Sarah Amalia Teichmann

A Community-Driven Single-Cell PBMC Reference Integrating Landmark Datasets Spanning Health and Disease

HARP integrates PBMC data from multiple studies to create a reference atlas with consensus annotations and identifies age, sex, and disease-related cellular modules.

STEER-seq: a recombinase based platform for pooled multimodal single-cell perturbation screening

STEER-seq enables pooled single-cell perturbation screening in hiPSCs by using defined genomic integration and barcode tracking to study transcription factor effects on cell identity.

A repair-associated bronchial epithelial differentiation trajectory through KRT14+ basal and hillock-like cells drives airway inflammation and remodelling in childhood-onset asthma

The paper identifies a novel asthma-associated epithelial differentiation trajectory involving KRT14+ basal cells and hillock-like cells that contributes to airway inflammation and remodelling in childhood-onset asthma.

An Integrated Atlas of the Human Kidney Spanning Health and Diseases

The paper integrates multiple single-cell and single-nucleus RNA-sequencing datasets to create a comprehensive Human Kidney Cell Atlas, identifying cell types, states, and disease-associated populations.

Building optimized single-cell reference atlases with scAtlasTb

The paper introduces scAtlasTb, a framework for building and optimizing single-cell reference atlases, demonstrating its application on three Human Cell Atlas projects.

An early CYP26A1/CRYAA progenitor-glial domain marks the presumptive macular region during human retinal development

The paper identifies a CYP26A1/CRYAA progenitor-glial domain in the human retina that marks the presumptive macula and links it to regional gliogenic maturation and specialized Muller glial populations.

Full-thickness spatial transcriptomics of the human uterus reveals basalis niche architecture and regeneration gradients during menstrual breakdown

This study uses spatial transcriptomics to map gene expression gradients in the human endometrium, revealing coordinated regeneration and niche architecture during menstrual breakdown.

A human developmental and adult brain atlas benchmarks dopaminergic stem cell models and cell therapy candidates

The paper benchmarks dopaminergic stem cell models and cell therapy candidates using a human brain atlas to identify off-target populations and lineage plasticity.

Multimodal Hypersampling of the adult human heart resolves tissue-specific cell states and disease-associated variants

This paper creates a detailed heart atlas using multimodal data to identify cell states and disease-associated genetic variants in specific heart regions.

An integrated multimodal pan-organ atlas of the female reproductive system across the lifespan contextualises gynaecological pathologies

This paper creates an integrated multimodal atlas of the female reproductive system across the lifespan, identifying cell types and linking them to gynaecological pathologies.

An integrated single cell and spatial omics atlas of human prenatal development

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

Single-Cell Profiling Reveals Developmental Trajectories and identifies SYK and TIM3 as Targets in some T Cell Lymphomas

This study uses single-cell transcriptomics to analyze T cell lymphomas, identifies developmental origins, and discovers SYK and TIM3 as potential therapeutic targets.

Perturbation-guided mapping of colorectal cancer cell states to causal mechanisms

This paper develops a continual learning framework to map colorectal cancer cell states to causal mechanisms through integration of single-cell data and perturbation experiments.

The Immunoregulatory Architecture of the Adult Oral Cavity

This paper presents a single-cell and spatial proteotranscriptomic atlas of human oral tissues, identifying fibroblasts as key immunoregulatory hubs and revealing changes in disease states.

Temporal Dynamics of Antigen-Specific T Cell Expansion in Primary SARS-CoV-2 Infection

The paper quantifies T cell response dynamics during primary SARS-CoV-2 infection, showing clone-intrinsic properties drive clonal kinetics and providing insights for vaccine design.

A single cell and spatial genomics atlas of human skin fibroblasts in health and disease

This study creates a spatial genomics atlas of human skin fibroblasts in health and disease, identifying six major populations and three disease-specific subtypes.

Decoding human B cell ontogeny in prenatal and adult bone marrow and in vitro models via single-cell multiomics

This study creates a single-cell multiomics atlas of B cell development in prenatal and adult bone marrow and in vitro models, identifying novel cell subsets and molecular signatures.

Malat1 regulates female Th2 cell cytokine expression through controlling early differentiation and response to IL2

This study shows Malat1 regulates cytokine expression in female Th2 cells by affecting early differentiation and IL2 response, but not in male cells.

Integrating multi-covariate disentanglement with counterfactual analysis on synthetic data enables cell type discovery and counterfactual predictions.

CellDISECT improves cell type discovery and counterfactual predictions by disentangling covariates and using synthetic data for training.

An atlas of TF driven gene programs across human cells

The paper creates a regulon atlas mapping TF activity across human cell types and uses it to link disease signatures to cell types and TFs, improving disease risk locus analysis.

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage

This paper describes the construction and usage of the Human Reference Atlas (HRA) v2.0, which integrates multiscale data across 36 organs and provides tools for analysis and visualization.

inVAE: Conditionally invariant representation learning for generating multivariate single-cell reference maps

inVAE improves cell state identification by disentangling biological and technical variation in single-cell data, outperforming existing methods across multiple human tissues.

multiDGD: A versatile deep generative model for multi-omics data

multiDGD is a deep generative model for multi-omics data that learns shared representations and enables data integration and association detection.

Single Cell Integration Characterises Metaplasia in Inflammatory Intestinal Diseases

The paper integrates single-cell RNA-seq datasets across the GI tract to identify epithelial metaplasia in inflammatory diseases, showing its role in inflammation through immune cell interactions.

Gene-level alignment of single cell trajectories

Genes2Genes aligns single-cell trajectories using a Bayesian DP framework, revealing gene-level mismatches and highlighting differences in T cell differentiation between in vitro and in vivo states.

Bin2cell reconstructs cells from high resolution Visium HD data

Bin2cell reconstructs cells from high-resolution Visium HD data by integrating morphology and gene expression, improving downstream analysis on mouse brain and human colorectal cancer data.

WebAtlas pipeline for integrated single cell and spatial transcriptomic data

WebAtlas integrates single cell and spatial transcriptomic data into a cloud-optimised format for interactive exploration.

A multiomic atlas of human early skeletal development

This study constructs a multiomic atlas of human early skeletal development using single-nuclei transcriptomics, epigenomics, and spatial transcriptomics to uncover regulatory mechanisms and cell states involved in bone and joint formation.

Integrating T-cell receptor and transcriptome for large-scale single-cell immune profiling analysis

The paper introduces mvTCR, a multimodal generative model for integrating TCR and transcriptome data to improve analysis of single-cell immune profiling data.

Developmental Dynamics of Human Cardiogenesis: A multi-omic reference and its disruption in Trisomy 21

This study develops a multi-omic reference of human cardiac development and identifies disruptions in Trisomy 21 hearts.