Graduate Faculty

701-231-8443

Marc D. Anderson, Ph.D.
Iowa State University, 1995
Department:
Biological Sciences
Research Interest:
Plant Stress Physiology

Eugene Berry, Ph.D.
Northeastern University, 1983
Department:
Veterinary and Microbiological Sciences
Research Interest:
Animal Virology

Xiwen Cai, Ph.D.
Washington State University, 1998
Department:
Plant Sciences
Research Interest:
Cytogenetics

Michael J. Christoffers, Ph.D.
University of Missouri-Columbia, 1998
Department:
Plant Sciences
Research Interest:
Weed Molecular Genetics

Edward L. Deckard, Ph.D.
University of Illinois, Champaign-Urbana, 1970
Department:
Plant Sciences
Research Interest:
Crop Physiology

Anne Denton, Ph.D.
University of Mainz, Germany, 1996
Department:
Computer Science
Research Interest:
Data Mining, Bioinformatics

Justin D. Faris, Ph.D.
Kansas State University, 1999
Department:
Plant Sciences
Research Interest:
Wheat Molecular Genetics

Marvin W. Fawley, Ph.D.
Miami University, 1985
Department:
Biological Sciences
Research Interest:
Evolutionary Biology

David P. Horvath, Ph.D.
Michigan State University, 1993
Department:
Plant Sciences
Research Interest:
Perennial Weed Physiology

Shahryar F. Kianian, Ph.D.
University of California-Davis, 1990
Department:
Plant Sciences
Research Interest:
Wheat Molecular Genetics

Phillip E. McClean, Ph.D.
Colorado State University, 1982
Department:
Plant Sciences
Research Interest:
Plant Molecular Genetics

Steven W. Meinhardt, Ph.D.
University of Illinois, Champaign-Urbana, 1984
Department:
Biochemistry and Molecular Biology
Research Interest:
Protein Structure/Function

Kendall Nygard, Ph.D.
Virginia Polytechnic Institute and State University, 1978
Department:
Computer Science
Research Interest:
Bioinformatics

William Perrizo, Ph.D.
University of Minnesota, 1972
Department:
Computer Science and Operation Research
Research Interest:
Distributed Database Systems, Centralized Database Systems

Birgit Pruess, Ph.D.
Ruhr- Universitat Bochum, Germany , 1991
Department:
Veterinary and Microbiological Sciences
Research Interest:
Microbial Physiology and Gene Regulation

Jack B. Rasmussen Ph.D.
Michigan State University, 1987
Department:
Plant Pathology
Research Interest:
Molecular Plant/Microbe Interactions

Mark Sheridan, Ph.D.
University of California-Berkeley, 1985
Department:
Biological Sciences
Research Interest:
Control of Growth, Development and Metabolism

Vasant A. Ubhaya, Ph.D.
University of California-Berkeley, 1971
Department:
Computer Science and Operations
Research
Research Interest:
Algorithm Analysis, Operations Research

Program Description

Genomics and Bioinformatics is an interdisciplinary graduate program that involves faculty from nine departments. Advanced research and study will focus on either functional or computation genomics. The program is designed to provide both M.S. and Ph.D. students the necessary skills and intellectual background to work cooperatively with others in a research area that takes a systems-wide approach to the study of the organization and expression of the many genes and their products expressed in an organism. Exposure to modern techniques and instrumentation will prepare the student for success in both industrial and academic careers.

Admissions Requirements

It is the intent of the program to admit students in either of two tracks. The Functional Genomics Track will be for students interested in the generation and application of genomic information. The Computational Bioinformatics Track is intended for students interested in using computer science and statistical approaches to analyze large amounts of genomic data.

The Genomics graduate program is open to qualified graduates of universities of recognized standing. The Graduate School minimum for the TOEFL examination applies. In addition, the following are the requirements to be admitted with full standing.

Functional Genomics Track: a B.S. degree with courses in genetics, physiology, biochemistry; an upper-division statistics class; an introductory biology class emphasizing molecular biology; and minimum undergraduate GPA is 3.0.

Computational Bioinformatics Track: a B.S. degree with courses in calculus, comparative computer languages, data structures, an upper-division statistics class, an introductory biology class emphasizing molecular biology, and minimum undergraduate GPA is 3.0

Students can be accepted conditionally into either track without meeting the course or GPA requirements, but will be required to meet those requirements while in residency.

Degree Requirements

Adviser and Graduate Committee:

During the first year, the student will select an adviser, form a graduate committee, and submit the Plan of Study to the Graduate School. The committee must include the student's major adviser, at least one other faculty member of the genomics program, and the Graduate School appointee. For Ph.D. students only, one member of the committee must be from outside the student's home college.

Core Courses
PLSC 611 Genomics – 3 cr
CSCI/MATH/STAT 732 Bioinformatics – 3 cr
PLSC 721/BIOC 721 Genomic Techniques – 2 cr
796 Current Topics in Genomics – 2 [2 x 1 cr. (MS)] or 3 [3 x 1 cr. (Ph.D.)] cr
790 Graduate Seminar – 1 (M.S.) or 2 (Ph.D.) cr

The Ph.D. Program

Functional Genomics Option

Ph. D. Core Courses – 13 cr
Support Courses (required unless on incoming transcript)
          BIOL 659 Evolution – 3 cr
          PLSC 631 Intermediate Genetics – 3 cr
          STAT 726 – Applied Regression and Analysis of Variance – 3 cr
Electives – minimum of 15 credits from the Physiology, Gene Expression, Genetics and Computational Elective areas; one course from each of the Physiology, Gene Expression, Genetics elective areas is required
Thesis Research – to 90 credits total
 (NOTE: a minimum of 15 didactic credits must be 700-level courses)

