A5004591041- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Cell Image Analysis Techniques
- Bioinformatics and Genomic Networks
- T-cell and B-cell Immunology
- Immune cells in cancer
- Immunotherapy and Immune Responses
- Evolution and Genetic Dynamics
- Image Processing Techniques and Applications
- Epigenetics and DNA Methylation
- Immune Cell Function and Interaction
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Evolutionary Game Theory and Cooperation
- Innovative Microfluidic and Catalytic Techniques Innovation
- Science Education and Perceptions
- Lung Cancer Research Studies
- Molecular Biology Techniques and Applications
- Biomedical and Engineering Education
- Social Media in Health Education
- Neuroinflammation and Neurodegeneration Mechanisms
- Microbial Community Ecology and Physiology
- Asthma and respiratory diseases
- Hematopoietic Stem Cell Transplantation
- Bacterial Identification and Susceptibility Testing
University of Lausanne
2023-2024
Ghent University
2018-2023
VIB-UGent Center for Inflammation Research
2018-2023
École Normale Supérieure de Lyon
2018-2022
Université Claude Bernard Lyon 1
2018-2022
Inserm
2018-2022
Centre National de la Recherche Scientifique
2018-2022
Centre International de Recherche en Infectiologie
2018-2022
Highlights•ZEB2 is highly expressed across the macrophage lineage•ZEB2 preserves tissue-specific identities of macrophages tissues•ZEB2 deficient are outcompeted by WT counterparts•LXRα crucial for Kupffer cell identity and maintained ZEB2SummaryHeterogeneity between different populations has become a defining feature this lineage. However, conserved factors remain largely unknown. The transcription factor ZEB2 best described its role in epithelial to mesenchymal transition; however, within...
Abstract Using single-cell-omics data, it is now possible to computationally order cells along trajectories, allowing the unbiased study of cellular dynamic processes. Since 2014, more than 50 trajectory inference methods have been developed, each with its own set methodological characteristics. As a result, choosing method infer trajectories often challenging, since comprehensive assessment performance and robustness still lacking. In facilitate comparison results these other gold standard,...
The diversity of mononuclear phagocyte (MNP) subpopulations across tissues is one the key physiological characteristics immune system. Here, we focus on understanding metabolic variability MNPs through network analysis applied to three large-scale transcriptional datasets: introduce (1) an ImmGen MNP open-source dataset 337 samples 26 tissues; (2) a myeloid subset Phase I (202 samples); and (3) mouse single-cell RNA sequencing (scRNA-seq) (51,364 cells) assembled based Tabula Muris Senis. To...
Abstract Bacteria in nature often thrive fragmented environments, like soil pores, plant roots or leaves, leading to smaller isolated habitats, shared with fewer species. This spatial fragmentation can significantly influence bacterial interactions, affecting overall community diversity. To investigate this, we contrast paired growth tiny picoliter droplets (1–3 cells per 35 pL up 3–8 species 268 pL) larger, uniform liquid cultures (about 2 million 140 µl). We test four interaction scenarios...
Abstract Bacteria in nature often proliferate highly patchy environments, such as soil pores, particles, plant roots or leaves. The resulting spatial fragmentation leads to cells being constrained smaller habitats, shared with potentially fewer other species. effects of microhabitats on the emergence bacterial interspecific interactions are poorly understood, but important for maintenance diversity at a larger scale. To study this more in-depth, we contrasted paired species-growth picoliter...
Abstract Motivation During the last decade, trajectory inference (TI) methods have emerged as a novel framework to model cell developmental dynamics, most notably in area of single-cell transcriptomics. At present, more than 70 TI been published, and recent benchmarks showed that even state-of-the-art only perform well for certain types but not others. Results In this work, we present TinGa, new is fast flexible, based on Growing Neural Graphs. We performed an extensive comparison TinGa five...
Bacterial species interactions significantly shape growth and behavior in communities, determining the emergence of community functions. Typically, these are studied through bulk population measurements, overlooking role cell-to-cell variability spatial context. This study uses real-time surface measurements thousands sparsely positioned microcolonies to investigate kinetic variations monocultures cocultures
The mechanisms underlying operational tolerance after hematopoietic stem cell transplantation in humans are poorly understood. We studied two independent cohorts of patients who underwent allogeneic from human leukocyte antigen–identical siblings. Primary was associated with long-lasting reshaping the recipients’ immune system compared to their healthy donors an increased proportion regulatory T subsets and decreased activation, proliferation, migration. Transcriptomics profiles also...
Abstract Interactions between species are thought to be crucial for modulating their growth and behaviour within communities, determinant the emergence of community functions. Several different interaction concepts exist, but there is no consensus on how interactions should quantified integrated in theory. Here we expand existing real-time measurements pure culture microcolony develop benchmark coculture experiments, show these can both parametrize kinetic interspecific effects. We follow...
Bacterial growth can be studied at the single cell level through time-lapse microscopy imaging. Technical advances in lead to increasing image quality, which turn allows visualize larger areas of growth, containing more and cells. In this context, use automated computational tools becomes essential. paper, we present STrack, a tool that track cells images fast efficient way. We compared it 3 recently published tracking on ranging over 6 different bacterial strains with various morphologies....
ABSTRACT Real-time imaging of bacterial cell division, population growth and behaviour is essential for our understanding microbial-catalyzed processes at the microscale. However, despite relative ease by which high resolution data can be acquired, extraction relevant features from images remains cumbersome. Here we present a versatile pipeline automated standalone or time-resolved image series, with standardized output easy downstream processing. The input consist phase-contrast without...
Abstract We dissect metabolic variability of mononuclear phagocyte (MNP) subpopulations across different tissues through integrative analysis three large scale datasets. Specifically, we introduce ImmGen MNP Open Source dataset that profiled 337 samples and extended previous effort which included 202 phagocytes their progenitors. Next, analysed Tabula Muris Senis to extract data for 51,364 myeloid cells from 18 tissues. Taken together, a compendium assembled in this work covers phagocytic...
In this work, we studied the generation of memory precursor cells following an acute infection by analyzing single-cell RNA-seq data that contained CD8 T collected during postinfection expansion phase. We used different tools to reconstruct developmental trajectory followed after activation. Cells exhibited a signature were identified and positioned on trajectory. found these precursors are generated continuously with increasing numbers arising over time. Similarly, expression genes...
Abstract In this work, we studied the generation of memory precursor cells following an acute infection by analyzing single-cell RNA-seq data that contained CD8 T collected during postinfection expansion phase. We used different tools to reconstruct developmental trajectory followed after activation. Cells exhibited a signature were identified and positioned on trajectory. found precursors are generated continuously with increasing numbers being over time. Similarly, expression genes...
In this work, we studied the generation of memory precursor cells following an acute infection by analyzing single-cell RNA-seq data that contained CD8 T collected during post-infection expansion phase. We used different tools to reconstruct developmental trajectory followed after activation. Cells exhibited a signature were identified and positioned on trajectory. found precursors are generated continuously with increasing numbers being over time. Similarly, expression genes associated...
Abstract Bacterial growth can be studied at the single cell-level through time-lapse microscopy imaging. Technical advances in lead to increasing image quality, which turn allows visualize larger areas of growth, containing more and cells. In this context, use automated computational tools becomes essential. paper, we present STrack, a tool that track cells images fast efficient way. We compared it three recently published tracking on ranging over six different bacterial strains, STrack...