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About the Genome Center

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UC Davis Genome Center Strategic Plan November 2003

 

 

Strategic Plan - November 2003

 THE UC DAVIS GENOME CENTER

UC Davis is in the enviable position of having a large number of talented labs across the biological spectrum.  However, we face the challenge of maintaining our position of leadership while assimilating the many new genomic technologies and high-throughput methodologies that are becoming available.

We therefore developed the concept that the UC Davis Genome Center would be the technological antenna in the genomics arena for the campus.  The Center should provide enabling genomics technology that is not readily available elsewhere to all research groups on campus who wish to use it.  However, given the speed of technological change, this technology service component cannot be static but must continually evolve.  Whatever is current today is likely soon to be outmoded.

Consequently, in order to keep the Genome Center current, there needs to be a core of faculty closely associated with it whose research interests require that the core technologies provided by the Center are maintained at the cutting edge.  This requirement led to the development of a strategic plan for the Genome Center in which an enabling core technology service component is developed, and outstanding faculty are recruited who will position the Center and UC Davis at the frontiers of genomics. The faculty will consist of ten wet lab scientists and seven bioinformaticists located in Center space.  These core faculty will be located on the 4th and 5th floors of the GBSF building, with the service core on the 1st floor. 

We envisage several levels of faculty participation in the Genome Center.  The 17 core Genome Center faculty will be almost exclusively new recruits and housed in the building.  Other faculty on campus with strong genomics components to their programs will be Associate Members of the Genome Center.  They will not be housed in Center space, but will be involved in many of the functions of the Center.  This includes the refinement and implementation of the strategic plan laid out below. In addition, all biology faculty on campus are potential users of the Genome Center; much of this use is expected to be occasional and ad hoc.

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Academic Focus and Faculty Composition

The Genome Center cannot be all things to all people; to be maximally effective our efforts need to be focused. The research of the Center will be focused on the phenotypic consequences of genetic variation. This is one of the major emerging challenges in biology, cutting across all disciplines and taxonomic categories. UC Davis is particularly well positioned to make significant advances in this area at both the fundamental and applied levels. The development of this focus will require a fusion of comparative, functional and structural genomics. This includes the integration of multiple levels of investigation, from areas as disparate as protein structure-function relationships, cellular physiology, population genetics and bioinformatics. Wet lab experimentation must be closely integrated with bioinformatics research. The GBSF building that will house the Center was designed with this in mind. Several, possibly the majority, of the core Genome Center faculty will have both wetlab and bioinformatics components to their research programs. 

Davis would be poorly served by a Genome Center that is focused on a single group of organisms. The taxonomic breadth of the organisms studied at Davis is virtually unequaled elsewhere, and is a key asset that we should exploit. We have a broad diversity of strengths, opportunities and needs across the spectrum of organismal biology. 

In our wet lab recruitments we will place the highest priority on hiring technology-driven biologists with broad research interests. We anticipate that several will have programs that span multiple taxonomic groups. In evaluating candidates we will place primary importance on whether they are using the optimal organism to address a biological question of central importance to the Center’s vision. We also will consider how many other faculty will be enabled by access to the technology the candidate uses. These matters will be more important hiring criteria than the specific organism they study, or the kingdom in which it occurs. We anticipate that the final distribution of faculty recruits will be approximately evenly divided among microbial, animal/ human and plant biologists. Hiring will be closely coordinated with interested groups across campus and will rely heavily on these groups to identify and recruit the best candidates. Our recruitment strategy will be designed both to build on existing campus strengths and to address currently unmet needs and opportunities.

Areas of strength that could be complemented by recruitments into the Genome Center include plant genomics, chromosome biology, population genetics, and infectious diseases. In plant biology, the campus is particularly strong in translational plant genomics. This provides the opportunity to make significant recruitments in rice genomics, which would have a concomitant impact of improving this critical food crop. Several aspects of chromosome biology also are particularly strong on campus. Knowledge of chromosome structure coming from genome projects is leading to insights as to how chromosomes function. This in turn is providing new tools for manipulating chromosomes, altering their behavior and potentially enabling targeted gene replacement. These abilities will impact many fields from cancer biology to neurosciences to plant breeding. Population genetics is also strong on campus; one or more hires in the area of mammalian population genetics would complement existing strengths. There are major programs on infectious diseases of both animals and plants on campus. These have multiple similarities on both the host and pathogen sides that could be studied productively at the genomic level. 

Areas of opportunity that could be addressed by recruitments to the Genome Center include microbial genomics, mammalian genetics and foods for health. There is a wealth of opportunities being created by the rapid increase in the number of fully sequenced bacterial genomes, and recently also of fungal genomes. Comparative microbial genomics is currently an unmet teaching and research opportunity at Davis. Faculty appointments in microbial genomics could also contribute to developing our breadth of expertise in host-pathogen interactions and infectious diseases. The Human Genome Project will obviously continue to provide new opportunities in all areas of biomedical research. The Genome Center needs to ensure that the campus as a whole participates in these emerging disciplines. In addition, there is growing momentum on campus for a ‘Foods for Health’ initiative to which the Center should and will contribute. 

