Genomics and Bioinformatics
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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.
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.
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 of 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 of 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.
Adviser and Graduate Committee
During the first year, the student will 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 and Bioinformatics program, and a third member from outside the student's home college. For Ph.D. students only, a fourth member of the committee serves as the Graduate School Representative (GSR). The GSR must be a full member of the graduate faculty, AND be either a tenured faculty member outside the committee chair’s/co-chairs' home department(s) OR a faculty member outside the primary college of the committee chair/co-chairs. For this interdisciplinary program, the GSR must ALSO be outside of the program. Additionally, the GSR must be clear of any conflicts of interest with either the student or the committee chair/co-chairs. Examples of possible conflicts of interest may include budgetary relationships, family or financial, personal relationships, or research and/or publication relationships between the GSR and either the student or the committee chair.
Ph.D. Program
FUNCTIONAL GENOMICS OPTION
- Ph.D. Core Courses 13 credits
- Support Courses (required unless on incoming transcript) BIOL 859 Evolution , PLSC 631 Intermediate Genetics, STAT 726 Applied Regression and Analysis of Variance
- 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
- Research to 90 credits total (NOTE: a minimum of 15 didactic credits must be 700-level courses)
BIOINFORMATICS OPTION
- Ph.D. Core Courses 13 credits
- Support Courses (required unless on incoming transcript) PLSC 731 Plant Molecular Genetics, STAT 661 Applied Regression Models, CSCI 796 Special Topics
- 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
- Research to 90 credits total (NOTE: a minimum of 15 didactic credits must be 700-level courses)
M.S. Program - Thesis Option
FUNCTIONAL GENOMICS OPTION
- M.S. Core Courses 11 credits
- 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 credits total
BIOINFORMATICS OPTION
- M.S. Core Courses 11 credits
- Electives - minimum of 9 credits; a minimum of one course must be from the Physiology, Gene Expression or Genetics Elective areas; the remainder of the courses must be from the Computational area
- Research to 30 credits total
M.S.Program - Comprehensive Study Option
FUNCTIONAL GENOMICS OPTION
- M.S. Core Courses 11 credits
- 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 credits
- Electives - minimum of 15 credits; a minimum of two courses must be from 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
- 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.
- 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.
- 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.
| Code | Title | Credits |
|---|---|---|
| Core Courses | 11 (M.S.) - 13 (Ph.D.) | |
| Genomics | ||
| Introduction To Bioinformatics | ||
| Genomics Techniques | ||
796 Current Topics in Genomics 2 (MS) or 3 cr. (Ph.D.) | ||
790 Graduate Seminar 1 (M.S.) or 2 (Ph.D.) cr | ||
| Code | Title | Credits |
|---|---|---|
| Electives | ||
| Physiology | ||
| ANSC 828 | Advanced Reproductive Biology | 3 |
| MICR 670 | Basic Immunology | 3 |
| MICR 680 | Microbial Physiology | 3 |
| MICR 781 | Advanced Bacterial Physiology | 3 |
| PPTH 751 | Physiology Of Plant Disease | 3 |
| ZOO 660 | Animal Physiology | 3 |
| ZOO 664 | Endocrinology | 3 |
| ZOO 682 | Developmental Biology | 3 |
| ZOO 866 | Advanced Animal Behavior | 3 |
| Gene Expression | ||
| BIOC 719 | Molecular Biology of Gene Expression and Regulation | 3 |
| BOT 820 | Advanced Cell Biology | 3 |
| MICR 775 | Molecular Virology | 3 |
| PLSC 731 | Plant Molecular Genetics | 3 |
| Genetics | ||
| BIOL 859 | Evolution | 3 |
| BIOL 796 | Special Topics | 3 |
| MICR 682 | Microbial Genetics | 3 |
| MICR 783 | Advanced Bacterial Genetics and Phage | 3 |
| PLSC 631 | Intermediate Genetics (required for Functional Genomics Option) | 3 |
| PLSC 741 | Cytogenetics | 4 |
| PLSC 751 | Advanced Plant Genetics | 3 |
| PLSC 780 | Population Genetics | 2 |
| PLSC 781 | Quantitative Genetics | 2 |
| PPTH 759 | Host-Parasite Genetics | 3 |
| Computational | ||
| CSCI 724 | Survey of Artificial Intelligence | 3 |
| CSCI 859 | Computational Methods in Bioinformatics | 3 |
| CSCI 760 | Dynamic Programming | 3 |
| CSCI 765 | Introduction To Database Systems | 3 |
| CSCI 783 | Topics In Software Systems | 3 |
| CSCI 796 | Special Topics ( Knowledge Discovery in Biological Data) | 3 |
| CSCI 796 | Special Topics (Signal Processing and Analysis in Bioinformatics) | 3 |
| MATH 684 | Mathematical Methods of Biological Processes | 3 |
| STAT 650 | Stochastic Processes | 3 |
| STAT 661 | Applied Regression Models (required for Bioinformatics Ph.D. option) | 3 |
| STAT 730 | Biostatistics | 3 |
| STAT 764 | Multivariate Methods | 3 |
| STAT 796 | Special Topics (required for Bioinformatics Ph.D. option) | 3 |
Peter Bergholz, Ph.D.
Michigan State University, 2007
Department: Veterinary and Microbiological Sciences
Research Interest: Bacterial Population and Landscape Genomics
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
Anne Denton, Ph.D.
University of Mainz, 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
Nathan Fisher, Ph.D.
University of Michigan, 2006
Department: Veterinary and Microbiological Sciences
Research Interest:Functional Genomics and Gene Exaptation
Timothy Friesen, Ph.D.
North Dakota State University, 2001
Department: Plant Pathology
Research Interest: Host-Pathogen Interactions of Cereals
Jill Hamilton, Ph.D.
University of British Columbia, 2012
Department: Biological Sciences
Research Interest: Plant Evolutionary Genomics
David P. Horvath, Ph.D.
Michigan State University, 1993
Department: Plant Sciences
Research Interest: Perennial Weed Physiology
Rick Jansen, Ph.D.
University of Minnesota, 2009
Department: Public Health
Research Interest: Molecular and Genomic Epidemiology
Zhaohui Liu, Ph.D.
North Dakota State University, 2006
Department: Plant Pathology
Research Interest: Host-Parasite Interactions of Wheat
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, 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
Katie Reindl, Ph.D.
North Dakota State University, 2006
Department: Biological Sciences
Research interest: Cancer cell biology
Saeed Salem, Ph.D.
Rensselaer Polytechnic Institute, 2009
Department: Computer Science
Research Interest: Bioinformatics Analysis of Biological Networks
Vasant A. Ubhaya, Ph.D.
University of California-Berkeley, 1971
Department: Computer Science and Operations Research
Research Interest: Algorithm Analysis, Operations Research
Changhui Yan, Ph.D.
Iowa State University, 2005
Department: Computer Science
Research interest: Computational Bioinformatics
Yarong Yang, Ph.D.
Northern Illinois University, 2010
Department: Statistics
Research interest: Bioinformatics