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PhD Courses

Students in the biomedical engineering PhD program are trained to solve problems related to human health using innovative engineering approaches. This training includes in-depth instruction in both the life sciences and quantitative disciplines. Our curriculum is flexible, allowing students to choose courses that align with their research area. A full description of our degree requirements can be found here.

BME PhD students can take courses offered by any of the Johns Hopkins divisions, including the Whiting School of Engineering, School of Medicine, and the Bloomberg School of Public Health. The Whiting School of Engineering offers a broad range of in-depth courses in engineering, mathematics, and computer science. The School of Medicine offers a variety of graduate courses in the life sciences, spanning topics such as neuroscience, molecular biology, genetics, cell structure and dynamics, pharmacology, cancer biology, and more. In addition to these courses from the graduate curriculum, some BME PhD students have the option to take courses from the first-year basic sciences medical curriculum at the School of Medicine. That is, these BME PhD students learn human biology alongside the medical students. This is an intensive curriculum covering topics such as molecules and cells, human anatomy, immunology, physiology, and neuroscience. Some students who choose this option devote their entire first academic year to these courses, while others take select courses from the medical curriculum. Please note that the number of seats available to BME PhD students in the medical curriculum courses (particularly Anatomy) is limited; priority will be given based on relevance of each course to the student’s research area.

To help guide students in their course selection, common courses related to each of the BME program’s seven core research areas are listed in the tracks below. Each course is annotated with one or more of the following designations to indicate how it counts toward fulfilling the PhD program degree requirements:

  • LS = Life Sciences
  • QE = Quantitative/Engineering
  • QE.ST = Quantitative/Engineering with Substantial Theory Content

A number of the courses listed in the tracks below can contribute toward the requirement for either life science or quantitative credits, but cannot contribute to both categories simultaneously. Required seminar and ethics courses do not satisfy the requirements of either category.

Students are not required to take courses from a single track. In fact, because biomedical engineering is interdisciplinary by nature, many students choose courses from more than one track to tailor their education to their unique research interests. Course offerings change frequently, and the lists below are not all-inclusive. Additional courses not listed here are likely acceptable for satisfying program requirements. Students are encouraged to consult their faculty advisors when selecting courses. Additionally, the program offers advising support for BME PhD students.

For a course to apply toward graduation, a grade of B- or higher is required. If a grade lower than B- is received, 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 co-directors.

Faculty advisors may strongly advise that students choose specific electives and/or specific numbers of electives related to specific 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 coursework in the responsible conduct of research.

