A5041922675- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Genomics and Chromatin Dynamics
- Immune Cell Function and Interaction
- T-cell and Retrovirus Studies
- Microfluidic and Bio-sensing Technologies
- Cytomegalovirus and herpesvirus research
- T-cell and B-cell Immunology
- Liver Disease Diagnosis and Treatment
- vaccines and immunoinformatics approaches
- Cancer Cells and Metastasis
- Genomics and Rare Diseases
- Cancer Genomics and Diagnostics
- Liver Diseases and Immunity
- Genetic Associations and Epidemiology
- Cancer Immunotherapy and Biomarkers
- CRISPR and Genetic Engineering
- Hepatitis B Virus Studies
- Gene expression and cancer classification
- Cell Image Analysis Techniques
- Diabetes and associated disorders
Stanford University
2025
Universitätsklinikum Tübingen
2024
University of Tübingen
2020-2023
University Children's Hospital Tübingen
2020-2023
ETH Zurich
2020
SIB Swiss Institute of Bioinformatics
2020
Abstract Hepatocellular carcinoma (HCC) can have viral or non-viral causes 1–5 . Non-alcoholic steatohepatitis (NASH) is an important driver of HCC. Immunotherapy has been approved for treating HCC, but biomarker-based stratification patients optimal response to therapy unmet need 6,7 Here we report the progressive accumulation exhausted, unconventionally activated CD8 + PD1 T cells in NASH-affected livers. In preclinical models NASH-induced therapeutic immunotherapy targeted at programmed...
The progression of non-alcoholic steatohepatitis (NASH) to fibrosis and hepatocellular carcinoma (HCC) is aggravated by auto-aggressive T cells. gut-liver axis contributes NASH, but the mechanisms involved consequences for NASH-induced liver cancer remain unknown. We investigated role gastrointestinal B cells in development HCC.
Improvements in single-cell RNA-seq technologies mean that studies measuring multiple experimental conditions, such as time series, have become more common. At present, few computational methods exist to infer series-specific transcriptome changes, and therefore typically used unsupervised pseudotime methods. While these identify cell subpopulations the transitions between them, they are not appropriate for identifying genes vary coherently along series. In addition, orderings estimate based...
We report Cytopath, a method for trajectory inference that takes advantage of transcriptional activity information from the RNA velocity single cells to perform inference. Cytopath performs this task by defining Markov chain model, simulating an ensemble possible differentiation trajectories, and constructing consensus trajectory. show can recapitulate topological molecular characteristics process under study. In our analysis, we include trajectories with varying bifurcated, circular,...
Objective Liver metastases are often resistant to immune checkpoint inhibitor therapy (ICI) and portend a worse prognosis compared with other locations. Regulatory T cells (Tregs) one of several immunosuppressive implicated in ICI resistance liver tumours, but the role played by Tregs residing within surrounding tumour is unknown. Design Flow cytometry single-cell RNA sequencing were used characterise hepatic before after therapy. Results We found that murine houses Treg population that,...
Abstract Single-cell RNA sequencing (scRNAseq) protocols measure the abundance of expressed transcripts for single cells. Gene expression profiles cells (cell-states) represent functional properties cell and are used to cluster cell-states that have a common identity (cell-type). Standard clustering methods scRNAseq data perform hard based on KNN graphs. This approach implicitly assumes variation among within does not correspond changes in properties. Differentiation is directed process...
A bstract Trajectory inference from single-cell RNA sequencing data bears the potential to systematically reconstruct complex differentiation processes, however inferring trajectories that accurately model biological characteristics of varied processes continues be a challenge, notwithstanding many available solutions. In general, trajectory and pseudotime methods have so far suffered ambiguity static transcriptome snapshots lacking concept directionality rate transcriptional activity. We...
Abstract Single-cell RNA-sequencing (scRNA-seq) has transformed our ability to resolve cellular properties across systems. However, current scRNA-seq platforms are one-size-fits-all approaches that tailored toward large cell inputs (> 1,000 cells), rendering them inefficient and costly when processing small, individual tissue samples. This important drawback tends be resolved by loading bulk samples, but this yields confounded mosaic population read-outs. To overcome these technological...
A bstract In chronic infections CD8 + T cells acquire a state termed “exhaustion” which is characterized by impaired effector functions and expression of co-inhibitory receptors as response to continuous TCR stimulation. Recently, the pool exhausted has been shown harbor multiple functionally distinct populations with memory-like effector-like features, though differentiation lineage relations between these are unclear. this work we present comprehensive scRNAseq time-series analysis from...