Graduate

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 credit)

Winter: Genes to Society (GTS)

ME: 800.639 (GTS 1): Immunology, 13 days (5 credits)
ME: Micro/Infectious disease, 20 days (8 credits)
ME: Dermatology, 3 days, (1 credit)
ME: Hematology/Oncology, 17 days (7 credits)
ME: 800.610 (GTS 5): Nervous systems and special senses, 33 days (13 credits)
Part 1: Neuroanatomy
Part 2: Function
ME: 800.610 (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)
580.429 Systems Bioengineering III (systems biology)
and 1-2 courses from Quantitative Biology Electives

or Alternate Track 2

ME: 440.811 Neuroscience Cognition I (5 credits)
ME: 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 (3 credits)
520.636 Feedback Control in Biological Signaling Pathways (3 credits)
540.409 Modeling Dynamics and Control for Chemical and Biological Systems (3 credits)
540.659 Bioengineering in Regenerative Medicine (3 credits)
580.420 Build-a-Genome (4 credits)
580.626 Structure and Function of the Auditory and Vestibular Brain (3 credits)
580.630 Theoretical Neuroscience (4 credits)
580.682 Computational Models of the Cardiac Myocyte (3 credits)
580.688 Foundations of Computational Biology and Bioinformatics II (3 credits)
580.690 Systems Biology of Cell Regulation (3 credits)

Mathematics/Applied Mathematics Electives

110.405 Analysis (4 credits)
580.691 Learning Theory (3 credits)
110.607 Complex Variables (3 credits)
550.426 Introduction to Stochastic Processes (4 credits)
550.430 Introduction to Statistics (4 credits)
550.437 Statistics Information and Vision (3 credits)
550.471 Combinatorial Analysis (4 credits)
550.620 Probability Theory I (4 credits)
550.621 Probability Theory II (4 credits)
550.626 Stochastic Processes II (3 credits)
550.636 Statistical Inference (2 credits)
550.632 Multivariate Statistical Inference
550.672 Graph Theory (4 credits)
550.692 Matrix Analysis and Linear Algebra (4 credits)
550.723 Markov Chains (3 credits)
670.619 Fundamental Physics and Chemistry of Nanomaterials (3 credits)
ME: 510.707 Statistics and Data Analysis Using R (1.5 credits)

Engineering Courses With Substantial Theory Content

520.447 Introduction to Information Theory and Coding (3 credits)
580.691 Learning Theory (3 credits)
520.601 Introduction to Linear Dynamical Systems (3 credits)
520.621 Nonlinear System Theory (3 credits)
520.651 Random Signals (4 credits)
530.659 Applied Analysis for Engineers and Scientists [no record]
530.730 Finite Element Methods (3 credits)
530.761 Mathematical Methods of Engineering I (3 credits)
530.762 Mathematical Methods of Engineering II (4 credits)
540.641 Micro- and Nanoscale Transport Phenomena (3 credits)
540.652 Advanced Transport Phenomena (3 credits)
550.630 Statistical Theory (4 credits)
550.661 Foundations of Optimization (3 credits)
580.639. Models of Neuron (3 credits)
580.677 Advanced Topics in Magnetic Resonance Imaging (3 credits)

Exams and Evaluations

  • For complete information about requirements, exams and evaluation view the BME PhD guidelines.

Evaluation of Student Progress

The primary mechanism with which the program director can follow your progress in the program is via the online progress report form. As you enroll in courses, embark on laboratory rotations, take your Doctoral Board Exam, hold a thesis committee, write a manuscript, give a talk, etc., you must update this form. You are required to check and update the form at least every three months. The form is an accurate record of all your academic activities during your PhD years. The data in this form is kept confidential, and is available to only you, the program director, and the program administrator. The data are used to monitor your progress in the program.

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 one semester of a BME or BME-relevant course. Alternatively, students may teach their own courses. 

Research Rotations

Depending on the type of admission offer received, some students may conduct research rotations in multiple 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 of BME, students must obtain approval from the program director. Students must select a thesis research mentor by the end of the summer following program year one.

Write and Present a Thesis Proposal to the BME Committee

Within 12 months after passing the DBO examination, each student must submit a written proposal for dissertation research and present it orally to their thesis committee. The written proposal should follow the format of an NIH fellowship 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.

Approval of the Dissertation by Two Readers

The completed dissertation must be read and approved by two faculty readers acceptable to the BME PhD program. 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 one additional faculty member.