Skip to Content

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 

Several of the courses listed in the tracks below can contribute toward the requirement for either life science or quantitative credits, but a single course cannot contribute to both categories simultaneously. Required seminar and ethics courses do not satisfy the requirements of either category. Courses offered by the JHU Engineering for Professionals (EP) program generally do not count for credit toward graduation, with a limited number of exceptions noted in the list below. 

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) 
  • EN.580.711 Quantitative Methods in BME (1 credit, QE) 
  • 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.520.651 Foundations of Probabilistic Machine Learning (4 credits, QE.ST) 
  • EN.520.659 Machine Learning for Medical Applications (3 credits, QE.ST) 
  • EN.520.665 Machine Perception (3 credits, QE.ST) 
  • EN.553.636 Introduction to Data Science (4 credits, QE.ST) 
  • EN.553.650 Computational Molecular Medicine (4 credits, LS, QE.ST) 
  • EN.553.739 Statistical Pattern Recognition Theory & Methods (3 credits, QE.ST) 
  • EN.601.779 Machine Learning: Advanced Topics (3 credits, QE.ST) 
  • EN.601.668 Machine Translation (3 credits, QE.ST) 
  • ME.250.770 Clinical Data Analysis with Python (QE.ST) 
  • ME.250.783 Imaging Informatics and Deep Learning (QE.ST) 
  • ME.250.771 Introduction to Precision Medicine Data Analysis (QE) 
  • ME.330.809 Analytical Methods of Clinical Pharmacology (QE) 
  • ME.510.707 Statistics and Data Analysis Using R (QE.ST) 
  • PH.140.628 Data Science for Public Health I (QE.ST) 
  • PH.140.629 Data Science for Public Health II (QE.ST) 
  • PH.140.644 Statistical Machine Learning: Methods, Theory, and Applications (QE.ST) 
  • PH.140.664 Causal Inference in Medicine and Public Health I (QE) 
  • PH.140.665 Causal Inference in Medicine and Public Health II (QE) 
  • PH.140.731 Advanced Data Science I (QE.ST) 
  • PH.140.732 Advanced Data Science II (QE.ST) 
Genomics & Systems Biology
  • EN.580.428 Genomic Data Visualization (3 credits, LS, QE) 
  • EN.580.446 Physical Epigenetics (3 credits, LS, QE) 
  • 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.580.635 Applied Bioelectrical Engineering (3 credits, LS, 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.580.743 Advanced Topics in Genomic Data Analysis (3 credits, QE) 
  • EN.525.626 Feedback Control in Biological Signaling Pathways (3 credits, QE.ST) 
  • EN.540.409 Dynamic Modeling and Control (4 credits, QE.ST) 
  • EN.540.618 Metabolic Dysfunctions and Related Diseases (2 credits, LS, QE) 
  • EN.540.645 Junk Food Junkies (3 credits, LS) 
  • EN.601.646 Sketching and Indexing for Sequences (3 credits, QE.ST) 
  • EN.601.647 Computational Genomics: Sequences (3 credits, LS, QE.ST) 
  • EN.601.649 Computational Genomics: Applied Comparative Genomics (3 credits, LS, QE.ST) 
  • EN.601.651 Introduction to Computational Immunogenomics (3 credits, QE) 
  • ME.250.957 Database Querying in Health (QE) 
  • ME.330.809 Analytical Methods of Clinical Pharmacology (QE) 
  • ME.800.723 Computational Genomics Methods (QE) 
  • ME.800.786 Scientific Foundations of Medicine – Pharmacology (LS) 
  • PH.120.608 Gene Editing, Therapy, and Manipulation (LS) 
  • PH.140.686 Advanced Methods for Statistical Genetics and Genomics (QE.ST) 
Imaging & Medical Devices
  • EN.580.627 Deep Learning for Medical Imaging (3 credits, QE.ST) 
  • EN.580.631 Introduction to Computational Medicine: Imaging (2 credits, QE.ST) 
