Advanced technologies are essential to biomedical progress, and CISID is committed to both driving innovation and to providing access to a range of enabling technologies and expertise. Researchers in the CISID community will be able to leverage the advances that emerge from the Innovation Labs as well as the Broad’s professionally run scientific platforms.

Broad Institute Scientific Platforms

The Broad provides access to the following technology platforms:

CISID Innovation Labs

In addition, CISID has established three Innovation Labs at the Broad with the goal of 1) pushing the technology envelop to enable scientists to ask and address critical questions relevant to infectious disease research; and 2) democratizing the pursuit of cutting-edge science by making critically-needed, enabling technologies accessible to the scientific community.

Microbial 'Omics Collaborative (MOC) Innovation Lab

MOC was established to develop and make accessible transformative genomics and transcriptomics methods and technologies that enable and advance CISID research. Work in MOC focuses on the 3 interconnected areas listed below, with an emphasis on applying 'omics methods directly to samples isolated from animal models of infection and human tissue obtained from CISID’s clinical research units, which allows us to begin understanding the interactions between host and pathogen in new ways.

For more information on the Microbial ‘Omics Collaborative Innovation Lab, contact Jonathan Livny, PhD.


Jonathan Livny, PhD

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415 Main St. Rm. 2021 Cambridge, MA 02142

Characterizing heterogeneity

Increasing the scale in which the variability of disease progression and outcome among patient populations can be studied and the resolution at which heterogeneity within individual infections can be interrogated. Methods in this area include higher-throughput, lower cost generation of microbial sequencing libraries and single-cell transcriptional profiling of pathogens in infection-derived samples.

Profiling cell-cell interactions

Enabling parallel profiling of cellular responses to infection in microbial pathogens, their hosts, and the resident microbiome to elucidate the complex interactions that govern infectious disease. Technologies include improved methods for enrichment of microbe-derived nucleic acids from infected cells and tissues and from diverse patient samples.

Mapping spatial and temporal dynamics

Developing improved ‘omics-based approaches to study the progression of infection over space and time as pathogens traverse diverse host niches and distinct stages of infection. These methods focus on extraction of nucleic acids and generation of sequencing libraries from low biomass samples and challenging sample types, as well as the interrogation of host and pathogen transcriptional programs within the spatial context of infected tissues.

Immune Profiling Innovation Lab

We are creating technologies that will enable us to understand the complete infection history of patients by deciphering systemic and tissue immune states before, during, and after an infectious challenge. One of the therapeutic goals is to understand how, when, and in which patients the growing portfolio of immune-modulating therapies can be deployed during an infection.

For more information on the Immune Profiling Innovation Lab, contact Jacques Deguine, Ph.D.


Jacques Deguine, Ph.D

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415 Main St. Rm. 7007 Cambridge, MA 02142

Scaling serological approaches

We aim to scale both phage and yeast-display systems to profile existing antibodies responses to pathogens, commensal microbes and self-antigens in serum.

Charting immune repertoires

By combining sorting approaches, single cell sequencing and functional evaluation of isolated T and B cell receptors, we aim to enable at scale mapping of adaptive immune responses.

Functional profiling of responses

Cytokine profiling of stimulated cells reveals distinct functional profiles both in healthy subjects and during acute and chronic infections. We will track responses to a range a stimuli, including a range of pathogens of interests.