Jana M. Braunger
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View article: A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines
A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines Open
Population-scale resources of genetic, molecular, and cellular information form the basis for understanding human genomes, charting the heritable basis of disease and tracing the effects of mutations. Pooled perturbation assays, probing th…
View article: Remodeling of cytoskeleton, chromatin, and gene expression during mechanical rejuvenation of aged human dermal fibroblasts
Remodeling of cytoskeleton, chromatin, and gene expression during mechanical rejuvenation of aged human dermal fibroblasts Open
Aging is associated with a progressive decline in cellular function. To reset the aged cellular phenotype, various reprogramming approaches, including mechanical routes, have been explored. However, the epigenetic mechanisms underlying cel…
View article: A genome-scale single cell CRISPRi map of<i>trans</i>gene regulation across human pluripotent stem cell lines
A genome-scale single cell CRISPRi map of<i>trans</i>gene regulation across human pluripotent stem cell lines Open
Population-scale resources of genetic, molecular, and cellular information form the basis for understanding human genomes, charting the heritable basis of disease, and tracing the effects of mutations. Pooled perturbation assays applied to…
View article: Guide assignment in single-cell CRISPR screens using crispat
Guide assignment in single-cell CRISPR screens using crispat Open
Motivation Pooled single-cell CRISPR screens have emerged as a powerful tool in functional genomics to probe the effect of genetic interventions at scale. A crucial step in the analysis of the resulting data is the assignment of cells to g…
View article: Guide assignment in single-cell CRISPR screens using crispat
Guide assignment in single-cell CRISPR screens using crispat Open
Motivation Pooled single cell CRISPR screens have emerged as a powerful tool in functional genomics to probe the effect of genetic interventions at scale. A crucial step in the analysis of the resulting data is the assignment of cells to g…
View article: Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging
Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging Open
Human life expectancy is constantly increasing and aging has become a major risk factor for many diseases, although the underlying gene regulatory mechanisms are still unclear. Using transcriptomic and chromosomal conformation capture (Hi‐…
View article: Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO
Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO Open
Factor analysis is a widely used method for dimensionality reduction in genome biology, with applications from personalized health to single-cell biology. Existing factor analysis models assume independence of the observed samples, an assu…
View article: MEFISTO: Data for tutorials
MEFISTO: Data for tutorials Open
Data and pre-trained MEFISTO model to run the vignettes and tutorials provided at https://biofam.github.io/MOFA2/MEFISTO.html.* Evodevo application: Input data is provided as evodevo.csv and evodevo.RData, the trained MEFISTO model is prov…
View article: decoupleR: ensemble of computational methods to infer biological activities from omics data
decoupleR: ensemble of computational methods to infer biological activities from omics data Open
Summary Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present deco…
View article: decoupleR: Ensemble of computational methods to infer biological activities from omics data
decoupleR: Ensemble of computational methods to infer biological activities from omics data Open
Summary Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present deco…
View article: MEFISTO: Data for tutorials
MEFISTO: Data for tutorials Open
Data and pre-trained MEFISTO model to run the vignettes and tutorials provided at https://biofam.github.io/MOFA2/MEFISTO.html.* Evodevo application: Input data is provided as evodevo.csv and evodevo.RData, the trained MEFISTO model is prov…
View article: Identifying temporal and spatial patterns of variation from multi-modal data using MEFISTO
Identifying temporal and spatial patterns of variation from multi-modal data using MEFISTO Open
Factor analysis is among the most-widely used methods for dimensionality reduction in genome biology, with applications from personalized health to single-cell studies. Existing implementations of factor analysis assume independence of the…