Annual Report 2005

PROGRESS REPORT - Year 1

1.   What has been accomplished so far?

Pre-Year 1

Goal:   Plan the Initiative hiring process, and prepare for likely needs to strengthen the computational infrastructure in the Center for Genome Research and Biocomputing (CGRB).

Outcome:   The hiring of three new faculty (one of which could be at the Assoc. or Full Prof. level) was planned.   The CGRB computational infrastructure was expanded (more nodes in cluster, new servers for core facilities) and an additional computational scientist (Chris Sullivan) was hired.

Year 1

Goal:   Hire three new faculty in Computational and Genome Biology.

Outcome:   A consortium of departments, colleges and centers with high interest in the CGBI Initiative (Center for Genome Research and Biocomputing, Environmental Health Sciences Center, the Departments of Botany and Plant Pathology, Biochemistry and Biophysics, Microbiology, Environmental and Molecular Toxicology, Zoology, and the Colleges of Agricultural Sciences, Science and Pharmacy) all agreed in principle to support the hiring of three new faculty.   A search committee was formed with representatives of each department and college.   Key outcomes of the search as follows:

• Major, international search was done for three new faculty.   The original plan was designed to bring in two faculty in year 1, and one faculty in year 2.   We executed the search, however, to enable hiring three in year 1 if the candidates warranted three offers.
• Application closing date was May 23, 2005, and the search finished with approximately 115 applicants
• Interviews were conducted with 11 candidates, with 7 on-site interviews completed by August 20, 2005. FOUR outstanding candidates were identified, and strategies to hire all four were pursued with the College of Science and College of Agricultural Sciences.
• Three positions converted to FOUR positions.   One position was split into two, but with the same resource commitment from CGBI.   CAS and CoS committed to provided the additional funding necessary to make the offers.   Offers are in progress for Dee Denver (Zoology), Todd Mockler (Bot. and Plant Path), Erica Bakker (Horticulture) and Michael Freitag (Biochem./Biophysics).  
• A fifth candidate, Jeff Chang, was recruited into the CGBI after being hired in the Department of Botany and Plant Pathology through a different search.   The CGBI committed additional funds for start-up and salary.   He will begin March 1, 2006.

2.   Plans for 2005-06 (completion of Year 1)

Goal:   Completion of offers to candidates - An important component of these searches was to offer peer-competitive salaries and startup packages.   This was seen as necessary to the Initiative.   Offers were made to:

DEE DENVER - anticipated start date April 1, 2006

PH.D. (2002) University of Missouri-Kansas City

Post-doctoral Advisor (2002-2005) Michael Lynch, Indiana University

Recruiting Department/College:   Department of Zoology/College of Science

Research Area: Genome and transcriptome evolution in C. elegans

TODD MOCKLER - anticipated start date June 30, 2006

PH.D. (2002) University of California-Los Angeles

Post-doctoral Advisor (2002-present) Joanne Chory, The Salk Institute

Recruiting Department/College:   Department of Botany and Plant Pathology/College of Agricultural Sciences

Research Area: Functional genomics and whole-genome expression profiling in Arabidopsis

ERICA BAKKER - anticipated start date - June 30, 2006

PH.D. (2001) Wageningen University

Post-doctoral Advisor (2001-present)   Martin Kreitman, University of Chicago, Department of Ecology and Evolution

Recruiting Department/College :   Department of Horticulture/College of Agricultural Sciences

Research Area: Genome evolution in Arabidopsis

MICHAEL FREITAG - anticipated start date July 1, 2006

PH.D. (1996) Oregon Graduate Institute of Science and Technology

Post-doctoral Advisor (1996-present) Eric Selker, University of Oregon

Recruiting Department/College:   Departments of Microbiology or Biochemistry and Biophysics/College of Science

Research Area: Epigenomics in Neurospora

JEFFREY CHANG - anticipated start date March 1, 2006

PH.D. (1999) University of California-Davis

Post-doctoral Advisor (1999-present) Jeff Dangl, University of North Carolina-Chapel Hill

Hired by Department of Botany and Plant Pathology, beginning March 1, 2006

College of Science and College of Agricultural Sciences

Research Area: Genomics, biochemistry and evolution of bacterial type III effector systems

Once offers are accepted, work will shift to ensure they set their laboratories up efficiently and quickly.

Goal:  Initiate Renovation of MCB Curriculum.   Plans for the new faculty to teach in the MCB Graduate Program will be further developed.   We are specifically interested in upgrading four existing courses and initiating three new courses in computational and genome biology.   Of course, progress in defining future instruction in year 1, prior to arrival of faculty, will be limited.

Goal:  Attract and elevate profile of graduate students in computational and genome biology in the MCB Graduate Program.   Two fellowships for GRAs will be offered to attract a cadre of Ph.D. students to the program for enrollment in 2006-2007.   Recruitment activities begin in late Fall, 2005.

Goal:  Enhance and relocate the CGRB computational infrastructure.   The existing room housing our distributed servers, compute cluster and network infrastructure is located in unreliable and unsecured space.   We seek to have a plan in place to move the infrastructure to ALS, possibly in space already occupied by the CGRB,

3.   Where you want to be when your initiative is fully developed/matured?

• Major strength in Computational and Genome Biology at OSU.   Strong impact on existing departments and programs through infusion of new faculty, new graduate students and new or revised core facilities.   We envision OSU being recognized as a major force in these areas of science, which will serve to attract students, faculty, postdoctorals and stature to OSU.
• Recognition as an excellent destination for graduate students in computational and genome-based biology.   They will be accommodated through formulation of a new track – Computational and Genome Biology – within the MCB Graduate Program
• Major new community resources and core facilities, primarily through the CGRB, enabling high-throughput and computation-intensive bioscience.   This will serve to attract new grant money broadly across OSU.
• Recognition as a center of high-impact discovery, attracting donors and gift-givers to OSU.

4.   A few simplified metrics that will be easy for others to understand

• Leveraged approximately $3.1 million from CGRB, Research Office and Colleges to combine with Provost's Initiative funds.
• Funds originally proposed for THREE new faculty were leveraged to provide support for FIVE new faculty in four departments.
• Within five years, each faculty is projected to generate $450,000/yr in external grant funding.
• Both salary and start-up packages offered are recognized as peer-competitive by our external advisors (Brian Staskawicz of UC Berkeley, and Steve Kay of The Scripps Research Institute).
• Five new or revised courses to be offered by MCB Graduate Program within three years.

5.   Other helpful information (examples include student credit hours that will be/could be generated; new dollars that will be generated from the dollars invested; a summary of what OSU gets for this investment)

• In addition to research funding to new faculty, the Initiative and new CGRB investment will continue to fuel high-value, grant-generating activities from existing programs.   Examples of early payoffs from these investments include funding for projects like the Oceanic Microbial Genome project ($3.3 million, Moore Foundation; PI:   Giovannoni), Arabidopsis Small RNA project ($1.7 million, NSF; PI: Carrington), the Poplar tree genome project ($1.2 million, DOE; PIs:   Strauss and Brunner), and the renewal of the Marine Freshwater Biomedical Research Center ($2.1 million, NIH; Director: Williams).

Progress Report prepared by:  

James C. Carrington

Director, Center for Genome Research and Biocomputing, and

Co-coordinator, Computational and Genome Biology Initiative