Research

Uniting our lab group's diverse interests is a commitment to improve global health. We are interested in interactions of microbes with the human host in a wide range of contexts, from infection to beneficial colonization to everything in between. We engage in both fundamental research (to understand these complex systems) and translational research to make real-world impact.

One of our unique strengths is that we combine insights and approaches from multiple fields, including : 1) tools for high-resolution, quantitative measurements and 2) computational analyses to give rise to capabilities that haven't previously been possible, but are necessary to understand complex systems like the human-microbe interface and 3) quantitative ideas and tools from biophysics, dynamical systems, and engineering.

For example, in the context of infections, we develop rapid ultrasensitive diagnostics of infectious diseases (including several COVID-19 related projects and antibiotic resistance projects). In another example, we are interested in the interplay of food, gut microbes, and biophysics in human health. We have a number of projects (see the example of our celiac disease project at NIH RePORTER) in which we collaborate with clinicians to understand interactions of microbes with the human host.

In the past, our lab pioneered technologies for performing chemistry in droplet-based microfluidics and other devices, and these technologies are now widely used by many others. Innovative ideas that have been incubating in our lab continue to lead to new, significant projects.

We gratefully acknowledge support from the following agencies (past and present):

Army Research Office (ARO)
"MURI: Dissecting microbiome-gut-brain circuits for microbial modulation of host cognition in response to diet and stress"

Bill & Melinda Gates Foundation (BMGF)
"Determining the Detectable–to–Infectious Interval of SARS-CoV-2"

Burroughs Wellcome Fund (BWF)
"A microfluidic diagnostic platform to advance regulatory science"

Combating Antibiotic Resistant Bacteria (CARB-X)
"dAST - Digital antimicrobial susceptibility testing"
*Consortium organized by Boston University that includes federal sponsors BARDA, NIH and the Wellcome Trust

Jet Propulsion Laboratory (JPL)
"Ultra-sensitive RNA-based Functional Analysis (URFA) for viable microbial bioburden of spacecraft and associated surfaces"

Kenneth Rainin Foundation (KRF)
Innovator Award: "Tools for quantitative spatial analysis of mucosal gut microbiota in IBD"

National Institutes of Health (NIH)
"Novel tools to comprehensively map dynamic organization of RNA and DNA in
higher-order nuclear structures within single cells"

"Tissue destruction and healing in Celiac Disease"

National Science Foundation (NSF)
"RAPID: COVID-19 diagnostics for limited resource settings via improved sample preparation"
"EFRI-MIKS: Control of signaling and function by design with spatially pre-structured microbial communities"

Defense Advanced Research Projects Agency (DARPA)
"Digital single-molecule LRS diagnostics on SlipChip"
"BRICS: Enhancing Synthetic Biology With BioFARMs: Biologically Functional Assemblies
of Robust Microenvironments"
"CLIPS: Cohesive Living Protective Surfaces"
"Implementation of a synthetic Anammox biogranular technology in the main wastewater treatment line"

Department of Defense (DoD)
"Threshold-switchable particles (TSPs) to control internal hemorrhage"

Defense Threat Reduction Agency (DTRA)
"Single-molecule Antimicrobial Susceptibility Testing of Biothreat Bacterial Pathogens"

California Institute of Technology
Ronald & Maxine Linde Center for New Initiatives
Caltech's Merkin Institute for Translational Research (Merkin)
Joan & Jerry Doren
Center for Environmental Microbial Interactions (CEMI)
Jacobs Institute for Molecular Engineering for Medicine (JIMEM)
Caltech Innovation Initiative (CI2)
Resnick Sustainability Institute (RSI)
Caltech Space-Health Innovation Fund (established by the Translational Research Institute for Space Health, TRISH)
Donna & Benjamin M. Rosen Bioengineering Center (Rosen)
Caltech Center for Sensing to Intelligence (S2I)

Our research has also been supported previously by: American Chemical Society, Office of Naval Research, Searle Scholars Program, Alfred P. Sloan Foundation, Research Corporation for Science Advancement, Arnold & Mabel Beckman Foundation, Institute for Collaborative Biotechnologies, and the Camille & Henry Dreyfus Foundation.