  • EN.580.635 Applied Bioelectrical Engineering (3 credits, LS, 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.601.661 Computer Vision (3 credits, QE.ST) 
  • ME.250.783 Imaging Informatics and Deep Learning (QE.ST) 
  • ME.420.702 Radiological Physics and Dosimetry (QE) 
  • ME.420.703 Radiation Therapy Physics (LS, QE) 
  • ME.800.726 Electron Microscopy: Principles and Practices (QE) 
  • PH.330.622 Neuroimaging: Methods and Applications in Mental and Behavioral Health (QE) 
Neuroengineering
  • EN.580.462 Representations of Choice (3 credits, LS, 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.580.656 Introduction to Rehabilitation Engineering (3 credits, QE) 
  • EN.580.674 Introduction to Neuro-Image Processing (3 credits, QE.ST) 
  • EN.580.697 Biomedical Data Design I (4 credits, QE.ST) 
  • EN.580.638 Biomedical Data Design II (4 credits, QE.ST) 
  • EN.580.742 Neural Implants and Interfaces (3 credits, LS, QE.ST) 
  • EN.520.645 Audio Signal Processing (3 credits, QE.ST) 
  • AS.050.603 Intro to Cognitive Neuroscience (3 credits, LS) 
  • AS.050.626 Foundations of Cognitive Science (3 credits, LS) 
  • AS.050.636 Intro to Neurolinguistics (LS) 
  • AS.050.637 Reading the Mind: Computational Cognitive Neuroscience of Vision (3 credits, LS, QE.ST) 
  • AS.050.653 Cognitive Science in Artificial Intelligence (3 credits, QE) 
  • AS.050.665 Cracking the code: Theory and modeling of information coding in neural activity (LS, QE) 
  • AS.050.675 Probabilistic Models of the Visual Cortex (LS, QE) 
  • AS.080.620 Theoretical and Computational Neuroscience (LS, QE) 
  • ME.120.727 Neuroanatomy for the Medical Illustrator (LS) 
  • ME.200.650 Genes to Society – Nervous Systems and Special Senses (LS) 
  • ME.370.650 Genes to Society – Mind, Brain, Behavior (LS) 
  • 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.440.882 Computational Principles of Biological Vision (LS) 
  • PH.330.622 Neuroimaging: Methods and Applications in Mental and Behavioral Health (QE) 
  • PH.330.623 Brain and Behavior in Mental Disorders (LS) 
Translational Cell & Tissue Engineering and/or Immunoengineering
  • EN.580.453 Immunoengineering Principles and Applications (3 credits, LS, QE) 
  • 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.580.644 Biomedical Applications of Glycoengineering (3 credits, LS) 
  • 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.580.754 Cell & Tissue Engineering Lab (4 credits, LS) 
  • EN.510.610 Fundamentals of Biomaterials (3 credits, QE) 
  • EN.510.636 Biomaterials for Cell Engineering (3 credits, QE) 
  • EN.520.773 Advanced Topics in Microsystems Fabrication (4 credits, QE) 
  • EN.530.410 Biomechanics of the Cell (3 credits, LS, QE) 
  • EN.530.672 Biosensing and BioMEMS (3 credits, QE.ST) 
  • EN.540.622 Introduction to Polymeric Materials (3 credits, QE) 
  • EN.540.626 Fundamentals of Cell Bioengineering (3 credits, LS, QE) 
  • EN.540.637 Application of Molecular Evolution to Biotechnology (3 credits, LS, QE) 
  • EN.601.651 Introduction to Computational Immunogenomics (3 credits, QE) 
  • AS.030.623 Molecular Synthetic Biology (3 credits, LS, QE) 
  • AS.030.677 Advanced Organic Synthesis I (3 credits, LS) 
  • ME.250.611 Micro/Infectious Disease (LS) 
  • ME.250.619 Immunology (LS) 
  • ME.250.703 Graduate Immunology (LS) 
  • ME.250.714 HIV Biology (LS) 
  • ME.510.706 Fundamentals of Cancer: Cause to Cure (LS) 
  • PH.120.627 Stem Cells and the Biology of Aging and Disease (LS) 
  • PH.260.623 Fundamental Virology (LS) 

Electives

Medical School Basic Sciences Curriculum
  • ME.130.600 Scientific Foundations of Medicine – Human Anatomy (LS) 
  • ME.800.781 Scientific Foundations of Medicine – Macromolecules (LS) 
  • ME.800.782 Scientific Foundations of Medicine – Cell Physiology (LS) 
  • ME.800.784 Scientific Foundations of Medicine – Metabolism (LS) 
  • ME.800.785 Scientific Foundations of Medicine – Genetics 
  • ME.800.787 SFM including Macromolecules, Cell physiology, Metabolism, and Genetics (LS) 
  • ME.800.783 Scientific Foundations of Medicine – Histopathology (LS) 
  • ME.800.786 Scientific Foundations of Medicine – Pharmacology (LS) 
  • ME.250.611 Genes to Society – Micro/Infectious Disease (LS) 
  • ME.250.619 Genes to Society – Immunology (LS) 
  • ME.250.622 Genes to Society – Hematology (LS) 
  • ME.200.650 Genes to Society – Nervous Systems and Special Senses (LS) 
  • ME.370.650 Genes to Society – Mind, Brain, Behavior (LS) 
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.300.713 Pathology for Graduate Students: Basic Mechanisms (LS) 
  • ME.300.716 Pathology for Graduate Students: Immunology/Infectious Disease (LS) 
  • ME.330.707 Graduate Pharmacology I (LS) 
  • ME.330.709 Organic Mechanisms in Biology (LS) 
  • ME.330.715 Graduate Pharmacology II (LS) 
  • ME.340.713 Microbial Pathogenesis (LS) 
  • ME.360.728 Pathways and Regulation (LS) 
  • ME.360.720 Organ Physiology (recommended for cardiovascular focus) (LS) 
  • ME.710.745 Evolving Concepts of the Gene (LS) 
  • ME.800.709 Cellular and Molecular Basis of Disease (LS) 
  • ME.800.723 Computational Genomics Methods (QE) 
Engineering for Professionals (EP) Program Courses Accepted for BME Credit
  • EN.525.626 Feedback Control in Biological Signaling Pathways (3 credits, QE.ST) 
  • EN.585.744 Biomedical Applications of Glycoengineering (3 credits, LS) 
Core 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.520.618 Modern Convex Optimization (3 credits, QE.ST) 
  • EN.520.621 Introduction to Nonlinear Systems (3 credits, QE.ST) 
  • EN.520.622 Principles of Complex Networked Systems (3 credits, QE.ST) 
  • EN.520.635 Digital Signal Processing (3 credits, QE.ST) 
  • EN.520.647 Information Theory (3 credits, QE.ST) 
  • EN.525.626 Feedback Control in Biological Signaling Pathways (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.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.553.764 Modeling, Simulation, and Monte Carlo (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) 
  • ME.250.770 Clinical Data Analysis with Python (QE.ST) 
  • PH.140.615 Statistics for Laboratory Scientists I (QE.ST) 
  • PH.140.616 Statistics for Laboratory Scientists II (QE.ST) 
  • PH.140.621 Statistical Methods in Public Health I (QE.ST) 
  • PH.140.622 Statistical Methods in Public Health II (QE.ST) 
  • PH.140.646 Essentials of Probability and Statistical Inference I (QE.ST) 
  • PH.140.647 Essentials of Probability and Statistical Inference II (QE.ST) 
  • PH.140.648 Essentials of Probability and Statistical Inference III (QE.ST) 
  • PH.140.649 Essentials of Probability and Statistical Inference IV (QE.ST) 
  • PH.140.651 Methods in Biostatistics I (QE.ST) 
  • PH.140.652 Methods in Biostatistics II (QE.ST) 
  • PH.140.731 Statistical Theory I (QE.ST) 
  • PH.140.732 Statistical Theory II (QE.ST) 
  • PH.140.776 Statistical Computing (QE.ST) 
Additional Public Health Courses
  • PH.221.615 Health Emergencies in Large Populations (H.E.L.P.) (LS) 
  • PH.221.634 Stress Management for Relief Workers (LS) 
  • PH.221.701 Gender Analysis in Health Research (LS) 
  • PH.221.660 Systems Science in Public Health: Basic Modeling and Simulation Methods (QE.ST) 
  • PH.222.644 Cellular Biochemistry of Nutrients (LS) 
  • PH.222.652 Nutrition in Disease Treatment and Prevention (LS) 
  • PH.260.665 Biological Basis of Aging (LS) 
  • PH.330.606 Digital and Mobile Health Research in Public Mental Health (LS) 
  • PH.340.682 Pharmacoepidemiology Methods (QE.ST) 
  • PH.340.721 Epidemiologic Inference in Public Health I (QE.ST) 
  • PH.340.725 Methods for Clinical and Translational Research (QE) 

Evaluation of Student Progress

The primary mechanism with which the program directors 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 (DBO), hold a thesis committee meeting, 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. These data entries are used to monitor your progress in the program. 

The Doctoral Board Oral (DBO) Examination 

Upon completion of a majority of the required course work, PhD students must pass a Doctoral Board Oral (DBO) examination. 

Learn more about the details of the preliminary and final Doctoral 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. Paid TA positions in the Engineering for Professionals (EP) program cannot be counted for credit toward the TA requirement. 

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 directors. 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. 

 

View Student Resources Page

Read the Johns Hopkins University privacy statement here.

Accept