Induction of metabolic quiescence defines the transitional to follicular B cell switch
  • Farmer et al.,
  • Science Signaling,
  • 2019
Biology
Genomics
Immunology
Toby Aicher
Alex K. Shalek
The next quarter century
  • Ablasser et al.,
  • Immunity,
  • 2019
Biology
Genomics
Immunology
Alex K. Shalek
Germline-encoded affinity for cognate antigen enables vaccine amplification of a human broadly neutralizing response against influenza virus
  • Sangesland et al.,
  • Immunity,
  • 2019
Biology
Genomics
Immunology
Infectious Disease
Medicine
Sam Kazer
Alex K. Shalek
Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression
  • Tsankov et al.,
  • Development,
  • 2019
Biology
Genomics
Marc Wadsworth II
Sam Allon
Ben Mead
Riley Drake
Alex K. Shalek
Highly efficient, massively-parallel single-cell RNA-Seq reveals cellular states and molecular features of human skin pathology
  • Hughes T.K. et al.,
  • bioRxiv,
  • 2019
Biology
Genomics
Immunology
R&D
Technology
Travis Hughes
Marc Wadsworth II
José Ordovas-Montañes
Alex K. Shalek
Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection
  • Kazer S.W. et al.,
  • bioRxiv,
  • 2019
Biology
Genomics
Immunology
Infectious Disease
Sam Kazer
Toby Aicher
Shaina Carroll
José Ordovas-Montañes
Carly Ziegler
Sarah Nyquist
Alex K. Shalek
Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing
  • Aicher et al.,
  • Single-Cell Methods,
  • 2019
R&D
Technology
Toby Aicher
Shaina Carroll
Marc Wadsworth II
Travis Hughes
Alex K. Shalek
Mechanisms of lymphoma clearance induced by high-dose alkylating agents
  • Lossos et al.,
  • Cancer Discovery,
  • 2019
Biology
Cancer
Immunology
Kellie Kolb
Jay Prakadan
Alex K. Shalek
Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration
  • Pepe-Mooney et al.,
  • Cell Stem Cell,
  • 2019
Biology
Cell Atlas
Medicine
José Ordovas-Montañes
Alex K. Shalek
Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
  • van Galen et al.,
  • Cell,
  • 2019
Marc Wadsworth II
Travis Hughes
Alex K. Shalek
Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer
  • Hamza B. et al.,
  • PNAS,
  • 2019
Biology
Cancer
Computational Methods
R&D
Technology
Jay Prakadan
Andrew Navia
Peter Winter
Riley Drake
Alejandro Gupta
Alex K. Shalek
Linking single-cell measurements of mass, growth rate, and gene expression
  • Kimmerling R.J. et al.,
  • Genome Biology,
  • 2018
Biology
Cancer
Genomics
Physics
R&D
Technology
Jay Prakadan
Alejandro Gupta
Riley Drake
Alex K. Shalek
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
Allergic Inflammatory Memory in Human Respiratory Epithelial Progenitor Cells
  • Ordovas-Montanes et al.,
  • Nature,
  • 2018
Biology
Cell Atlas
Immunology
Medicine
José Ordovas-Montañes
Sarah Nyquist
Marko Vukovic
Marc Wadsworth II
Travis Hughes
Sam Kazer
Alex K. Shalek
Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
  • Mead B.E.* et al.,
  • BMC Biology,
  • 2018
Ben Mead
José Ordovas-Montañes
Travis Hughes
Marc Wadsworth II
Alex K. Shalek
Linking single-cell measurements of mass, growth rate, and gene expression
  • Kimmerling et al.,
  • BioRxiv,
  • 2018
Chemistry
Genomics
Technology
Jay Prakadan
Alejandro Gupta
Riley Drake
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
Science Forum: The Human Cell Atlas
  • Regev A. et al.,
  • eLife,
  • 2017
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Medicine
Technology
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
Scaling by shrinking: empowering single-cell ‘omics’ with microfluidic devices
  • Prakadan et al.,
  • Nature Reviews Genetics,
  • 2017
Genomics
Technology
Jay Prakadan
Alex K. Shalek
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
  • Gierahn et al.,
  • Nature Methods,
  • 2017
Chemistry
Genomics
R&D
Technology
Travel
Marc Wadsworth II
Travis Hughes
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
Regulation of X-linked gene expression during early mouse development by Rlim
  • Wang et al.,
  • eLife,
  • 2016
Biology
Genomics
Alex K. Shalek
Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
  • Genshaft et al.,
  • Genome Biology,
Biology
Chemistry
Genomics
R&D
Technology
Alex Genshaft
Jay Prakadan
Carly Ziegler
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 II
Alex Genshaft
Travis Hughes
Carly Ziegler
Sam Kazer
Aleth Gaillard
Kellie Kolb
Alex K. Shalek
Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM
  • Wong et al.,
  • PNAS,
  • 2016
Chemistry
Genomics
Technology
Sam Kazer
Aleth Gaillard
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
Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics
  • Wadsworth II et al.,
  • Genome Biology,
  • 2015
Genomics
R&D
Technology
Marc Wadsworth II
Travis Hughes
Alex K. Shalek
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
  • Macosko et al.,
  • Cell,
  • 2015
Genomics
R&D
Technology
Alex K. Shalek
Deconstructing transcriptional heterogeneity in pluripotent stem cells
  • Kumar et al.,
  • Nature,
  • 2014
Biology
Genomics
Alex K. Shalek
Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL
  • Wang et al.,
  • Blood,
  • 2014
Cancer
Genomics
Alex K. Shalek
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
  • Shalek et al.,
  • Nature,
  • 2014
Biology
Genomics
Alex K. Shalek
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
  • Patel et al.,
  • Science,
  • 2014
Cancer
Genomics
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
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
  • Lohr et al.,
  • Nature Biotechnology,
  • 2014
Biology
Cancer
Genomics
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
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
Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells
  • Shalek et al.,
  • PNAS,
  • 2010
Chemistry
Genomics
Physics
R&D
Technology
Alex K. Shalek