Background & Interests









Biography
Alex K. Shalek, PhD, is the J. W. Kieckhefer Professor in the Institute for Medical Engineering & Science and the Department of Chemistry, and an Extramural Member of The Koch Institute for Integrative Cancer Research at MIT. He is also an Institute Member of the Broad Institute, a Member of the Ragon Institute, an Assistant in Immunology at MGB, and an Instructor in Health Sciences & Technology at HMS. 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). His lab’s research is directed towards the development and application of new approaches to elucidate cellular and molecular features that inform tissue-level function and dysfunction across the spectrum of human health and disease. Dr. Shalek and his work have received numerous honors including a NIH New Innovator Award, a Beckman Young Investigator Award, a Searle Scholar Award, a Pew-Stewart Scholar Award, the Avant-Garde (DP1 Pioneer) Award from the National Institute for Drug Abuse (NIDA), and an Alfred P. Sloan Research Fellowship in Chemistry, as well as the 2019-2020 Harold E. Edgerton Faculty Achievement Award at MIT and the 2020 HMS Young Mentor Award.
Publications

Quantitative characterization of tissue states using multiomics and ecological spatial analysis






Transcriptomic analysis of whole staged ovarian follicles reveals stage-specific folliculogenesis signatures in mice







A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients






Artificial variables help to avoid over-clustering in single-cell RNA sequencing







Adapting systems biology to address the complexity of human disease in the single-cell era






Programs, origins and immunomodulatory functions of myeloid cells in glioma









A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment







Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2
















scRNA-seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with uncomplicated malaria






Deep profiling deconstructs features associated with memory CD8+ T cell tissue residence



