Single Cell Genomics Day: A (Virtual) Practical Workshop

Details

When:Friday June 12, 2026 10:00 AM to 5:00 PM EDT
Livestream:All talks will be openly livestreamed on this website. Registration is not required. The livestream link will be added when available.
Single Cell Genomics Day 2026 flyer

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Agenda

10:00 — 10:40 AMRahul Satija NYGC and NYU
Single-cell genomics: Recent advances and future directions
10:40 — 11:00 AMDingchang Lin Johns Hopkins University
Genetically encoded assembly recorder temporally resolves cellular history
11:00 — 11:40 AMXin Jin Scripps Research
Towards a functional brain genome
11:40 AM — 12:00 PMCoffee break
12:00 — 12:20 PMSydney Blattman Memorial Sloan Kettering Cancer Center
Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity.
12:20 — 12:40 PMAmanda Urke Harvard University
Protein-guided RNA barcoding links transcriptomes to synaptic architecture.
12:40 — 1:20 PMAnshul Kundaje Stanford University
Deep learning the regulatory code of fetal development and cellular reprogramming from single cell chromatin accessibility
1:20 — 2:00 PMLunch
2:00 — 2:45 PMAviv Regev Genentech
From Cell Atlases to Medicines, with AI
2:45 — 3:05 PMAlex Bradu NYGC
Genome-wide single-cell perturbation screens with VIPerturb-seq
3:05 — 3:20 PMBreak
3:20 — 3:40 PMKevin Chao Harvard University
TimeVault: A genetically encoded device for transcriptome storage in mammalian cells
3:40 — 4:20 PMJunyue Cao Rockefeller University
Scalable genomic approaches to investigate cellular dynamics in aging and disease
4:20 — 4:40 PMMoritz Schaefer Stanford University
Biomedical Data Analysis with Language-Multimodal AI
4:40 — 4:50 PMWrap-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.

Previous years