Courses by Research Area

Required Courses for all First Year BME PhD Students
  • EN: 580.781 BME Seminar (1 credit)
  • EN: 580.710 Ethical Challenges in BME (2 credits) – New for 2022
  • ME: 210.801 Special Studies in BME
  • ME: 800.811 Introduction to Responsible Conduct of Research
    • Alternative: AS: 360.625 Responsible Conduct of Research – May be taken in place of ME: 800.811 for Homewood-based students
Biomedical Data Science and Computational Medicine
  • EN: 580.475 Biomedical Data Science (2 credits, QE.ST)
  • EN: 580.477 Biomedical Data Science Laboratory (1 credit, QE.ST)
  • EN: 580.485 Computational Medicine: Cardiology (2 credits, LS, QE.ST)
  • EN: 580.487 Computational Medicine: Cardiology Laboratory (1 credit, LS, QE.ST)
  • EN: 580.631 Introduction to Computational Medicine: Imaging (2 credits, QE.ST)
  • EN: 580.633 Introduction to Computational Medicine: The Physiome (2 credits, QE.ST)
  • EN: 580.640 Systems Pharmacology and Personalized Medicine (4 credits, QE.ST)
  • EN: 580.680 Precision Care Medicine I (4 credits, LS, QE.ST)
  • EN: 580.681 Precision Care Medicine II (4 credits, LS, QE.ST)
  • EN: 580.735 Advanced Seminars in Computational Medicine (1 credit, QE)
  • EN: 520.638 Deep Learning (3 credits, QE.ST)
  • EN: 520.650 Machine Intelligence (3 credits, QE.ST)
  • EN: 520.659 Machine Learning for Medical Applications (3 credits, QE.ST)
  • EN: 520.807 Current Topics in Language and Speech Processing (1 credit, QE)
  • EN: 601.779 Machine Learning: Advanced Topics (3 credits, QE.ST)
Genomics & Systems Biology
  • EN: 580.485 Computational Medicine: Cardiology (2 credits, LS, QE.ST)
  • EN: 580.487 Computational Medicine: Cardiology Laboratory (1 credit, LS, QE.ST)
  • EN: 580.633 Introduction to Computational Medicine: The Physiome (2 credits, QE.ST)
  • EN: 580.639 Models of the Neuron (4 credits, LS, QE.ST)
  • EN: 580.640 Systems Pharmacology and Personalized Medicine (4 credits, QE.ST)
  • EN: 580.658 Computing the Transcriptome (3 credits, QE.ST)
  • EN: 580.683 Annotate a Genome (3 credits, LS, QE)
  • EN: 580.688 Foundations of Computational Biology and Bioinformatics (4 credits, QE.ST)
  • EN: 520.636 Feedback Control in Biological Signaling Pathways (3 credits, QE.ST)
  • EN: 540.409 Dynamic Modeling and Control (4 credits, QE.ST)
  • ME: 800.638 Pharmacology (LS)
  • ME: 800.723 Computational Genomics Methods (QE)
  • PH: 140.686 Advanced Methods for Statistical Genetics and Genomics (QE.ST)
Imaging & Medical Devices
  • EN: 580.631 Introduction to Computational Medicine: Imaging (2 credits, QE.ST)
  • EN: 580.674 Introduction to Neuro-Image Processing (3 credits, QE.ST)
  • EN: 580.678 Biomedical Photonics (4 credits, QE.ST)
  • EN: 580.679 Principles and Applications of Modern X-ray Imaging and Computed Tomography (3 credits, QE.ST)
  • EN: 580.689 Modern Optical Microscopy: Theory and Practice (3 credits, QE.ST)
  • EN: 580.723 Introduction to MRI in Medicine (3 credits, QE.ST)
  • EN: 580.771 Principles of the Design of Biomedical Instrumentation (4 credits, QE.ST)
  • EN: 520.414 Image Processing and Analysis (3 credits, QE.ST)
  • EN: 520.605 Advanced Optical and Optoelectronic Instruments and Devices (3 credits, QE.ST)
  • EN: 520.613 Advanced Topics in Optical and Medical Imaging (3 credits, QE.ST)
  • EN: 520.631 Ultrasound and Photoacoustic Beamforming (3 credits, QE.ST)
  • EN: 520.632 Medical Imaging Systems (3 credits, QE.ST)
  • EN: 520.659 Machine Learning for Medical Applications (3 credits, QE.ST)
  • EN: 530.672 Biosensing and BioMEMS (3 credits, QE.ST)
  • EN: 601.655 Computer Integrated Surgery I (4 credits, QE.ST)
  • EN: 580.625 Structure and Function of the Auditory and Vestibular Systems (3 credits, LS, QE.ST)
  • EN: 580.639 Models of the Neuron (4 credits, LS, QE.ST)
  • EN: 580.674 Introduction to Neuro-Image Processing (3 credits, QE.ST)
  • EN: 580.697 Neuro Data Design I (4 credits, QE.ST)
  • EN: 580.638 Neuro Data Design II (4 credits, QE.ST)
  • EN: 580.742 Neural Implants and Interfaces (3 credits, QE.ST)
  • EN: 520.645 Audio Signal Processing (3 credits, QE.ST)
  • EN: 520.807 Current Topics in Language and Speech Processing (1 credit, QE)
  • AS: 080.620 Theoretical and Computational Neuroscience (LS, QE)
  • ME: 440.811 Neuroscience Cognition I (LS)
  • ME: 440.812 Neuroscience Cognition II (LS)
  • ME: 440.820 Circuits and Brain Disorders (LS)
  • ME: 440.718 Neurobiology (LS)
  • ME: 800.610 Nervous Systems and Special Senses, 33 days (LS)
  • ME: 800.610 Brain/Mind/Behavior, 12 days (LS)

*as of September 2021

Translational Cell & Tissue Engineering and Immunoengineering
  • EN: 580.637 Microphysiological Systems (3 credits, QE)
  • EN: 580.641 Cellular Engineering (4 credits, LS, QE.ST)
  • EN: 580.642 Tissue Engineering (3 credits, LS,QE)
  • EN: 580.646 Molecular Immunoengineering (3 credits, LS, QE)
  • EN: 580.647 Computational Stem Cell Biology (3 credits, LS, QE.ST)
  • EN: 580.752 Advanced Topics in Regenerative and Immune Engineering (4 credits, LS)
  • EN: 510.636 Biomaterials for Cell Engineering (3 credits, QE)
  • EN: 520.773 Advanced Topics in Microsystems Fabrication (4 credits, QE)
  • EN: 530.672 Biosensing and BioMEMS (3 credits, QE.ST)
  • ME: 250.611 Micro/Infectious Disease, 20 days (LS)
  • ME: 510.706 Fundamentals of Cancer: Cause to Cure (LS)
  • ME: 800.639 Immunology, 13 days (LS)
  • PH: 120.627 Stem Cells and the Biology of Aging and Disease (LS)
  • PH: 260.623 Fundamental Virology (LS)


