Optimizing the Cell Painting assay for image-based profiling

…, CH Lardeau, E Mouchet, S Singh, H Shafqat Abbasi… - Nature protocols, 2023 - nature.com
In image-based profiling, software extracts thousands of morphological features of cells
from multi-channel fluorescence microscopy images, yielding single-cell profiles that can be …

Predicting cell health phenotypes using image-based morphology profiling

…, F Piccioni, T Becker, H Shafqat-Abbasi… - Molecular biology of …, 2021 - Am Soc Cell Biol
Genetic and chemical perturbations impact diverse cellular phenotypes, including multiple
indicators of cell health. These readouts reveal toxicity and antitumorigenic effects relevant to …

[HTML][HTML] Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations

…, D Kuhn, D Hernandez, J Berstler, H Shafqat-Abbasi… - Nature …, 2024 - nature.com
The identification of genetic and chemical perturbations with similar impacts on cell morphology
can elucidate compounds’ mechanisms of action or novel regulators of genetic pathways…

An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes

H Shafqat-Abbasi, JM Kowalewski, A Kiss, X Gong… - Elife, 2016 - elifesciences.org
Shafqat-Abbasi et al. developed a method to analyse how … adopt two distinct migration modes,
which Shafqat-Abbasi et al. termed ’… Shafqat-Abbasi et al.’s method provides an analytical …

[PDF][PDF] FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity

N Wieder, JC Fried, C Kim, EH Sidhom, MR Brown… - Cell metabolism, 2023 - cell.com
Cellular exposure to free fatty acids (FFAs) is implicated in the pathogenesis of obesity-associated
diseases. However, there are no scalable approaches to comprehensively assess the …

[HTML][HTML] Disentangling membrane dynamics and cell migration; differential influences of F-actin and cell-matrix adhesions

JM Kowalewski, H Shafqat-Abbasi… - PloS one, 2015 - journals.plos.org
Cell migration is heavily interconnected with plasma membrane protrusion and retraction (collectively
termed “membrane dynamics”). This makes it difficult to distinguish regulatory …

Assessing the performance of the Cell Painting assay across different imaging systems

N Jamali, C Tromans-Coia, HS Abbasi, KA Giuliano… - Biorxiv, 2023 - biorxiv.org
Quantitative microscopy is a powerful method for performing phenotypic screens, from which
image-based profiling can extract a wealth of information, termed profiles. These profiles …

[HTML][HTML] Plasticity in the macromolecular-scale causal networks of cell migration

JG Lock, MJ Mamaghani, H Shafqat-Abbasi, X Gong… - PLoS …, 2014 - journals.plos.org
Heterogeneous and dynamic single cell migration behaviours arise from a complex multi-scale
signalling network comprising both molecular components and macromolecular modules…

Assessing the performance of the Cell Painting assay across different imaging systems

C Tromans‐Coia, N Jamali, HS Abbasi… - Cytometry Part …, 2023 - Wiley Online Library
Quantitative microscopy is a powerful method for performing phenotypic screens from which
image‐based profiling can extract a wealth of information, termed profiles. These profiles …

[HTML][HTML] Pervasive mislocalization of pathogenic coding variants underlying human disorders

…, C Reno, WW Qian, X Xiong, H Shafqat-Abbasi… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Widespread sequencing has yielded thousands of missense variants predicted or confirmed
as disease-causing. This creates a new bottleneck: determining the functional impact of …