Single Cell Genomics Day: A Practical Workshop
Recent developments in molecular biology, microfluidics, and computational biology have transformed the field of single cell genomics. 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 Third Annual Single Cell Genomics Day on Friday, March 22, 2019. 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 not to fully describe the details of each method, but instead to highlight the intuition and key use cases that can help motivate new users to get started.
- Learn about cutting-edge molecular technologies including: single nucleus ATAC-seq, spatial measurements of single cell expression, and multi-modal profiling approaches.
- Hear about recent updates to widely used commerical systems, and contrasting home-brew workflows.
- Get a practical introduction to recently developed computational techniques, including methods for data integration, organism-scale developmental reconstruction, and deep learning applications for single cell data.
- Share ideas, troubleshoot experiments, and ask questions
- Hear keynote presentations from:
- Jeff Moffitt Harvard Medical School
- Darren Cusanovich University of Arizona
- Jeff Farrell Harvard Unviersity
Single Cell Genomics Day will be held at NYU Center for Genomics and Systems Biology, with check in beginning at 8:30 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.
We would like to acknowledge the generous support of the Chan Zuckerberg Initiative, which allowed us to provide a video livestream of all presentations. We will be posting slides, references, and selected videos from the workshop in the near future.
|9:00 — 9:45||Rahul Satija
Download Slides, Summary and References
Single-cell genomics: Recent advances and future directions
View the talk here
|9:45 — 10:15||Peter Smibert
NYGC Technology Innovation Lab|
Multi-modal single-cell analysis
Topics: ECCITE-Seq, single cell chromatin+RNA, single cell calling cards
|10:15 — 11:00||Jeff Moffitt
Harvard Medical School|
Imaging the transcriptome: Mapping the brain with MERFISH
|11:00 — 11:15||Coffee Break|
|11:15 — 11:45||Grace Zheng
Dissecting complex systems with multidimensional data
Topics: scATAC-seq, spatial gene expression, surface protein + antigen receptors
|11:45 — 12:30||Darren Cusanovich
University of Arizona|
Single-cell genomics via Combinatorial Indexing: A scalable and adaptable framework
|12:30 — 13:15||Lunch|
|13:15 — 13:45||Andrew Butler, Shiwei Zheng
Introduction to Deep Learning methods for single-cell analysis
Topics: Neural networks, autoencoders, VAE, GAN
|13:45 — 14:30||Jeff Farrell
Reconstruction of developmental trajectories during zebrafish embryogenesis
|14:30 — 15:00||Tim Stuart
Integration and harmonization of single-cell data
Topics: Batch correction, cross-modal integration, transfer learning
Below, we list a few useful resources for those who would like to a brief introduction to the field prior to the workshop.