Any
substitutions of required courses require prior approval by the graduate
program director or associate graduate program director. A grade of B or better is necessary.
YEAR 1
Semester
1: One course from each Track (A,B,C)
TRACK A:
Physics and Chemistry of Living Matter
Biophysical
Chemistry I 16:160:537 (3)
TRACK B: Data, Computation, and Statistics
1. A computer science master's-level course or the
equivalent (by arrangement with the graduate program director or associate director in quantitative biomedicine)
2. One of the following statistics courses (by
arrangement with the graduate program director in statistics and biostatistics):
Intermediate
Statistical Analysis 01:960:384 (3)
Basic Applied Statistics 01:960:484 (3)
Regression Analysis
16:960:563 (3)
Survey Sampling
16:960:576 (3)
Interpretation of Data I 16:960:586 (3)
Interpretation of Data II 16:960:587 (3)
Data Mining
16:960:588 (3)
Design of Experiments 16:960:590
(3)
Statistic Theory for Research Workers 16:960:501 (3) (Prereq: undergraduate precalculus)
Bayesian Analysis 16:215:571 (3)
3. A bioinformatics course:
Undergraduate
Genetics:
Genome Evolution
01:447:352 (3)
Evolutionary Genetics 01:447:486 (3)
Biotech and Plant Biology:
Bioinformatics 11:126:485 (3) (Biotech) and
16:765:585:01 (Plant Biology) (3)
Graduate
Business
and Science:
Clinical Research in Informatics 16:137:580 (3)
Bioinformatics: Tools for Genomic Analysis 16:137:617 (3)
TRACK C:
Quantitative Modeling in Biology
Dynamical Models in Biology 16:848:504 (3)
Conversational Mathematical Modeling 11:216:458 (3)
An
applied math modeling course (by arrangement with the graduate program director
or associate director in quantitative biomedicine)
Semester 2
: Two courses
from Track A or B or C and one course from another Track
TRACK A:
Physics and
Chemistry of Living Matter
Physics of Living Matter
16:1848:617:01 (3)
Biophysical
Chemistry II 16:160:538 (3)
TRACK B: Data, Computation, and Statistics
1. A computer science master's-level course or the
equivalent (by arrangement with the graduate program director or associate director in quantitative biomedicine)
2. One of the following statistics courses (by
arrangement with the graduate program director in statistics and biostatistics):
Intermediate
Statistical Analysis 01:960:384 (3)
Basic Applied Statistics 01:960:484 (3)
Regression Analysis
16:960:563 (3)
Survey Sampling
16:960:576 (3)
Interpretation of Data I 16:960:586 (3)
Interpretation of Data II 16:960:587 (3)
Data Mining
16:960:588 (3)
Design of Experiments 16:960:590 (3)
Statistic Theory for Research Workers 16:960:501 (3) (Prereq: undergraduate precalculus)
3. A bioinformatics course:
Undergraduate:
Genetics:
Quantitative Biology and Bioinformatics 01:447:302 (3)
Genome Evolution 01:447:352 (3)
Ecology, Evolution, and Natural Resources:
Conversational
Mathematical Modeling 11:216:458 (3)
Fundamentals of Genomics 11:216:465 (3)
Graduate:
Biomedical Engineering:
Computer Integrated Interventions in Medicine
16:125:623 (3)
Business and Science:
Bioinformatics:
Tools for Genomic Analysis
16:137:617 (3)
Chemistry
and Chemical Biology:
Data
Science and Structural Biology
16:160:579:02 (2)
TRACK
C: Quantitative Modeling in Biology
Dynamical
Models in Biology 16:848:504 (3)
(Note:
not always offered)
Mathematics
of Cancer 01:640:459 (3) (Note: not always
offered)
Biomedical
Mathematical Methods 16:125:501 (3)
An applied math modeling course (by arrangement
with the graduate program director or associate director in quantitative biomedicine)
YEAR 2
Seminar in
Quantitative Biomedicine (2 X 1 cr):
16:118:616:01
Fall and
Spring
Specialized electives course(s) (1 credit in a relevant area of study) This may consist of regular
courses, minicourses, or other approved
offerings.
