Shalek Lab
Shalek Lab

Menu

  • Home
  • Team
    • Nucleus
    • Bonds
    • Join
  • Research
    • Technology
    • Systems
  • Diversity
    • Diversity Statement
    • Expectations
    • Research Ethics
    • Values
  • Publications
  • Resources
  • News
  • Giving
  • Contact
  • Publications
    Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation
    • Kummerlowe et al.,
    • Science Translational Medicine,
    • 2022
    Biology
    Cell Atlas
    Genomics
    Immunology
    Infectious Disease
    Microbiology
    Conner Kummerlowe
    Travis Hughes
    Nolawit Mulugeta
    Ira Fleming
    Marko Vukovic
    Benjamin Doran
    Toby Aicher
    Marc Wadsworth II
    José Ordovas-Montañes
    Alex K. Shalek
    Deciphering the immunopeptidome in vivo reveals new tumour antigens
    • Jaeger et al.,
    • Nature,
    • 2022
    Biology
    Cancer
    Genomics
    Immunology
    Peter Winter
    Alex K. Shalek
    How to ensure the Human Cell Atlas benefits humanity
    • Majumder et al.,
    • Nature,
    • 2022
    Cell Atlas
    Alex K. Shalek
    Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
    • Gideon et al.,
    • Immunity,
    • 2022
    Biology
    Cell Atlas
    Genomics
    Immunology
    Infectious Disease
    Microbiology
    Travis Hughes
    Constantine Tzouanas
    Marc Wadsworth II
    Conner Kummerlowe
    Sarah Nyquist
    Samira Ibrahim
    José Ordovas-Montañes
    Alex K. Shalek
    A single-cell liver atlas of Plasmodium vivax infection
    • Mancio-Silva et al.,
    • Cell Host & Microbe,
    • 2022
    Biology
    Cell Atlas
    Genomics
    Immunology
    Infectious Disease
    Microbiology
    Technology
    Marc Wadsworth II
    Travis Hughes
    Alex K. Shalek
    Cellular and transcriptional diversity over the course of human lactation
    • Nyquist et al.,
    • PNAS,
    • 2022
    Biology
    Cell Atlas
    Genomics
    Immunology
    Medicine
    Sarah Nyquist
    Patricia Gao
    Riley Drake
    Kellie Kolb
    Ben Mead
    Alex K. Shalek
    Brittany Goods
    Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation
    • Mead et al.,
    • Nature Biomedical Engineering,
    • 2022
    Biology
    Computational Methods
    Genomics
    Immunology
    Medicine
    R&D
    Technology
    Ben Mead
    Marko Vukovic
    Conner Kummerlowe
    José Ordovas-Montañes
    Alex K. Shalek
    JAK inhibition in a patient with a STAT1 gain-of-function variant reveals STAT1 dysregulation as a common feature of aplastic anemia
    • Rosenberg et al.,
    • Med,
    • 2022
    Biology
    Genomics
    Immunology
    Medicine
    Travis Hughes
    Alex K. Shalek
    Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
    • Song et al.,
    • Nature Communications,
    • 2022
    Biology
    Cancer
    Genomics
    Immunology
    R&D
    Marc Wadsworth II
    Alex K. Shalek
    Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
    • Raghavan et al.,
    • Cell,
    • 2021
    Cancer
    Computational Methods
    Genomics
    Immunology
    Medicine
    R&D
    Technology
    Peter Winter
    Andrew Navia
    Jennyfer Galvez-Reyes
    Nolawit Mulugeta
    Alex K. Shalek
    Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity
    • Genshaft et al.,
    • bioRxiv,
    • 2021
    Biology
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Infectious Disease
    R&D
    Technology
    Alex Genshaft
    Mike Vilme
    Riley Drake
    Ira Fleming
    Nancy Tran
    Constantine Tzouanas
    Jasmin Joseph-Chazan
    Alex K. Shalek
    Aggregated Mycobacterium tuberculosis Enhances the Inflammatory Response
    • Rodel et al.,
    • Frontiers in Microbiology,
    • 2021
    Biology
    Genomics
    Immunology
    Infectious Disease
    Microbiology
    Carly Ziegler
    Alex K. Shalek
    Allelic variation in class I HLA determines CD8+ T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2
    • Francis et al.,
    • Science Immunology,
    • 2021
    Biology
    Genomics
    Immunology
    Infectious Disease
    Alex K. Shalek
    Cellular and transcriptional diversity over the course of human lactation
    • Nyquist et al.,
    • bioRxiv,
    • 2021
    Biology
    Cell Atlas
    Genomics
    Immunology
    Vincent Miao
    Patricia Gao
    Riley Drake
    Kellie Kolb
    Ben Mead
    Alex K. Shalek
    Brittany Goods
    Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip
    • Bein et al.,
    • Frontiers in Pharmacology,
    • 2021
    Biology
    Genomics
    Immunology
    Infectious Disease
    Medicine
    R&D
    Technology
    Vincent Miao
    Andrew Navia
    Carly Ziegler
    José Ordovas-Montañes
    Alex K. Shalek
    Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice
    • Hamza et al.,
    • Nature Communications,
    • 2021
    Biology
    Cancer
    Genomics
    Immunology
    Physics
    R&D
    Technology
    Nolawit Mulugeta
    Alex K. Shalek
    Single cell biology—a Keystone Symposia report
    • Cable et al.,
    • Annals of the New York Academy of Sciences,
    • 2021
    Biology
    Cell Atlas
    Genomics
    Alex K. Shalek
    Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases
    • Prakadan et al.,
    • Nature Communications,
    • 2021
    Biology
    Cancer
    Genomics
    Immunology
    Medicine
    Jay Prakadan
    Andrew Navia
    Kellie Kolb
    Marc Wadsworth II
    Alex K. Shalek
    A Treatment-Naive Cellular Atlas of Pediatric Crohn’s Disease Predicts Disease Severity and Therapeutic Response
    • Zheng et al.,
    • bioRxiv,
    • 2021
    Biology
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Medicine
    Benjamin Doran
    Kyle Kimler
    Alex K. Shalek
    José Ordovas-Montañes
    Identification of immune correlates of fatal outcomes in critically ill COVID-19 patients
    • Youngs et al.,
    • PLOS Pathogens,
    • 2021
    Biology
    Genomics
    Immunology
    Infectious Disease
    Vincent Miao
    Alex K. Shalek
    HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells
    • Fardoos et al.,
    • JCI Insight,
    • 2021
    Genomics
    Immunology
    Infectious Disease
    Sarah Nyquist
    Alex K. Shalek
    Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes
    • Genshaft et al.,
    • Nature Communications,
    • 2021
    Genomics
    R&D
    Technology
    Alex Genshaft
    Carly Ziegler
    Constantine Tzouanas
    Ben Mead
    Andrew Navia
    Alex K. Shalek
    Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
    • Ziegler et al.,
    • Cell,
    • 2021
    Biology
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Infectious Disease
    Carly Ziegler
    Vincent Miao
    Andrew Navia
    Josh Bromley
    Micayla George
    Riley Drake
    Alex K. Shalek
    José Ordovas-Montañes
    Expression of Foxp3 by T follicular helper cells in end-stage germinal centers
    • Jacobsen et al.,
    • Science,
    • 2021
    Biology
    Genomics
    Immunology
    Sam Allon
    Alex K. Shalek
    The cellular architecture of the antimicrobial response network in human leprosy granulomas
    • Ma et al.,
    • Nature Immunology,
    • 2021
    Biology
    Genomics
    Immunology
    Infectious Disease
    Microbiology
    Travis Hughes
    Marc Wadsworth II
    Alex K. Shalek
    Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells
    • Jiang et al.,
    • JCI Insight,
    • 2021
    Biology
    Genomics
    Immunology
    Infectious Disease
    Ira Fleming
    Alex K. Shalek
    High-fat diet-activated fatty acid oxidation mediates intestinal stemness and tumorigenicity
    • Mana et al.,
    • Cell Reports,
    • 2021
    Biology
    Genomics
    Constantine Tzouanas
    Alex K. Shalek
    Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas
    • Amoozgar et al.,
    • Nature Communications,
    • 2021
    Cancer
    Genomics
    Immunology
    Medicine
    Sam Kazer
    Alex K. Shalek
    COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
    • Delorey et al.,
    • Nature,
    • 2021
    Biology
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Infectious Disease
    Statistics
    Carly Ziegler
    Alex K. Shalek
    Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation in severe disease
    • Kummerlowe et al.,
    • bioRxiv,
    • 2021
    Biology
    Genomics
    Immunology
    Infectious Disease
    Conner Kummerlowe
    Travis Hughes
    Nolawit Mulugeta
    Ira Fleming
    Marko Vukovic
    Benjamin Doran
    José Ordovas-Montañes
    Alex K. Shalek
    MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection
    • Khuzwayo et al.,
    • Frontiers in Immunology,
    • 2021
    Biology
    Genomics
    Immunology
    Infectious Disease
    Microbiology
    Jay Prakadan
    Sam Kazer
    Alex K. Shalek
    Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation
    • Dwyer et al.,
    • Science Immunology,
    • 2021
    Biology
    Genomics
    Immunology
    José Ordovas-Montañes
    Sam Allon
    Marko Vukovic
    Travis Hughes
    Sarah Nyquist
    Alex K. Shalek
    Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
    • Goods et al.,
    • JCI Insight,
    • 2021
    Biology
    Genomics
    Immunology
    Medicine
    Brittany Goods
    Riley Drake
    Ira Fleming
    Alex K. Shalek
    How are methodological developments enabling insights into cell behavior in cellular communities?
