Genomics, Phenomics, and Bioinformatics

It is the intent of the program to admit students into one of three tracks. The Functional Genomics track will be for students interested in the generation and application of genomic information. The Bioinformatics track is intended for students interested in using computational and statistical approaches to analyze large amounts of genomic data. The Phenomics track will be attractive to students interested in the application of high-throughput equipment to measure important traits necessary for full expression of the traits necessary for the organism to productively complete its life cycle.

The 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 Bachelor of Science (B.S.) degree with an introductory biology class emphasizing molecular biology; with courses in genetics, physiology, biochemistry; an upper-division statistics class.  A minimum undergraduate GPA of 3.0.

Bioinformatics and Phenomics tracks: a B.S. degree with an introductory biology class emphasizing molecular biology; with courses in calculus, upper-division statistics class, calculus or matrix algebra, and programming language experience.  A minimum undergraduate GPA of 3.0.

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

Adviser and Supervisory Committee

During the first year, the student will form a supervisory 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, Phenomics, 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). Requirements for GSR can be found here.

Master's Requirements

Functional Genomics - Thesis Option
Core Courses
PLSC 611Genomics3
CSCI/MATH/STAT 732Introduction To Bioinformatics3
PLSC 721Genomics 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 Seminar1
Electives: At least one course from two elective areas9
798 Master's Thesis (6-10)
Total Credits30

Functional Genomics Comprehensive Study Option
PLSC 611Genomics3
CSCI 732Introduction To Bioinformatics3
PLSC 721Genomics Techniques ( or)2
BIOC 674Methods of Recombinant DNA Technology3
796 Current Topics (1 credit, 2 semesters)2
790 Graduate Seminar1
Electives: At least one course from two elective areas
797 Master's Paper4
Total Credits30

Bioinformatics - Thesis Option
PLSC 611Genomics3
CSCI 732Introduction To Bioinformatics3
CSCI 859Computational Methods in Bioinformatics3
796 Current Topics ( 1 credit, two semesters)2
790 Graduate Seminar1
Electives: At least one course from two elective areas9
798 Master's Thesis6-10
Total Credits30

Bioinformatics Comprehensive Study Option
PLSC 611Genomics3
CSCI 732Introduction To Bioinformatics3
CSCI 859Computational Methods in Bioinformatics3
796 Current Topics (1 credit, 2 semesters)2
790 Graduate Seminar1
Electives: At least one course from two elective areas15
797 Master's Paper 4
Total Credits30

Phenomics Thesis Option
CSCI 679Introduction to Data Mining3
ABEN 747Numerical Modeling of Environmental and Biological Systems3
Physiology Elective3
796 Special Topics (1 credit, 2 semesters)2
790 Graduate Seminar1
Electives: At least one course from two elective areas9
798 Master's Thesis6-10
Total Credits30

