CD4+ T cells re-wire granuloma cellularity and regulatory networks to promote immunomodulation following Mtb reinfection
CD4+ T cells re-wire granuloma cellularity and regulatory networks to promote immunomodulation following Mtb reinfection
  • Bromley et al.,
  • Immunity,
  • 2024
Computational Methods Computational Methods
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Josh Bromley Josh Bromley
Sarah Nyquist Sarah Nyquist
LAT encodes T cell activation pathway balance
LAT encodes T cell activation pathway balance
  • Rubin et al.,
  • bioRxiv,
  • 2024
Computational Methods Computational Methods
Immunology Immunology
Microbiology Microbiology
Adam Rubin Adam Rubin
Alex K. Shalek Alex K. Shalek
Tyler Dao Tyler Dao
Distinct olfactory mucosal macrophage populations mediate neuronal maintenance and pathogen defense
Distinct olfactory mucosal macrophage populations mediate neuronal maintenance and pathogen defense
  • Wellford et al.,
  • Mucosal Immunology,
  • 2024
Infectious Disease Infectious Disease
Medicine Medicine
Microbiology Microbiology
Alex K. Shalek Alex K. Shalek
José Ordovas-Montañes José Ordovas-Montañes
Marko Vukovic Marko Vukovic
Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease
Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease
  • Winter et al.,
  • Biorxiv,
  • 2024
Cancer Cancer
Microbiology Microbiology
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Charles P. Couturier Charles P. Couturier
Jennyfer Galvez-Reyes Jennyfer Galvez-Reyes
Michelle Ramseier Michelle Ramseier
Nolawit Mulugeta Nolawit Mulugeta
Peter Winter Peter Winter
Impact of variants and vaccination on nasal immunity across three waves of SARS-CoV-2
Impact of variants and vaccination on nasal immunity across three waves of SARS-CoV-2
  • Long et al.,
  • biorxiv,
  • 2024
Infectious Disease Infectious Disease
Medicine Medicine
Andrew Navia Andrew Navia
Carly Ziegler Carly Ziegler
Josh Bromley Josh Bromley
José Ordovas-Montañes José Ordovas-Montañes
Kyle Kimler Kyle Kimler
Micayla George Micayla George
Riley Drake Riley Drake
Samira Ibrahim Samira Ibrahim
Tasneem Jivanjee Tasneem Jivanjee
Vincent Miao Vincent Miao
Comprehensive multi-site profiling of the malignant pleural mesothelioma micro-environment identifies candidate molecular determinants of histopathologic type
Comprehensive multi-site profiling of the malignant pleural mesothelioma micro-environment identifies candidate molecular determinants of histopathologic type
  • Severson et al.,
  • biorxiv,
  • 2024
Cancer Cancer
Computational Methods Computational Methods
Alex K. Shalek Alex K. Shalek
Travis Hughes Travis Hughes
Systematic deconstruction of myeloid cell signaling in tuberculosis granulomas reveals IFN-γ, TGF-β, and time are associated with conserved myeloid diversity
Systematic deconstruction of myeloid cell signaling in tuberculosis granulomas reveals IFN-γ, TGF-β, and time are associated with conserved myeloid diversity
  • Peters et al.,
  • biorxiv,
  • 2024
Alex K. Shalek Alex K. Shalek
Josh Bromley Josh Bromley
Sarah Nyquist Sarah Nyquist
Travis Hughes Travis Hughes
Single-cell and spatiotemporal profile of ovulation in the mouse ovary
Single-cell and spatiotemporal profile of ovulation in the mouse ovary
  • Huang et al.,
  • bioRxiv,
  • 2024
Biology Biology
Computational Methods Computational Methods
Alex K. Shalek Alex K. Shalek
Brittany Goods Brittany Goods
Daniela Russo Daniela Russo
Intrahepatic plasma cells, but not atypical memoryB cells, associate with clinical phases of chronichepatitis B
Intrahepatic plasma cells, but not atypical memoryB cells, associate with clinical phases of chronichepatitis B
  • Osmani et al.,
  • European Journal of Immunology,
  • 2024
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Jasmin Joseph-Chazan Jasmin Joseph-Chazan
B cell heterogeneity in human tuberculosis highlights compartment-specific phenotype and functional roles
B cell heterogeneity in human tuberculosis highlights compartment-specific phenotype and functional roles
  • Krause et al.,
  • Nature Communications,
  • 2024
Biology Biology
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data
Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data
  • Zhu et al.,
  • bioRxiv,
  • 2024
Computational Methods Computational Methods
Alex K. Shalek Alex K. Shalek
Bokai Zhu Bokai Zhu
An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection
An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection
  • Ziegler et al.,
  • American Society for Microbiology,
  • 2024
Computational Methods Computational Methods
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Carly Ziegler Carly Ziegler
Josh Bromley Josh Bromley
José Ordovas-Montañes José Ordovas-Montañes
Micayla George Micayla George
Riley Drake Riley Drake
Sam Kazer Sam Kazer
Vincent Miao Vincent Miao
A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing
A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing
  • DenAdel et al.,
  • bioRxiv,
  • 2024
Computational Methods Computational Methods
Microbiology Microbiology
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Michelle Ramseier Michelle Ramseier
Peter Winter Peter Winter
Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
  • Nwizu et al.,
  • bioRxiv,
  • 2024
Computational Methods Computational Methods
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Michelle Ramseier Michelle Ramseier
Peter Winter Peter Winter
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
A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment
A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment
  • Zhu et al.,
  • bioRxiv,
  • 2024
Computational Methods Computational Methods
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Bokai Zhu Bokai Zhu
Congenital T cell activation impairs transitional to follicular B cell maturation in humans
Congenital T cell activation impairs transitional to follicular B cell maturation in humans
  • Allard-Chamard et al.,
  • bioRxiv,
  • 2024
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Michelle Ramseier Michelle Ramseier
Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
  • Nwizu et al.,
  • bioRxiv,
  • 2024
Computational Methods Computational Methods
Genomics Genomics
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Michelle Ramseier Michelle Ramseier
Peter Winter Peter Winter
Pro-inflammatory feedback loops define immune responses to pathogenic Lentivirus infection
Pro-inflammatory feedback loops define immune responses to pathogenic Lentivirus infection
  • Wilk et al.,
  • Genome Medicine,
  • 2024
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Ira Fleming Ira Fleming
Jennyfer Galvez-Reyes Jennyfer Galvez-Reyes
Sam Kazer Sam Kazer
Vincent Miao Vincent Miao
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
CD4 + T cells are homeostatic regulators during Mtb reinfection
CD4 + T cells are homeostatic regulators during Mtb reinfection
  • Bromley et al.,
  • bioRxiv,
  • 2024
Biology Biology
Computational Methods Computational Methods
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Dennis Wang Dennis Wang
Josh Bromley Josh Bromley
Sarah Nyquist Sarah Nyquist
Son Nguyen Son Nguyen

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