Biography

Alex K. Shalek is currently the Pfizer-Laubach Career Development Associate Professor at MIT, as well as a Core Member of the Institute for Medical Engineering and Science (IMES), an Associate Professor of Chemistry, and an Extramural Member of The Koch Institute for Integrative Cancer Research.  He is also an Institute Member of the Broad Institute, an Associate Member of the Ragon Institute, an Assistant in Immunology at MGH, and an Instructor in Health Sciences and Technology at HMS.  His research is directed towards the creation and implementation of new approaches to elucidate cellular and molecular features that inform tissue-level function and dysfunction across the spectrum of human health and disease. This encompasses both the development of broadly enabling technologies as well as their application to characterize, model, and rationally control complex multicellular systems. Dr. Shalek received his bachelor’s degree summa cum laude from Columbia University and his Ph.D. from Harvard University in chemical physics under the guidance of Hongkun Park, and performed postdoctoral training under Hongkun Park and Aviv Regev (Broad/MIT).

Publications

Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection
  • Wilk et al.,
  • bioRxiv,
  • 2023
  • Infectious Disease
  • Immunology
  • Genomics
  • 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
  • Cancer
  • Technology
  • Genomics
  • R&D
  • Biology
  • Immunology
  • Alex K. Shalek
Mepolizumab targets multiple immune cells in aspirin-exacerbated respiratory disease
  • Buchheit et al.,
  • Journal of Allergy and Clinical Immunology,
  • Immunology
  • Medicine
  • Biology
  • Genomics
  • 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,
  • Cell Atlas
  • Genomics
  • Biology
  • 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
  • Technology
  • Immunology
  • R&D
  • Genomics
  • 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,
  • Immunology
  • Infectious Disease
  • Biology
  • Cell Atlas
  • Genomics
  • 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
  • Infectious Disease
  • Immunology
  • Genomics
  • Cell Atlas
  • Alex K. Shalek
Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2–Mediated Myocarditis
  • Tucker et al.,
  • Circulation,
  • Cell Atlas
  • Biology
  • 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,
  • Immunology
  • Genomics
  • Biology
  • José Ordovas-Montañes
  • Marko Vukovic
  • Alex K. Shalek
Compressed phenotypic screens for complex multicellular models and high-content assays
  • Mead et al.,
  • bioRxiv,
  • 2023
  • Cancer
  • Genomics
  • Technology
  • Biology
  • Chemistry
  • Statistics
  • Computational Methods
  • R&D
  • 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
  • Immunology
  • Genomics
  • Technology
  • R&D
  • Peter Winter
  • Andrew Navia
  • Alex K. Shalek
NIAID Workshop on T Cell Technologies
  • Gondré-Lewis et al.,
  • Nature Immunology,
  • Genomics
  • Biology
  • Computational Methods
  • Immunology
  • R&D
  • Cell Atlas
  • Alex K. Shalek
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
  • Jaiswal et al.,
  • BMC Genomics,
  • Infectious Disease
  • Biology
  • Cell Atlas
  • Computational Methods
  • Genomics
  • R&D
  • Immunology
  • 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,
  • Infectious Disease
  • Immunology
  • Genomics
  • Biology
  • 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
  • Genomics
  • R&D
  • Technology
  • Biology
  • 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,
  • Genomics
  • Cancer
  • Biology
  • 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,
  • Cell Atlas
  • Cancer
  • Immunology
  • Biology
  • Genomics
  • 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,
  • Computational Methods
  • R&D
  • Immunology
  • Biology
  • Cell Atlas
  • Genomics
  • 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,
  • Cancer
  • Genomics
  • Immunology
  • Biology
  • 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
  • Infectious Disease
  • Microbiology
  • Cell Atlas
  • Immunology
  • Biology
  • Genomics
  • 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
  • Genomics
  • Immunology
  • Biology
  • Cancer
  • 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
  • Immunology
  • Infectious Disease
  • Microbiology
  • Cell Atlas
  • Genomics
  • Biology
  • 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
  • Cell Atlas
  • Microbiology
  • Genomics
  • Immunology
  • Biology
  • Technology
  • Infectious Disease
  • Marc Wadsworth II
  • Travis Hughes
  • Alex K. Shalek
Cellular and transcriptional diversity over the course of human lactation
  • Nyquist et al.,
  • PNAS,
  • 2022
  • Medicine
  • Cell Atlas
  • Immunology
  • Biology
  • Genomics
  • 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
  • Medicine
  • R&D
  • Computational Methods
  • Genomics
  • Biology
  • Technology
  • Immunology
  • 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
  • Medicine
  • Genomics
  • Immunology
  • Biology
  • 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
  • Genomics
  • Biology
  • R&D
  • Immunology
  • Cancer
  • Marc Wadsworth II
  • Alex K. Shalek
Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
  • Raghavan et al.,
  • Cell,
  • 2021
  • Immunology
  • Computational Methods
  • Genomics
  • Technology
  • Cancer
  • R&D
  • Medicine
  • 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
  • R&D
  • Infectious Disease
  • Biology
  • Cell Atlas
  • Immunology
  • Genomics
  • Computational Methods
  • 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,
  • Immunology
  • Infectious Disease
  • Microbiology
  • Genomics
  • Biology
  • 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
  • Genomics
  • Biology
  • Immunology
  • Infectious Disease
  • Alex K. Shalek
Cellular and transcriptional diversity over the course of human lactation
  • Nyquist et al.,
  • bioRxiv,
  • 2021
  • Immunology
  • Biology
  • Cell Atlas
  • Genomics
  • 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
  • Technology
  • Infectious Disease
  • Genomics
  • R&D
  • Immunology
  • Medicine
  • 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,
  • Physics
  • Genomics
  • Immunology
  • Biology
  • Technology
  • R&D
  • Cancer
  • 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
  • Genomics
  • Cell Atlas
  • Alex K. Shalek
Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases
  • Prakadan et al.,
  • Nature Communications,
  • 2021
  • Medicine
  • Immunology
  • Genomics
  • Biology
  • Cancer
  • 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
  • Genomics
  • Immunology
  • Cell Atlas
  • Computational Methods
  • 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
  • Technology
  • R&D
  • Genomics
  • 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
  • Infectious Disease
  • Cell Atlas
  • Computational Methods
  • Genomics
  • Immunology
  • Biology
  • 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
  • Immunology
  • Biology
  • Genomics
  • 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
  • Microbiology
  • Immunology