Physiology Electives
ANSC 663Physiology of Reproduction3
BIOL 660Animal Physiology3
BIOL 662Physiological Ecology3
BIOL 664Endocrinology3
BIOL 683Cellular Mechanisms of Disease3
BIOL 825Biology of Aging3
BIOL 861Advanced Physiology - Physiology of Extremes3
MICR 6503
MICR 680Microbial Physiology3
PPTH 751Physiology Of Plant Disease3
PLSC 686Applied Crop Physiology3
PLSC 750Crop Stress Physiology3
PSCI 747Cardiovascular Pharmacology3
PSCI 762Advanced Biopharmaceutics2
PSCI 765Cancer Cell Biology2
Gene Expression
BIOC 660Foundations of Biochemistry and Molecular Biology I3
BIOC 683Cellular Signal Transduction Processes and Metabolic Regulation3
BIOC 719Molecular Biology of Gene Expression and Regulation3
BIOC 723Structural Basis of Membrane Transport and Signaling3
BIOL 682Developmental Biology3
BIOL 820Advanced Cell Biology3
MICR 7753
PLSC 731Plant Molecular Genetics3
Genetics and Genomics Electives
ANSC 6573
ANSC 7501
ANSC 7511
ANSC 7521
BIOL 679Biomedical Genetics and Genomics3
BIOL 859Evolution3
BIOL 860Evolutionary Ecology3
BIOL 862Environment and Adaptation3
MICR 681Microbial Genomics with Computational Laboratory3
MICR 682Microbial Genetics3
MICR 783Advanced Bacterial Genetics and Phage3
PLSC 631Intermediate Genetics (required for Functional Genomics Option)3
PLSC 7414
PLSC 751Advanced Plant Genetics3
PLSC 782Population and Quantitative Genetics4
PPTH 755Population Biology of Plant Pathogens3
PPTH 759Host-Parasite Genetics3
PSCI 617Pharmacogenomics2
Computer Science, Statistics, and Computational Biology Electives
ANSC 850Linear Models in Animal Breeding1
ANSC 851Genetic Prediction1
ANSC 852Applied Variance Component Estimation1
ANSC 8561
BIOL 842Quantitative Biology3
BIOL 877Analysis of Population and Demographic Data3
CSCI 679Introduction to Data Mining3
CSCI 724Survey of Artificial Intelligence3
CSCI 736Computational Intelligence3
CSCI 765Introduction to Database Systems3
CSCI 8793
MATH 630Graph Theory3
MATH 636Combinatorics3
MATH 684Mathematical Methods of Biological Processes3
MATH 830Graph Theory3
MATH 839Topics in Combinatorics and Discrete Mathematics3
MATH 867Topics in Applied Mathematics3
MICR 7243
PLSC 749Applied Plant Molecular Breeding3
PH 674Epidemiology3
PH 706Essentials of Epidemiology3
PH 731Biostatistics3
PH 750Epidemiologic Methods I2
PH 752Epidemiologic Methods II2
PLSC 724Field Design I3
STAT 650Stochastic Processes3
STAT 661Applied Regression Models (required for Bioinformatics Ph.D. option)3
STAT 711Basic Computational Statistics using R3
STAT 712Applied Statistical Machine Learning3
STAT 713Introduction to Data Science3
STAT 714Statistical Big Data Visualization3
STAT 725Applied Statistics3
STAT 764Multivariate Methods3
STAT 840Introduction to Statistical Design and Analysis of Gene Expression Experiments3
STAT 851Bayesian Statistical Inference3
STAT 860Statistical Machine Learning3
Modeling and Sensing Electives
ABEN 747Numerical Modeling of Environmental and Biological Systems3
ABEN 758Applied Computer Imaging and Sensing for Biosystems3
CE 725Biomaterials-Materials in Biomedical Engineering3
CSCI 628Artificial Intelligence, Ethics, and the Environment3
GEOG 655Introduction to Geographic Information Systems4
GEOG 656Advanced Geographic Information Systems3
GEOG 670Remote Sensing3
GEOG 680Geographic Information Systems Pattern Analysis and Modeling3
PAG 654Applications of Precision Agriculture3

Doctoral Requirements

Functional Genomics
PLSC 611Genomics3
CSCI 732Introduction To Bioinformatics3
PLSC 721Genomics Techniques (or)2
or BIOC 674 Methods of Recombinant DNA Technology
796 Current Topics (1 credit, 3 semesters)3
790 Graduate Seminar (1 credit, 2 semesters)2
Requested Core Courses (unless in M.S. transcript)
PLSC 631Intermediate Genetics3
STAT 726Applied Regression and Analysis of Variance3
Graduate Evolution Course
Electives: At least one course from three elective areas15
899 Doctoral Dissertationup to 90

Bioinformatics Option
PLSC 611Genomics3
CSCI 732Introduction To Bioinformatics3
CSCI 859Computational Methods in Bioinformatics3
796 Current Topics (1 credit, 3 semesters)3
790 Graduate Seminar (1 credit, 2 semesters)2
Required Core Courses (unless in M.S. transcript)
CSCI 679Introduction to Data Mining3
CSCI 765Introduction to Database Systems3
STAT 661Applied Regression Models3
Electives: At least one course from three elective areas15
899 Doctoral Dissertationup to 90

Phenomics Option
CSCI 679Introduction to Data Mining3
ABEN 747Numerical Modeling of Environmental and Biological Systems3
Physiology Course3
796 Current Topics (1 credit, 3 semesters)3
790 Graduate Seminar (1 credit, 2 semesters)2
STAT 726Applied Regression and Analysis of Variance3
CSCI 765Introduction to Database Systems3
Electives: At least one course from three elective areas15
899 Doctoral Dissertationup to 90