    • Piddini et al.,
    • Cell Systems,
    • 2021
    Biology
    Genomics
    Immunology
    Alex K. Shalek
    Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
    • Muus et al.,
    • Nature Medicine,
    • 2021
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Infectious Disease
    Statistics
    Sam Allon
    Sarah Nyquist
    Marc Wadsworth II
    Carly Ziegler
    Alex K. Shalek
    A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
    • Delorey et al.,
    • bioRxiv,
    • 2021
    Biology
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Infectious Disease
    Statistics
    Carly Ziegler
    Alex K. Shalek
    Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
    • Ziegler et al.,
    • bioRxiv,
    • 2021
    Biology
    Genomics
    Immunology
    Infectious Disease
    Microbiology
    Carly Ziegler
    Vincent Miao
    Andrew Navia
    Josh Bromley
    Micayla George
    Riley Drake
    Alex K. Shalek
    José Ordovas-Montañes
    Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage
    • Askenase et al.,
    • Science Immunology,
    • 2021
    Biology
    Genomics
    Immunology
    Medicine
    Brittany Goods
    Shaina Carroll
    Riley Drake
    James Gatter
    Alex K. Shalek
    Spatiotemporal single-cell profiling reveals that invasive and tissue-resident memory donor CD8+ T cells drive gastrointestinal acute graft-versus-host disease
    • Tkachev et al.,
    • Science Translational Medicine,
    • 2021
    Biology
    Cell Atlas
    Genomics
    Immunology
    Medicine
    Jim Kaminski
    José Ordovas-Montañes
    Alex K. Shalek
    Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
    • Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia et al.,
    • medRxiv,
    • 2020
    Biology
    Cell Atlas
    Genomics
    Immunology
    Infectious Disease
    Carly Ziegler
    Vincent Miao
    Andrew Navia
    Josh Bromley
    José Ordovas-Montañes
    Alex K. Shalek
    Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential
    • Huang et al.,
    • Cell,
    • 2020
    Biology
    Genomics
    Immunology
    Carly Ziegler
    Marko Vukovic
    José Ordovas-Montañes
    Alex K. Shalek
    Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
    • Pae et al.,
    • Journal of Experimental Medicine,
    • 2020
    Biology
    Genomics
    Immunology
    Sam Allon
    José Ordovas-Montañes
    Alex K. Shalek
    The Human Cell Atlas and equity: lessons learned
    • Majumder et al.,
    • Nature Medicine,
    • 2020
    Cell Atlas
    Genomics
    Alex K. Shalek
    Single cell and spatial transcriptomics defines the cellular architecture of the antimicrobial response network in human leprosy granulomas
    • Ma et al.,
    • bioRxiv,
    • 2020
    Biology
    Cell Atlas
    Genomics
    Immunology
    Infectious Disease
    Travis Hughes
    Marc Wadsworth II
    Alex K. Shalek
    Functional compensation precedes recovery of tissue mass following acute liver injury
    • Walesky et al.,
    • Nature Communications,
    • 2020
    Biology
    Genomics
    Immunology
    Kellie Kolb
    Ira Fleming
    Alex K. Shalek
    Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
    • Pae et al.,
    • bioRxiv,
    • 2020
    Biology
    Genomics
    Immunology
    Sam Allon
    José Ordovas-Montañes
    Alex K. Shalek
    Inflammasomes within hyperactive murine dendritic cells stimulate long-lived T cell-mediated anti-tumor immunity
    • Zhivaki et al.,
    • Cell Reports,
    • 2020
    Biology
    Cancer
    Genomics
    Immunology
    Medicine
    Benjamin Doran
    Ira Fleming
    Alex K. Shalek
    Evolution and diversity of immune responses during acute HIV infection
    • Kazer et al.,
    • Immunity,
    • 2020
    Biology
    Immunology
    Infectious Disease
    Medicine
    Sam Kazer
    Alex K. Shalek
    Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
    • Goods et al.,
    • biorXiv,
    • 2020
    Biology
    Genomics
    Immunology
    Medicine
    Brittany Goods
    Riley Drake
    Ira Fleming
    Alex K. Shalek
    Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
    • Song et al.,
    • bioRxiv,
