. Natural Resources and Environmental Issues 15:257-264. Special Issue: 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.


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

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. 20:47–62. In: Proceedings of the 20th Annual Kansas State University Conference on Applied Statistics in Agriculture. Ed. Gary L. Gadbury. New Prairie Press, Manhattan, KS.

[(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. (PMID:17293521)

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.


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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 formation in fermented dairy products. In Biotechnology in Flavor Production, 1st Edition. Ed. F. Belanger; Blackwell Publishing Ltd., Oxford.

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. (PMID: 16751541)

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. 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.


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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. Volume 18. Methods in Biotechnology: Microbial Products and Biotransformation. pp. 333-343. Humana Press, Totowa, NJ USA. ISBN 1588295486

41. (aci)* Weimer, B., and B. Dias. 2004. Volatile Sulfur detection in fermented foods. Ed. J.-L. Barredo. Volume 18. Methods in Biotechnology: Microbial Products and Biotransformation. pp. 397-403. Humana Press, Totowa, NJ USA. ISBN 1588295486

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

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

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


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

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.

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

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

director 100k pathogen genome sequencing …bart c. weimer, professor 1 director 100k pathogen...

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