Single-Cell Profiling and Engineering

Matthew Thomson – Principal Investigator
Brian Williams – Director
Technology Development

The mission of the Single-cell Profiling and Engineering Center (SPEC) is to unlock the potential of single-cell genomics for human health and basic research by advancing the technology and collaborating with innovative, diverse research groups across the Caltech campus. We provide scientific consulting, workflow training, instrumentation, and reagents to facilitate research projects across a wide range of applications and biological systems, including the mammalian brain, the immune system, and novel model organisms like the jellyfish or beetle.

Our central focus is to enable Caltech and the wider scientific community to wield single-cell profiling measurements as an experimental engine for rational engineering of cell state and function. We develop technologies that enable high-throughput perturbational experiments to close the loop between experimental manipulation and single-cell responses. By iterating through an array of drugs, biomolecules, doses, or genetic circuits, we can decipher the causal relationship between perturbation and cellular responses, at unprecedented transcriptional resolution. We envision that such high-dimensional profiling data can be used in the design of synthetic cell states for basic research or therapeutic applications.

Resources and Outreach:

  • We collaborate with the Caltech community on technology development projects.
  • We help with methodology development of new cell isolation protocols for novel biological systems—such as beetle glands or sea urchin embryos.
  • We train and provide expertise on single-cell library prep and sequencing methods.
  • We host workshops and seminars on cutting-edge single-cell profiling technologies.
  • We provide guidance and advice on single-cell data approaches and analysis tools.


  • Chromium controller
  • Miseq
  • Bioanalyzer
  • BluePippin
  • BSL2 culture facility
  • Nanodrop/Qubit/Plate reader


Brian Williams


117 Kerckhoff
Mail Code 156-29

Matthew Thomson

Principal Investigator

Principal Investigator
Biology and Biological Engineering
152 Beckman Behavioral Biology (BBB)
Mail Code 216-76