  • Infectious Disease
  • 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
  • Infectious Disease
  • Biology
  • Genomics
  • Immunology
  • Ira Fleming
  • Alex K. Shalek
High-fat diet-activated fatty acid oxidation mediates intestinal stemness and tumorigenicity
  • Mana et al.,
  • Cell Reports,
  • 2021
  • Genomics
  • Biology
  • Constantine Tzouanas
  • Alex K. Shalek
Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas
  • Amoozgar et al.,
  • Nature Communications,
  • 2021
  • Medicine
  • Immunology
  • Cancer
  • Genomics
  • Sam Kazer
  • Alex K. Shalek
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
  • Delorey et al.,
  • Nature,
  • 2021
  • Statistics
  • Computational Methods
  • Biology
  • Infectious Disease
  • Cell Atlas
  • Genomics
  • Immunology
  • 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
  • Genomics
  • Biology
  • 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
  • Immunology
  • Biology
  • Microbiology
  • Infectious Disease
  • Genomics
  • 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
  • Immunology
  • Genomics
  • Biology
  • 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
  • Genomics
  • Medicine
  • Biology
  • Immunology
  • 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
  • Infectious Disease
  • Computational Methods
  • Statistics
  • Immunology
  • Genomics
  • 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
  • Statistics
  • Genomics
  • Biology
  • Immunology
  • Infectious Disease
  • Computational Methods
  • Cell Atlas
  • Carly Ziegler
  • Alex K. Shalek
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
  • Ziegler et al.,
  • bioRxiv,
  • 2021
  • Microbiology
  • Infectious Disease
  • Biology
  • Immunology
  • Genomics
  • 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,
  • Immunology
  • Genomics
  • Medicine
  • Biology
  • 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
  • Genomics
  • Cell Atlas
  • Biology
  • Medicine
  • Immunology
  • 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
  • Immunology
  • Cell Atlas
  • Biology
  • Genomics
  • 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,
  • Genomics
  • Immunology
  • Biology
  • 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,
  • Biology
  • Genomics
  • Immunology
  • Infectious Disease
  • Cell Atlas
  • 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,
  • Immunology
  • Genomics
  • Biology
  • 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
  • Cancer
  • Genomics
  • Biology
  • Medicine
  • Immunology
  • Benjamin Doran
  • Ira Fleming
  • Alex K. Shalek
Evolution and diversity of immune responses during acute HIV infection
  • Kazer et al.,
  • Immunity,
  • Immunology
  • Infectious Disease
  • Biology
  • 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
  • Medicine
  • Genomics
  • Immunology
  • Biology
  • 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
  • Cancer
  • Immunology
  • Biology
  • Genomics
  • Marc Wadsworth II
  • Alex K. Shalek
Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics
  • Kotliar et al.,
  • Cell,
  • Genomics
  • Infectious Disease
  • Immunology
  • Cell Atlas
  • Biology
  • 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
  • Cell Atlas
  • Genomics
  • Infectious Disease
  • Biology
  • Immunology
  • 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
  • Chemistry
  • R&D
  • Biology
  • Technology
  • Genomics
  • Cell Atlas
  • Immunology
  • 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
  • Computational Methods
  • Biology
  • 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,
  • Biology
  • Immunology
  • Genomics
  • 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
  • Cell Atlas
  • Cancer
  • Medicine
  • Technology
  • Genomics
  • Immunology
  • Computational Methods
  • 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
  • Immunology
  • Genomics
  • Biology
  • Infectious Disease
  • Computational Methods
  • 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,
  • Genomics
  • Biology
  • 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
  • Immunology
  • Biology
  • Genomics
  • 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
  • Infectious Disease
  • Genomics
  • Immunology
  • Biology
  • Travis Hughes
  • Marc Wadsworth II
  • Nancy Tran
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Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
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  • bioRxiv,
  • 2020
  • Computational Methods
  • Medicine
  • Genomics
  • Immunology
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Computational Methods for Single-Cell RNA Sequencing
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  • Annual Reviews,
  • Genomics
  • Biology
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High-throughput organoid screening enables engineering of intestinal epithelial composition
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  • 2020
  • R&D
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  • Genomics
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SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
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  • 2020
  • Genomics
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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
  • Immunology
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  • Marc Wadsworth II
  • Sam Kazer
  • Travis Hughes
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  • Ben Mead
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  • Alex K. Shalek
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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
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  • Immunology
  • Cell Atlas
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Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
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  • 2020
  • Microbiology
  • Infectious Disease
  • Genomics
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The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
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  • Cell,
  • 2020
  • Genomics
  • Cancer
  • Biology
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Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
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  • 2020
  • Genomics
  • Computational Methods
  • Technology
  • R&D
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Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
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  • Nature Medicine,
  • 2020
  • Genomics
  • Immunology
  • Infectious Disease
  • Computational Methods
  • Biology
  • Statistics
  • Sam Kazer
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  • José Ordovas-Montañes
  • Vincent Miao
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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,
  • Medicine
  • Infectious Disease
  • Genomics
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  • Biology
  • Computational Methods
