Meetings & Courses Program

Crossroads of Biology

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Single Cell & Spatial Transcriptomics Analysis 
June 25 - July 13, 2026

Key Dates
Application Deadline: March 27th, 2026 CLOSED
Arrival: June 25th by 6pm EST
Departure: July 13th around 12pm EST

The 2026 Single Cell & Spatial Transcriptomics  Course is no longer taking applications.



CSHL Courses are intensive, running all day and often including evenings and weekends; students are expected to attend all sessions and reside on campus for the duration of the course.

Instructors

Nicholas Navin, MD Anderson Cancer Center, Houston, TX
Julea Vlassakis, Rice University, Houston, TX

Co-Instructors
Mandovi Chatterjee, Harvard Medical School, Boston
Sanja Vickovic, NYGC and Columbia University, New York, NY 


See the roll of honor - who's taken the course in the past.


Video about the course.

The goal of this two-week course is to teach students cutting-edge wet-lab approaches for single cell analysis, and to provide familiarity with basic bioinformatic approaches to single cell data. Modules of the course will be taught by scientists with expertise in distinct areas of single cell analysis.

Topics:

  • Droplet-based single cell RNA-seq using RNA Flex Technology.

  • Spatial Transcriptomics of tissues using Visium HD

  • Single-Cell Protein Electrophoresis

  • Single-Cell Mass Spectrometry

  • Introduction to single-cell data analysis (R / Unix)

  • Single-cell RNA and DNA data analysis

  • Spatial Transcriptomics data analysis methods

  • and more


2026 Invited Speakers
James Eberwine, University of Pennsylvania, Philadelphia, PA
Rong Fan, Yale University, Cheshire, CT
Bill Flynn, The Jackson Laboratory for Genomic Medicine, CT
Daniel Fürth, Uppsala University, Sweeden
Peter Kharchenko, Harvard Medical School, Boston
Siran Li, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Maddison Masaelie, DeepCell, Menlo Park, CA
Orit Rosenblatt-Rosen, Genentech, San Francisco, CA
Peter Sims, Columbia University, New York, NY
Chloe Villani, Mass General Hospital and Harvard Medical School, Boston, MA
Chenxu Zhu, New York Genome Center & Weill Cornell Medicine, New York, NY 

Major support for this course is provided by the Eunice Kennedy Shriver National Institute of Child Health & Human Development of the National Institutes of Health. 

Additional funding provided by Howard Hughes Medical Institute.

We would like to thank the following company for their generous donation in making this course possible


We would like to acknowledge the following companies that provided invaluable equipment support:
10x Genomics, Aligned Genetics/Logos Biosystems, Calibre Scientific, and Sutter Instrument

Cost (including board and lodging): $5,720 USD

No fees are due until you have completed the full application process and are accepted into the course.

Students are further expected to bring a laptop computer with specified bioinformatic packages pre-installed.

Before applying, ensure you have:
  1. Personal statement/essay;
  2. Letter(s) of recommendation;
  3. Curriculum vitae/resume (optional);
  4. Financial aid request (optional).
    More details.

If you are not ready to fully apply but wish to express interest in applying, receive a reminder two weeks prior to the deadline, and tell us about your financial aid requirements, click below: