Sarah A. Teichmann
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View article: GZMK+CD8+ T cells target a specific acinar cell type in Sjögren's disease
GZMK+CD8+ T cells target a specific acinar cell type in Sjögren's disease Open
Using single-cell and spatial transcriptomics and proteomics, this study identifies a selective loss of PRR4⁺CST3⁺WFDC2⁻ seromucous acinar cells and a rise in GZMK⁺CD8⁺ T cells in Sjögren's disease, revealing distinct immune-mediated epith…
View article: Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base
Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base Open
The Iterative Bleaching Extends Multiplexity (IBEX) imaging method is an iterative immunolabeling and chemical bleaching method that enables highly multiplexed imaging of diverse tissues. Development of the IBEX method and related software…
View article: A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues
A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues Open
Fibroblasts sculpt the architecture and cellular microenvironments of various tissues. Here we constructed a spatially resolved atlas of human skin fibroblasts from healthy skin and 23 skin diseases, with comparison to 14 cross-tissue dise…
View article: Decoding human B cell ontogeny in prenatal and adult bone marrow and in vitro models via single-cell multiomics
Decoding human B cell ontogeny in prenatal and adult bone marrow and in vitro models via single-cell multiomics Open
In humans, the bone marrow becomes the primary site for B lymphopoiesis during the second trimester of pregnancy and continues throughout life. Prenatal and adult B cell progenitors play distinct roles in the aetiology and pathology of pae…
View article: <i>Malat1</i> regulates female Th2 cell cytokine expression through controlling early differentiation and response to IL-2
<i>Malat1</i> regulates female Th2 cell cytokine expression through controlling early differentiation and response to IL-2 Open
Identifying cell intrinsic regulators of immune sexual dimorphism is critical for treatment of several immunopathologies. We show that Malat1 is required for appropriate cytokine expression in female but not male T helper 2 (Th2) cells. Ma…
View article: Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation
Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation Open
Predicting transcriptional responses to genetic perturbations is challenging in functional genomics. While recent methods aim to infer effects of untested perturbations, their true predictive power remains unclear. Here, we show that curre…
View article: Single-cell transcriptomics identifies chondrocyte differentiation dynamics in vivo and in vitro
Single-cell transcriptomics identifies chondrocyte differentiation dynamics in vivo and in vitro Open
Developing in vitro chondrocytes that replicate in vivo development would benefit musculoskeletal disease modeling and regenerative medicine. Although current methodologies have made progress, challenges such as off-target differentiation …
View article: Temporal multi-omics analysis of COVID-19 in end-stage kidney disease
Temporal multi-omics analysis of COVID-19 in end-stage kidney disease Open
Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. We performed longitudinal single-cell immune profiling of ESKD patients with COVID-19. Transcriptome, surface proteome, and immunoreceptor sequencing data w…
View article: Integrating multi-covariate disentanglement with counterfactual analysis on synthetic data enables cell type discovery and counterfactual predictions
Integrating multi-covariate disentanglement with counterfactual analysis on synthetic data enables cell type discovery and counterfactual predictions Open
Single-cell gene expression is influenced by diverse covariates such as genomics protocol, tissue origin, donor attributes, and microenvironment, which are challenging to disentangle. We present CellDISECT, a novel method combining disenta…
View article: An atlas of TF driven gene programs across human cells
An atlas of TF driven gene programs across human cells Open
Combinations of transcription factors (TFs) regulate gene expression and determine cell fate. Much effort has been devoted to understanding TF activity in different tissues and how tissue-specificity is achieved. However, ultimately gene r…
View article: The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods
The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods Open
The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the…
View article: The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods
The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods Open
The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the…
View article: The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques
The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques Open
Multiplexed imaging is a powerful approach in spatial biology, although it is complex, expensive and labor-intensive. Here, we present the IBEX Knowledge-Base, a central resource for reagents, protocols and more, to enhance knowledge shari…
View article: The cellular and molecular cardiac tissue responses in human inflammatory cardiomyopathies after SARS-CoV-2 infection and COVID-19 vaccination
The cellular and molecular cardiac tissue responses in human inflammatory cardiomyopathies after SARS-CoV-2 infection and COVID-19 vaccination Open
Myocarditis, characterized by inflammatory cell infiltration, can have multiple etiologies, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or, rarely, mRNA-based coronavirus disease 2019 (COVID-19) vaccina…
View article: Leveraging protein structural information to improve variant effect prediction
Leveraging protein structural information to improve variant effect prediction Open
Despite massive sequencing efforts, understanding the difference between human pathogenic and benign variants remains a challenge. Computational variant effect predictors (VEPs) have emerged as essential tools for assessing the impact of g…
View article: A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung disease
A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung disease Open
Alveolar type 2 (AT2) cells maintain lung health by acting as stem cells and producing pulmonary surfactant. AT2 dysfunction underlies many lung diseases, including interstitial lung disease (ILD), in which some inherited forms result from…
View article: A single cell and spatial genomics atlas of human skin fibroblasts in health and disease
A single cell and spatial genomics atlas of human skin fibroblasts in health and disease Open
Fibroblasts are critical cells that shape the architecture and cellular ecosystems in multiple tissues. Understanding fibroblast heterogeneity and their spatial context in health and disease has enormous clinical relevance. In this study, …
View article: inVAE: Conditionally invariant representation learning for generating multivariate single-cell reference maps
inVAE: Conditionally invariant representation learning for generating multivariate single-cell reference maps Open
Single-cell data is driving new insights into the spatiotemporal dynamics of cells and individual disease susceptibility. However, accurately identifying cell states across diverse cohorts remains challenging, as both biological variation …