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 …
Cell Painting: a decade of discovery and innovation in cellular imaging
Modern quantitative image analysis techniques have enabled high-throughput, high-content
imaging experiments. Image-based profiling leverages the rich information in images to …
imaging experiments. Image-based profiling leverages the rich information in images to …
Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView
Optical pooled screening (OPS) is a scalable method for linking image-based phenotypes
with cellular perturbations. However, it has thus far been restricted to relatively low-plex …
with cellular perturbations. However, it has thus far been restricted to relatively low-plex …
Building, benchmarking, and exploring perturbative maps of transcriptional and morphological data
The continued scaling of genetic perturbation technologies combined with high-dimensional
assays such as cellular microscopy and RNA-sequencing has enabled genome-scale …
assays such as cellular microscopy and RNA-sequencing has enabled genome-scale …
A pooled cell painting CRISPR screening platform enables de novo inference of gene function by self-supervised deep learning
Pooled CRISPR screening has emerged as a powerful method of mapping gene functions
thanks to its scalability, affordability, and robustness against well or plate-specific …
thanks to its scalability, affordability, and robustness against well or plate-specific …
Gene-level representation learning via interventional style transfer in optical pooled screening
Optical pooled screening (OPS) combines automated microscopy and genetic perturbations
to systematically study gene function in a scalable and cost-effective way. Leveraging the …
to systematically study gene function in a scalable and cost-effective way. Leveraging the …
Biological cartography: Building and benchmarking representations of life
The continued scaling of genetic perturbation technologies combined with high-dimensional
assays (microscopy and RNA-sequencing) has enabled genome-scale reverse-genetics …
assays (microscopy and RNA-sequencing) has enabled genome-scale reverse-genetics …
Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens
Single-nucleotide variants (SNVs) in key T cell genes can drive clinical pathologies and
could be repurposed to improve cellular cancer immunotherapies. Here, we perform …
could be repurposed to improve cellular cancer immunotherapies. Here, we perform …
NIS-Seq enables cell-type-agnostic optical perturbation screening
CI Fandrey, M Jentzsch, P Konopka, A Hoch… - Nature …, 2024 - nature.com
Optical pooled screening offers a broader-scale alternative to enrichment-based
perturbation screening, using fluorescence microscopy to correlate phenotypes and …
perturbation screening, using fluorescence microscopy to correlate phenotypes and …
Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView
Optical pooled screening (OPS) is a highly scalable method for linking image-based
phenotypes with cellular perturbations. However, it has thus far been restricted to relatively …
phenotypes with cellular perturbations. However, it has thus far been restricted to relatively …