Alex K. Shalek

Faculty Title: 

Pfizer-Laubach Career Development Assistant Professor, MIT  Core Member, Institute for Medical Engineering and Science, MIT Assistant Professor, Chemistry, MIT Associate Member, Ragon Institute of MGH, MIT, and Harvard Associate Member, Broad Institute of MIT and Harvard Assistant in Immunology, MGH Instructor, Health Sciences and Technology, HMS  


  • Chemistry
  • Institute for Medical Engineering & Science (IMES)



Phone Number: 

(617) 324-5670


Faculty Bio: 

Alex K. Shalek is currently the Pfizer-Laubach Career Development Assistant Professor at MIT, as well as a Core Member of the Institute for Medical Engineering and Science (IMES) and an Assistant Professor of Chemistry.  He is also an Associate Member of the Ragon and Broad Institutes, an Assistant in Immunology at MGH, and an Instructor in Health Sciences and Technology at HMS.  His research is directed towards the development and application of new technologies that facilitate understanding of how cells collectively perform systems-level functions in healthy and diseased states.  Dr. Shalek received his bachelor's degree summa cum laude from Columbia University and his Ph.D. from Harvard University in chemical physics under the guidance of Hongkun Park, and performed postdoctoral training under Hongkun Park and Aviv Regev (Broad/MIT).  To date, his interdisciplinary research has focused on realizing and utilizing nanoscale manipulation and measurement technologies to examine how small components (molecules, cells) drive systems of vast complexity (cellular responses, population behaviors). DEGREES PhD in Chemical Physics, Harvard University, 2011 AM in Chemical Physics, Harvard University, 2006 BA in Chemical Physics, Columbia University, 2004   SELECTED AWARDS/SOCIETIES Pfizer-Laubach Career Development Professorship, MIT, 2017-2020 Associate Scientific Advisor, Science Translational Medicine, 2016 NIH New Innovator, 2015 Beckman Young Investigator, 2015 Searle Scholar, 2015 “Follow That Cell” Competition First Place (Team Member), 2015 Hermann L.F. Von Helmholtz Career Development Professor, 2014-Present Broad Institute-Israel Partnership for Cell Circuit Research Collaborative Grant, 2013 Excellence Award, Broad Institute, 2013 Dudley R. Herschbach Teaching Award, Harvard University, 2006 Certificate of Distinction in Teaching, Harvard University, 2005 National Science Foundation Graduate Research Fellowship, 2005-2008 Phi Beta Kappa, Columbia University, 2004 John Jay Scholar, Columbia University, 2000-2004 Dean’s List, Columbia University, 2000-2004

Research Areas: 

Research Summary: 

Research in the Shalek Lab is directed towards the creation and implementation of new technologies to understand how cells collectively perform systems-level functions in healthy and diseased states. To examine the rules that govern ensemble cellular behaviors, we employ a comprehensive, five-step approach: first, we identify the fundamental elements that comprise our systems; second, we decipher the salient characteristics that differentiate each element; third, we explore how environmental signals impact the molecular computations each element makes; fourth, we examine how direct interactions between elements influence each other; and, finally, we investigate how the foregoing factors cooperatively drive ensemble phenomena. At each step, as we face technical limitations and pressing biological needs, we develop and apply innovative methodologies to empower a deeper, more mechanistic inquiry. Our technology development leverages recent advances in genomics, chemical biology, and nanotechnology to establish cross-disciplinary platforms for in-depth profiling and precise manipulation of cells and their interactions. Examples include microdevices for massively-parallel single-cell genomics, strategies for simultaneously measuring diverse cellular variables, microfluidic tools for controlling the cellular microenvironment, and approaches for engineering and profiling cell-cell interactions. Our biological applications focus on the roles of cellular heterogeneity and cell-to-cell communication in driving immune responses. Current studies examine how: innate and adaptive immune cells coordinate balanced responses to environmental changes; host cell-pathogen interactions evolve across time and tissues during HIV-1 and M. Tuberculosis infection; and, tumor cells evade immune responses. Overall, our goal is to realize broadly-applicable experimental and computational platforms to uncover common cellular motifs that inform healthy and diseased immune responses. Using this information, we aim to help transform how the community thinks about single cells, cell-cell interactions, diseased tissues and processes, and therapeutics to create a new paradigm for understanding and designing systems-level multicellular behaviors.   SELECTED PUBLICATIONS Gierahn, T.#, Wadsworth II, M.H. #, Hughes, T.K. #, Bryson, B.D., Butler, A., Satija, R., Fortune, S., Love, J.C.*, and Shalek, A.K.*, “Seq-Well: A Portable, Low-cost Platform for Single-Cell RNA-Seq of Low-Input Samples,” Nature Meth., 14, 395 (2017). Tirosh, I. #, Izar, B. #, Prakadan, S.M., Wadsworth II, M.H., Tracy, D., Trombetta, J.J., Rotem, A., Rodman, C., Lian, C., Murphy, G., Fallahi-Sichani, M., Dutton-Regester, K., Lin, J.R., Cohen, O., Shah, P., Lu, D., Genshaft, A., Hughes, T.K., Ziegler, C.G.K., Kazer, S.W., Gaillard, A., Kolb, K.E., Villani, A.C., Johannessen, C.M., Andreev, A.Y., van Allen, E.M., Bertagnolli, M., Sorger, P.K., Sullivan, R.J., Flaherty, K.T., Frederick, D.T., Jané-Valbuena, J., Yoon, C.*, Rozenblatt-Rosen, O.*, Shalek, A.K.*, Regev, A.*, and Garraway, L.*, “Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq,” Science, 352, 189 (2016). Macosko, E.Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A.R., Kamitaki, N., Martersteck, E.M., Trombetta, J.J., Weitz, D.A., Sanes, J.R., Shalek, A.K., Regev, A., and McCarroll, S.A., “Genome-wide expression profiling of thousands of individual cells using nanoliter droplets,” Cell, 161, 1202 (2015). Shalek, A.K.#, Satija, R.#, Shuga, J.#, Trombetta, J.J., Lu, D., Gennert, D., Chen, P., Gertner, R.S., Gaublomme, J.T., Yosef, N., Schwartz, S., Fowler, B., Weaver, S., Wang, J., Wang, X., Ding, R., Raychowdhury, R., Friedman, N., Hacohen, N., Park, H.*, May, A.P.*, and Regev, A.*, “Large-Scale Single-Cell RNA-Seq Reveals Strategies for Regulating Cell-to-Cell Dynamic Variability through Paracrine Signaling,” Nature, 510, 363 (2014). Shalek, A.K.#, Satija, R.#, Adiconis, X., Gertner, R.S., Gaublomme, J.T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D., Trombetta, J.J., Gennert, D., Gnirke, A., Goren, A., Hacohen, N., Levin, J.Z., Park, H., and Regev, A., “Single-Cell Transcriptomics Reveals Bimodality in Expression and Splicing in Immune Cells,” Nature, 498, 236 (2013). Yosef, N.#, Shalek, A.K.#, Gaublomme, J.T.#, Jin, H., Lee, Y., Awasthi, A., Wu, C., Karwacz, K., Xiao, S., Jorgolli, M., Gennert, D., Satija, R., Shakya, A., Lu, D.Y., Trombetta, J.J., Pillai, M., Ratcliffe, P.J., Coleman, M.L., Bix, M., Tantin, D., Hongkun Park, H., Kuchroo, V.K., and Regev, A., “Dynamic Regulatory Network Controlling Th17 Cell Differentiation,” Nature, 496, 461 (2013). A full list of Professor Shalek’s publications can be found on his website.