Single Cell Genomics Day: A Practical Workshop


Where: NYU Center for Genomics and Systems Biology
When: Friday, January 24, 2020 9:00 AM to 5:00 PM EST
Livestream: The workshop is concluded, but we will rebroadcast the livestream on this website starting at Thursday, 2/6 at 9:30PM EST. The rebroadcast will include breaks.
Registration: You can register for the waitlist to attend in-person here


9:30 am — 10:15 am Rahul Satija New York Genome Center (NYGC) and New York University (NYU)
Single-cell genomics: Recent advances and future directions
View the talk here
10:15 am — 10:45 am Eleni Mimitou NYGC Technology Innovation Lab
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New technologies for single-cell multi-omic analysis
10:45 am — 11:25 am Kun Zhang University of California, San Diego
Integrative single-cell RNA and chromatin analysis of human brain
11:25 am — 11:45 am Coffee Break
11:45 am — 12:15 pm Yuhan Hao NYGC / NYU
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Defining cellular identity based on multiple modalities
12:15 pm — 12:55 pm Jimmie Ye University of California, San Francisco
Multiplexed single cell genomics
12:55 pm — 2:15 pm Lunch Break
2:15 pm — 2:55 pm Aviv Regev Broad Institute, MIT, HHMI
Cell Atlases as Road Maps to Health and Disease
2:55 pm — 3:25 pm Tim Stuart NYGC
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Analyzing single-cell ATAC-seq datasets
3:25 pm — 3:40 pm Break
3:40 pm — 4:20 pm Roser Vento-Tormo Sanger Institute
Immunogenomics, one cell at a time
4:20 pm — 4:50 pm Andrew Butler, Paul Hoffman NYGC/NYU
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Analyzing spatially-resolved transcriptomic datasets


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 Fourth Annual Single Cell Genomics Day on Friday, January 24, 2020. This workshop will begin with an overview of exciting developments in the field over the past year, followed by in-depth presentations with an emphasis on practical details and considerations. 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, including: paired RNA-seq and ATAC-seq from the same nucleus, and spatial measurements of single cell expression.
  • Get a practical introduction to recently developed computational techniques, including algorithms for inferring cell-cell interactions, and analytical tools for spatial transcriptomics datasets.
  • Learn about strategies for massively multiplexed experimental design, and new approaches to understand the effects of human genetic variation on cellular heterogeneity.
  • Hear about recent updates from the Human Cell Atlas, a global initiative to create comprehensive reference maps of all human cells.
  • Share ideas, troubleshoot experiments, and ask questions.
  • Hear keynote presentations from:
    • Kun Zhang University of California, San Diego
    • Jimmie Ye University of California, San Francisco
    • Roser Vento-Tormo Sanger Institute
    • Aviv Regev Broad Institute, Massachusets Institute of Technology, Howard Hughes Medical Institute

Single Cell Genomics Day will be held at NYU Center for Genomics and Systems Biology, with check in beginning at 9:00 AM. Please register in advance to attend in person. The workshop is free for all participants, thanks to generous support from the NYU Biology department and Center for Genomics and Systems Biology.


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.

Previous years