Author

Alex K Shalek

4Department of Chemistry, Massachusetts Institute of Technology; Cambridge, MA, USA. 5Institute for Medical Engineering & Science, Massachusetts Institute of Technology; Cambridge, MA, USA. 6Koch Institute for Integrative Cancer Research, Massachusetts In;

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Research Focus:clustering· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Research Focus:host-pathogen & immune response· 1 Organism:human· 1 Organism:non-human primate· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Alanna Callendrello· 1 shared Alexander A Smith· 1 shared Andrew McDavidiD· 1 shared Andrew W Simonson· 1 shared Cassaundra L Ameel· 1 shared Charles A Scanga· 1 shared Chloe K Slichter· 1 shared E Grace Bothwell· 1 shared

Activity by Year

2015-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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1 shared paperImmunology

Alanna Callendrello

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2 papers

Recent·Most cited

ImmunologybioRxivPreprintNov 3, 2026

Protection against disseminated disease following reinfection with Mycobacterium tuberculosis requires CD8+ lymphocytes

Andrew W Simonson, Michael C Chao, E Grace Bothwell…·JoAnne L Flynn

This study shows that CD8+ lymphocytes are essential for preventing Mtb dissemination during reinfection, highlighting their non-redundant role in concomitant immunity.

DOI 10.64898/2026.10.29.762796

non-human primateexperimental assay

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BioinformaticsbioRxivJun 15, 2015

MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA-seq data.

Greg Finak, Andrew McDavid, Masanao Yajima…·Raphael Gottardo

The paper introduces a statistical framework to analyze single-cell RNA-seq data by modeling bimodality and characterizing transcriptional changes and heterogeneity.

DOI 10.1186/s13059-015-0844-5

humanscRNA-seq

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