Genomics and Bioinformatics
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 |
|---|---|---|
| Functional Genomics - Thesis Option | ||
| Core Courses | ||
| PLSC 611 | Genomics | 3 |
| CSCI/MATH/STAT 732 | Introduction To Bioinformatics | 3 |
| PLSC 721 | Genomics Techniques ( BIOC 674 is 3 credits) | 2 |
| or BIOC 674 | Methods of Recombinant DNA Technology | |
| 796 Current Topics in Genomics (1 credit, 2 semesters) | 2 | |
| 790 Graduate Seminar | 1 | |
| Electives: At least one course from two elective areas | 9 | |
| 798 Master's Thesis (6-10) | ||
| Total Credits | 30 | |
| Code | Title | Credits |
|---|---|---|
| Functional Genomics Comprehensive Study Option | ||
| PLSC 611 | Genomics | 3 |
| CSCI 732 | Introduction To Bioinformatics | 3 |
| PLSC 721 | Genomics Techniques ( or) | 2 |
| BIOC 674 | Methods of Recombinant DNA Technology | 3 |
| 796 Current Topics (1 credit, 2 semesters) | 2 | |
| 790 Graduate Seminar | 1 | |
| Electives: At least one course from two elective areas | ||
| 797 Master's Paper | 4 | |
| Total Credits | 30 | |
| Code | Title | Credits |
|---|---|---|
| Bioinformatics - Thesis Option | ||
| PLSC 611 | Genomics | 3 |
| CSCI 732 | Introduction To Bioinformatics | 3 |
| CSCI 859 | Computational Methods in Bioinformatics | 3 |
| 796 Current Topics ( 1 credit, two semesters) | 2 | |
| 790 Graduate Seminar | 1 | |
| Electives: At least one course from two elective areas | 9 | |
| 798 Master's Thesis | 6-10 | |
| Total Credits | 30 | |
| Code | Title | Credits |
|---|---|---|
| Bioinformatics Comprehensive Study Option | ||
| PLSC 611 | Genomics | 3 |
| CSCI 732 | Introduction To Bioinformatics | 3 |
| CSCI 859 | Computational Methods in Bioinformatics | 3 |
| 796 Current Topics (1 credit, 2 semesters) | 2 | |
| 790 Graduate Seminar | 1 | |
| Electives: At least one course from two elective areas | 15 | |
| 797 Master's Paper | 4 | |
| Total Credits | 30 | |
| Code | Title | Credits |
|---|---|---|
| Phenomics Thesis Option | ||
| CSCI 679 | Introduction to Data Mining | 3 |
| ABEN 747 | Numerical Modeling of Environmental and Biological Systems | 3 |
| Physiology Elective | 3 | |
| 796 Special Topics (1 credit, 2 semesters) | 2 | |
| 790 Graduate Seminar | 1 | |
| Electives: At least one course from two elective areas | 9 | |
| 798 Master's Thesis | 6-10 | |
| Total Credits | 30 | |
| Code | Title | Credits |
|---|---|---|
| Physiology Electives | ||
| ANSC 663 | Physiology of Reproduction | 3 |
| BIOL 660 | Animal Physiology | 3 |
| BIOL 662 | Physiological Ecology | 3 |
| BIOL 664 | Endocrinology | 3 |
| BIOL 683 | Cellular Mechanisms of Disease | 3 |
| BIOL 825 | Biology of Aging | 3 |
| BIOL 861 | Advanced Physiology - Physiology of Extremes | 3 |
| MICR 650 | 3 | |
| MICR 680 | Microbial Physiology | 3 |
| PPTH 751 | Physiology Of Plant Disease | 3 |
| PLSC 686 | Applied Crop Physiology | 3 |
| PLSC 750 | Crop Stress Physiology | 3 |
| PSCI 747 | Cardiovascular Pharmacology | 3 |
| PSCI 762 | Advanced Biopharmaceutics | 2 |
| PSCI 765 | Cancer Cell Biology | 2 |
| Gene Expression | ||
| BIOC 660 | Foundations of Biochemistry and Molecular Biology I | 3 |
| BIOC 683 | Cellular Signal Transduction Processes and Metabolic Regulation | 3 |
| BIOC 719 | Molecular Biology of Gene Expression and Regulation | 3 |
