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 …

CellProfiler 3.0: Next-generation image processing for biology

C McQuin, A Goodman, V Chernyshev… - PLoS …, 2018 - journals.plos.org
CellProfiler has enabled the scientific research community to create flexible, modular image
analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new …

Opportunities and obstacles for deep learning in biology and medicine

T Ching, DS Himmelstein… - Journal of the …, 2018 - royalsocietypublishing.org
Deep learning describes a class of machine learning algorithms that are capable of
combining raw inputs into layers of intermediate features. These algorithms have recently …

[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 …

High-throughput methods in the discovery and study of biomaterials and materiobiology

L Yang, S Pijuan-Galito, HS Rho, AS Vasilevich… - Chemical …, 2021 - ACS Publications
The complex interaction of cells with biomaterials (ie, materiobiology) plays an increasingly
pivotal role in the development of novel implants, biomedical devices, and tissue …

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 …

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 …

[HTML][HTML] Repurposing high-throughput image assays enables biological activity prediction for drug discovery

J Simm, G Klambauer, A Arany, M Steijaert… - Cell chemical …, 2018 - cell.com
In both academia and the pharmaceutical industry, large-scale assays for drug discovery are
expensive and often impractical, particularly for the increasingly important physiologically …

Image-based cell phenotyping with deep learning

A Pratapa, M Doron, JC Caicedo - Current opinion in chemical biology, 2021 - Elsevier
A cell's phenotype is the culmination of several cellular processes through a complex
network of molecular interactions that ultimately result in a unique morphological signature …