Genome Center membership

Join the Genome Center

We invite all UC Davis faculty who are interested in genomics research to consider becoming Members of the Genome Center.

The Genome Center

The UC Davis Genome Center, located in the Genome and Biomedical Sciences Facility, provides state-of-the-art genomics technologies to enhance the research of all campus faculty who wish to use such approaches. Genomics is interpreted broadly to embrace multiple levels of global analysis, including proteomics, metabolomics, and bioinformatics. A second objective of the Genome Center is to promote and coordinate genomics-related research on campus.

We oversee technology service cores for DNA technologies and expression analysis, proteomics, metabolomics, and bioinformatics. Services are provided based on recharge rates that reflect the actual cost of doing the analysis, thus providing cost-effective access to these technologies. These services are also available to off-campus users if we have extra capacity. In most cases, services involve Genome Center staff performing high-throughput, quality-controlled analyses of user-provided samples. For certain technologies, there are opportunities to train on and use equipment separate from that used by Genome Center staff. Please contact the core managers if you have any questions.

Faculty Affiliation with the Genome Center

There are three levels of faculty participation in the Genome Center:

  1. Genome Center Faculty
  2. Genome Center Members
  3. Occasionalad hoc users

There are currently fifteen Faculty resident in the Genome Center. The role of Genome Center Faculty, in addition to performing their own research, is to provide leadership in technology development and implementation. All faculty on campus that are actively engaged in genomics research — as judged by the criteria below — may become Genome Center Members. The third level of participation are ad hoc users that only require occasional access to the service cores (which are available to all campus faculty at the same recharge rates).

Benefits of Membership

Genome Center Members have the opportunity to provide input into the development of the Genome Center, particularly with respect to the technology service cores. This will primarily be through a Genomics Advisory Committee, comprised of six faculty members — selected from and by Genome Center Members — who represent the diversity of genomics interests on campus. This committee is expected to meet at least twice per year to review and provide input into the development of the Genome Center as well as genomics on campus in general. One member from the Genomics Advisory Committee will be invited to attend the monthly Genome Center Faculty meetings to represent the campus faculty.

In addition, each technology service core has an oversight committee comprising Genome Center Faculty and Members who are major users of that particular service core. Members will be invited to participate in events organized by the Genome Center designed to encourage collaborative genomics-related research across campus.

The Genome Center will provide Members with supporting documentation to assist in the submission of grant proposals. Genome Center Members will also have the opportunity to participate in training and research grants coordinated by the Genome Center and will have web-based access to applications from students and postdocs who apply through the Genome Center website.

Application for Membership

Initially, Genome Center Members will be self-selecting. All UC Davis faculty who feel they fulfill the criteria below and who wish to join may do so. In order to maintain an active membership, after one year and every three years thereafter, Members will be reviewed by the Genomics Advisory Committee according to the following criteria:

  1. Evidence of an active research program. Membership will require demonstration of an active research program in an area of genomics or bioinformatics. Evidence of an active program includes the training of students in genomics or bioinformatics>, the publication of genomics research in peer-reviewed journals and the ability to obtain extramural funds sufficient for the maintenance of an active research program in genomics and/or bioinformatics.
  2. Service in the development of genomics on campus. Active participation in the activities and administration of genomics on campus, including but not limited to one or more of the following: service on Genome Center committees, involvement in recruitment of Genome Center faculty and staff, active participation in genomics-related seminar programs, and/or teaching in genomics-related courses.

For this initial membership, please submit the following as e-mail attachments to Ernie Hoftyzer (eahoftyzer@ucdavis.edu):

  • A brief curriculum vitae (two pages maximum). Please use keywords to describe the genomics and bioinformatics resources that you currently use.
  • A description of services that you anticipate using and/or would like the Genome Center to develop. Please add links to personal and lab webpages (if any). This information will be used to develop a webpage of genomics researchers at Davis. If this information is already web accessible, please indicate your interest in being a Genome Center Member and direct us to your website.

Rather than develop a separate database, we will utilize the one administered by the CBS Dean’s office to minimize redundancy and the problems of keeping the information current. Please visit the College of Biological Sciences Faculty Directory and login to initiate or update your entry. You will need your Kerberos ID and passphrase. Under ‘research interests’ please describe the specific genomics aspects of your research. You will not be considered a Genome Center Member until this entry is completed.

