Master of Science (M.S.) In Bioinformatics
Crop Sciences Concentration

Overview

The Department of Crop Sciences offers a concentration within the campus-wide M.S. program in Bioinformatics that focuses on the agricultural and life sciences.

The discipline of Bioinformatics addresses the need to manage and interpret the data that is being massively generated by genomic and proteomic research. This discipline represents the convergence of biology, computer and information technology sciences, and encompasses analysis and interpretation of biomolecular data, modeling of biological phenomena, and development of algorithms and statistical approaches. With current technology, scientific discovery occurs in a global arena and data are stored and archived massively in databases, disseminated through cable or wireless conduits, and analyzed. This includes information on genomes, biomolecules, biomolecular circuitry, and biological processes at the molecular, cellular, organismal and population levels. Our world expects substantial pay-offs from the analysis of multi-dimensional data structures, including proactive control and clear understanding of chemical, biological and cosmological processes. Ultimately, we expect a better life. The College of Agricultural, Consumer and Environmental Sciences (ACES) and the Department of Crop Sciences have a comprehensive mission that relates to agriculture, food, and environment, and is driven mainly by a human-community dimension. This involves addressing important issues in biology. Within this framework, bioinformatics plays an important role in the management and exploitation of microbial, plant and animal genomic resources.

Students interested in our Bioinformatics program may come with undergraduate training in one of the following areas: (a) biological and agricultural sciences, (b) statistical, mathematical and computer sciences, (c) informatics and engineering sciences. Graduates from the bioinformatics program will be able to integrate basic and applied concepts in the three areas and applied them to biotechnology and medical research.

Degree Requirements For The M. S. In Bioinformatics

The Crop Sciences concentration within the M.S. in Bioinformatics is offered in both thesis and non-thesis versions.

The thesis option, requires a minimum of 32 hours, including 28 hours of coursework with at least 12 hours at the 500-level and 8 hours within the Department of Crop Sciences. Of the 32 hours, a minimum of 12 hours must be within a General core, equally distributed between Fundamental Bioinformatics, Biology, and Computer Science courses. The General core complies with the requirements of the campus-wide Master of Science in Bioinformatics. In addition, a minimum of 7 hours of courses in Computational, Quantitative and Statistical Biology must be completed, together with a minimum of 5 hours of electives. Within the Computational, Quantitative and Statistical Biology core, the students must take CPSC 440 (Applied Statistical Methods I) or CPSC 540 (Applied Statistical Methods II). No double counting is possible; the same course cannot be used to satisfy the General core and the Computational, Quantitative and Statistical Biology core requirements simultaneously. The courses approved for the General core and the Computational, Quantitative and Statistical Biology core are listed below. Electives can be satisfied with any graduate-level course; however, students must select elective courses in consultation with their departmental advisor and are strongly encouraged to select from among courses offered by the Department of Crop Sciences. Students must also complete a minimum of 4 hours of thesis within Crop Sciences research (CPSC 599). Students are required to register each semester for 1 hr of seminar in one of the sections of Crop Sciences. A student may be exempted from seminar for the semester or register for a seminar in another department upon the recommendation of his/her advisor and approval of the graduate coordinator. Students are required to present a seminar on their thesis research during the last semester of their study program.

With the permission of their advisor, students in the Department of Crop Sciences may choose to pursue a non-thesis option within the M.S. in Bioinformatics. The non-thesis option requires a minimum of 36 hours with the same course requirements specified in the thesis option. Supplementary requirements towards satisfying the 36 hours include an additional minimum of 3 hours of General Core courses, an additional minimum of 3 hours of Computational, Quantitative and Statistical Biology core courses, and an additional minimum of 3 additional hours of elective courses, for a minimum total of 9 hours. The student may incorporate supervised research experiences including internships and projects to complete the remaining required hours of the non-thesis option. No course can be used to satisfy more than one requirement.

Courses

1. General courses
   1. Fundamental Bioinformatics (4 hours)
      

      CPSC 569 / ANSC 542		Applied Bioinformatics
      ANSC 543 / CHBE 571 / STAT 530 / MCB 571		Bioinformatics

   2. Crop Science (4 hours)
      

      CPSC 452		Genetics of Higher Organisms
      CPSC 568		Recombinant DNA Technology Lab
      CPSC 566 / HORT 566		Plant Gene Regulation

   3. Computer Science (4 hours)
      

      CS 411		Database Systems
      CS 473		Algorithms

2. Courses in Computational, Quantitative and Statistical Biology
   At least 7 hours distributed as follows:
   1. One required course to be selected between:
      

      CPSC 440		Applied Statistical Methods I
      CPSC 540		Applied Statistical Methods II

   2. And at least one elective course to be selected among:

      ANSC 441   Human Genetics ANSC 444   Applied Animal Genetics ANSC 445   Statistical Methods ANSC 446   Population Genetics ANSC 447   Quantitative Genetics ANSC 543   Bioinformatics ANSC 545   Statistical Genomics CPSC 432   Genetic Toxicology CPSC 440   Applied Statistical Methods I CPSC 540   Applied Statistical Methods II CPSC 541   Regression Analysis (approval in progress) CPSC 452   Genetics of Higher Organisms CPSC 453   Principles of Plant Breeding CPSC 454   Plant Breeding Methods CPSC 558   Quantitative Plant Breeding CPSC 563   Molecular Cytogenetics CPSC 564   Molecular Marker Data Analyses CPSC 567   Bioinformatics and Systems Biology CPSC 569   Applied Bioinformatics LIS 451   Introduction to Network Systems LIS 501   Info Org and Access BIOP 420   Molecular Biophysics BIOP 541   Macromolecular Modeling CHEM 470   Computational Chemical Biology CHEM 574   Genomics, Proteomics, and Bioinformation

      CS 400   Data Structures, Non-CS Majors CS 411   Database Systems CS 413   Introduction to Combinatorics CS 418   Computer Graphics CS 420   Intro to Parallel Programming CS 446   Machine Learning & Pattern Recognition CS 450   Introduction to Numerical Analysis CS 473   Algorithms CS 484   Computer Data Acquisition Sys. CS 512   Data Mining CS 519   Scientific Visualization CS 542   Artificial Neural Networks CS 571   Information Theory STAT 424   Analysis of Variance STAT 425   Applied Regression and Design STAT 429   Time Series Analysis STAT 525   Computational Statistics STAT 571   Multivariate Analysis VP 554   Molecular and Evolutionary Epidemiology MCB 421   Microbial Genetics MCB 432   Computing in Molecular Biology IB 402   Molecular Evolution IB 405   Ecological Genetics IB 504   Genomic Analysis of Insects

3. Elective Graduate Courses
   At least two courses (5 hours) selected by the student in consultation with his/her advisor. Crop Sciences courses are highly recommended.