The recruitments in bioinformatics will occur in tandem with the wet lab recruits, and share a common vision. Priority areas for hiring will be those that meet a need for specific expertise in areas of importance to the strategic plan for the center. These include protein structure prediction, small molecule bioinformatics, statistics, human population genetics, comparative genomics (at multiple levels from sequences to systems), databases (design, construction and integration), and complex traits. 

It is important that faculty recruitment be balanced among the senior, mid-career, and junior ranks. Senior faculty will have well-established, well-funded research programs that will contribute to meeting our Garamendi obligations, and will provide both national and international visibility, and campus-wide leadership in genomics. The mid-career and junior faculty will be the future of the Center and likely will provide much of its drive for ongoing technological innovation. We will aim to hire approximately one third full professors, one third associate professors, and one third assistant professors. There may be an initial emphasis on recruiting at the senior level, as high-profile hires can help attract the strongest candidates at lower levels.

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Space

The Genome Center will be located in the GBSF building, which is scheduled for occupancy on July 1, 2004. The core faculty will be housed primarily on the 4th floor and part of the 5th floor. The core facilities will be housed on the 1st floor. Even with this new building the Center will be acutely short of space. Our allocation does not provide enough lab space for ten large genomics programs. From the outset of the building planning process we knew this would be the case. However, the amount of space was constrained by the maximum budget threshold for the building ($100M) and the maximum number of floors possible without triggering additional seismic requirements. Therefore, it will not be possible to accommodate existing faculty from campus in the Genome Center. Relocation of such faculty into the Center is also undesirable as their appropriate role is to act as bridges for transferring advanced technologies from the Center to the wider campus community. Also, it is likely that large genomics programs for core faculty will have to be accommodated by such programs having space in the GBSF and in their home departments. Although this is less desirable than collocation of all programs, it will also help integration of Genome Center activities with the rest of campus.
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Technology Service Component

The Genome Center will aim to provide enabling genomic technologies that are not readily available elsewhere either on or off campus. The Genome Center will not provide access to technologies where the campus already has good service resources, as presently is the case for DNA sequencing. When radical technological advances occur, such as the ability to sequence of hundreds of kb at a time, we will assess what the Genome Center’s role should be in providing the campus with access to the new technologies. 

We currently envision at least four initial service foci: high-throughput genotyping, analysis of macromolecular complexes, analysis of small molecules, and bioinformatics.

Genotyping: The ability to perform low-cost, high-throughput genotyping will revolutionize many areas of biology, from pharmacogenomics to ecology and plant breeding. Currently, there is no single genotyping technology that suits all purposes, and costs are still an order of magnitude too high for routine large-scale analysis. However, technologies are advancing rapidly and costs falling in concert. The Genome Center will provide a variety of genotyping technologies as they become cost-effective for the levels of demand anticipated on campus. This will include upstream sample processing as well as downstream data analysis support. It may also provide BAC library and physical mapping technologies, depending on whether these are areas of expertise of the hired faculty.

Macromolecular Complexes: Many areas of biological investigation will be advanced by the ability to rapidly analyze macromolecular complexes. The Genome Center will develop and provide the service to purify intact macromolecular complexes from microbes, animals and plants and then to identify their constituent components. This core will rely heavily on advanced separation technologies and mass spectroscopy and will complement existing campus strengths in structural biology and cryoEM.

Analysis of Small Molecules: The ultimate result of changes in patterns of gene expression is often the alteration of the small molecule composition of the cell. The technology is now becoming available for in-depth analysis of the small molecule composition of cells. However, the complete characterization of the output from such analyses remains challenging. The Genome Center will develop and implement a service for in-depth analysis of a variety of types of small molecules as well as for interpretation of the experimental data. This again will rely heavily on mass spectroscopy. 

Bioinformatics: Bioinformatics is often both the key and the bottleneck to gleaning new biological knowledge from high-throughput experiments. A wide variety of computational and analytic methods are used, depending on the biological question being asked and the experimental system and procedures used. Examples include sequence assembly and analysis, macromolecular structure prediction, inference and analysis of pathways and regulatory networks, database design, development and integration, and statistical analysis. The Center will provide access to a bioinformatics core that will assist in developing the bioinformatics resources needed in specific high demand applications. This core will provide some level of training in the use of bioinformatics tools and some access to large-scale computing resources. It may also host and support specialized genomics databases.

The costs of each of these services will be recharged in a manner designed to make them accessible to the broadest spectrum of researchers. Equipment will be bought through grant support with matching funds from the campus. Salaries for core technological support will be subsidized by the campus. The cost of the consumables will be recharged, along with a small amount of personnel and equipment depreciation costs.

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Coordination with other faculty

Neither the technology service component nor the recruitment of faculty will be possible without extensive consultation, input and commitment from faculty throughout campus. There will be the necessary advisory and search committees to ensure that this occurs. 

The forgoing is the strategic plan for the Genome Center as it currently stands. It has evolved greatly over the past four years and will undergo further refinement in light of additional input from the faculty and experience as it is implemented.

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