scRNA-Seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with clinical malaria
  • Morang’a et al.,
  • medRxiv,
  • 2023
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Riley Drake
Vincent Miao
Alex K. Shalek
Single-cell RNA sequencing of liver fine-needle aspirates captures immune diversity in the blood and liver in chronic hepatitis B patients
  • Genshaft et al.,
  • Hepatology,
  • 2023
Biology
Cell Atlas
Genomics
Immunology
R&D
Technology
Alex Genshaft
Mike Vilme
Riley Drake
Ira Fleming
Nancy Tran
Constantine Tzouanas
Jasmin Joseph-Chazan
Alex K. Shalek
Comparative analysis of cell–cell communication at single-cell resolution
  • Wilk et al.,
  • Nature Biotechnology,
  • 2023
Computational Methods
Genomics
R&D
Statistics
Alex K. Shalek
Engineering kinetics of TLR7/8 agonist release from bottlebrush prodrugs enables tumor-focused immune stimulation
  • Bhagchandani et al.,
  • Science Advances,
  • 2023
Biology
Cancer
Chemistry
Genomics
Immunology
Medicine
R&D
Technology
Evelyn Yuzhou Tong
Michelle Ramseier
Alex K. Shalek
PI3Kβ controls immune evasion in PTEN-deficient breast tumours
  • Bergholz et al.,
  • Nature,
Biology
Cancer
Genomics
Immunology
Medicine
Michelle Ramseier
Jay Prakadan
Alex K. Shalek
Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection
  • Wilk et al.,
  • bioRxiv,
  • 2023
Genomics
Immunology
Infectious Disease
Sam Kazer
Ira Fleming
Vincent Miao
Jennyfer Galvez-Reyes
Alex K. Shalek
A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery
  • Crouchet et al.,
  • Nature Communications,
  • 2023
Biology
Cancer
Genomics
Immunology
R&D
Technology
Alex K. Shalek
Mepolizumab targets multiple immune cells in aspirin-exacerbated respiratory disease
  • Buchheit et al.,
  • Journal of Allergy and Clinical Immunology,
Biology
Genomics
Immunology
Medicine
Marko Vukovic
Alex K. Shalek
José Ordovas-Montañes
An ex vivo ovulation system enables the discovery of novel ovulatory pathways and nonhormonal contraceptive candidates
  • Zhang et al.,
  • Biology of Reproduction,
Biology
Cell Atlas
Genomics
Brittany Goods
Alex K. Shalek
Vitrification preserves murine ovarian follicular cell transcriptome in a 3D encapsulated in vitro follicle growth system
  • Wang et al.,
  • Biology of Reproduction,
Biology
Genomics
Immunology
R&D
Technology
Riley Drake
Daniela Russo
Alex K. Shalek
Brittany Goods
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity
  • Bui et al.,
  • Nature Communications,
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19
  • Bernardes et al.,
  • Immunity,
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2–Mediated Myocarditis
  • Tucker et al.,
  • Circulation,
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Alex K. Shalek
IL-5Rα marks nasal polyp IgG4- and IgE-expressing cells in aspirin-exacerbated respiratory disease
  • Buchheit et al.,
  • Journal of Allergy and Clinical Immunology,
Biology
Genomics
Immunology
José Ordovas-Montañes
Marko Vukovic
Alex K. Shalek
Compressed phenotypic screens for complex multicellular models and high-content assays
  • Mead et al.,
  • bioRxiv,
  • 2023
Biology
Cancer
Chemistry
Computational Methods
Genomics
R&D
Statistics
Technology
Ben Mead
Conner Kummerlowe
Ivy Liu
Walaa Kattan
Thomas Nok Hin Cheng
Peter Winter
Alex K. Shalek
Spatially Resolved Single-Cell Assessment of Pancreatic Cancer Expression Subtypes Reveals Co-expressor Phenotypes and Extensive Intratumoral Heterogeneity
  • Williams et al.,
  • Cancer Research,
  • 2023
Cancer
Genomics
Immunology
R&D
Technology
Peter Winter
Andrew Navia
Alex K. Shalek
NIAID Workshop on T Cell Technologies
  • Gondré-Lewis et al.,
  • Nature Immunology,
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
R&D
Alex K. Shalek
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
  • Jaiswal et al.,
  • BMC Genomics,
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
R&D
Sarah Nyquist
Tasneem Jivanjee
Samira Ibrahim
Josh Bromley
James Gatter
Alex K. Shalek
HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control
  • Fardoos et al.,
  • Frontiers in Immunology,
Biology
Genomics
Immunology
Infectious Disease
Sarah Nyquist
Sam Kazer
Son Nguyen
Alex K. Shalek
Single-cell transcriptomics of staged oocytes and somatic cells reveal novel regulators of follicle activation
  • Chen et al.,
  • Reproduction,
  • 2023
Biology
Genomics
R&D
Technology
Daniela Russo
Riley Drake
Alex K. Shalek
Brittany Goods
Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells
  • Morris et al.,
  • Cell Reports,
Biology
Cancer
Genomics
Immunology
Travis Hughes
Alex K. Shalek
Single-Cell Multiomics Reveals Clonal T-Cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm
  • DePasquale et al.,
  • Frontiers in Immunology,
Biology
Cancer
Cell Atlas
Genomics
Immunology
Charles P. Couturier
Alex K. Shalek
Identification and tracking of alloreactive T cell clones in Rhesus Macaques through the RM-scTCR-Seq platform
  • Gerdemann et al.,
  • Frontiers in Immunology,
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
R&D
Technology
Jim Kaminski
Alex K. Shalek
PI3K activation allows immune evasion by promoting an inhibitory myeloid tumor microenvironment
  • Collins et al.,
  • Journal for Immunotherapy of Cancer,
Biology
Cancer
Genomics
Immunology
Medicine
Marc Wadsworth II
Travis Hughes
Alex K. Shalek
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
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,
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,
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,
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
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
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
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,
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,
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,
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,
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