Graduate Programs

Checklist

The program is interdisciplinary and it is therefore expected that there will be diverse backgrounds in the students admitted to this program. To ensure that all fundamental knowledge is adequately present, candidates may need to complete courses, which depend on the candidates’ backgrounds. For example, a student with an experimental biology background needs to take programming courses. The courses are thus individualized for each candidate based on their previous experience and research activities to be pursued where applicable. Some candidates may already possess this background information. In such circumstances, the candidate’s Thesis Committee may award credit for previous experience. These courses can be at the undergraduate level but do not count towards the 30 credits in the case of the Master’s and 72 credits in case of the PhD degrees. Students with sufficient background can start taking graduate level classes counting towards the graduate degree in their junior year, but the majority will do so in their senior year.  The program will be flexible given the expected diverse backgrounds of the students, and will offer boot-camp style activities at the beginning of each core class in order to account for the differences in backgrounds, where students from one background will help teach students with other backgrounds to acquire complementary skills.

PhD Qualifying Process

Core Curriculum – The three required core classes must be completed in the first two full academic years for all doctoral candidates, except where remedial classes or prerequisites need to be taken prior. Students must obtain a grade of B- or better in each class and have a cumulative GPA of 3.0 or higher to be eligible to take the qualifying examination at the end of the succeeding spring semester. If not allowed to complete the qualifying examination at the end of the spring semester, students will be discouraged from the PhD program and encouraged, rather, to finish with a Master’s degree.

PhD Qualifying Examination – All first-year Quantitative Biosciences and Engineering PhD students are expected to successfully complete the qualifying examination at the end of the first year to remain in good standing in the program. The examination covers material from the core curriculum plus the theoretical background of their chosen area of research. If a student performs below the expectations of the faculty administering the oral exam, a student may need to finish with a Master’s degree.

PhD Thesis Proposal – A student’s PhD thesis committee administers the PhD Thesis Proposal defense. The PhD proposal defense should occur no later than the student’s fourth semester. While the proposal itself should focus on the central topic of the student’s research, during the proposal defense, candidates may expect to receive a wide range of questions from the Committee. This would include all manner of questions directly related to the proposal. Candidates, however, should also expect questions related to the major concept areas of Biology within the context of a candidate’s research focus. The Committee formally reports the results of the PhD proposal defense to the Quantitative Biosciences and Engineering Program Director using the Committee Reporting form developed by the Office of Graduate Studies.

Upon completion of these steps and upon completion of all required coursework, candidates are admitted to candidacy. Following successful completion of coursework and the PhD qualifying process, candidates must also submit a thesis and successfully complete the PhD Defense of Thesis examination before the PhD Thesis Committee.

BIOL500. CELL BIOLOGY AND BIOCHEMISTRY + LAB. 4.0 Semester Hrs.

This specially designed core course for Integrative Graduate Program in Quantitative Biosciences and Engineering will provide students with deep biological insight as well as hands-on experience of studying a biological question at the level of the cell, including gene expression and localization of proteins in eukaryotic cells, to the level  of the protein, from molecular biology of the gene to characterization of posttranslational modifications, and protein purification and biochemical and biophysical characterization of protein structure and dynamics. These fundamental properties will be linked to protein activity and function.

BIOL510. APPLIED BIOINFORMATICS. 3.0 Semester Hrs.

In this course, the concepts and tools of bioinformatics and computational biology will be covered in detail. Examples relating to the other two core required classes, BIOL500: Cell biology and biochemistry, and BIOL520: Systems biology will be presented. The molecular biology of genomics and proteomics will be presented and the techniques for collecting, storing, retrieving and processing such data will be discussed. Topics include the analysis of DNA, RNA and protein sequences, gene recognition, gene expression, protein structure prediction, molecular dynamics simulations and  modeling evolution. Students will use BLAST and other online tools for the exploration of genome, proteome and other available databases. In parallel, there will be an introduction to programming languages frequently used in bioinformatics (Perl, Python, Matlab, R, etc.). Practical applications to biological research and disease will be presented and students will be given opportunities to use this suite of tools. Prerequisites: CSCI261, MATH323 or equivalent.

BIOL520. SYSTEMS BIOLOGY. 3.0 Semester Hrs.

This course is at the interface of mathematical biology and systems biology and will be closely aligned with the experimental lab course, BIOL500: Cell biology and biochemistry. The goal of this course is to apply the tools of experimental and computational biology to the analysis of gene systems, protein systems, metabolic systems, and signaling systems and pathways. We will cover the principles and applications of technologies that are used to measure and perturb genotypes and phenotypes. We will learn how to use these data sets to build mathematical models of biological systems. Prerequisite: course in differential equations.