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Immunology
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,
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,
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,
Biology
Genomics
Immunology
Sam Allon
José Ordovas-Montañes
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,
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,
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,
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
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
Transcriptional subtype-specific microenvironmental crosstalk and tumor cell 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,
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
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,
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
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,
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
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,
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
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
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
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 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
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 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
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 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
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 II
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 T
H
17 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
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