    • 2020
    Biology
    Cancer
    Genomics
    Immunology
    Marc Wadsworth II
    Alex K. Shalek
    Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics
    • Kotliar et al.,
    • Cell,
    • 2020
    Biology
    Cell Atlas
    Genomics
    Immunology
    Infectious Disease
    Travis Hughes
    Marc Wadsworth II
    Nancy Tran
    Alex K. Shalek
    Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
    • Gideon et al.,
    • bioRxiv,
    • 2020
    Biology
    Cell Atlas
    Genomics
    Immunology
    Infectious Disease
    Travis Hughes
    Marc Wadsworth II
    Conner Kummerlowe
    Sarah Nyquist
    José Ordovas-Montañes
    Alex K. Shalek
    Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
    • Hughes et al.,
    • Immunity,
    • 2020
    Biology
    Cell Atlas
    Chemistry
    Genomics
    Immunology
    R&D
    Technology
    Travis Hughes
    Marc Wadsworth II
    José Ordovas-Montañes
    Alex K. Shalek
    Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
    • Berger et al.,
    • Nature Communications,
    • 2020
    Biology
    Computational Methods
    Statistics
    Sarah Nyquist
    Alex K. Shalek
    Innate Lymphoid Cell Activation and Sustained Depletion in Blood and Tissue of Children Infected with HIV from Birth Despite Antiretroviral Therapy
    • Singh et al.,
    • Cell Reports,
    • 2020
    Biology
    Genomics
    Immunology
    Infectious Disease
    Sam Kazer
    Alex K. Shalek
    The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
    • Raghavan et al.,
    • bioRxiv,
    • 2020
    Biology
    Cancer
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Medicine
    Technology
    Peter Winter
    Andrew Navia
    Jennyfer Galvez-Reyes
    Nolawit Mulugeta
    Alex K. Shalek
    A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood
    • Sangesland et al.,
    • Cell Reports,
    • 2020
    Biology
    Computational Methods
    Genomics
    Immunology
    Infectious Disease
    Sam Kazer
    James Gatter
    Alex K. Shalek
    Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease
    • Mitsialis et al.,
    • Gastroenterology,
    • 2020
    Biology
    Genomics
    Immunology
    José Ordovas-Montañes
    Marko Vukovic
    Alex K. Shalek
    Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states
    • Tkachev et al.,
    • bioRxiv,
    • 2020
    Biology
    Genomics
    Immunology
    Jim Kaminski
    José Ordovas-Montañes
    Alex K. Shalek
    Single-cell profiling of Ebola virus infection ​in vivo​ reveals viral and host transcriptional dynamics
    • Kotliar et al.,
    • bioRxiv,
    • 2020
    Biology
    Genomics
    Immunology
    Infectious Disease
    Travis Hughes
    Marc Wadsworth II
    Nancy Tran
    Alex K. Shalek
    Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
    • Bassler et al.,
    • bioRxiv,
    • 2020
    Computational Methods
    Genomics
    Immunology
    Medicine
    Marc Wadsworth II
    Travis Hughes
    Alex K. Shalek
    Computational Methods for Single-Cell RNA Sequencing
    • Hie et al.,
    • Annual Reviews,
    • 2020
    Biology
    Computational Methods
    Genomics
    Sarah Nyquist
    Alex K. Shalek
    High-throughput organoid screening enables engineering of intestinal epithelial composition
    • Mead et al.,
    • bioRxiv,
    • 2020
    Biology
    Genomics
    Medicine
    R&D
    Technology
    Ben Mead
    Marko Vukovic
    José Ordovas-Montañes
    Alex K. Shalek
    SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
    • Sungnak et al.,
    • Nature Medicine,
    • 2020
    Biology
    Genomics
    Immunology
    Infectious Disease
    José Ordovas-Montañes
    Alex K. Shalek
    SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
    • Ziegler et al.,
    • Cell,
    • 2020
    Biology
    Cell Atlas
    Genomics
    Immunology
    Infectious Disease
    Statistics
    Carly Ziegler
    Sam Allon
    Sarah Nyquist
    Vincent Miao
    Constantine Tzouanas
    Marc Wadsworth II
    Sam Kazer
    Travis Hughes
    Benjamin Doran
    James Gatter
    Marko Vukovic
    Ben Mead
    Shaina Carroll
    Alex K. Shalek
    José Ordovas-Montañes
    Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
    • Muus et al.,
    • bioRxiv,
    • 2020
    Biology
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Infectious Disease
    Statistics
    Sam Allon
    Sarah Nyquist
    José Ordovas-Montañes
    Marc Wadsworth II
    Carly Ziegler
    Alex K. Shalek
    Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
    • Cao et al.,
    • bioRxiv,
    • 2020
    Biology
    Genomics
    Immunology
    Infectious Disease
    Microbiology
    José Ordovas-Montañes
    Alex K. Shalek
    The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
    • Rozenblatt-Rosen et al.,
    • Cell,
    • 2020
    Biology
    Cancer
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Medicine
    Alex K. Shalek
    Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
    • Ding et al.,
    • Nature Biotechnology,
    • 2020
    Computational Methods
    Genomics
    R&D
    Technology
    Travis Hughes
    Marc Wadsworth II
    Shaina Carroll
    Alex K. Shalek
    Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
    • Kazer et al.,
    • Nature Medicine,
    • 2020
    Biology
    Computational Methods
    Genomics
    Immunology
    Infectious Disease
    Statistics
    Sam Kazer
    Toby Aicher
    Shaina Carroll
    José Ordovas-Montañes
    Vincent Miao
    Carly Ziegler
    Sarah Nyquist
    Alex K. Shalek
    SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues
    • Ziegler et al.,
    • SSRN,
    • 2020
    Biology
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Infectious Disease
    Medicine
    Carly Ziegler
    Sam Allon
    Sarah Nyquist
    Vincent Miao
    Marc Wadsworth II
    Sam Kazer
    Travis Hughes
    Benjamin Doran
    James Gatter
    Marko Vukovic
    Constantine Tzouanas
    Shaina Carroll
    Alex K. Shalek
    José Ordovas-Montañes
    Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
    • Genshaft et al.,
    • bioRxiv,
    • 2020
    Biology
    Cancer
    Chemistry
    Genomics
    R&D
    Technology
    Alex Genshaft
    Carly Ziegler
    Constantine Tzouanas
    Ben Mead
    Andrew Navia
    Alex K. Shalek
    Distribution and storage of inflammatory memory in barrier tissues
    • Ordovas-Montanes et al.,
    • Nature Reviews Immunology,
    • 2020
    Biology
    Genomics
    Immunology
    Infectious Disease
    José Ordovas-Montañes
    Alex K. Shalek
    Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies
    • Martin-Gayo et al.,
    • Cell Reports,
    • 2020
    Biology
    Genomics
    Immunology
    Infectious Disease
    Medicine
    Kellie Kolb
    Alex K. Shalek
    Identification of a master regulator of differentiation in toxoplasma
    • Waldman et al.,
    • Cell,
    • 2020
    Biology
    Genomics
    Immunology
    Infectious Disease
    Microbiology
    Marc Wadsworth II
    Alex K. Shalek
    Prevention of tuberculosis in macaques after intravenous BCG immunization
    • Darrah et al.,
    • Nature,
    • 2020
    Biology
    Genomics
    Immunology
    Infectious Disease
    Medicine
    Marc Wadsworth II
    Travis Hughes
    Alex K. Shalek
    TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures
    • Tu et al.,
    • Nature Immunology,
    • 2019
    Biology
    Cell Atlas
    Genomics
    Immunology
    R&D
    Technology
    Alex K. Shalek
    Revisiting airway epithelial remodeling in type 2 immunity: Beyond goblet cell metaplasia
    • Barrett et al.,
    • Journal of Allergy and Clinical Immunology,
    • 2019
    Biology
    Genomics
    Immunology
    Alex K. Shalek
    Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes
    • Huang et al.,
    • bioRxiv,
    • 2019
    Biology
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Carly Ziegler
    Marko Vukovic
    José Ordovas-Montañes
    Alex K. Shalek
    Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration
    • Menon et al.,
    • Nature Communications,
    • 2019
    Biology
    Cell Atlas
    Genomics
    Immunology
    Medicine
    Brittany Goods
    Alex K. Shalek
    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
    Voices in methods development
    • Anikeeva et al.,
