Single Cell Genomics Day: A (Virtual) Practical Workshop


When:Friday April 7, 2023 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)
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Single-cell genomics: Recent advances and future directions
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10:40 — 11:20 AMSamantha Morris Washington University in St. Louis
New genomic technologies to deconstruct and control cell identity
11:20 — 11:40 AMCoffee Break
11:40 AM — 12:20 PMSten Linnarsson Karolinska Institute
Cellular diversity of the developing and adult human nervous system
12:20 — 12:40 PMSanja Vickovic NYGC, Columbia University
Spatial host-microbiome sequencing
12:40 — 1:00 PMBrian Cleary Boston University
Compressed Perturb-seq: highly efficient screens from regulatory circuits using random composite perturbations.
1:00 — 1:40 PMLunch Break
1:40 — 2:00 PMJackson Weir Harvard University, Chen Lab
Slide-tags: A new methodology for generating spatially localized single cell genomics data
2:00 — 2:20 PMMadeline Kowalski NYGC/NYU, Satija Lab
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Characterizing heterogeneity in post-transcriptional regulation with single-cell sequencing
2:20 — 2:40 PMJohn Blair NYGC/NYU, Satija Lab
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Reconstructing regulatory networks from multimodal single cell data
2:40 — 3:00 PMHelen Kang Stanford University, Engreitz Lab
Variant-to-Gene-to-Program: an approach to trace the path between GWAS variants and common disease
3:00 — 3:20 PMCoffee Break
3:20 — 4:00 PMJay Shendure University of Washington
Global views of mammalian development, from zygote to pup
4:00 — 4:20 PMGesmira Molla, Yuhan Hao NYGC/NYU, Satija Lab
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Strategies for massively scalable single-cell analysis
4:20 — 4:40 PMSydney Shaffer University of Pennsylvania
Tracing lineages and cell states from metaplasia to cancer


Recent developments in molecular biology, microfluidics, 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 seventh annual Single Cell Genomics Day on Friday, April 7, 2023. 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, cellular recording, lineage tracing, and spatial profiling.
  • Discover powerful new computational approaches for transcriptional and post-transcriptional network reconstruction, integrating sequencing and imaging datasets, and scalable processing of millions of cells.
  • Share ideas, troubleshoot experiments, and ask questions.

Due to the COVID-19 pandemic, Single Cell Genomics Day will take place virtually in 2023. 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.