Phenotypic drug discovery: recent successes, lessons learned and new directions

F Vincent, A Nueda, J Lee, M Schenone… - Nature Reviews Drug …, 2022 - nature.com
Many drugs, or their antecedents, were discovered through observation of their effects on
normal or disease physiology. For the past generation, this phenotypic drug discovery …

Image-based profiling for drug discovery: due for a machine-learning upgrade?

SN Chandrasekaran, H Ceulemans, JD Boyd… - Nature Reviews Drug …, 2021 - nature.com
Image-based profiling is a maturing strategy by which the rich information present in
biological images is reduced to a multidimensional profile, a collection of extracted image …

Optimizing the Cell Painting assay for image-based profiling

BA Cimini, SN Chandrasekaran, M Kost-Alimova… - 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 used …

[HTML][HTML] Data-analysis strategies for image-based cell profiling

JC Caicedo, S Cooper, F Heigwer, S Warchal, P Qiu… - Nature …, 2017 - nature.com
Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic
differences among a variety of cell populations. It paves the way to studying biological …

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

MA Bray, S Singh, H Han, CT Davis, B Borgeson… - Nature protocols, 2016 - nature.com
In morphological profiling, quantitative data are extracted from microscopy images of cells to
identify biologically relevant similarities and differences among samples based on these …

Evaluation of deep learning strategies for nucleus segmentation in fluorescence images

JC Caicedo, J Roth, A Goodman, T Becker… - Cytometry Part …, 2019 - Wiley Online Library
Identifying nuclei is often a critical first step in analyzing microscopy images of cells and
classical image processing algorithms are most commonly used for this task. Recent …

Learning representations for image-based profiling of perturbations

N Moshkov, M Bornholdt, S Benoit, M Smith… - Nature …, 2024 - nature.com
Measuring the phenotypic effect of treatments on cells through imaging assays is an efficient
and powerful way of studying cell biology, and requires computational methods for …

Evaluating batch correction methods for image-based cell profiling

J Arevalo, E Su, JD Ewald, R van Dijk… - Nature …, 2024 - nature.com
High-throughput image-based profiling platforms are powerful technologies capable of
collecting data from billions of cells exposed to thousands of perturbations in a time-and cost …

Optical pooled screens in human cells

D Feldman, A Singh, JL Schmid-Burgk, RJ Carlson… - Cell, 2019 - cell.com
Genetic screens are critical for the systematic identification of genes underlying cellular
phenotypes. Pooling gene perturbations greatly improves scalability but is not compatible …

[HTML][HTML] Chemical probes and drug leads from advances in synthetic planning and methodology

CJ Gerry, SL Schreiber - Nature Reviews Drug Discovery, 2018 - nature.com
Screening of small-molecule libraries is a productive method for identifying both chemical
probes of disease-related targets and potential starting points for drug discovery. In this …