Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas
JE Rood, A Hupalowska, A Regev - Cell, 2024 - cell.com
Comprehensively charting the biologically causal circuits that govern the phenotypic space
of human cells has often been viewed as an insurmountable challenge. However, in the last …
of human cells has often been viewed as an insurmountable challenge. However, in the last …
Pooled Genome-Scale CRISPR Screens in Single Cells
D Schraivogel, LM Steinmetz… - Annual Review of …, 2023 - annualreviews.org
Assigning functions to genes and learning how to control their expression are part of the
foundation of cell biology and therapeutic development. An efficient and unbiased method to …
foundation of cell biology and therapeutic development. An efficient and unbiased method to …
Scalable genetic screening for regulatory circuits using compressed Perturb-seq
Pooled CRISPR screens with single-cell RNA sequencing readout (Perturb-seq) have
emerged as a key technique in functional genomics, but they are limited in scale by cost and …
emerged as a key technique in functional genomics, but they are limited in scale by cost and …
Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens
Summary The mammalian SWI/SNF (mSWI/SNF or BAF) family of chromatin remodeling
complexes play critical roles in regulating DNA accessibility and gene expression. The three …
complexes play critical roles in regulating DNA accessibility and gene expression. The three …
Cross-modality matching and prediction of perturbation responses with labeled Gromov-Wasserstein optimal transport
It is now possible to conduct large scale perturbation screens with complex readout
modalities, such as different molecular profiles or high content cell images. While these …
modalities, such as different molecular profiles or high content cell images. While these …
[HTML][HTML] Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes
Genetic studies have associated thousands of enhancers with breast cancer. However, the
vast majority have not been functionally characterized. Thus, it remains unclear how variant …
vast majority have not been functionally characterized. Thus, it remains unclear how variant …
Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors
Understanding a cell's expression response to genetic perturbations helps to address
important challenges in biology and medicine. This includes the inference of gene circuits …
important challenges in biology and medicine. This includes the inference of gene circuits …
Active learning for efficient discovery of optimal gene combinations in the combinatorial perturbation space
J Qin, HH Wessels, C Fernandez-Granda… - arXiv preprint arXiv …, 2024 - arxiv.org
The advancement of novel combinatorial CRISPR screening technologies enables the
identification of synergistic gene combinations on a large scale. This is crucial for …
identification of synergistic gene combinations on a large scale. This is crucial for …
A supervised contrastive framework for learning disentangled representations of cell perturbation data
CRISPR technology, combined with single-cell RNA-Seq, has opened the way to large scale
pooled perturbation screens, allowing more systematic interrogations of gene functions in …
pooled perturbation screens, allowing more systematic interrogations of gene functions in …
Guide assignment in single-cell CRISPR screens using crispat
JM Braunger, B Velten - bioRxiv, 2024 - biorxiv.org
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 …
to probe the effect of genetic interventions at scale. A crucial step in the analysis of the …