Master of Science Degree in
Epidemiology and Clinical Research

The Adult and Pediatric Divisions of Infectious Diseases coordinate an interdisciplinary program in Infectious Diseases for students. The requirements for the Infectious Diseases Track are identical to those of the Master's Program in Epidemiology and Clinical Research except students:

1. are not required to take EPI 251: Design and Conduct of Clinical Trials (encouraged, yet not required)
2. are required to take EPI 231: Epidemiology of Infectious Diseases
3. are required to take 6 credits from the list of Infectious Disease electives.
4. are encouraged to attend ID seminars in the Division of Infectious Diseases (https://med.stanford.edu/id/events.html) 

Infectious Disease Electives:

EPI 237: Practical Approaches to Global Health Research
How do you come up with an idea for health research overseas? How do you develop a research question, concept note, and get your project funded? How do you manage personnel in the field, difficult cultural situations, or unexpected problems? How do you create a sampling strategy, select a study design, and ensure ethical conduct with human subjects? This course takes students through the process of health research in under-resourced countries from the development of the initial research question and literature review to securing support and detailed planning for field work. Students progressively develop and receive weekly feedback on a concept note to support a funding proposal addressing a research question of their choosing. Aims at graduate students; undergraduates in their junior or senior year may enroll with instructor consent. This course is restricted to undergraduates unless they have completed 85 units or more.

EPI 247: Epidemic Intelligence (HUMBIO 57)
We will cover: the components of public health systems in the US; principles of outbreak investigation and disease surveillance; different types of study design for field investigation; visualization and interpretation of public health data, including identification and prevention of biases; and implementation of disease control by public health authorities. Students will meet with leaders of health departments of the state and the county and will be responsible for devising and conducting their own investigation of a health problem. HUMBIO students must enroll in HUMBIO 57. EPI students must enroll in EPI 247.

CEE 274D: Pathogens and Disinfection
Introduction to epidemiology, major pathogens and infectious diseases, the immune system, movement and survival of pathogens in the environment, transfer of virulence and antibiotic resistance genes, and pathogen control, with an emphasis on public health engineering measures (disinfection). Prerequisite: 274A.

CEE 274P: Environmental Health Microbiology Lab (offered various years)
Microbiology skills including culture-, microscope-, and molecular-based detection techniques. Focus is on standard and EPA-approved methods to enumerate and isolate organisms used to assess risk of enteric illnesses, such as coliforms, enterococci, and coliphage, in drinking and recreational waters including lakes, streams, and coastal waters. Student project to assess the microbial water quality of a natural water. Limited enrollment; priority to CEE graduate students. An application form must be filed and approved before admission to the class.

CEE 371C: SARS-CoV-2 in the Environment
Two years ago, the general public did not know about coronaviruses, and no one knew of SARS-CoV-2. Today, the world has changed as a result of the global pandemic caused by this virus, and every 3 year old can say "coronavirus". In this course, we will explore how research filled critical knowledge gaps related to environmental fate and transport of viruses allowed us to better understand the transmission of SARS-CoV-2 and inform public health policies on masking and social distancing. We will also discuss the flow of scientific discoveries and knowledge from laboratory to the public during the pandemic and how typical outlets for dissemination of science were or were not effective during the crisis. This course will involve substantial reading of the peer-reviewed and popular literature, and lively discussions and debate. Course likely will be offered remote synchronous

EARTHSYS 114/214: Global Change and Emerging Infectious Disease (ESS 213, HUMBIO 114)
The changing epidemiological environment. How human-induced environmental changes , such as global warming, deforestation and land-use conversion, urbanization, international commerce, and human migration, are altering the ecology of infectious disease transmission, and promoting their re-emergence as a global public health threat. Case studies of malaria, cholera, hantavirus, plague, and HIV. 

GENE 208: Gut Microbiota in Health and Disease (BIOE 221G, MI 221)
Preference to graduate students. Focus is on the human gut microbiota. Students enrolling for 3 units receive instruction on computational approaches to analyze microbiome data and must complete a related project.

