Molecularly defined atlases of complex tissues from in situ single-cell transcriptomics
Imagine the ability to peer within tissues and to identify and localize the individual RNA molecules expressed within each and every one of the cells within those tissues. With this ability one could discovery and identify cell types based on their gene expression profiles and reveal the activation state of cells based on changes in their gene expression all while mapping out their detailed spatial organization and interactions within intact tissues!
We are developing and utilizing in situ single-molecule imaging methods to realize this vision, and we are leveraging these technologies to create cellular atlases - molecularly defined, cell-type-and-state annotated maps of tissues. With these atlases, we are tackling a wide range of biological questions!
Massively multiplexed single-molecule imaging with multiplexed error robust fluoresence in situ hybridization (MERFISH)
We massively multiplex single-molecule RNA imaging by using binary barcodes, read out bit-by-bit through sequential rounds of single-molecule imaging, to image and identify hundreds to thousands of different RNA molecules within single cells.
Similar approaches can be employed to measure properties of the genome and proteome.
Similar approaches can be employed to measure properties of the genome and proteome.
In situ single-cell transcriptome imaging
We use massively multiplexed single-cell gene expression measurements to reveal gene regulatory processes, map the internal organization of the transcriptome within single cells, and discover and map cell types within complex tissues.
We perform these measurements at very high levels of throughput - imaging hundreds to thousands of different RNA molecules within hundreds of thousands of individual cells, and we have ongoing projects to push this throughput to even higher levels.
State-of-the-art high-resolution fluorescence microscopy, fluid handling, automation, and computational analysis
We develop novel approaches to high-resolution fluorescence microscopy and microfluidic solutions for rapid, repetitive staining of a wide range of biological samples to enable in situ single-cell measurements of the genome, transcriptome, and proteome.
We couple these instrumentation efforts with the development of high-performance and high-efficiency image analysis methods to rapidly convert the terabytes of imaging data we collect into novel biological insights.
Our team
We are a growing team of biologists, chemists, physicists, engineers, and computational biologists.
We share a common passion for tackling new biological questions by developing new imaging technologies.
Interested in learning more? Contact us!
Research
In situ single-cell 'omics promises the exciting ability to directly image and quantify the genome, transcriptome, and proteome within single cells within intact tissues!
We develop the novel microscopy techniques, fluid-handling methodologies, and computational tools that will drive continued innovations in in situ single-cell 'omics.
We apply these exciting new approaches to unravel long-standing and fundamental biological questions in a wide range of systems, most notably the microbiome-host interface in mammals.
The Team
We are a dynamic and collaborative group of biologists, chemists, computational scientists, physicists, and engineers with a collective interest in developing novel image-based 'omics approaches and using these methodologies to tackle fundamental biological questions.
Join Us
We are actively recruiting team members with all levels of experience!
Join us in our efforts to develop the tools necessary to create molecularly defined maps of complex tissues and to use these maps to tackle some exciting biological questions!