Design of small molecule HIV inhibitors (Rizzo).
The newly developed Computational Biology track in the Department of Applied Mathematics and Statistics is designed for those students whose interests lie in solving biological problems using computational and mathematical approaches. The program accommodates students with diverse backgrounds, including those whose primary background is in biology or chemistry as well as those with a background in mathematics or computer science.
Please refer to the Graduate Bulletin for further information about university and department-wide requirements.
The M.S. degree in the Department of Applied Mathematics and Statistics requires the satisfactory completion of a minimum of 30 graduate credits. All credits in satisfaction of the degree must be at the graduate level. In addition, the average for all courses taken must be B or higher, and at least 18 credits of all courses taken must carry a grade of B or higher. The student pursues a program of study planned in consultation with an academic advisor; the core courses listed below form the foundation of the Computational Biology specialization. The program and any subsequent modifications require approval by the graduate studies director.
The course sequence outlined for the Masters program provides the framework for the first years of study in the doctoral program. A two component qualifying exam must be passed to continue in the doctoral program. Additional requirements of the doctoral program include a preliminary examination (covering a proposed research plan for the dissertation), completion of a dissertation representing a significant and original contribution to the scientific literature, and an oral defense of the dissertation.
The course requirements provide the student with the fundamentals of both biology and applied mathematics, as well as in specific methods and applications in computational biology. It is expected that the student will choose a set of electives to provide in depth specialization. Students with less formal training in either math or biology may wish to audit an undergraduate course concurrently with, or prior to, taking the graduate level courses in that area.
Electives may also be chosen from any area relevant to computational biology, based on the specific interests of the student. The student is encouraged to consult with a faculty adviser in advance of choosing electives. Likely areas of specialization may include:
As with the other tracks in the department, the qualifying exam for the doctoral program consists of two parts: the Common Exam taken early in the spring semester of the first year, and the Area Exam taken a year later. Both cover the material from the core course sequence.
The common exam is a written exam, consisting of two parts. Part A of the exam covers the fundamentals of Linear Algebra and Advanced Calculus, as covered in AMS 510; all doctoral students in AMS take this portion of the exam. Part B of the exam is specific to Computational Biology, and consists of questions covering the basics of Computational Structural Biology (AMS 535) and Bioinformatics (CSE 549).
The area exam in computational biology is an oral exam based on the student's specific course sequence. The student is examined by a panel of at least three faculty and must answer questions from those courses the student has covered in each of these three key areas: fundamentals of biology and/or biochemistry (CHE 541/MCB 520 or alternate); fundamentals of applied mathematics (AMS 507, AMS 530); methods and applications in computational biology (AMS 533) as well as in the particular elective courses the student has taken. The oral format is chosen to allow greater flexibility in dealing with a range of students having different focus areas and in assessing the student's understanding of biological systems. Students should consult with the examination committee well prior to the exam in order to determine which areas/courses will be emphasized.
For a student entering in the fall semester, the following outline provides a suggested sequence through the first four semesters of the track.
This page is maintained by David F. Green <dfgreen@ams.sunysb.edu>. Last updated: Mon Oct 6 13:14:31 2008.Copyright © 2006 Department of Applied Math & Statistics - Stony Brook University. All rights reserved.