Examples of
minicourses in molecular biosciences (16:695:622-635):
The Cillium, Organelle of the 21st Century
Cancer and Clinical Oncology
Cancer Genes and Cells
Evolution of Emerging Viruses
Noncoding Regulatory RNA
Toll-Like Receptors in Health and Disease
Molecular Biology of Cancer
P53
Understanding the Ubiquitin/Proteasome System and Its Involvement in Disease
Neural Circuit Microscopy
Pluripotent and Somatic Stem Cells
Regenerative Medicine - Stem Cell Therapy
Neurodevelopmental Disorders
Genetic Systems and Structures
Genetics and Cell Biology of Fertilization
Examples of regular courses of possible interest:
Fundamentals of Molecular Biosciences 16:695:538 (6)
Experimental Methods in Molecular Biosciences 16:695:539
(2)
Molecular
Biology of Cells 16:148:514 (3)
Molecular
Biology and Biochemistry 16:115:511/512
and 16:694:407/408 (3 each)
Biochemistry 16:115: 503 or 504 (4)
Molecular
Basis of Physiology 16:761:580 (3)
Genetic
Systems and Structures 16:848:617:02 (3)
Human
Genetics 16:681:535 (3)
Cancer 01:447:495
(3)
Cell and
Molecular Pharmacology: Principles of Drug Action and Targeting 16:718:680 (3)
Drug
Delivery: Fundamentals and Applications
16:125:590 (3)
Introduction to Applied Mathematics 01:640:321 (3)
Biocontrol,
Modeling, and Computation 16:125:572 (3)
Thermal
Physics 01:750:351 (3)
Quantum
Mechanics and Atomic Physics 01:750:361 (3)
Advanced
Topics in Statistical Mechanics
and
Biological Physics 16:750:677
(3)
Physical
Chemistry: Biochemical Systems
01:160:341 or 342 (3)
Concepts in Nanochemistry 16:160:579:01 (3)
Computational Chemistry 16:160:579:04 (3)
Chemical
Thermodynamics 16:160:525 (3)
Thermodynamics
and Kinetics 16:160:541:01 (3)
Structural
Biology, Structural Biophysics, and Chemical Biology of Transcription/Structural
Biology/Biophysics 16:160:580 (3)
Communicating Science 16:718:560 (0)
Graduate Writing
16:355:502 (0)
Winter Session of any Year(s) in Graduate School
Interdisciplinary Quantitative Biology
Boot Camp 16:848:601 (1)
Interdisciplinary Quantitative Biology
Boot Camp 16:848:615 (2)
Ethical
Conduct in Scientific Research
Available in most science- or engineering-oriented
graduate programs and online as well.
Responsible
and Ethical Research I 16:486:501 (0)
Introduction
to Research 16:160:603 (1)
Ethical Scientific Conduct 16:115:556 (1)
Research Rotations
In the first year, students typically engage in one-three
rotations (16:848:621
and 622; 1 credit per rotation). Rotations provide the opportunity to explore
research (for two months per rotation) in the quest of finding a research group in which to do one's dissertation
research. The format for lab rotations varies
depending upon the research group. Students may be given an independent
laboratory research project and/or may assist other members of the lab in data
acquisition and analysis. During this time, the student attends and
participates in laboratory group meetings and related events. Students are responsible for arranging their own
laboratory rotations by contacting faculty with whom they are interested in
having rotations. Students should talk
with faculty about their interest at the beginning of the first year (or,
better yet, before arriving), as labs fill up quickly.
Teaching Requirement
Assistant teaching (normally in
the form of TAs; 6 credits/semester) is formally
required for the equivalent of one semester.
A possible alternative to doing a TA could be assisting with the teaching of a course (by arrangement with the professor).
This might consist of such activities as preparing and performing
demonstrations, preparing and grading quizzes, and/or preparing and providing a
lecture. This kind of alternative teaching can be arranged upon agreement with
the graduate program director and the professor teaching the course (and can be
indicated on the student transcript as "Teaching Apprenticeship").
Examination and Thesis Requirements
A.
Written Qualifying Exam
(End of Year 1)
Students will have a written qualifying exam at the
end of their first year of graduate school during which they will demonstrate
their working knowledge of the course material learned in the first year of
graduate school. The questions will be
provided and graded by the course instructors.
Students will either pass the exam, be given a chance to retake the exam
(or course) and retested, or will be terminated from the program, depending on
their performance.
B. Admission
of Candidacy Exam (By End of Year 2)
Students will have a written and oral
admission-of-candidacy exam with the Admission of Candidacy Exam Committee,
focused on the student's proposed thesis research.
1)
Written component:
Students prepare a written proposal for their
thesis research that must be not exceed 20 pages single-spaced (not including
references). The preparation of the
proposal is intended to educate the student (i.e., about the work that has been done in the field to date and
the techniques that will be useful for the work [e.g., the how to and the principles]) and to promote creative
thinking about the outstanding problems in the field and ways to solve these
problems. The student should obtain the application for admission to candidacy
for the doctoral degree from the office of the graduate school and submit it to
the chair of the committee at the time of the examination.
2) Oral component:
The student will defend the proposal and
show relevant knowledge in an oral presentation of approximately 30 minutes in
duration. The date for this component of the qualifying exam should be
set up with the committee members at least two weeks before the scheduled date
of the exam. The Exam Committee will meet after the exam and decide among
the following three options: (1) Pass; (2) Fail; (3) Fail with an opportunity
to repeat the exam. In the case of option #3, the student must repeat the
exam within three months after the first exam. Repeat exams will be graded as
Pass or Fail only. If the student passes Exam B, the members of the
candidate's committee and the graduate director will sign the application for
admission to candidacy
for the doctoral degree (see Forms). This form must be returned to the
office of the associate director of graduate studies. If the student does
not pass the qualifying exam, she or he may be eligible to earn a master's degree at
this stage. (See section on quantitative biomedicine master's program.)
Students are expected to submit and defend a dissertation
within five years of starting the program.