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  • Sam Allon
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  • Marc Wadsworth II
  • Sam Kazer
  • Travis Hughes
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Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
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  • 2020
  • Genomics
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  • Biology
  • Cancer
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Distribution and storage of inflammatory memory in barrier tissues
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  • Infectious Disease
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Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies
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  • Genomics
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Identification of a master regulator of differentiation in toxoplasma
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  • Cell,
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  • Microbiology
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Prevention of tuberculosis in macaques after intravenous BCG immunization
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  • Immunology
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TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures
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  • 2019
  • Technology
  • Cell Atlas
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Revisiting airway epithelial remodeling in type 2 immunity: Beyond goblet cell metaplasia
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Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes
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  • Biology
  • Immunology
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Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration
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  • Genomics
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Induction of metabolic quiescence defines the transitional to follicular B cell switch
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The next quarter century
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Voices in methods development
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  • R&D
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Germline-encoded affinity for cognate antigen enables vaccine amplification of a human broadly neutralizing response against influenza virus
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  • Immunity,
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Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression
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  • Genomics
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Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells
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  • Medicine
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A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases
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  • Genomics
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Intra- and inter-cellular rewiring of the human colon during ulcerative colitis
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  • Cell,
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Highly efficient, massively-parallel single-cell RNA-Seq reveals cellular states and molecular features of human skin pathology
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  • 2019
  • Genomics
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Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis
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  • Nature,
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  • Immunology
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Identification of a Master Regulator of Differentiation in Toxoplasma
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  • Microbiology
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Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection
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  • 2019
  • Immunology
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Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing
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  • 2019
  • Technology
  • R&D
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Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection
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  • Medicine
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Mechanisms of lymphoma clearance induced by high-dose alkylating agents
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  • Biology
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Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration
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  • Medicine
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Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
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  • Cell,
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Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer
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  • 2019
  • Cancer
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  • Computational Methods
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Linking single-cell measurements of mass, growth rate, and gene expression
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  • Genome Biology,
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  • Physics
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Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses
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  • Infectious Disease
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T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation
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  • Genomics
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Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis
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  • Computational Methods
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The Human Cell Atlas White Paper
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Allergic Inflammatory Memory in Human Respiratory Epithelial Progenitor Cells
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  • Cell Atlas
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Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
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Linking single-cell measurements of mass, growth rate, and gene expression
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  • BioRxiv,
  • 2018
  • Technology
  • Chemistry
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A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers
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  • Genome Biology,
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  • Genomics
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Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells
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  • Cell,
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  • Immunology
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Science Forum: The Human Cell Atlas
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  • Immunology
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Reduced cellular diversity and an altered basal progenitor cell state inform epithelial barrier dysfunction in human type 2 immunity
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  • 2017
  • Medicine
  • Immunology
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Single-cell analyses to tailor treatments
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  • Infectious Disease
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Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies
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  • 2017
  • Immunology
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IFNγ-Dependent Tissue-Immune Homeostasis is Co-opted in the Tumor Microenvironment
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  • Cell,
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  • Immunology
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Scaling by shrinking: empowering single-cell ‘omics’ with microfluidic devices
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  • Genomics
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Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
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  • Genomics
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  • R&D
  • Travel
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Circulating CXCR5+CXCR3+PD-1lo Tfh-like Cells in HIV-1 Controllers with Neutralizing Antibody Breadth
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  • Infectious Disease
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Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion
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  • Immunity,
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  • Infectious Disease
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Regulation of X-linked gene expression during early mouse development by Rlim
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  • Biology
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Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
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  • Chemistry
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  • Genomics
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Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
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  • Cancer
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Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM
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  • 2016
  • Technology
  • Genomics
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Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression
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  • Immunity,
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  • Genomics
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A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages
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  • Biology
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Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity
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  • Cell,
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  • Genomics
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Oct1 and OCA-B are selectively required for CD4 memory T cell function
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Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses
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  • Infectious Disease
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Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics
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  • R&D
  • Genomics
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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
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  • Cell,
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  • R&D
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Deconstructing transcriptional heterogeneity in pluripotent stem cells
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Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL
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  • Blood,
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  • Cancer
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Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing
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  • 2014
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Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
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Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
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  • Science,
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  • Genomics
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Heterogeneity in immune responses: from populations to single cells
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  • Immunology
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Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells
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  • Cell,
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  • Genomics
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Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
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  • Genomics
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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
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Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
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Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli
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Dynamic regulatory network controlling TH17 cell differentiation
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  • Immunology
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Probing Enzymatic Activity inside Living Cells Using a Nanowire−Cell “Sandwich” Assay
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  • 2013
  • Technology
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Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits
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Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits
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  • Genomics
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Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells
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  • 2010
  • Physics
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Photoinduced Interfacial Charging and “Explosion” of Monolayer Pentacene Islands
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  • Physics
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