Upcoming Talks and Events

Events on January 14, 2019
WCMC: Hands-on LC-MS Data processing and Statistics
Starts: 12:00 am
Ends: January 19, 2019 - 12:00 am
Location: UC Davis Conference Center, 550 Alumni Ln, Davis, CA 95616, USA
Description: Registration: http://ucanr.edu/survey/survey.cfm?surveynumber=15575

This course will feature hands-on training with real-world metabolomics data covering LC/MS compound identification, data processing, statistical analysis, network mapping and data interpretation.

We will instruct using a variety of software, workflows, and algorithms but also give theoretical background information and overviews. We will focus on utilizing open source software and only refer to commercial or vendor software when necessary.

All participants will be trained on laptops that were specifically purchased for course training, with all software already installed and data available to use.

The course will include:

untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
The course fees are $ 2,500 per participant to cover expenses for instructors, organization, materials and meals.

more Info:

Jeannette Martins

email: jmartins@ucdavis.edu

phone: +1-530-754-5357

Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.
Events on May 16, 2019
WCMC: Best practice in operating mass spectrometers in Metabolomics
Starts: 12:00 am
Ends: May 20, 2019 - 12:00 am
Location: Genome and Biomedical Sciences Facility, 451 Health Science Dr, Davis, CA 95616, USA
Description: Registration: https://goo.gl/forms/TGeuALrTMfTpGh0O2

This course will enhance your standing and expertise to prepare and successfully run samples in a metabolomic laboratory. It is designed to provide hands-on practical exercises using gas and liquid chromatography coupled to mass spectrometry (GC-MS & LC-MS). The course will focus on untargeted data acquisition in metabolomics with both nominal mass and accurate mass instruments. You will learn how to operate the instruments, how to collect metabolite profiles on complex samples and how to prepare and derivatize samples, troubleshoot instruments, acquire data and perform data quality control routines (QA/QC). Overall, you will receive comprehensive understanding of the current best practices in the metabolomics laboratory.

The course will include:


1. Fundamentals of mass spectrometry, chromatography, and metabolomics.
2. hands-on exercises on sample preparation, including extraction and derivatization
of complex samples for untargeted metabolomics profiling
3. Hands-on exercises to learn how to operate both gas and liquid chromatography
coupled to mass spectrometry (GC-MS & LC-MS).
4. quality control routines (QA/QC) in order to ensure comparable data, reproducibility, and instrument performance.
Events on August 19, 2019
International Summer Sessions in Metabolomics
Starts: 12:00 am
Ends: August 31, 2019 - 12:00 am
Location: UC Davis Alumni Center
Description: Registration: https://docs.google.com/forms/d/e/1FAIpQLSeVnMXxhkMtlET-RGDgW99jA3lr1wS4hypU0kI6O1yGV0GqBg/viewform?usp=sf_link

Contact: Jeannette Martins jmartins@ucdavis.edu

Please, contact us now if you need letters of support to obtain funding from your home institutions.

The West Coast Metabolomics Center organizes an instructional course for researchers for researcher which need a deeper and broader understanding in the field of Metabolomics. This course will span 12 days from August 19-30, 2019.

In order to serve the group interests best and have interesting open discussions we have a small class of 22 participants. The participants come always from all over the world and have a very diverse research background.

The course will include:

study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
sample preparation and quality control
in-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
exercises on flux analysis in cancer cells by isotope tracer analysis
untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
Past course participation:
2018 course: 25 researchers from USA, Brazil, China, Japan, Korea, Taiwan, Russia, Norway, Germany, Poland, Canada
2017 course: 24 researchers from USA, Saudi-Arabia, China, , Korea, Italy, Denmark, Iran, United Kingdom
2016 course: 23 researchers from USA, Saudi-Arabia, China, Thailand, Japan, Italy, Brazil, Chile, Korea, and Canada.
2015 course: 21 researchers from USA, China, Germany, Brazil, Switzerland, Denmark, Canada, Korea, Malaysia, and Netherlands.
2014 course: 20 researchers from USA, New Zealand, Italy, Denmark, China, Canada, Turkey and Switzerland
2013 course: 20 researchers from USA, New Zealand, Costa Rica, Denmark, Luxembourg, Brazil, Columbia, Japan, Korea and Taiwan.
For questions, please contact our program representative Jeannette Martins (jmartins@ucdavis.edu).

Visiting Scientists
Participation in this course is mandatory for visiting international researchers who want to engage in collaborative research projects.
The minimum time span for such collaborative visits is 3 months, preferred is 12 months.
An additional payment of $500 for the visa has to be paid prior to arrival at UC Davis.

Each year, up to five international researchers have started such research visits, funded by agencies in their home countries.
Please contact us at least 6 months in advance to help you with letters of support, booking your course, and obtaining a visa for you.
Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.

Categories