Program Requirements

General Program Requirements:
Number of Credits Required Beyond the Baccalaureate: 36

Required Courses:

Core Courses
BIOL 5312Biostatistics3
BIOL 5403Genomics3
BIOL 8003Introduction to Graduate Research3
Select one of the following:3
CIS 5015
Scripting for Sciences and Business
CIS intermediate- or advanced-level coding course
Concentration Courses12
Biological Data Analysis
BIOL 5466
Contemporary Biology
CIS 5523
Knowledge Discovery and Data Mining
Two electives selected from the following:
CIS 5002
Database Design & Programming
CIS 5011
Programming and Data Structure
CIS 5516
Principles of Data Management
CIS 5526
Machine Learning
Evolutionary Genomics
BIOL 5509
Computational Genomics
BIOL graduate course in Population Genetics
Two electives selected from the following:
BIOL 5112
Fundamentals of Genomic Evolutionary Medicine
BIOL 5128
Genomics and Infectious Disease Dynamics
BIOL 5241
Genomics and Evolutionary Biology of Parasites and Other Dependent Species
Evolutionary Medicine
BIOL 5112
Fundamentals of Genomic Evolutionary Medicine
BIOL 5128
Genomics and Infectious Disease Dynamics
BIOL 5241
Genomics and Evolutionary Biology of Parasites and Other Dependent Species
BIOL 5509
Computational Genomics
Structural Bioinformatics
BIOL 5411
Structural Bioinformatics I
CHEM 5412
Structural Bioinformatics II
Two electives selected from the following:
BIOL 5112
Fundamentals of Genomic Evolutionary Medicine
BIOL 5509
Computational Genomics
CHEM 5102
Data Analysis and Evidence
CHEM 5302
Statistical Thermodynamics
Research Courses12
BIOL 9994
Preliminary Examination Preparation
BIOL 9998
Pre-Dissertation Research / Elevation to Candidacy
BIOL 9999
Dissertation Research
Total Credit Hours36

Additional Requirements:
All graduate-level courses must be passed with a "B-" or better.

All Ph.D. candidates must have experience teaching at Temple University. A minimum teaching requirement of one term may be satisfied by serving as a Teaching Assistant in a Bioinformatics-affiliated department.

Attendance at scheduled departmental colloquia is required.

Culminating Events:
Preliminary Examination:
The student independently prepares a written proposal and submits it to the Graduate Committee by April 1 of the student's fourth term. The proposal should follow the general format of a postdoctoral proposal to a federal granting agency (e.g., NIH). It should include background surrounding a particular research problem, including literature related to the problem, and a detailed methodological plan for investigating the problem. The sections of the written proposal should include Title; Abstract (not to exceed 300 words); Specific Aims; Background and Significance; Preliminary Data; Experimental Design (including Rationale, Specific Methods, Interpretation of Possible Results, and Pitfalls and Alternative Strategies); and References. The preliminary exam proposal should be 15 to 20 pages in length. The research advisor is not to make direct contributions.

The Area Committee has two weeks in which to review the written proposal, and the student is allowed only one re-write. If the proposal is not accepted after the first re-write, the student is considered to have failed the exam. If the written proposal is accepted, an oral examination is scheduled through the Graduate Secretary and held within two weeks. The oral examination tests the student's understanding of the background and substance of the research proposal and her/his understanding of the area of specialization in which the research is embedded.

The preliminary examination is administered by the Preliminary Examination Committee. The student’s primary research advisor is allowed to attend but must remain silent unless called upon by the Committee for clarification or advice. A minimum of three examiners serve on the Preliminary Examination Committee. The full exam, both written and oral, is graded by the Preliminary Examination Committee, and one of the following grades is assigned: Pass or Fail. The evaluators look for a breadth and depth of understanding of specific research areas, a critical application of that knowledge to specific biological phenomena, and an ability to write a proposal in a manner consistent with scientists in the student's specialization. The student is notified of the grade the day the exam is taken. A passing grade requires a 2/3 majority of the Preliminary Examination Committee. If a student receives a grade of Fail, s/he may retake the exam one additional time. Examinations that are to be retaken must be completed before October 1 of the following academic year.

Dissertation:
The doctoral dissertation is an original bioinformatics study that demonstrates the student's knowledge of research methods and mastery of her/his primary area of research.

The Doctoral Advisory Committee includes a minimum of four members: three from the list of CST faculty affiliated with the Bioinformatics Ph.D. program, including the advisor, and one from outside the College of Science and Technology. Departmental/affiliated faculty members must be Graduate Faculty or equivalent research faculty and are chosen by the student and advisor. The Doctoral Advisory Committee is to be formed within 2 to 3 months after successful completion of the preliminary examination, with the exception of the outside member who may be chosen just prior to the dissertation defense. The student may petition the Biology Department Graduate Committee to change an advisor or committee member.

The Doctoral Examination is to consist of a formal departmental colloquium open to the public, but conducted by the Doctoral Advisory Committee. The student then meets with the Dissertation Examining Committee after the colloquium for the dissertation defense. The penultimate version of the dissertation must be approved by the Doctoral Advisory Committee at least two weeks before the Graduate School deadline for submission of final copies.

The scheduling of the dissertation defense is to be arranged by the dissertation advisor. The Graduate School must be notified at least ten working days in advance. Announcements of the dissertation defense are posted around the Biology Department and the host department as well as advertised via e-mail or listserv.