PhD program course information

In-depth training in life sciences is achieved in one of two ways. First, incoming PhD students may enroll in the first year basic sciences curriculum of the Johns Hopkins University School of Medicine. That is, you will learn human biology with the medical students. This is a unique and intensive curriculum covering a broad range of topics including molecules and cells, human anatomy, immunology, physiology and neuroscience. Students choosing this option typically devote their entire first academic year to these courses. This curriculum is an excellent way to build a broad and solid foundation in the life sciences.

Students may also consider the alternative life sciences curricula. These curricula have been carefully designed to provide training in areas of the life sciences that are appropriate to each of the program’s research areas. This option is of particular value to students who enter the program having a strong background in the life sciences. In-depth training in engineering, mathematics and computer science is achieved through elective courses, with choice of electives reflecting the research interests of each student. Detailed curricula have been developed in each of the program’s research areas to assist students in making these choices.

For a course to apply toward graduation, a grade of B- or higher is required. If a grade lower than B- is received, then that course must be repeated. If it is not possible to repeat the course, then an alternate course may be taken but must be approved by the Program Director.

Faculty advisors may strongly advise that students choose specific electives and/or specific numbers of electives of particular importance to each of the research and training areas. In such cases, this additional course work is not a requirement of the BME PhD Program.

All PhD candidates in the School of Medicine are required to take a course in the responsible conduct of research.

First Year Basic Sciences Curriculum of the School of Medicine

Fall: Scientific Foundations of Medicine (SFM)

ME:130.600 (SFM1): Anatomy, 35 days (12 credits)
ME:800.638 (SFM2): Macromolecules, Cell physiology, Metabolism, and Genetics, 30 days (12 credits)
ME:800.654 (SFM3): Histology and pathobiology, 7 days (2 credits)
ME:330.602 (SFM4): Pharmacology, 7 days (1 credits)

Winter: Genes to Society (GTS)

GTS 1: Immunology I, 13 days (5 credits)
GTS 2: Micro/Infectious disease, 20 days (8 credits)
GTS 3: Dermatology, 3 days, (1 credits)
GTS 4: Hematology/Oncology, 17 days (7 credits)
GTS 5: Nervous systems and special senses, 33 days (13 credits)
           Part 1: Neuroanatomy.
           Part 2: Function.
GTS 6: Brain/Mind/Behavior, 12 days (5 credits)
Physiology - Organ systems (recommended for cardiovascular focus) (7 credits) offered by Departments of Physiology and BME

Alternate Life Sciences Tracks

Alternate Track 1

Two of the following (each 4 credits):
580.421 Systems Bioengineering I (cardiovascular)
580.422 Systems Bioengineering II (neuroscience)
580.423 Systems Bioengineering III (systems biology)
and 1-2 courses from Quantitative Biology Electives

or Alternate Track 2

440.811 Neuroscience Cognition I (5 credits)
440.812 Neuroscience Cognition II (7 credits)
and 1-2 courses from Quantitative Biology Electives

or Alternate Track 3

Biochemistry, Cell and Molecular Biology Core:
100.709 Macromolecular Structure and Analysis (1 credits)
100.710 Biochemical and Biophysical Principles (1.5 credits)
260.708 Genetics (1.5 credits)
260.709 Molecular Biology and Genomics (1.5 credits)
330.709 Organic Mechanisms in Biology (3 credits)
360.728 Pathways and Regulation (1 credit)
110.728 Cell Structure and Dynamics (1 credit)
800.707 Bioinformatics (1 credit)
and 1-2 courses from Quantitative Biology Electives

Quantitative Biology Electives

520.610 Computational Functional Genomics
520.636 Feedback Control in Biological Signaling Pathways
540.409 Modeling Dynamics and Control for Chemical and Biological Systems
540.659 Bioengineering in Regenerative Medicine
580.420 Build-a-Genome
580.460 Physiological Fluid Mechanics
580.625 Ion Channels
580.626 Structure and Function of the Auditory and Vestibular Brain
580.630 Theoretical Neuroscience
580.635 Bioelectromagnetic Phenomena
580.639 Models of Neuron
580.682 Computational Models of the Cardiac Myocyte
580.687 Foundations of Computational Biology I
580.688 Foundations of Computational Biology and Bioinformatics II
580.690 Systems Biology of Cell Regulation

