William D. Beavis
Citizenship: USA.
Birthplace: Ypsilanti, Michigan.
Addresses:
Positions held
Professor, and GF Sprague Chair, Department of Agronomy, Iowa State University, (Sept 2007 to present).
Chief Science Officer, NCGR, Santa Fe, NM (October 2000 to Sept., 2007).
Adjunct Professor, Department of Mathematics and Statistics, University of New Mexico (November, 2002 – Sept. 2007).
Adjunct Assistant Professor, Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico (January 2003 – December 2006).
Adjunct Research Scientist, Lovelace Respiratory Research Institute, Albuquerque, New Mexico (January 2004 – present).
Board of Directors, National Center for Genome Resources (NCGR), Santa Fe, NM (July 2001 to present).
Board of Directors, New Mexico Biomedical and Biotechnology Association (January, 2002 – January, 2004).
Board of Directors, New Mexico Technology Research Collaborative (January, 2003 – 2005).
Director of Science Programs, NCGR, Santa Fe, NM (June 1999 to October 2000).
Program Leader for Complex Traits, NCGR, Santa Fe, NM (September 1998-June 1999).
Research Statistician, Pioneer Hi-Bred, Int’l, Johnston, IA (1987-1998).
Data Manager, Sorghum Breeding Department, Pioneer Hi-Bred, Int’l, Plainview, TX (1986-1987).
Education
Ph.D., 1986, Plant Breeding Major, Statistics Minor, Iowa State University, Ames, IA.
M.S., 1981, Interdisciplinary Biology-Statistics, New Mexico State University, Las Cruces, NM.
B.S., 1978, Range Management, Humboldt State University, Arcata, CA.
Research Support:
Current:
10/01/04 – 9/31/09 (NCGR - $2,620,000)
NIH-NIAID
Role: Co-PI
Title: Immunity to Infections and Vaccines
Objectives: The goal of this proposal is to identify the genetic factors (alleleic variants at candidate genes underlying QTL) responsible for various types of immunological responses to infections and vaccines. The PI, Dr. Jeff Gulcher of deCode Genetics, will utilize their access to the medical records, familial records and genotypes of the “Icelandic” population to identify QTL. NCGR is responsible for data analyses that will link genotypes and gene expression and for development of a public immunological response database.
3/01/05 – 2/28/07 ($100,000)
NIH-NIAID
Role: Co – PI
Title: Genetic Analysis of Murine Pulmonary Immunity.
Objectives: The goal of the proposal is to identify genetic factors responsible for the pulmonary immune response to a fungal pathogen, Cryptococcus neoformans (Cne) using segregating progeny from a cross inbred strains of mice exhibiting distinct Th1 and Th2 immune responses to Cne.
Pending:
06/01/08-06/01/10 ($200,000)
USDA-NRI/PGI
Role: co-PI
Title: Training Maize Breeders for Sustainable Bioenergy Maize Production
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Completed:
10/1/05 – 9/30/07 ($1,760,000)
NSF-MGI (05-512)
Role: Co-PI
Title: Population Resource and Genome Sequence of the Vegetable Pathogen Phytophthora capsici
Objectives: Sequence five strains of Phytophthora Capsici using a novel sequencing technology. Utilize comparative genomics methods to develop gene models for oomycetes and evaluate sequence variability within this species relative to the genomic variability among Phytophthora species.
9/1/05 – 8/31/07 ($1,700,000)
NSF-BDI
Role: Co-PI
Title: Virtual Plant Information Network
Objectives: Develop a semantic web services platform based on both BioMOBY and plant ontologies. Register several plant information resources with the platform and demonstrate the utility of the platform through development of a Plant-Google like interface.
01/01/02-12/31/06 ($5,740,00)
USDA-ARS
Role:PI
Title: Model Plant Initiative, Legume Information System
Objectives: The objective of the initiative is to leverage computational tools and information resources from model organisms to economically important crops. LIS represents the first project of the Model Plant Initiative. LIS has developed automated annotation tools for genomic sequences from Medicago truncatula, the model legume, and integrated the information with genetic and genomic information from a dozen legume crop species such as soybean. The integrated information and associated bioinformatics tools are publicly accessible to legume researchers via http://www.comparative-legumes.org/lis/. In 2006 I transferred the role of PI to Dr. Greg May.
