Single Cell and Spatial Technologies





Course Description and Assignments

Single cell and spatial technologies allowed us to surpass granularity and context barriers, revolutionizing cancer research. They permit the investigation of cellular transcriptional programs, tumor clonal evolution, or immune cell receptors in unparalleled resolution, while spatial methods enable the fine-grained characterization of the tumor microenvironment and cell-cell communication in situ.

In this course we will focus on existing and upcoming technologies and how they can shape the scope of basic and translational cancer research. We will start with a general introduction to the methods, their capabilities, and shortcomings, and then proceed to discuss cutting-edge applications and still open research questions.


Each session will also incorporate walkthroughs of analyses, experiments, and recent publications, as well as 30’ of interactive discussion.

Registered participants will formulate a one-page example of a cancer research application using these technologies.

Session Dates and Times

Priority will be given to graduate students taking the course for credit. In order to receive credit, students must attend all sessions and complete the assignment. Postdocs may register but will only be granted access to the course as space allows.


First session – Tuesday May 4, 4-6:00pm, Zoom
Ioannis Vlachos
Yered Pita-Juarez

Second session – Tuesday May 11, 4-6:00pm, Zoom
Ioannis Vlachos
Yered Pita-Juarez

Third session – Thursday May 13, 4-6:00pm, Zoom
Ioannis Vlachos
Yered Pita-Juarez

Course Director & Instructor
Ioannis Vlachos, PhD, co-Director of the Bioinformatics Program, Cancer Research Institute, Beth Israel Deaconess Medical Center / Director of Bioinformatics, Precision RNA Medicine Core, HMS Initiative for RNA Medicine / Broad Institute of MIT and Harvard

Guest Lecturer
Yered Pita-Juarez, PhD, Postdoctoral Research Fellow, Beth Israel Deaconess Medical Center / Harvard Medical School / Broad Institute of MIT and Harvard.

Curriculum Fellow
Jelena Patrnogic, PhD (