Alex K. Shalek

Alex K. Shalek

Background & Interests

Biology Biology
Chemistry Chemistry
Genomics Genomics
Getting Swole Getting Swole
Hot Stuff Hot Stuff
I Want a Hot Body, but I also Want Tacos I Want a Hot Body, but I also Want Tacos
Immunology Immunology
R&D R&D
Top Shelf Top Shelf

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
Quantitative characterization of tissue states using multiomics and ecological spatial analysis
  • Ding et al.,
  • Nature Genetics,
  • 2025
Computational Methods Computational Methods
Genomics Genomics
Technology Technology
Alex K. Shalek Alex K. Shalek
Bokai Zhu Bokai Zhu
Transcriptomic analysis of whole staged ovarian follicles reveals stage-specific folliculogenesis signatures in mice
Transcriptomic analysis of whole staged ovarian follicles reveals stage-specific folliculogenesis signatures in mice
  • VanBenschoten et al.,
  • bioRxiv,
  • 2025
Biology Biology
Chemistry Chemistry
Computational Methods Computational Methods
Alex K. Shalek Alex K. Shalek
Brittany Goods Brittany Goods
Daniela Russo Daniela Russo
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
  • Pita-Juarez et al.,
  • Genome Biology,
  • 2025
Computational Methods Computational Methods
Genomics Genomics
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Carly Ziegler Carly Ziegler
Artificial variables help to avoid over-clustering in single-cell RNA sequencing
Artificial variables help to avoid over-clustering in single-cell RNA sequencing
  • DenAdel et al.,
  • AJHG,
  • 2025
Computational Methods Computational Methods
R&D R&D
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Michelle Ramseier Michelle Ramseier
Peter Winter Peter Winter
Adapting systems biology to address the complexity of human disease in the single-cell era
Adapting systems biology to address the complexity of human disease in the single-cell era
  • Fischer et al.,
  • Nature Reviews Genetics,
  • 2025
Computational Methods Computational Methods
Genomics Genomics
Alex K. Shalek Alex K. Shalek
David Fischer David Fischer
Peter Winter Peter Winter
Programs, origins and immunomodulatory functions of myeloid cells in glioma
Programs, origins and immunomodulatory functions of myeloid cells in glioma
  • Miller et al.,
  • Nature,
  • 2025
Cancer Cancer
Immunology Immunology
Medicine Medicine
Technology Technology
Alex K. Shalek Alex K. Shalek
Charles P. Couturier Charles P. Couturier
David Fischer David Fischer
Evelyn Yuzhou Tong Evelyn Yuzhou Tong
A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment
A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment
  • Zhu et al.,
  • Nature Communications,
  • 2025
Medicine Medicine
Microbiology Microbiology
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Bokai Zhu Bokai Zhu
Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2
Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2
  • Walsh et al.,
  • Nature Immunology,
  • 2025
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Medicine Medicine
Andrew Navia Andrew Navia
Carly Ziegler Carly Ziegler
Josh Bromley Josh Bromley
José Ordovas-Montañes José Ordovas-Montañes
Kyle Kimler Kyle Kimler
Micayla George Micayla George
Riley Drake Riley Drake
Samira Ibrahim Samira Ibrahim
Tasneem Jivanjee Tasneem Jivanjee
Vincent Miao Vincent Miao
scRNA-seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with uncomplicated malaria
scRNA-seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with uncomplicated malaria
  • Morang’a et al.,
  • Experimental Biology and Medicine,
  • 2025
Computational Methods Computational Methods
Infectious Disease Infectious Disease
Microbiology Microbiology
Alex K. Shalek Alex K. Shalek
Riley Drake Riley Drake
Deep profiling deconstructs features associated with memory CD8+ T cell tissue residence
Deep profiling deconstructs features associated with memory CD8+ T cell tissue residence
  • Scott et al.,
  • Immunity,
  • 2024
Computational Methods Computational Methods
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Zoë Steier Zoë Steier