Prof. Alex Shalek

Professor of Chemistry
Core Member, Institute for Medical Engineering and Science
Member, Ragon Institute
Institute Member, Broad Institute
Assistant in Immunology Massachusetts General Hospital (MGH)
Instructor, Health Sciences and Technology, Harvard Medical School (HMS)

Primary DLC

Department of Chemistry

MIT Room: E25-348A


Jeff Gahan

Areas of Interest and Expertise

Single Cells
Systems Biology
Cellular Circuits
Synthetic Biology
Molecular Biology
Chemical Biology
Mucosal Immunology
Precision Medicine
Tumor Immunology
Computational Biology

Research Summary

Research in the Shalek group is directed towards the development and application of new technologies that will facilitate an understanding of how cells collectively perform systems-level functions in healthy and diseased states. With respect to technology development, the group is leveraging recent advances in nanotechnology and chemical biology to establish a host of core, cross-disciplinary platforms that will collectively enable them to extensively profile and precisely control cells and their interactions within the context of complex systems. With respect to biological applications, the group is focusing on how cellular heterogeneity and cell-to-cell communication drive ensemble-level decision-making in the immune system, with an emphasis on "two-body" interactions (such as those between host cells and pathogens (e.g., HIV, TB), the innate and adaptive immune systems, and tumors and immune infiltrate). Their is to not only realize broadly applicable experimental tools, but also to help transform the way in which we think about single cells, cell-cell interactions, diseased cellular states, and therapeutics, creating a new paradigm for understanding and designing systems-level cellular behaviors in multicellular organisms.

Recent Work

  • Video


    April 4, 2023Conference Video Duration: 36:38
    Does Cell State Matter in Cancer? 

    AI in LIfe Science 2018 - Alex Shalek

    December 4, 2018Conference Video Duration: 28:23

    Identifying and Rationally Modulating Cellular Drivers of Enhanced Immunity

    Immune homeostasis requires constant collaboration between a diverse and dynamic set of cell types. Within our immune tissues, distinct cellular subsets must work together to defend against pathogenic threats, maintain tolerance, and establish memory. While surveying multiple healthy individuals enables exploration of potential ensemble immune solutions, contrasts against outliers of health and disease can reveal deviations that underscore diagnostic, therapeutic, and prophylactic features of enhanced function or dysfunction. Here, I will discuss how we can leverage single-cell genomic approaches – and, in particular, single-cell RNA-Seq – to explore the extensive functional diversity among immune cells within and across individuals, and uncover, from the bottom-up, distinct cell types and states associated with improved immunity. Moreover, I will discuss emerging experimental and computational strategies for altering ensemble cellular responses through targeted intra- or extracellular induction of these preferred types and states.

    2018 MIT AI in Life Sciences and Healthcare Conference