Description of funding. The MPI has been funded through a congressional appropriation and administered though a CRA from USDA-ARS. In 2006 appropriations are for $1.9M; ~$200K is used for overhead at USDA-ARS, ~$850K will support the development of a Comparative Legume Biology Program at Ames, Iowa, and ~$will support the mission of LIS that will be expanded from software engineering to include Bioinformatics Research at NCGR.
5/1/05 – 4/30/08 ($3,000,000)
NSF/PGRP
Role: Co-PI
Title: Soymap, an Integrated Map of Soybean
Objectives: Develop biological and information resources for investigation of structural and functional genomics of polyploidy in soybean. NCGR is responsible for make the data available through LIS. In 2006 I transferred the role of Co-PI to Dr. Greg May in April 2006.
10/1/06 – 12/31/06 ($225,000)
Role: PI
Title: A Legume Information Network
Objectives: Demonstrate the capability of semantic web services to interoperate a set of legume data and analysis tools from more than a single web-site in a network for purposes of identifying potential genomic orthologs among legume species.
04/01/01–09/31/04 ($500,000) NSF–BDI
Role: PI
Title: GeneX: An Internet Accessible Gene Expression Database
Objectives: The goal of the project was to develop a modular software system for data from RNA expression arrays consisting of a relational database, a common data exchange format, curation tool, query tool, and set of analysis tools in an Open Source licensing environment. The software was developed and distributed through SourceForge and seven manuscripts were produced from the project.
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09/01/99-08/31/2004 (total-$5,429,525 / NCGR-$1,931,527)
NSF-BDI
Role: Institutional representative and Co-PI
Title: AtIR-An Arabidopsis thaliana Information Resource
Objectives: In collaboration with Chris Somerville at the Carnegie Institute of Washington the objective of this project was to develop the Arabidopsis Information Resource (TAIR). All software development, except the user interface was done at NCGR. Development of the user interface and curation were done at Carnegie. Hosting and maintenance of TAIR has been at NCGR since 1999, but will be migrating to Carnegie in 2006.
02/01/03–12/31/2003 ($100,000)
USAID
Role: PI
Title: Comparative Map Viewer: an integrated bioinformatic tool to display and compare genetic information on a consensus map.
Objectives: Advance understanding of the genetic and environment bases of drought resistance through comparative cereal genomics. We used ISYS and its comparative mapping components to cross-evaluate five types of information: 1) structural, chromosomal positional data on drought-relevant genes; 2) phenotypic QTL field and experimental data; 3) gene expression information; 4) metabolic and gene regulatory pathway information; and 5) meta-data, such as annotated genes from literature references.
11/01/00 – 10/31/03 (total-$1,292,814 / NCGR-$83,649)
European Union 5th Framework.
Role: Co-PI
Title: Gene-Mine
Objectives: Our role in the GeneMine project was to develop a modular software system for lettuce germplasm and genomic information consisting of application and analysis tools, a common user interface and relational database for purposes of germplasm and biodiversity conservation. Our contribution, as the sole non-European organization of a ten-member team, consisted of porting relevant aspects of the data model from the Arabidopsis Information Resource to GeneMine and providing the interface to applications being developed by other GeneMine partners.
07/01/01-06/31/02 ($148,000)
Consultive Group for International Agricultural Research
Role: Principle Investigator
Title: Comparative Map and Trait Viewer
Objectives: We developed a software interface between the International Crop Information System and NCGR’s Integration System (ISYS) to accommodate integration of germplasm and genomic data resources.
03/01/02-02/29/03 ($18,000)
International Maize and Wheat Improvement Center
Role:Principle Investigator
Title: Comparative Map and Trait Viewer.
Objectives: We enhanced ISYS and comparative map viewing software systems to combine QTL experiments into a unified, consensus view so that plant breeders working at international centers can utilize molecular information to accelerate crop improvement.
12/31/00-12/31/01 ($35,000)
Rockefeller Foundation
Role: Institutional Represenative
Title: International Bioinformatics Workshop.
Objectives: We provided a workshop in bioinformatics for international scientists at the NCGR facilities in Santa Fe.
10/01/99-9/30/01 ($35,000)
USDA-NRI/AGI
Role: Co-PI
Title: Development of Resources for Functional Genomics in Pig
Objectives: We analyzed expressed sequence tags from the porceine genome and predicted their genetic locations based on sequence similarities to human ESTs and cytogenetic and radiation hybrid maps of the human ESTs.
06/01/99-06/01/01 ($60,000)
USDA-NRI/PGI
Role: PI
Title: Infromatics Based Comparative Mapping
Objectives: We developed a comparative map viewer that utilized sequence similarities and genetic locus names as objects for comparisons between linkage maps from related plant species.