| BIOC 723 | Structural Basis of Membrane Transport and Signaling | 3 |
| BIOL 682 | Developmental Biology | 3 |
| BIOL 820 | Advanced Cell Biology | 3 |
| MICR 775 | 3 | |
| PLSC 731 | Plant Molecular Genetics | 3 |
| Genetics and Genomics Electives | ||
| ANSC 657 | 3 | |
| ANSC 750 | 1 | |
| ANSC 751 | 1 | |
| ANSC 752 | 1 | |
| BIOL 679 | Biomedical Genetics and Genomics | 3 |
| BIOL 859 | Evolution | 3 |
| BIOL 860 | Evolutionary Ecology | 3 |
| BIOL 862 | Environment and Adaptation | 3 |
| MICR 681 | Microbial Genomics with Computational Laboratory | 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 | 4 | |
| PLSC 751 | Advanced Plant Genetics | 3 |
| PLSC 782 | Population and Quantitative Genetics | 4 |
| PPTH 755 | Population Biology of Plant Pathogens | 3 |
| PPTH 759 | Host-Parasite Genetics | 3 |
| PSCI 617 | Pharmacogenomics | 2 |
| Computer Science, Statistics, and Computational Biology Electives | ||
| ANSC 850 | Linear Models in Animal Breeding | 1 |
| ANSC 851 | Genetic Prediction | 1 |
| ANSC 852 | Applied Variance Component Estimation | 1 |
| ANSC 856 | 1 | |
| BIOL 842 | Quantitative Biology | 3 |
| BIOL 877 | Analysis of Population and Demographic Data | 3 |
| CSCI 679 | Introduction to Data Mining | 3 |
| CSCI 724 | Survey of Artificial Intelligence | 3 |
| CSCI 736 | Computational Intelligence | 3 |
| CSCI 765 | Introduction to Database Systems | 3 |
| CSCI 879 | 3 | |
| MATH 630 | Graph Theory | 3 |
| MATH 636 | Combinatorics | 3 |
| MATH 684 | Mathematical Methods of Biological Processes | 3 |
| MATH 830 | Graph Theory | 3 |
| MATH 839 | Topics in Combinatorics and Discrete Mathematics | 3 |
| MATH 867 | Topics in Applied Mathematics | 3 |
| MICR 724 | 3 | |
| PLSC 749 | Applied Plant Molecular Breeding | 3 |
| PH 674 | Epidemiology | 3 |
| PH 706 | Essentials of Epidemiology | 3 |
| PH 731 | Biostatistics | 3 |
| PH 750 | Epidemiologic Methods I | 2 |
| PH 752 | Epidemiologic Methods II | 2 |
| PLSC 724 | Field Design I | 3 |
| STAT 650 | Stochastic Processes | 3 |
| STAT 661 | Applied Regression Models (required for Bioinformatics Ph.D. option) | 3 |
| STAT 711 | Basic Computational Statistics using R | 3 |
| STAT 712 | Applied Statistical Machine Learning | 3 |
| STAT 713 | Introduction to Data Science | 3 |
| STAT 714 | Statistical Big Data Visualization | 3 |
| STAT 725 | Applied Statistics | 3 |
| STAT 764 | Multivariate Methods | 3 |
| STAT 840 | Introduction to Statistical Design and Analysis of Gene Expression Experiments | 3 |
| STAT 851 | Bayesian Statistical Inference | 3 |
| STAT 860 | Statistical Machine Learning | 3 |
| Modeling and Sensing Electives | ||
| ABEN 747 | Numerical Modeling of Environmental and Biological Systems | 3 |
| ABEN 758 | Applied Computer Imaging and Sensing for Biosystems | 3 |
| CE 725 | Biomaterials-Materials in Biomedical Engineering | 3 |
| CSCI 628 | Artificial Intelligence, Ethics, and the Environment | 3 |
| GEOG 655 | Introduction to Geographic Information Systems | 4 |
| GEOG 656 | Advanced Geographic Information Systems | 3 |
| GEOG 670 | Remote Sensing | 3 |
| GEOG 680 | Geographic Information Systems Pattern Analysis and Modeling | 3 |
| PAG 654 | Applications of Precision Agriculture | 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