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.