Single-Cell Genomics

Single-cell genomics is driving a measurement revolution in biology. Droplet-based single-cell profiling techniques allow us to interrogate the chemical state (mRNA, DNA, chromatin) of thousands of single cells at once—an exponential scaling of throughput from just a few years ago. Single-cell measurements show us how different cell types can collectively respond to a disease or treatment. These insights can lead to the development of new drugs and interventions that can mobilize the right cells against cancer or neurodegeneration, or generate entirely synthetic cell types that are useful in rejuvenation or repair.


Photo of student working in SPEC lab communal space

We develop technology that leverages single-cell genomics for manipulating and engineering synthetic cells and tissues.

First formed as a Beckman Institute Pilot Center in the fall of 2017, the Single-Cell Profiling and Engineering Center brings single-cell genomic capabilities to the Caltech campus and drives new technology development. We focus on two core competencies:

Scaling up experimentation. We both apply and develop new technologies  that make it possible to learn how populations of cells respond to hundreds of different chemical and genetic levers. These experiments will teach us how to program new and useful functions into populations of cells.

Machine learning. We develop computational tools that harness ideas from classical information theory to extract meaningful insights from single-cell datasets. Among these tools is a platform based on probabilistic models that can automatically rank drugs, classify diseases, and discover cell-type specific responses.

To learn more, explore our publications.

We support diverse projects across the Caltech campus, including neural systems engineering, human health and medicine, as well as ecology, evolution, and developmental biology. Our work includes:

  • Consulting and collaborating with the Caltech community to apply single-cell profiling to their projects
  • Developing new cell isolation protocols for unusual systems—such as beetle glands or sea urchin embryos
  • Providing training and expertise on single-cell library prep and sequencing methods
  • Offering guidance on single-cell data analysis tools

Want to Collaborate?


Dedicated to fostering the early development of cutting-edge research, the Beckman Institute supports new avenues of discovery and significant technological advances in the chemical and biological sciences. SPEC and other Resource Centers within the Beckman Institute strive to develop technology, practices, and an environment of collaboration that will lead to the Institute’s goals of creating great practical benefits for society and humankind.


Bioinformatics Resource Center

The BRC provides in-depth bioinformatics services and consulting. They consult on a range of topics including single-cell RNA-seq data analysis, transcriptome assembly, and ChIP-seq data.


The BI CLOVER Center facilitates optogenetic studies, custom viral vector development, and tissue clearing projects across Caltech through infrastructure and reagent sharing, training, and more.

Functional Genomics Resource Center

FGRC develops experimental and computational methods for functional genomics, including RNA-seq, small pools of cells and single cells, ChIP-seq, long distance chromosomal interactions, and more.