Program Overview

---

Education

PhD Program

The PhD program offers two tracks:

• AIM PhD Track
• BIG PhD Track

Master's Program

The Master's program includes:

• Admissions
  • International Applicants
  • Information Sessions
  • Tuition and Financial Aid
  • MMSc-BMI FAQs
• MMSc-BMI Curriculum
  • MMSc-BMI Electives
• MMSc-BMI Thesis
• Financial Aid Opportunities
  • INDECS Scholarship
• Student and Alumni Profiles
  • Current MBI Students
  • MBI Class of 2025
  • MBI Class of 2024
  • MBI Class of 2023
  • MBI Class of 2022
  • MBI Class of 2021
  • MBI Class of 2020
  • MBI Class of 2019
  • MBI Class of 2018
  • MBI Class of 2017
  • MBI Class of 2016
  • MBI Class of 2015

Summer Institute

The Summer Institute includes:

• Admissions
• Curriculum
• FAQ
• Student Projects
• Student Testimonials

Clinical Informatics Lecture Series

The Clinical Informatics Lecture Series includes:

• CME Evaluation
• Mailing List
• Past Series
• Past Series
• Past Series
• Past Series
• Past Series
• Past Series 2019–2020

Bootcamps

Bootcamps are available.

NLM BIRT Fellowship

The NLM BIRT Fellowship includes:

• BIRT Fellow Profiles
  • BIRT Alumni, 2019 - 2024
  • BIRT Alumni, 2013 - 2018
• Connections: Career Paths in Biomedical Informatics

Courses

Available courses include:

• AISC 610 - Computationally-Enabled Medicine
• BMI 701 - Foundations in Biomedical Informatics I
• BMI 702 - Foundations of AI in Medicine
• BMI 706 - Data Visualization for Biomedical Applications
• BMI 709 - Biomedical Web Applications with R/Python Shiny
• BMI 710 - Single-Cell Analysis for Functional Genomics of Disease
• BMI 711 - Integrative Analyses for Rare Genetic Disease Diagnostics
• BMI 712 - AI in Medical Imaging
• BMI 714 - Advanced Coding and Statistics for Biomedical Informatics
• BMI 717 - Conduct and Communication of Science
• BMI 718 - Reading, Writing, and Evaluating Scientific Literature
• BMI 719 - Design and Execution of Scientific Projects
• BMI 741 - Health Information and Technology: From Ideation to Implementation
• BMIF 201 - Concepts in Genome Analysis
• BMIF 202 - Artificial Intelligence in Medicine I
• BMIF 203 - Artificial Intelligence in Medicine II
• BMIF 204 - Foundations of Clinical Data and its Applications
• BMIF 301 - AI in Medicine Clinical Experience I
• BMIF 302 - AI in Medicine Clinical Experience II

Single-Cell Analysis for Functional Genomics of Disease

Course Description

Single-cell technologies promise unparalleled insights into human biology, but first, these data require a new computational and statistical toolkit. In this course, we will compare single-cell and bulk data analysis paradigms, and explore new methods to quality control, analyze, and interpret single-cell-RNA-sequencing data. Students will learn about single-cell technologies and experimental design, build pipelines to process sequencing data, and use R packages for quality control and analysis. Students will learn about frameworks for interpreting single-cell data - eg., trajectories, differential abundance - and use them to answer biological questions with single-cell datasets in diverse domains. We will conclude by exploring the application of single-cell technologies to disease cohorts with spatial profiling, reference mapping, and multimodal approaches. Class activities will include lectures, coding activities, and paper discussions.

Prerequisites

• R and basic command-line operations (BMI 714 or equivalent)
• Basic statistics (BMI 714, or equivalent)
• Familiarity with genomic data analysis is recommended (BST 281, BST 282, or equivalent; may be taken concurrently)

Faculty

Aparna Nathan, Lecturer in Biomedical Informatics, Associate Director, Master of Medical Sciences in Biomedical Informatics (MMSc-BMI) Program

Spring 2 2026

• Room: First class session will meet in TMEC 106. All subsequent class sessions will meet in Countway 403.
• Meeting Times: Thursdays, 9:00am - 11:00am
• First Class Meeting: Thursday, March 26, 2026
• Final Class Meeting: Thursday, May 7, 2026

Cross-Registration

Registration for HMS courses is not available until January. Students who are not in the Master of Medical Sciences in Biomedical Informatics program who wish to cross-register for this course must submit a petition in my.harvard that summarizes their interest in the course and how they have satisfied the prerequisites. Cross-reg petitions will be reviewed on a first-come, first-served basis beginning January 23, 2026. Students can and should submit petitions before this date, but they will not be approved ahead of time.

Research Areas

Available research areas include:

• Artificial Intelligence
• Biomedical Discovery Infrastructure
• Clinical Decision Making
• Computational Omics
• Evolutionary Genetics
• Genes and Environment
• Learning Health Systems
• Microbial Genomics
• Taxonomy of Disease

Projects

Available projects include:

• 4CE
• 4DN DCIC
• AIM PhD Track
• AIM-AHEAD
• CCB
• CGAP
• Confluence
• CHARM
• GenTB
• HuBMAP Data Portal
• IGVF
• MAIDA
• MOMA
• NEXUS
• NHLBI BioData Catalyst
• People Heart Study
• Precision Medicine Annual Conference
• ProCyon
• RAISE
• RANT
• SMaHT Data Portal
• SAIL
• TDC
• ToolUniverse
• UDN

Faculty

Core faculty members include:

• Paul Avillach
• Michael Baym
• Tianxi Cai
• Maha Farhat
• Nils Gehlenborg
• Isaac Kohane
• Heng Li
• Arjun (Raj) Manrai
• Luke O'Connor
• Peter Park
• Chirag Patel
• Pranav Rajpurkar
• Shamil Sunyaev
• Kun-Hsing Yu
• Marinka Zitnik

Events

Available events include:

• DBMI Calendar
• Event Submission Guidelines
• Entrepreneurs Salon (BIES)
• Omenn Lecture
• Open Insights Seminars
• Precision Medicine Annual Conference
• RAISE Symposium
• SAIL Annual Conference

Careers

Available career opportunities include:

• Faculty
• Postdoctoral Fellowships
• Curriculum Fellowships
• Associates and Research Associates
• Professional Staff

About DBMI

The Department of Biomedical Informatics includes:

• DBMI Mission and Vision
• Department Leadership
• Administration
• DBMI Technology Development Core
• Core for Computational Biomedicine
• Resources
• Contact Us