Graduate Life Science Courses, Including the Biochemistry, Cellular and Molecular Biology (BCMB) Core Curriculum
  • ME: 100.714 Single-Molecule Single-Cell Biophysics (LS)
  • ME: 100.715 Proteins and Nucleic Acids II (LS)
  • ME: 100.716 Analysis of Macromolecules (LS)
  • ME: 110.728 Cell Structure and Dynamics (LS)
  • ME: 110.733 Principles of Genetics (LS)
  • ME: 260.709 Molecular Biology and Genomics (LS)
  • ME: 260.711 Transcription Mechanisms (LS)
  • ME: 300.710 Pathobiology and Disease Mechanisms (LS)
  • ME: 330.707 Graduate Pharmacology I (LS)
  • ME: 330.709 Organic Mechanisms in Biology (LS)
  • ME: 330.715 Graduate Pharmacology II (LS)
  • ME: 360.720 Organ Physiology (recommended for cardiovascular focus) (LS)
  • ME: 360.728 Pathways and Regulation (LS)
  • ME: 710.745 Evolving Concepts of the Gene (5 credits, LS)
  • ME: 800.709 Cellular and Molecular Basis of Disease (LS)
  • ME: 800.723 Computational Genomics Methods (QE)
Medical School Basic Sciences Curriculum
  • ME.130.600 Scientific Foundations of Medicine-Human Anatomy
  • ME.800.787 Scientific Foundations of Medicine (inc. Macromolecules, Cell Physiology, Metabolism and Genetics)
  • ME.800.783 Scientific Foundations of Medicine: Histopathology
  • ME.800.786 Scientific Foundations of Medicine: Pharmacology
  • ME.200.650 Genes to Society – Nervous System and Special Senses
  • ME.250.611 Genes to Society – Micro/Infectious Disease
  • ME.250.619 Genes to Society – Immunology
  • ME.250.622 Genes to Society – Hematology
  • ME.370.650 Genes to Society – Mind, Brain, Behavior
Quantitative/Engineering Courses with Substantial Theory Content
  • AS: 110.405 Real Analysis (4 credits, QE.ST)
  • AS: 110.607 Complex Variables (3 credits, QE.ST)
  • EN: 580.691 Learning, Estimation, and Control (3 credits, QE.ST)
  • EN: 553.426 Introduction to Stochastic Processes (4 credits, QE.ST)
  • EN: 553.430 Introduction to Statistics (4 credits, QE.ST)
  • EN: 553.471 Combinatorial Analysis (4 credits, QE.ST)
  • EN: 553.620 Introduction to Probability (4 credits, QE.ST)
  • EN: 553.630 Introduction to Statistics (4 credits, QE.ST)
  • EN: 553.632 Bayesian Statistics (3 credits, QE.ST)
  • EN: 553.672 Graph Theory (4 credits, QE.ST)
  • EN: 553.692 Mathematical Biology (3 credits, QE.ST)
  • EN: 520.618 Modern Convex Optimization (3 credits, QE.ST)
  • EN: 520.621 Introduction to Nonlinear Systems (3 credits, QE.ST)
  • EN: 520.647 Information Theory (3 credits, QE.ST)
  • EN: 530.610 Quantitative Cell Mechanics (3 credits, QE.ST)
  • EN: 530.616 Introduction to Linear Systems Theory (3 credits, QE.ST)
  • EN: 540.652 Advanced Transport Phenomena (3 credits, QE.ST)
  • EN: 560.601 Applied Math for Engineers (3 credits, QE.ST)
  • ME: 510.707 Statistics and Data Analysis Using R (QE.ST)
  • PH: 140.615 Statistics for Laboratory Scientists I (QE.ST)
  • PH: 140.616 Statistics for Laboratory Scientists II (QE.ST)
  • PH: 140:651 Methods in Biostatistics I (QE.ST)
  • PH: 140:652 Methods in Biostatistics II (QE.ST)

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.

Learn more about the details of the preliminary and final Graduate Board Examinations, as well as scheduling, here.

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. 

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