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Education support:
Graduate Students:
Brian Munneke, Purdue University (PhD, May 2001)
Guy Brock, University of New Mexico (PhD, May 2003)
Reka Howard, Iowa State University (PhD, expected 2011)
Post Doctoral advisees:
Dr. Karen Schlauch (George Mason University)
Dr. Brian Shiloff (Exagen Corp)
Dr. Lisa Astuto (Sandia National Laboratories)
Dr. Baohong Guo (Iowa State University)
Classes taught:
Agronomy 513 Quantitative Methods for Agronomy 2008 Iowa State University
Techniques for identification of QTL:
1995 Cold Spring Harbor
1994 Cold Spring Harbor
1993 Cold Spring Harbor
1993 Iowa State University
1992 University of Minnesota
1991 Iowa State University
1991 Pioneer Hi-Bred soybean breeders
1990 Pioneer Hi-Bred corn breeders
1990 Pioneer Hi-Bred research directors
Techniques for generating linkage maps:
1994 Cold Spring Harbor
1993 Cold Spring Harbor
1991 Pioneer Hi-Bred soybean breeders
1990 Pioneer Hi-Bred corn breeders
1990 Pioneer Hi-Bred research directors
Introductory Statistics for Laboratory Experiments:
1993 Pioneer Hi-Bred, AMB labs
1993 Pioneer Hi-Bred, Disease Resistance and Insect Bioassay labs
1989 Pioneer Hi-Bred, Biotech Research Assoc
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Other Professional Activities:
2005 – 2007. Science advisory board to NSF funded CREST (Centers for Research Excellence in Science & Technology) award to the New Mexico Center for Bioinformatics & Computational Biology
2004- Lead review of the USDA-ARS Soybean Genomics and Improvement Laboratory, Beltsville, Md.
2003- present. Scientific advisory board to NSF-PGI funded project on structural genomics and association genetics of maize evolution.
2002 – present. Advisory Board to NSF-PGI funded project on functional genomics of root growth and root signaling under drought.
2001 – 2004 . Advisory Board to USDA-IFAFS funded project on Compositae Genomics Project.
2000 - 2002. Advisory Board to NSF-PGRI funded project on the Cotton Genome Project.
1999 - 2002. Advisory Board to NSF-PGRI funded project on soybean functional genomics.
1998. Panel Manager for the Plant Genome Panel of the National Research Initiative Competitive Grants Program, CSRS, USDA.
1997 Member of the Genome Panel for the National Research Initiative Competitive Grants Program, CSRS, USDA.
1997. Chair of the Gordon Research Conference on Quantitative Genetics and Biotechnology.
1996 - present. Associate Editor of Genetical Research, Cambridge.
1995 - 1996. Review panel for MILQTL program at the University of Liege, Belgium.
1994. Member of the Genome Panel for the National Research Initiative Competitive Grants Program, CSRS, USDA.
1992 – 1994. Member of the genetic nomenclature and database committees of the Maize Genome
1990 - present. Referee 5-10 manuscripts per year for Genetics, Theoretical and Applied Genetics, Crop Science, Trends in Genetics, Trends in Plant Science.
1990 - 1995. Review competitive grant proposals submitted to PHI.
1993 - 1994. Chair of maize mapping team at PHI.
1992 - 1994. Heterosis committee member at PHI.
1992 - 1995. Guest lecturer for classes at Cold Spring Harbor, Iowa State University and University of Minnesota.
1992 - 1994. Served on graduate student committees at Iowa State University.
Honors:
2002 Elected to the Board of Directors for the New Mexico Biomedical and Biotech Association
2001. Elected to the Board of Directors for the National Center for Genome Resources.
1998. Recognition for development of a useful Maize RFLP map conferred by the Department of Biotechnology at Pioneer Hi-Bred.
1993. Elected to chair the Gordon Research Conference on Quantitative Genetics and biotechnology for 1997.
1985. Iowa State University Research Excellence Award. This award is conferred upon the top ten percent of the dissertations submitted to the graduate college.
1985. Awarded a competitive mini-grant from the Iowa State Graduate College for cooperative work with the University of Minnesota on isolation and electrophoretic separation in enzyme- restricted mtDNA from Avena species.
Honor Societies:
1983 Gamma Sigma Delta.
1980 Sigma XI.
Referenced Publications- Click Here
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