Bioinformatics Option

Ph. D. Core Courses – 13 cr
Support Courses (required unless on incoming transcript)
          CSCI 668 – Database System Design – 3 cr
          PLSC 631 – Intermediate Genetics – 3 cr
          STAT 661 – Applied Regression Models – 3 cr
          CSCI 796 – Computational Methods in Bioinformatics – 3 cr
Electives - minimum of 15 credits; a minimum of three courses must be from the Computational area and a minimum of one course must be from either the Physiology, Gene Expression or Genetics Elective areas
Thesis Research – to 90 credits total 
 (NOTE: a minimum of 15 didactic credits must be 700-level courses)

Elective Areas

Physiology
ARSC 728 – Advanced Reproductive Biology – 3 cr
BIOC 718 – Metabolic Regulation – 3 cr
BOT 780 – Plant Metabolism and Stress Physiology – 3 cr
BOT 784 – Photobiology – 3 cr
MICR 670 - Basic Immunology – 3 cr
MICR 680 – Bacterial Physiology – 3 cr
MICR 781 – Advanced Bacterial Physiology – 3 cr
PPTH 751 – Physiology of Plant Disease – 3 cr
ZOO 660 – Animal Physiology – 4 cr
ZOO 664 - Endocrinology – 3 cr
ZOO 682 – Developmental Biology – 3 cr
ZOO 764 – Neuroendocrine and Endocrine Systems – 3 cr
ZOO 766 – Neurophysiology – 3 cr

Gene Expression
BIOC 719 – Molecular Biology of Gene Expression and Regulation – 3 cr
BOT/ZOOL 720 – Advanced Cell Biology – 3cr
MICR 775 – Molecular Virology – 3 cr
PLSC 731 – Plant Molecular Genetics – 3 cr

Genetics
BIOL 659 – Evolution – 3 cr (required for Functional Genomics Ph.D. Option)
BIOL 796 – Molecular Evolution and Phylogenetics – 3 cr
MICR 682 – Bacterial Genetics and Phage – 2 cr
MICR 783 – Adv. Bacterial Genetics and Phage – 2 cr
PLSC 631 – Intermediate Genetics – 3 cr (required for Functional Genomics Option)
PLSC 741 – Cytogenetics – 4 cr
PLSC 751 – Advanced Genetics – 3 cr
PLSC 780 – Population Genetics – 2 cr
PLSC 781 – Quantitative Genetics – 2 cr
PPTH 759 – Host-Parasite Genetics – 3 cr

Computational
CSCI 724 – Survey of Artificial Intelligence – 3 cr
CSCI 759 – Computational Methods in Bioinformatics – 3 cr
CSCI 760 – Dynamic Programming – 3 cr
CSCI 765 – Introduction to Database Systems – 3 cr
CSCI 783 – Data Mining– 3 cr
CSCI 796 – Knowledge Discovery in Biological Data – 3 cr
CSCI 796 – Signal Processing and Analysis in Bioinformatics – 3 cr
MATH 635 – Mathematical Models of Biological Processes– 3 cr
MATH 647 – Molecular Topology – 3 cr
STAT 650 – Stochastic Processes – 3 cr
STAT 651 – Bayesian Statistical Decision Theory – 3 cr
STAT 661 – Applied Regression Models – 3 cr (required for Bioinformatics Ph.D. option)
STAT 731 – Biostatistics – 3 cr
STAT 764 – Multivariate Methods – 3 cr
STAT 796 – Computational Statistics – 3 cr (required for Bioinformatics Ph.D. option)

The M.S. Program -- Thesis Option

Functional Genomics Option
M.S. Core Courses – 11 cr
Electives – minimum of 9 credits from the Physiology, Gene Expression, and Genetics areas; a minimum of one course must be selected from each of two of these areas
Research – to 30 cr total

Bioinformatics Option
M.S. Core Courses – 11 cr
Electives - minimum of 9 credits; a minimum of one course must be from the the Physiology, Gene Expression or Genetics Elective areas; the remainder of the courses must be from the Computational area
Research – to 30 cr total

The M.S. Program -- Comprehensive Study Option

Functional Genomics Option
M.S. Core Courses – 11 cr
Electives – minimum of 15 credits from the Physiology, Gene Expression, and Genetics areas; a minimum of one course must be selected from each of two of these areas
Masters Paper – to minimum of 30 credit total

Bioinformatics Option
M.S. Core Courses – 11 cr
Electives - minimum of 15 credits; a minimum of two courses must be from the the Physiology, Gene Expression or Genetics Elective areas; the remainder of the courses must be from the Computational area
Masters Paper – to minimum of 30 credit total

Examinations

1. Qualifying Exam (Ph.D. only):
   This exam consists of written and oral portions. The student will complete a written exam that emphasizes the application of materials presented in the core courses. The members of the genomics graduate program will submit these questions. The oral exam will be administered by the student's graduate committee and will focus on material beyond the core courses that are specific to the research of the student. Upon completion of the qualifying exam, the student will be accepted as a Ph.D. candidate.
2. Final Exam (M.S. and Ph.D.):
   The final exam will be an oral defense of the student's research results. The student's graduate committee will administer the exam.
3. Comprehensive Study Option Paper (M.S. only):
   M.S. students pursuing the Comprehensive Study Option will be required to complete an in-depth paper of a specific topic relevant to Genomics. The paper will be reviewed and accepted by the student's graduate committee.

Research

The student is required to perform original research in an area of genomics. This will be under the direction of the student's major adviser. To promote cross-disciplinary research, the student is encouraged to collaborate with a student in the other track. This does not apply to M.S. students pursuing the Comprehensive Study Option.