Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses
  • Douam F. et al.,
  • Nature Communications,
  • 2018
Biology
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Carly Ziegler
T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation
  • Biton et al.,
  • Cell,
  • 2018
Genomics
Immunology
Medicine
José Ordovas-Montañes
Alex K. Shalek
A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade
  • Jerby-Arnon et al.,
  • Cell,
  • 2018
Alex K. Shalek
Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis
  • Smillie et al.,
  • BioRxiv,
  • 2018
Biology
Cell Atlas
Computational Methods
Immunology
Medicine
José Ordovas-Montañes
Alex K. Shalek
High-Frequency, Functional HIV-Specific T-Follicular Helper and Regulatory Cells Are Present Within Germinal Centers in Children but Not Adults
  • Roider et al.,
  • frontiers in Immunology,
  • 2018
Toby Aicher
Sam Kazer
Alex K. Shalek
Allergic Inflammatory Memory in Human Respiratory Epithelial Progenitor Cells
  • Ordovas-Montanes J. et al.,
  • Nature,
  • 2018
Biology
Cell Atlas
Immunology
Medicine
José Ordovas-Montañes
Sarah Nyquist
Travis Hughes
Marc Wadsworth
Sam Kazer
Alex K. Shalek
A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers
  • Martin-Gayo et al.,
  • Genome Biology,
  • 2018
Computational Methods
Genomics
Immunology
Infectious Disease
Medicine
Kellie Kolb
José Ordovas-Montañes
Alex K. Shalek
Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells
  • Gaya M. et al.,
  • Cell,
  • 2017
Genomics
Immunology
Andrew Navia
Alex K. Shalek
Reduced cellular diversity and an altered basal progenitor cell state inform epithelial barrier dysfunction in human type 2 immunity
  • Jose Ordovas-Montanes et al.,
  • BioRxiv,
  • 2017
Cell Atlas
Immunology
Medicine
José Ordovas-Montañes
Sarah Nyquist
Marc Wadsworth
Travis Hughes
Sam Kazer
Alex K. Shalek
Single-cell analyses to tailor treatments
  • Shalek A.K. et al.,
  • Science Translational Medicine,
  • 2017
Immunology
Infectious Disease
Medicine
Technology
Alex K. Shalek
Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies
  • Nandin I.S. et al.,
  • Journal of Experimental Medicine,
  • 2017
Genomics
Immunology
Infectious Disease
Medicine
Microbiology
Sam Kazer
José Ordovas-Montañes
Alex K. Shalek
IFNγ-Dependent Tissue-Immune Homeostasis is Co-opted in the Tumor Microenvironment
  • Nirschl et al.,
  • Cell,
  • 2017
Cancer
Genomics
Immunology
Jay Prakadan
Alex K. Shalek
Circulating CXCR5+CXCR3+PD-1lo Tfh-like Cells in HIV-1 Controllers with Neutralizing Antibody Breadth
  • Martin-Gayo et al.,
  • JCI Insight,
  • 2017
Biology
Immunology
Infectious Disease
Kellie Kolb
Alex K. Shalek
Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion
  • Ranasinghe et al.,
  • Immunity,
  • 2016
Biology
Immunology
Infectious Disease
Sam Kazer
Alex K. Shalek
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
  • Tirosh et al.,
  • Science,
  • 2016
Biology
Cancer
Genomics
Medicine
Jay Prakadan
Marc Wadsworth
Alex Genshaft
Travis Hughes
Carly Ziegler
Sam Kazer
Aleth Gaillard
Kellie Kolb
Alex K. Shalek
Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression
  • Kløverpris et al.,
  • Immunity,
  • 2016
Biology
Genomics
Immunology
Infectious Disease
Sam Kazer
Alex K. Shalek
A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages
  • Kimmerling et al.,
  • Nat. Commun.,
  • 2016
Biology
Genomics
Immunology
R&D
Technology
Alex Genshaft
Sam Kazer
Alex K. Shalek
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity
  • Gaublomme et al.,
  • Cell,
  • 2015
Biology
Genomics
Immunology
Alex K. Shalek
Oct1 and OCA-B are selectively required for CD4 memory T cell function
  • Shakya et al.,
  • J. Exp. Med.,
  • 2015
Biology
Genomics
Immunology
Alex K. Shalek
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses
  • Avraham et al.,
  • Cell,
  • 2015
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Technology
Alex K. Shalek
Heterogeneity in immune responses: from populations to single cells
  • Satija et al.,
  • Trends in Immunology,
  • 2014
Genomics
Immunology
Technology
Alex K. Shalek
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
  • Shalek et al.,
  • Nature,
  • 2013
Biology
Genomics
Immunology
Alex K. Shalek
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli
  • Gat-Viks et al.,
  • Nature Biotechnology,
  • 2013
Biology
Immunology
Alex K. Shalek
Dynamic regulatory network controlling TH17 cell differentiation
  • Yosef et al.,
  • Nature,
  • 2013
Biology
Genomics
Immunology
Alex K. Shalek
Probing Enzymatic Activity inside Living Cells Using a Nanowire−Cell “Sandwich” Assay
  • Na et al.,
  • Nano Letters,
  • 2013
Biology
Chemistry
Immunology
Technology
Alex K. Shalek
Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits
  • Chevrier et al.,
  • Cell,
  • 2011
Genomics
Immunology
Infectious Disease
Alex K. Shalek