Physiology Electives
ANSC 663Physiology of Reproduction3
BIOL 662Physiological Ecology3
BIOL 664Endocrinology3
BIOL 683Cellular Mechanisms of Disease3
BIOL 825Biology of Aging3
MICR 6503
MICR 680Microbial Physiology3
MICR 7853
PPTH 751Physiology Of Plant Disease3
PLSC 686Applied Crop Physiology3
PLSC 750Crop Stress Physiology3
PSCI 747Cardiovascular Pharmacology3
PSCI 762Advanced Biopharmaceutics2
PSCI 765Cancer Cell Biology2
Gene Expression Electives
BIOC 660Foundations of Biochemistry and Molecular Biology I3
BIOC 683Cellular Signal Transduction Processes and Metabolic Regulation3
BIOC 719Molecular Biology of Gene Expression and Regulation3
BIOC 723Structural Basis of Membrane Transport and Signaling3
BIOL 682Developmental Biology3
BIOL 820Advanced Cell Biology3
MICR 7753
PLSC 731Plant Molecular Genetics3
Genetics and Genomics Electives
ANSC 6573
ANSC 7501
ANSC 7511
ANSC 7521
BIOL 679Biomedical Genetics and Genomics3
BIOL 859Evolution3
BIOL 860Evolutionary Ecology3
BIOL 862Environment and Adaptation3
MICR 681Microbial Genomics with Computational Laboratory3
MICR 682Microbial Genetics3
PPTH 755Population Biology of Plant Pathogens3
PPTH 759Host-Parasite Genetics3
PLSC 631Intermediate Genetics3
PLSC 7413
PLSC 751Advanced Plant Genetics3
PLSC 782Population and Quantitative Genetics4
PSCI 617Pharmacogenomics2
Computer Science, Statistics, and Computational Biology Electives
ANSC 850Linear Models in Animal Breeding1
ANSC 851Genetic Prediction1
ANSC 852Applied Variance Component Estimation1
ANSC 8561
BIOL 842Quantitative Biology3
BIOL 877Analysis of Population and Demographic Data3
CSCI 679Introduction to Data Mining3
CSCI 724Survey of Artificial Intelligence3
CSCI 736Computational Intelligence3
CSCI 765Introduction to Database Systems3
CSCI 8793
MATH 630Graph Theory3
MATH 636Combinatorics3
MATH 830Graph Theory3
MATH 839Topics in Combinatorics and Discrete Mathematics3
MATH 864Calculus Of Variations3
MATH 867Topics in Applied Mathematics3
MICR 7243
PLSC 749Applied Plant Molecular Breeding3
PH 674Epidemiology3
PH 706Essentials of Epidemiology3
PH 731Biostatistics3
PH 750Epidemiologic Methods I2
PH 752Epidemiologic Methods II2
PLSC 724Field Design I3
STAT 650Stochastic Processes3
STAT 661Applied Regression Models3
STAT 711Basic Computational Statistics using R3
STAT 712Applied Statistical Machine Learning3
STAT 713Introduction to Data Science3
STAT 714Statistical Big Data Visualization3
STAT 725Applied Statistics3
STAT 726Applied Regression and Analysis of Variance3
STAT 764Multivariate Methods3
STAT 840Introduction to Statistical Design and Analysis of Gene Expression Experiments3
STAT 851Bayesian Statistical Inference3
STAT 860Statistical Machine Learning3
Modeling and Sensing Electives
ABEN 747Numerical Modeling of Environmental and Biological Systems3
ABEN 758Applied Computer Imaging and Sensing for Biosystems3
CE 725Biomaterials-Materials in Biomedical Engineering3
CSCI 628Artificial Intelligence, Ethics, and the Environment3
GEOG 655Introduction to Geographic Information Systems4
GEOG 656Advanced Geographic Information Systems3
GEOG 665Remote Sensing of the Environment3
GEOG 670Remote Sensing3
GEOG 680Geographic Information Systems Pattern Analysis and Modeling3
PAG 654Applications of Precision Agriculture3

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 graduate program faculty will submit these questions. The oral exam will be administered by the student's supervisory 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: The final exam will be an oral defense of the student's research results. The student's supervisory committee will administer the exam.