Single Cell Genomics Day: A (Virtual) Practical Workshop
Details
| When: | Friday June 12, 2026 10:00 AM to 5:00 PM EDT |
| Livestream: | The livestream has ended. |
Agenda
| 10:00 — 10:40 AM | Rahul Satija
NYGC and NYU Single-cell genomics: Recent advances and future directions |
| 10:40 — 11:00 AM | Dingchang Lin
Johns Hopkins University Genetically encoded assembly recorder temporally resolves cellular history |
| 11:00 — 11:40 AM | Xin Jin
Scripps Research Towards a functional brain genome |
| 11:40 AM — 12:00 PM | Coffee break |
| 12:00 — 12:20 PM | Sydney Blattman
Memorial Sloan Kettering Cancer Center Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity. |
| 12:20 — 12:40 PM | Amanda Urke
Harvard University Protein-guided RNA barcoding links transcriptomes to synaptic architecture. |
| 12:40 — 1:20 PM | Anshul Kundaje
Stanford University Deep learning the regulatory code of fetal development and cellular reprogramming from single cell chromatin accessibility |
| 1:20 — 2:00 PM | Lunch |
| 2:00 — 2:45 PM | Aviv Regev
Genentech From Cell Atlases to Medicines, with AI |
| 2:45 — 3:05 PM | Alex Bradu
NYGC Genome-wide single-cell perturbation screens with VIPerturb-seq |
| 3:05 — 3:20 PM | Break |
| 3:20 — 3:40 PM | Kevin Chao
Harvard University TimeVault: A genetically encoded device for transcriptome storage in mammalian cells |
| 3:40 — 4:20 PM | Junyue Cao
Rockefeller University Scalable genomic approaches to investigate cellular dynamics in aging and disease |
| 4:20 — 4:40 PM | Moritz Schaefer
Stanford University Biomedical Data Analysis with Language-Multimodal AI |
| 4:40 — 4:50 PM | Wrap-up and closing |
Description
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 tenth annual Single Cell Genomics Day on Friday, June 12, 2026. 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.
Single Cell Genomics Day will take place virtually in 2026. 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.