Tal Ashuach
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View article: Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+
Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+ Open
Genetic screens mediated via CRISPR-Cas9 combined with high-content readouts have emerged as powerful tools for biological discovery. However, computational analyses of these screens come with additional challenges beyond those found with …
View article: Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation
Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation Open
Our findings suggest a generalizable framework for exploring gene regulatory programs and their dynamics across developmental processes; this includes a comprehensive approach to studying the effects of disease-associated variation on tran…
View article: NF-κB inhibitor alpha controls SARS-CoV-2 infection in ACE2-overexpressing human airway organoids
NF-κB inhibitor alpha controls SARS-CoV-2 infection in ACE2-overexpressing human airway organoids Open
As SARS-CoV-2 continues to spread worldwide, tractable primary airway cell models that recapitulate the cell-intrinsic response to arising viral variants are needed. Here we describe an adult stem cell-derived human airway organoid model o…
View article: Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation
Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation Open
Background Increasing evidence suggests that a substantial proportion of disease-associated mutations occur in enhancers, regions of non-coding DNA essential to gene regulation. Understanding the structures and mechanisms of regulatory pro…
View article: Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework Open
The advent of perturbation-based massively parallel reporter assays (MPRAs) technique has facilitated the delineation of the roles of non-coding regulatory elements in orchestrating gene expression. However, computational efforts remain sc…
View article: Hepatitis C virus infects and perturbs liver stem cells
Hepatitis C virus infects and perturbs liver stem cells Open
Hepatitis C virus (HCV) is the leading cause of death from liver disease. How HCV infection causes lasting liver damage and increases cancer risk remains unclear. Here, we identify bipotent liver stem cells as novel targets for HCV infecti…
View article: Best practices for perturbation MPRA—a computational evaluation framework of sequence design strategies
Best practices for perturbation MPRA—a computational evaluation framework of sequence design strategies Open
The advent of the perturbation-based massively parallel reporter assays (MPRAs) technique has enabled delineating of the roles of non-coding regulatory elements in orchestrating gene expression. However, computational efforts remain scant …
View article: MultiVI: deep generative model for the integration of multimodal data
MultiVI: deep generative model for the integration of multimodal data Open
Jointly profiling the transcriptome, chromatin accessibility and other molecular properties of single cells offers a powerful way to study cellular diversity. Here we present MultiVI, a probabilistic model to analyze such multiomic data an…
View article: NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids
NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids Open
As SARS-CoV-2 continues to spread worldwide, tractable primary airway cell models that accurately recapitulate the cell-intrinsic response to arising viral variants are needed. Here we describe an adult stem cell-derived human airway organ…
View article: Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation
Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation Open
Gene regulatory elements play a key role in orchestrating gene expression during cellular differentiation, but what determines their function over time remains largely unknown. Here, we perform perturbation-based massively parallel reporte…
View article: Hepatitis C Virus Infects and Perturbs Liver Stem Cells
Hepatitis C Virus Infects and Perturbs Liver Stem Cells Open
Summary Hepatitis C virus (HCV) is the leading cause of death from liver disease. How HCV infection causes lasting liver damage and increases cancer risk beyond viral clearance remains unclear. We identify bipotent liver stem cells as nove…
View article: MultiVI - Intermediate datasets, notebooks, and scripts
MultiVI - Intermediate datasets, notebooks, and scripts Open
All intermediate analyses, datasets, scripts, and notebooks to reproduce all results in the MultiVI manuscript.
View article: MultiVI - Intermediate datasets, notebooks, and scripts
MultiVI - Intermediate datasets, notebooks, and scripts Open
All intermediate analyses, datasets, scripts, and notebooks to reproduce all results in the MultiVI manuscript.
View article: MultiVI - Intermediate datasets, notebooks, and scripts
MultiVI - Intermediate datasets, notebooks, and scripts Open
All intermediate analyses, datasets, scripts, and notebooks to reproduce all results in the MultiVI manuscript.
View article: MultiVI - Intermediate datasets, notebooks, and scripts
MultiVI - Intermediate datasets, notebooks, and scripts Open
All intermediate analyses, datasets, scripts, and notebooks to reproduce all results in the MultiVI manuscript.
View article: MultiVI: deep generative model for the integration of multi-modal data
MultiVI: deep generative model for the integration of multi-modal data Open
Jointly profiling the transcriptional and chromatin accessibility landscapes of single-cells is a powerful technique to characterize cellular populations. Here we present MultiVI, a probabilistic model to analyze such multiomic data and in…
View article: Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans
Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans Open
Emerging evidence indicates a fundamental role for the epigenome in immunity. Here, we used a systems biology approach to map the epigenomic and transcriptional landscape of immunity to influenza vaccination in humans at the single-cell le…
View article: PeakVI: A Deep Generative Model for Single Cell Chromatin Accessibility Analysis
PeakVI: A Deep Generative Model for Single Cell Chromatin Accessibility Analysis Open
A bstract Single-cell ATAC sequencing (scATAC-seq) is a powerful and increasingly popular technique to explore the regulatory landscape of heterogeneous cellular populations. However, the high noise levels, degree of sparsity, and scale of…
View article: PeakVI intermediate results, trained models, notebooks.
PeakVI intermediate results, trained models, notebooks. Open
Intermediate result files, notebooks, and trained models used to generate figures in the PeakVI manuscript.
View article: PeakVI intermediate results, trained models, notebooks.
PeakVI intermediate results, trained models, notebooks. Open
Intermediate result files, notebooks, and trained models used to generate figures in the PeakVI manuscript.
View article: scvi-tools: a library for deep probabilistic analysis of single-cell omics data
scvi-tools: a library for deep probabilistic analysis of single-cell omics data Open
A bstract Probabilistic models have provided the underpinnings for state-of-the-art performance in many single-cell omics data analysis tasks, including dimensionality reduction, clustering, differential expression, annotation, removal of …
View article: Massively parallel reporter perturbation assay uncovers temporal regulatory architecture during neural differentiation
Massively parallel reporter perturbation assay uncovers temporal regulatory architecture during neural differentiation Open
Gene regulatory elements play a key role in orchestrating gene expression during cellular differentiation, but what determines their function over time remains largely unknown. Here, we performed perturbation-based massively parallel repor…
View article: Wimmers et al. custom scATAC analysis scripts
Wimmers et al. custom scATAC analysis scripts Open
Custom analysis scripts for scATAC analysis related to Wimmers et al.'s manuscript titled: "Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination i…
View article: Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction
Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction Open
Epigenomic regulation and lineage-specific gene expression act in concert to drive cellular differentiation, but the temporal interplay between these processes is largely unknown. Using neural induction from human pluripotent stem cells (h…