Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment
Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment
  • Yao et al.,
  • bioRxiv,
  • 2024
Biology Biology
Cancer Cancer
Alex K. Shalek Alex K. Shalek
Bokai Zhu Bokai Zhu
Glycan-costumed virus-like particles promote type 1 anti-tumor immunity
Glycan-costumed virus-like particles promote type 1 anti-tumor immunity
  • Lensch et al.,
  • biorxiv,
  • 2024
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Ankit Basak Ankit Basak
Engineering kinetics of TLR7/8 agonist release from bottlebrush prodrugs enables tumor-focused immune stimulation
Engineering kinetics of TLR7/8 agonist release from bottlebrush prodrugs enables tumor-focused immune stimulation
  • Bhagchandani et al.,
  • Science Advances,
  • 2023
Biology Biology
Cancer Cancer
Chemistry Chemistry
Genomics Genomics
Immunology Immunology
Medicine Medicine
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Evelyn Yuzhou Tong Evelyn Yuzhou Tong
Michelle Ramseier Michelle Ramseier
PI3Kβ controls immune evasion in PTEN-deficient breast tumours
PI3Kβ controls immune evasion in PTEN-deficient breast tumours
  • Bergholz et al.,
  • Nature,
  • 2023
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Jay Prakadan Jay Prakadan
Michelle Ramseier Michelle Ramseier
A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery
A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery
  • Crouchet et al.,
  • Nature Communications,
  • 2023
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Compressed phenotypic screens for complex multicellular models and high-content assays
Compressed phenotypic screens for complex multicellular models and high-content assays
  • Mead et al.,
  • bioRxiv,
  • 2023
Biology Biology
Cancer Cancer
Chemistry Chemistry
Computational Methods Computational Methods
Genomics Genomics
R&D R&D
Statistics Statistics
Technology Technology
Alex K. Shalek Alex K. Shalek
Ben Mead Ben Mead
Conner Kummerlowe Conner Kummerlowe
Ivy Liu Ivy Liu
Peter Winter Peter Winter
Thomas Nok Hin Cheng Thomas Nok Hin Cheng
Walaa Kattan Walaa Kattan
Spatially Resolved Single-Cell Assessment of Pancreatic Cancer Expression Subtypes Reveals Co-expressor Phenotypes and Extensive Intratumoral Heterogeneity
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 Cancer
Genomics Genomics
Immunology Immunology
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Peter Winter Peter Winter
Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells
Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells
  • Morris et al.,
  • Cell Reports,
  • 2023
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Travis Hughes Travis Hughes
Single-Cell Multiomics Reveals Clonal T-Cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm
Single-Cell Multiomics Reveals Clonal T-Cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm
  • DePasquale et al.,
  • Frontiers in Immunology,
  • 2023
Biology Biology
Cancer Cancer
Cell Atlas Cell Atlas
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Charles P. Couturier Charles P. Couturier
PI3K activation allows immune evasion by promoting an inhibitory myeloid tumor microenvironment
PI3K activation allows immune evasion by promoting an inhibitory myeloid tumor microenvironment
  • Collins et al.,
  • Journal for Immunotherapy of Cancer,
  • 2023
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Marc Wadsworth II Marc Wadsworth II
Travis Hughes Travis Hughes
Deciphering the immunopeptidome in vivo reveals new tumour antigens
Deciphering the immunopeptidome in vivo reveals new tumour antigens
  • Jaeger et al.,
  • Nature,
  • 2022
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Peter Winter Peter Winter
Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
  • Song et al.,
  • Nature Communications,
  • 2022
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
R&D R&D
Alex K. Shalek Alex K. Shalek
Marc Wadsworth II Marc Wadsworth II
Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
  • Raghavan et al.,
  • Cell,
  • 2021
Cancer Cancer
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Medicine Medicine
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Jennyfer Galvez-Reyes Jennyfer Galvez-Reyes
Nolawit Mulugeta Nolawit Mulugeta
Peter Winter Peter Winter
Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice
Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice
  • Hamza et al.,
  • Nature Communications,
  • 2021
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
Physics Physics
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Nolawit Mulugeta Nolawit Mulugeta
Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases
Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases
  • Prakadan et al.,
  • Nature Communications,
  • 2021
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Jay Prakadan Jay Prakadan
Kellie Kolb Kellie Kolb
Marc Wadsworth II Marc Wadsworth II
Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas
Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas
  • Amoozgar et al.,
  • Nature Communications,
  • 2021
Cancer Cancer
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Sam Kazer Sam Kazer
Inflammasomes within hyperactive murine dendritic cells stimulate long-lived T cell-mediated anti-tumor immunity
Inflammasomes within hyperactive murine dendritic cells stimulate long-lived T cell-mediated anti-tumor immunity
  • Zhivaki et al.,
  • Cell Reports,
  • 2020
Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Benjamin Doran Benjamin Doran
Ira Fleming Ira Fleming
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
  • Raghavan et al.,
  • bioRxiv,
  • 2020
Biology Biology
Cancer Cancer
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Medicine Medicine
Technology Technology
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Jennyfer Galvez-Reyes Jennyfer Galvez-Reyes
Nolawit Mulugeta Nolawit Mulugeta
Peter Winter Peter Winter
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
  • Rozenblatt-Rosen et al.,
  • Cell,
  • 2020
Biology Biology
Cancer Cancer
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
  • Genshaft et al.,
  • bioRxiv,
  • 2020
Biology Biology
Cancer Cancer
Chemistry Chemistry
Genomics Genomics
R&D R&D
Technology Technology
Alex Genshaft Alex Genshaft
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Ben Mead Ben Mead
Carly Ziegler Carly Ziegler
Constantine Tzouanas Constantine Tzouanas
Mechanisms of lymphoma clearance induced by high-dose alkylating agents
Mechanisms of lymphoma clearance induced by high-dose alkylating agents
  • Lossos et al.,
  • Cancer Discovery,
  • 2019
Biology Biology
Cancer Cancer
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Jay Prakadan Jay Prakadan
Kellie Kolb Kellie Kolb
Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
  • van Galen et al.,
  • Cell,
  • 2019
Alex K. Shalek Alex K. Shalek
Marc Wadsworth II Marc Wadsworth II
Travis Hughes Travis Hughes
Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer
Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer
  • Hamza B. et al.,
  • PNAS,
  • 2019
Biology Biology
Cancer Cancer
Computational Methods Computational Methods
R&D R&D
Technology Technology
Alejandro Gupta Alejandro Gupta
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Jay Prakadan Jay Prakadan
Peter Winter Peter Winter
Riley Drake Riley Drake
Linking single-cell measurements of mass, growth rate, and gene expression
Linking single-cell measurements of mass, growth rate, and gene expression
  • Kimmerling R.J. et al.,
  • Genome Biology,
  • 2018
Biology Biology
Cancer Cancer
Genomics Genomics
Physics Physics
R&D R&D
Technology Technology
Alejandro Gupta Alejandro Gupta
Alex K. Shalek Alex K. Shalek
Jay Prakadan Jay Prakadan
Riley Drake Riley Drake
A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade
A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade
  • Jerby-Arnon et al.,
  • Cell,
  • 2018
Alex K. Shalek Alex K. Shalek
Single-cell analyses to tailor treatments
Single-cell analyses to tailor treatments
  • Shalek A.K. et al.,
  • Science Translational Medicine,
  • 2017
Immunology Immunology
Infectious Disease Infectious Disease
Medicine Medicine
Technology Technology
Alex K. Shalek Alex K. Shalek
IFNγ-Dependent Tissue-Immune Homeostasis is Co-opted in the Tumor Microenvironment
IFNγ-Dependent Tissue-Immune Homeostasis is Co-opted in the Tumor Microenvironment
  • Nirschl et al.,
  • Cell,
  • 2017
Cancer Cancer
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Jay Prakadan Jay Prakadan
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
  • Tirosh et al.,
  • Science,
  • 2016
Biology Biology
Cancer Cancer
Genomics Genomics
Medicine Medicine
Aleth Gaillard Aleth Gaillard
Alex Genshaft Alex Genshaft
Alex K. Shalek Alex K. Shalek
Carly Ziegler Carly Ziegler
Jay Prakadan Jay Prakadan
Kellie Kolb Kellie Kolb
Marc Wadsworth II Marc Wadsworth II
Sam Kazer Sam Kazer
Travis Hughes Travis Hughes
Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL
Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL
  • Wang et al.,
  • Blood,
  • 2014
Cancer Cancer
Genomics Genomics
Alex K. Shalek Alex K. Shalek
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
  • Patel et al.,
  • Science,
  • 2014
Cancer Cancer
Genomics Genomics
Alex K. Shalek Alex K. Shalek
Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells
Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells
  • Suvà et al.,
  • Cell,
  • 2014
Biology Biology
Cancer Cancer
Genomics Genomics
Alex K. Shalek Alex K. Shalek
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
  • Lohr et al.,
  • Nature Biotechnology,
  • 2014
Biology Biology
Cancer Cancer
Genomics Genomics
Alex K. Shalek Alex K. Shalek
Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia
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 Cancer
Genomics Genomics
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek