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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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,
• 2023
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

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 T_H17 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