    • Nature Methods,
    • 2019
    Computational Methods
    Genomics
    R&D
    Technology
    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
    Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells
    • Reitman et al.,
    • Nature Communications,
    • 2019
    Biology
    Cancer
    Genomics
    Medicine
    Alex K. Shalek
    A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases
    • Gawel et al.,
    • Genome Medicine,
    • 2019
    Biology
    Computational Methods
    Genomics
    Immunology
    Medicine
    Alex K. Shalek
    Intra- and inter-cellular rewiring of the human colon during ulcerative colitis
    • Smillie et al.,
    • Cell,
    • 2019
    Biology
    Cell Atlas
    Genomics
    Immunology
    José Ordovas-Montañes
    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
    Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis
    • Ardain A. et al.,
    • Nature,
    • 2019
    Biology
    Immunology
    Infectious Disease
    Sam Kazer
    Alex K. Shalek
    Identification of a Master Regulator of Differentiation in Toxoplasma
    • Waldman B.S. et al.,
    • bioRxiv,
    • 2019
    Biology
    Infectious Disease
    Microbiology
    Marc Wadsworth II
    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
    Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection
    • Ndhlovu et al.,
    • Science Translational Medicine,
    • 2019
    Genomics
    Immunology
    Medicine
    Sam Kazer
    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
    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
    The Human Cell Atlas White Paper
    • Regev A. et al.,
    • Arxiv,
    • 2018
    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 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
    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
    Science Forum: The Human Cell Atlas
    • Regev A. et al.,
    • eLife,
    • 2017
    Biology
    Cell Atlas
    Computational Methods
    Genomics
    Immunology
    Medicine
    Technology
    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 II
    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
    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
    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
    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,
    • 2016
    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
    MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
    • Finak et al.,
    • Genome Biology,
    • 2015
    Computational Methods
    Statistics
    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
    Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing
    • Trombetta et al.,
    • Current Protocols in Molecular Biology,
    • 2014
    R&D
    Technology
    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
    Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells
    • Suvà et al.,
    • Cell,
    • 2014
    Biology
    Cancer
    Genomics
    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
    Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
    • Gifford et al.,
    • Cell,
    • 2013
    Biology
    Genomics
    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
    Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia
    • Shalek et al.,
    • Nano Letters,
    • 2012
    Cancer
    Genomics
    R&D
    Technology
    Alex K. Shalek
    Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits
    • Robinson et al.,
    • Nature Nanotechnology,
    • 2012
    Biology
    Chemistry
    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
    Photoinduced Interfacial Charging and “Explosion” of Monolayer Pentacene Islands
    • Chen L. et al.,
    • Nano Lett,
    • 2005
    Chemistry
    Physics
    R&D
    Technology
    Alex K. Shalek

Topic

  • Cancer
  • Computational Methods
  • Genomics
  • Immunology
  • Infectious Disease
  • Nanotechnology
  • Pre-Prints
  • Review
  • Technology Development

By Year

    • 2022
    • 2021
    • 2020
    • 2019
    • 2018
    • 2017
    • 2016
    • 2015
    • 2014
    • 2013 and before
Copyright © 2023 Shalek Lab.
  • Accessibility