Sarah Amalia Teichmann

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

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.

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.

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

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.

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

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

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

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

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.

This paper develops a co-differentiation platform using human iPSCs to generate transplantable colonic tissue that mimics native mucosa and responds to biological signals.

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

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.

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.

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.

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

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.

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

The paper profiles immune cell RNA and protein expression across tissues and age to identify tissue-specific and age-related immune signatures.

This study uses single-cell transcriptomics to compare in vitro and in vivo chondrocyte differentiation, identifies off-target differentiation, and improves in vitro protocols by inhibiting FOXO1.

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

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.

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.

This study integrates single-cell and spatial transcriptomics with histopathology to identify cellular and molecular changes in lung alveolar damage during COVID-19 progression.

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

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

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.

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.

The paper traces the origin of four synchronous renal tumours in a child to an early embryonic MTOR mutation, showing its role in tumour development and clinical implications.