Computational Medicine

icm.jhu.edu

Picture1The Institute for Computational Medicine (ICM) is proud to offer an undergraduate minor in Computational Medicine, the first educational program in CM, reflecting Johns Hopkins University’s leadership in this field. Like the ICM itself, the undergraduate minor in Computational Medicine is integrative and multidisciplinary. The 18 ICM Core Faculty who serve as advisors to the undergraduate minor hold primary and joint appointments in multiple Johns Hopkins University departments and schools including Biomedical Engineering, Computer Science, Electrical and Computer Engineering, Mechanical Engineering, Applied Mathematics and Statistics (WSE); Neurosurgery, Emergency Medicine, Medicine, and the Divisions of Cardiology and Health Sciences Informatics (SOM); and Health Policy and Management (BSPH).

With a minor in CM, undergraduates will have a solid grounding in the development and application of computational methods in multiple key areas of medicine. Specifically, undergraduates will understand how mathematical models can be constructed from biophysical laws or experimental data, and how predictions from these models facilitate diagnosis and treatment of a disease. Undergraduates will become conversant with a wide variety of statistical, deterministic and stochastic modeling methods, skills that are essential to the advancement of modern medicine, and are prized both in academic research and industrial research. 

CM research at ICM is sub-divided into four key areas: Computational Molecular MedicineComputational Physiological MedicineComputational AnatomyComputational Healthcare. Techniques for and applications in each of these four key subareas are introduced during the required core courses, exposing undergraduates to the breadth of Computational Medicine, and enabling each student to identify a preferred area of interest:

  • Computational Physiological Medicine develops mechanistic models of biological systems in disease, and applies the insights gained from these models to develop improved diagnostics and therapies. Therapies could be diverse drugs, electrical stimulation, mechanical support devices and more.
  • Computational Molecular Medicine harnesses the enormous amount of disease-relevant data produced by next-generation sequencing, microarray and proteomic experiments of large patient cohorts, using statistical models to identify the drivers of disease and the susceptible links in disease networks.
  • Computational Anatomy uses medical imaging to analyze the variation in structure of human organs in health and disease. Such image analysis has been integrated into clinical workflows to assist in the diagnosis and prognosis of complex diseases.
  • Computational Healthcare is an emerging field devoted to understanding populations of patients and their interaction with all aspects of the healthcare process.

CM is distinct from Computational Biology in its focus on human health, disease, and treatment; translation to and application in the clinic is a near-term goal of all CM research. Applications of CM are as broad as medicine itself, and include: identification of optimal drugs using associated genomic and proteomic biomarkers; discovery of image-based biomarkers for diagnosis and prognosis; design and dynamic adjustment of individualized non-drug therapies such as deep brain stimulation, cardiac stimulation, and cochlear implants; modeling and learning from patient EHR data to improve patient outcomes and efficiency of care; optimization of healthcare policy decisions by quantitative analysis; and more. CM is one of the pillars of the University’s Strategic Initiative in Individualized Health.

Computational Medicine (CM) is an emerging discipline devoted to the development of quantitative approaches for understanding the mechanisms, diagnosis and treatment of human disease through applications of mathematics, engineering and computational science. The core approach of CM is to develop computational models of the molecular biology, physiology, and anatomy of disease, and apply these models to improve patient care. CM approaches can provide insight into and across many areas of biology, including genetics, genomics, molecular networks, cellular and tissue physiology, organ systems, and whole body pharmacology.

Minor Prerequisites 

Before attempting the minor, undergraduates will have taken the following courses. For a course to count towards the minor, a minimum grade of C- is required (courses graded as ‘S/U’ do not satisfy prerequisites):

  1. Calculus I 
  2. Calculus II
  3. Probability and Statistics: either a single course covering both (e.g. EN.553.310 or EN.553.311) or a course devoted to each (e.g., EN.553.420 and EN.553.430) – this may be taken concurrent with core course EN.580.431 
  4. At least one (1) additional course in mathematics or applied mathematics (at least 3 credits)
  5. At least one (1) computer programming course (at least 3 credits)
  6. At least one (1) biological sciences course (at least 3 credits)

Core Courses

The required core courses for the minor are Introduction to Computational Medicine I (EN.580.431) and either Computational Molecular Medicine (EN.553.450) or Foundations of Computational Biology and Bioinformatics II (EN.580.488).

EN.580.431 covers computational anatomy and physiology and will be jointly taught by ICM faculty from multiple departments.

EN.550.450 focuses on molecular medicine and computational healthcare while EN.580.488 introduces probabilistic modeling and information theory applied to biological sequence analysis. Both courses require background in probability theory and statistics.

Core courses may not be taken concurrently.

Distinguished Seminar Series

Students enrolled in the Computational Medicine Minor are REQUIRED to attend 6 ICM Distinguished Seminars in person by graduation. Documentation of seminar attendance is two-fold: (1) Students must sign-in at every seminar attended and (2) students must complete the online Seminar Attendance Form. Contact ICM Administrative Office for further details. 