Mathematics/Applied Mathematics Electives

110.405 Analysis
580.691 Learning Theory
110.607 Complex Variables
550.426 Introduction to Stochastic Processes
550.430 Introduction to Statistics
550.437 Statistics Information and Vision
550.471 Combinatorial Analysis
550.491 Applied Analysis for Engineers and Scientists
550.620 Probability Theory I
550.621 Probability Theory II
550.626 Stochastic Processes II
550.630 Statistical Theory
550.631 Statistical Inference
550.632 Multivariate Statistical Inference
550.672 Graph Theory
550.692 Matrix Analysis and Linear Algebra
550.723 Markov Chains
670.619 Fundamental Physics and Chemistry of Nanomaterials

Engineering Courses With Substantial Theory Content

520.447 Introduction to Information Theory and Coding
580.691 Learning Theory
520.601 Introduction to Linear Dynamical Systems
520.621 Nonlinear System Theory
520.651 Random Signals
530.659 Applied Analysis for Engineers and Scientists
530.661 Applied Mathematics for Engineering  Note: This couse is cancelled for 2016–17.
530.730 Finite Element Methods
530.761 Mathematical Methods of Engineering I
530.762 Mathematical Methods of Engineering II
540.641 Micro- and Nanoscale Transport Phenomena
540.652 Advanced Transport Phenomena
550.661 Foundations of Optimization
580.677 Advanced Topics in Magnetic Resonance Imaging

Exams and Evaluations

Evaluation of Student Progress

An Advisory Committee of three faculty members will be chosen by each student. The student should meet with the Advisory Committee members each semester until the Graduate Board Oral (GBO) examination is passed. These meetings will serve two purposes. First, they will permit students to seek advice on courses and potential research topics. Second, they will permit advisors to assess students' progress in the program. The mode of assessment will be left to individual advisors. Near the end of the first year, each student will present a paper to his/her Advisory Committee in a formal meeting. Students' progress will be evaluated at least once per year by the Junior Progress Committee appointed by the BME Committee. Satisfactory performance will be required both in course work and in advisory meetings.

The Graduate Board Oral (GBO) Examination

Upon completion of a majority of student's course work, he/she must pass a Graduate Board Oral (GBO) examination. Get details about the preliminary and final Graduate Board Oral Examinations. Get more information about the composition of the Graduate Board Oral Examination Committee and scheduling of the Graduate Board Oral Examination.

Teaching Requirement

Each student will assist in teaching two semesters of approved undergraduate courses organized by the BME Department. A TA Committee consisting of a faculty chair, Ph.D. program director, Ph.D. program coordinator, second and third year Ph.D. students, and Master's student, coordinates the assignment of students to teaching duties and must approve all assignments.

Research Rotations

Students are required to conduct research rotations in one to three laboratories. The purpose of these rotations is to gain experience with a range of  research opportunities and to assist in settling on a thesis project. Before conducting a rotation with faculty outside the BME Department, students must obtain approval from the BME Committee. During portions of the first year when courses are not in session, students must participate in a research rotation. Students must select a thesis research mentor by the end of the summer following program year 1.

Present a Thesis Proposal to the BME Committee

Within 12 months after passing the GBO examination, each student must submit a written proposal for dissertation research and present it orally to the BME Committee. The written proposal should follow the format of an NIH grant proposal. Particular attention should be paid to a clear exposition of the hypotheses to be tested, the methods to be used and their feasibility, and the interpretation of expected results. The BME Committee must ensure that the proposed project has both the financial and academic support of a suitable preceptor from a Ph.D. degree-granting program. Following presentation of the thesis proposal, the student's Advisory Committee will be disbanded, and a Thesis Advisory Committee will be named. This committee shall consist of the student's Ph.D. thesis mentor and at least 2 additional faculty. At least one faculty member must be a member of the BME committee.

Conduct Original Research and Describe It in a Dissertation

Upon approval of the BME Committee, research may be conducted in any graduate degree-granting program in the University. When research is conducted under a preceptor who does not have close ties to the BME Program, the student will select and the BME Committee must approve a co-advisor who is a BME Committee member. The progress of all students conducting research will be reviewed by the Senior Progress Committee at least once each year. Students are required to meet at least once per year with their full thesis committee.

Approval of the Dissertation by Two Readers

The completed dissertation must be read and approved by two faculty readers acceptable to the BME Committee. Ordinarily, one of the readers will be the thesis preceptor. Upon approval of the dissertation, the readers will submit a letter to the Graduate Board stating that they have read and approved the thesis and that it represents original work worthy of publication.

Pass a Final Oral Defense of the Dissertation

A final draft of the dissertation must be defended before a committee which will consist of the two principal readers and at least three additional faculty members. At least one defense committee member must be from outside both the Department of Biomedical Engineering and the Committee and at least one must be a member of the Department. The defense committee will be chaired by an individual other than the candidate's primary thesis advisor.