Single Cell Analysis
June 30 - July 15, 2023

Key Dates
Application DeadlineMarch 15, 2023
Arrival: June 29th by 6pm EST
Departure: July 15th 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.


David Chenoweth, University of Pennsylvania
Luciano Martelotto,
University of Adelaide, Australia
Michael McConnell,
Lieber Institute for Brain Development
Julea Vlassakis,
Rice University

Huaiying Zhang, Carnegie Mellon University

2023 Teaching Assistants
Mandovi Chaterjee, Harvard Medical School
Trinh Lam, University of California, Berkeley
Yang Liu, University of California, Berkeley
Maya Overton, University of California, Berkeley
Dylan Schaff, University of Pennsylvania
Rongwei Zhao, Carnegie Mellon University

2023 Computational Assistants
Trent A Gomberg, UCSD
Adam Klie, UCSD
Nicole A Lopez, UCSD

Deepak Pant, UCSD
Brian Yee, UCSD

COVID-19: All participants planning to attend in-person will be required to attest to recent COVID vaccination (within one year of the course’s start date) with an FDA or WHO approved vaccine. Additional safety measures will be in line with current NY and Federal Guidelines applicable in Summer 2023.


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.

  • Droplet- and microwell based single cell isolation
  • SplitSeq device-free single cell RNA librarypreparation
  • Single molecule FISH
  • Single cell western blot
  • Photoactivatable single cell probes
  • Single cell mass spectrometry 
  • Introductory single cell sequencing analysis

Speakers and Module Leaders Include:

Noorsher Ahmed, University of California, San Diego
Nancy Allbritton, University of Washington
James Eberwine, University of Pennsylvania
Rong Fan, Yale University
Jean Fan, Johns Hopkins University
Livnat Jerby, Stanford University
Liana Lareau, University of California, Berkeley
Clarence Mah, University of California, San Diego
Samantha Morris, Washington University in St. Louis
Charlie Roco,
Parse Biosciences
Elena Romanova, University of Illinois
Stas Rubakhin, University of Illinois
Sydney Shaffer, University of Pennsylvania
Peter Sims, Columbia University
Nikolai Slavov, Northeastern University
Longzhi Tan, Stanford University
Gene Yeo, University of California, San Diego

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 and Helmsley Charitable Trust.

We would like to acknowledge the following companies that provided invaluable equipment support:
Agilent Technologies, Cell MicrosystemsEppendorf North America, Hamamatsu Photonics, Molecular DevicesProteinSimple, Inc, Sutter Instrument Company, Thermo Fisher Scientific

Cost (including board and lodging): $4,660

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: