David R. Glass
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View article: Annotation-free discovery of disease-relevant cells in single-cell datasets
Annotation-free discovery of disease-relevant cells in single-cell datasets Open
In single-cell datasets, patient labels indicating disease status (e.g., “sick” or “not sick”) are typically available, but individual cell labels indicating which of a patient’s cells are associated with their disease state are generally …
View article: Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming
Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming Open
Hematopoietic stem and progenitor cell (HSPC) transplantation is an essential therapy for hematological conditions, but finer definitions of human HSPC subsets with associated function could enable better tuning of grafts and more routine,…
View article: Cell simulation as cell segmentation
Cell simulation as cell segmentation Open
View article: Terminal deoxynucleotidyl transferase and CD84 identify human multi-potent lymphoid progenitors
Terminal deoxynucleotidyl transferase and CD84 identify human multi-potent lymphoid progenitors Open
Lymphoid specification in human hematopoietic progenitors is not fully understood. To better associate lymphoid identity with protein-level cell features, we conduct a highly multiplexed single-cell proteomic screen on human bone marrow pr…
View article: Hallmarks of tumor-experienced T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy
Hallmarks of tumor-experienced T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy Open
Dysregulation of the bone marrow (BM) niche in multiple myeloma (MM) alters the composition and state of resident immune cells, potentially impeding anti-tumor immunity. One common mechanism of immune inhibition in solid tumors is the indu…
View article: Cell Simulation as Cell Segmentation
Cell Simulation as Cell Segmentation Open
Single-cell spatial transcriptomics promises a highly detailed view of a cell’s transcriptional state and microenvironment, yet inaccurate cell segmentation can render this data murky by misattributing large numbers of transcripts to nearb…
View article: Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma
Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma Open
Cutaneous T cell lymphomas (CTCLs) are skin cancers with poor survival rates and limited treatments. While immunotherapies have shown some efficacy, the immunological consequences of administering immune-activating agents to CTCL patients …
View article: 173 Deciphering the tumor microenvironment of renal cell carcinoma: integrating single-cell sequencing and <i>In Situ</i> spatial transcriptomics for comprehensive characterization of tumor-infiltrating T cells
173 Deciphering the tumor microenvironment of renal cell carcinoma: integrating single-cell sequencing and <i>In Situ</i> spatial transcriptomics for comprehensive characterization of tumor-infiltrating T cells Open
Background Renal cell carcinoma (RCC) is a prevalent and aggressive form of kidney cancer, with variable response rates to checkpoint blockade immunotherapies. While high T cell infiltration often indicates a favorable response to immunoth…
View article: Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors
Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors Open
Summary Hematopoietic stem and progenitor cell (HSPC) transplantation is an essential therapy for hematological conditions, but finer definitions of human HSPC subsets with associated function could enable better tuning of grafts and more …
View article: ATACseq data, processed files and scripts associated with paper 'Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming'
ATACseq data, processed files and scripts associated with paper 'Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming' Open
These are zipped bam and bed files, processed bulkATAC and scATAC objects and scripts for analysis of ATAC seq data generated from erythrocyte/megakaryocyte progenitors (EMP) and Macrophage/Dendritic cell progenitor (MDP) populations isola…
View article: Fcs files used in "Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors"
Fcs files used in "Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors" Open
Mass cytometry data from the manuscript, "Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors". This repository contains singlet-gated, viable, CD45+, batch-corrected cells from t…
View article: Fcs files used in "Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors"
Fcs files used in "Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors" Open
Mass cytometry data from the manuscript, "Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors". This repository contains singlet-gated, viable, CD45+, batch-corrected cells from t…
View article: Data used in "Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma"
Data used in "Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma" Open
Data generated from the clinical trials, CITN-10 (NCT02243579) and CITN-13 (NCT03063632), analyzing the in vivo responses to anti-PD-1 monotherapy or anti-PD-1 interferon-gamma combination therapy in patients with advanced mycosis fungoide…
View article: Data used in "Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma"
Data used in "Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma" Open
Data generated from the clinical trials, CITN-10 (NCT02243579) and CITN-13 (NCT03063632), analyzing the in vivo responses to anti-PD-1 monotherapy or anti-PD-1 interferon-gamma combination therapy in patients with advanced mycosis fungoide…
View article: Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics
Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics Open
Approximately 5 million dengue virus–infected patients progress to a potentially life-threatening severe dengue (SD) infection annually. To identify the immune features and temporal dynamics underlying SD progression, we performed deep imm…
View article: CD4+ T cells expressing CX3CR1, GPR56, with variable CD57 are associated with cardiometabolic diseases in persons with HIV
CD4+ T cells expressing CX3CR1, GPR56, with variable CD57 are associated with cardiometabolic diseases in persons with HIV Open
Persons with HIV (PWH) on long-term antiretroviral therapy (ART) have a higher incidence and prevalence of cardiometabolic diseases attributed, in part, to persistent inflammation despite viral suppression. In addition to traditional risk …
View article: Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics
Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics Open
Code to reproduce figures from "Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics" https://www.biorxiv.org/content/10.1101/2022.09.21.508901v1.full Batch-corrected …
View article: A Distinct Phenotype of Polarized Memory B cell holds IgE Memory
A Distinct Phenotype of Polarized Memory B cell holds IgE Memory Open
Allergen-specific IgE antibodies mediate allergic pathology in diseases such as allergic rhinitis and food allergy. Memory B cells (MBCs) contribute to circulating IgE by regenerating IgE-producing plasma cells upon allergen encounter. We …
View article: Expression of terminal deoxynucleotidyl transferase (TdT) identifies lymphoid-primed progenitors in human bone marrow
Expression of terminal deoxynucleotidyl transferase (TdT) identifies lymphoid-primed progenitors in human bone marrow Open
Lymphoid specification in human hematopoietic progenitors is not fully understood. To better associate lymphoid identity with protein-level cell features, we conducted a highly multiplexed single-cell proteomic screen on human bone marrow …
View article: Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics
Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics Open
Summary Approximately five million dengue virus-infected patients, particularly children, progress to a potentially life-threatening severe dengue (SD) infection annually. To identify the immune features and temporal dynamics underlying SD…
View article: Data science through the lens of systems immunology
Data science through the lens of systems immunology Open
View article: Supervised dimensionality reduction for exploration of single-cell data by HSS-LDA
Supervised dimensionality reduction for exploration of single-cell data by HSS-LDA Open
Single-cell technologies generate large, high-dimensional datasets encompassing a diversity of omics. Dimensionality reduction captures the structure and heterogeneity of the original dataset, creating low-dimensional visualizations that c…
View article: Human IL-10-producing B cells have diverse states that are induced from multiple B cell subsets
Human IL-10-producing B cells have diverse states that are induced from multiple B cell subsets Open
Regulatory B cells (Bregs) suppress immune responses through the secretion of interleukin-10 (IL-10). This immunomodulatory capacity holds therapeutic potential, yet a definitional immunophenotype for enumeration and prospective isolation …
View article: Supervised dimensionality reduction for exploration of single-cell data by Hybrid Subset Selection - Linear Discriminant Analysis
Supervised dimensionality reduction for exploration of single-cell data by Hybrid Subset Selection - Linear Discriminant Analysis Open
Single-cell technologies generate large, high-dimensional datasets encompassing a diversity of omics. Dimensionality reduction enables visualization of data by representing cells in two-dimensional plots that capture the structure and hete…
View article: Multi-Omic Single Cell Identification of Lin- CD34- Natural&nbsp;Killer Cell Progenitors in Human Hematopoiesis
Multi-Omic Single Cell Identification of Lin- CD34- Natural Killer Cell Progenitors in Human Hematopoiesis Open
View article: Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma
Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma Open
View article: Human IL-10-producing B cells have diverse states induced from multiple B cell subsets
Human IL-10-producing B cells have diverse states induced from multiple B cell subsets Open
Regulatory B cells (Bregs) can suppress immune responses through the secretion of IL-10 and other anti-inflammatory cytokines. This immunomodulatory capacity holds therapeutic potential, yet a definitional immunophenotype for enumeration a…
View article: Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma
Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma Open
Ductal carcinoma in situ (DCIS) is a pre-invasive lesion that is thought to be a precursor to invasive breast cancer (IBC). To understand how the tumor microenvironment (TME) changes with transition to IBC, we used Multiplexed Ion Beam Ima…
View article: Single-cell metabolic profiling of human cytotoxic T cells
Single-cell metabolic profiling of human cytotoxic T cells Open
View article: Single-cell metabolic profiling (scMEP) of human cytotoxic T cells
Single-cell metabolic profiling (scMEP) of human cytotoxic T cells Open
Datasets for Hartmann FJ et al. (2020) Single-cell metabolic profiling of human cytotoxic T cells. Nature Biotechnology Contains single-cell mass cytometry (CyTOF) datasets for metabolic analysis of human whole blood populations, in vi…