Meetings & Courses Program

Crossroads of Biology

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Single Cell & Spatial Transcriptomics Analysis 
July 1 - 19, 2027

Key Dates
Application Deadline: March 12, 2027
Arrival: July 1st, by 6pm EST
Departure: July 19th, around 12pm EST

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.  The programs are not offered for academic credit or completion of an academic program of study in the U.S.. 


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. 


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

Cost (including board and lodging): $5,895 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).  Stipend requests do not affect selection decisions by the Instructors.
    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: