Single Cell Genomics Day: A (Virtual) Practical Workshop


When:Friday March 29, 2024 10:00 AM to 5:00 PM EDT
Livestream:All talks will be openly livestreamed on this website and Youtube. Registration is not required.


10:00 — 10:40 AM (EST)Rahul Satija New York Genome Center (NYGC) and New York University (NYU)
Single-cell genomics: Recent advances and future directions
10:40 — 11:20 AMJason Buenrostro Harvard University
Single-cell epigenomics and the regulatory control of cells
11:20 AM — 11:40 AMMarie Schott & Daniel León-Periñán Max Delbrück Center, Rajewsky lab
Open-ST: High-resolution spatial transcriptomics in 3D in your lab
11:40 — 12:00 PMCoffee break
12:00 — 12:20 PMCaleb Lareau Memorial Sloan Kettering Cancer Center
Rare cell analyses with single-cell sequencing
12:20 — 12:40 PMCarol Dalgarno & Longda Jiang New York Genome Center, Satija lab
Single cell perturbation dictionaries
12:40 — 1:00 PMKamal Maher Broad Institute, Wang lab
Generalizing single-cell analysis methods to spatial data
1:00 — 1:40 PMLunch break
1:40 — 2:20 PMXiaowei Zhuang Harvard University
Spatially resolved single-cell genomics & cell atlas of the brain
2:20 — 2:40 PMYanay Rosen Stanford University, Leskovec lab
Universal cell embeddings: A foundation model for cell biology
2:40 — 3:00 PMCoffee break
3:00 — 3:40 PMIdo Amit Weizmann Institute
The power of ONE: Immunology in the age of spatial and single cell genomics
3:40 — 4:00 PMAustin Hartman Stanford University
Comparative analysis of multiplexed in situ gene expression profiling technologies
4:00 — 4:20 PMSandra Nakandakari Rockefeller University, Victora lab
Universal recording of cellular interactions


Recent developments in molecular biology, multiplexed imaging, and computational biology have transformed the field of single cell genomics, and have widespread biological applications. However, the breathtaking pace of technology development has given rise to a multitude of molecular protocols, commercial systems, and computational challenges.

The Satija Lab is excited to host the eighth annual Single Cell Genomics Day on Friday, March 29, 2024. This workshop will begin with an overview of exciting developments in the field over the past year, followed by in-depth presentations on exciting methods and techniques. Our goal is to empower you to utilize single cell genomics in your work. The workshop is free and open to beginners and experts alike.

Come to:

  • Learn about cutting-edge molecular technologies for multimodal single-cell analysis, scalable perturbation screens, time-resolved measurements, and spatial profiling.
  • Discover powerful new computational approaches for analyzing single cell data with AI language models, interpreting and benchmarking spatial technologies, and cross-species atlasing.
  • Hear keynote presentations from:
    • Ido Amit Weizmann Institute of Science
    • Jason Buenrostro Broad Institute
    • Xiaowei Zhuang Harvard University

Additional speakers and a full agenda will be posted to this website in advance of the workshop.

Single Cell Genomics Day will take place virtually in 2024. We are able to make all talks freely available via livestream thanks to support from the National Human Genome Research Institute to the Center for Integrated Cellular Analysis.

Additional resources

Below, we list a few useful resources for those who would like to a brief introduction to the field prior to the workshop.

Integrative single-cell analysis. (Stuart and Satija., 2019) [PubMed]
Our recent overview of multi-modal technologies and computational integration methods for single-cell data.

A practical guide to single cell RNA-seq for biomedical research and clinical applications. (Haque et al., 2017) [PubMed]
An excellent overview of single cell genomics, for those new to the field.

Choosing a single cell technology. (Satija Lab) [PDF Slides]
From our first single cell genomics day. Covers the strengths, weaknesses, and ideal uses cases for common technology platforms.

Computational and analytical challenges in single-cell transcriptomics. (Stegle, Teichmann, and Marioni, 2015) [PubMed]
A broad and comprehensive discussion of analytical challenges for single cell analysis.

Power analysis of single-cell RNA-sequencing experiments. (Svensson et al., 2017) [PubMed]
A comprehensive technical benchmarking of single cell technologies.

Methods and challenges in the analysis of single-cell RNA-sequencing data. (Camara, 2017) [Link]
A concise overview, focusing on recent analytical developments in the field.