HISTORY 343D: Emerging Diseases, Past and Present
This course will use our current experience with the COVID-19 pandemic as a lens to study the processes by which infectious diseases emerge. Because of recent developments in the "historicist sciences" (bioarchaeology and palaeogenetics), it is possible to piece together the origin stories of some of the world's most impactful diseases. How does a "microbe's-eye view" of disease emergence change our understanding of past (and present) pandemics? Is it possible that understanding emergence might help us better understand why certain diseases have continued to proliferate, refusing to yield to modern interventions?nnWe will focus on several major diseases transmitted between the Old and New Worlds before and after 1500. At issue is not simply the original spillover event (the transfer of a pathogen from one host species to humans), but the question of how these diseases exploit human connectivity to proliferate. These early globalizing stories will be compared with the story of SARS-CoV-2 as its own "origin story" continues to unfold. Given current critiques of the failures of "global health," what do these origin stories have to tell us about how diseases become "endemic"? Is humankind both the cause of its major diseases, but also doomed to endure them in perpetuity?

HRP 204: Models for Understanding and Controlling Global Infectious Diseases (HUMBIO 154D)
(HUMBIO students must enroll in HUMBIO 154D. Med/Graduate students must enroll in HRP 204.) This course introduces students to the dynamics of infectious diseases of global health importance, focusing on the use of mathematical models to characterize their transmission in populations. Relevant case examples of pathogens with differing natural history and transmission routes include tuberculosis, HIV, malaria, typhoid, and cholera, as well emerging infectious diseases such as Ebola and the 2019 novel coronavirus. Lectures will emphasize the theoretical basis underlying infectious disease dynamics and link them to in-class workshops and problem sets that will emphasize public health applications and will provide students with hands-on experience in creating and coding models. Students will learn the mathematical underpinnings of key topics in infectious disease transmission including herd immunity, the basic reproductive number, vaccine effects, social contact structure, host heterogeneities, and pathogen fitness. The course will teach students how to approach new questions in infectious disease transmission, from model selection, tradeoffs in model complexity or parsimony, parameterization, sensitivity and uncertainty analyses. Students will practice building models, evaluating the influence of model parameters, making predictions about disease trajectories, and projecting the impact of public health interventions. Prerequisites: HUMBIO 88 or 89 or STATS 141 or BIOSCI 141

ME 233: Data-driven modeling of COVID-19
How to design computational tools to understand the dynamics of the COVID-19 pandemic. Emphasis on mathematical epidemiology, infectious disease models, concepts of effective reproduction number and herd immunity, network modeling, outbreak dynamics and outbreak control, Bayesian methods, model calibration and validation, prediction and uncertainty quantification; Projects on statistic or mechanistic modeling of COVID-19. 

MI 115B: The Vaccine Revolution
Advanced seminar. Human aspects of viral disease, focusing on recent discoveries in vaccine development and emerging infections. Journal club format: students choose articles from primary scientific literature, write formal summaries, and synthesize them into a literature review. Emphasis is on analysis, experimental design, and interpretation of data. Oral presentations. Enrollment limited to 8. Prerequisite: prior enrollment in MI 116, The Human Virosphere or consent of instructor required.

MI 155A: Humans and Viruses I
Introduction to human virology integrating epidemiology, molecular biology, clinical sciences, social sciences, history, and the arts. Emphasis is on host pathogen interactions and policy issues. Topics: polio and vaccination, smallpox and eradication, yellow fever and history, influenza and genomic diversity, rubella and childhood infections, adenovirus and viral morphology, ebola and emerging infection, lassa fever and immune response.

MS&E 292: Health Policy Modeling
Primarily for master's students; also open to undergraduates and doctoral students. The application of mathematical, statistical, economic, and systems models to problems in health policy. Areas include: disease screening, prevention, and treatment; assessment of new technologies; bioterrorism response; and drug control policies.

*Additional Infectious Disease electives may be approved by student's advisor.