Elective Courses

Following satisfaction of the prerequisites, to complete the minor, undergraduates must take at least 6 CM courses totaling at least 18 credits. This includes two one-semester core courses plus four approved courses selected from those listed below. The following restrictions are noted:

  1. At most 3 of the 18 credits can consist of independent research in Computational Medicine, as defined and agreed to in advance by the minor advisor;
  2. The 18 credits will all be at 300-level or above, and courses must be passed at a C- level or above;
  3. At least 2 non-core/elective courses must be outside student’s home department;
  4. At least 2 non-core/elective courses must have a substantial biology or medicine component, as identified in the list below with an (M) designation;
  5. At least 1 non-core/elective course must have a substantial computational component in the area of "applied programming," as identified in the list below with an (C) designation;
  6. All courses must be passed at a C- level or above;
  7. A class may not be counted as both a prerequisite and an elective.

Students may suggest elective courses to be added to the list by completing a “Class Approval Request Form”. Requests should be made to Dr. Joshua Vogelstein and will be reviewed by the CM Minor Curriculum Committee.

Electrical and Computer Engineering
EN.520.315Introduction to Information Processing of Sensory Signals3
EN.520.432Medical Imaging Systems (M)3
EN.520.601Introduction to Linear Systems Theory3
EN.520.621Introduction To Nonlinear Systems3
Mechanical Engineering
EN.530.343Design and Analysis of Dynamical Systems3
EN.530.676Locomotion in Mechanical and Biological Systems (M)3
Chemical and Biomolecular Engineering
EN.540.400Project in Design: Pharmacokinetics (MC)3
EN.540.409Dynamic Modeling and Control (C)4
EN.540.421Project in Design: Pharmacodynamics (MC)3
Applied Mathematics and Statistics
EN.553.391Dynamical Systems4
EN.553.420Introduction to Probability4
EN.553.426Introduction to Stochastic Processes4
EN.553.430Introduction to Statistics4
EN.553.436Data Mining4
Biomedical Engineering
EN.580.430Systems Pharmacology and Personalized Medicine (MC)3
EN.580.445Networks (C)3
EN.580.460Theory of Cancer (MC)3
EN.580.468The Art of Data Science (C)3
EN.580.488Foundations of Computational Biology and Bioinformatics II (MC)3
EN.580.491Learning Theory (C)3
EN.580.689Computational Personal Genomics (MC)3
EN.580.694Statistical Connectomics (MC)3
EN.580.446Physical Epigenetics3
Computer Science
EN.601.448Computational Genomics: Data Analysis3
EN.601.447Computational Genomics: Sequences3
EN.601.455Computer Integrated Surgery I4
EN.601.461Computer Vision3
EN.601.476Machine Learning: Data to Models3
EN.601.350Introduction to Genomic Research3
EN.601.723Advanced Topics in Data-Intensive Computing3
EN.601.750Frontiers of Sequencing Data Analysis3

Declaring the Minor

Interested students should contact Alecia Flynn, ICM Administrative Coordinator, to receive guidance on declaring the minor:

Phone: 410-516-4116
Email: aflynn12@jhu.edu 

Specific questions regarding the minor requirements and courses can be directed to Dr. Joshua Vogelstein, Director of Undergraduate Studies for the CM minor.

Faculty

Director

Raimond Winslow
Director of Institute for Computational Medicine, Director of Center for Cardiovascular Bioinformatics and Modeling, Raj and Neera Singh Professor of Biomedical Engineering

Director of Undergraduate Studies

Joshua T. Vogelstein
Assistant Professor, Dept. of Biomedical Engineering

Undergraduate Advisors

William S. Anderson
Associate Professor, Dept. of Neurosurgery, Attending Neurosurgeon at The Johns Hopkins Hospital

Joel Bader
Professor, Dept. of Biomedical Engineering, Bioinformatics and Computational Biology Lab

Patrick Boyle
Assistant Research Professor, Dept. of Biomedical Engineering

Nicolas Charon
Assistant Professor, Dept. of Applied Mathematics and Statistics, Center for Imaging Sciences

Joshua Epstein
Professor of Emergency Medicine, Director of Center for Advanced Modeling in the Social, Behavioral and Health Sciences

Feilim Mac Gabhann
Associate Professor, Dept. of Biomedical Engineering

Donald Geman
Professor, Applied Mathematics and Statistics, Center for Imaging Sciences

Rachel Karchin
Associate Professor, Dept. of Biomedical Engineering, The William R. Brody Faculty Scholar

Michael I. Miller
Herschel and Ruth Seder Professor, Dept. of Biomedical Engineering, Director of Center for Imaging Sciences

Rajat Mittal
Professor, Dept. of Mechanical Engineering

Tilak Ratnanather
Associate Research Professor, Dept. of Biomedical Engineering

Suchi Saria
Assistant Professor, Dept. of Computer Science

Sridevi Sarma
Associate Professor, Dept. of Biomedical Engineering

Natalia Trayanova
Murray B. Sachs Professor, Dept. of Biomedical Engineering

Rene Vidal
Professor, Dept. of Biomedical Engineering, Computer Science, Mechanical Engineering, and Electrical and Computer Engineering, Director of Vision Dynamics and Learning Lab

Laurent Younes
Professor and Chair, Dept. of Applied Mathematics and Statistics