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

Rosmarinic Acid as a Candidate in a Phenotypic Profiling Cardio-/Cytotoxicity Cell Model Induced by Doxorubicin

(2020) Qiao Zhang et al.   MOLECULES

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

Fluopack screening platform for unbiased cellular phenotype profiling

(2020) Zhao B. Kang et al.   Scientific Reports

Zebrafish Avatars towards Personalized Medicine—A Comparative Review between Avatar Models

(2020) Bruna Costa et al.   Cells

Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes

(2020) Björn Eismann et al.   JOURNAL OF CELL SCIENCE

Structure and Function of the Bacterial Protein Toxin Phenomycin

(2020) Bente K. Hansen et al.   STRUCTURE

Multiparametric Assays for Accelerating Early Drug Discovery

(2020) Alexander Herholt et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

High-Content Phenotypic Profiling in Esophageal Adenocarcinoma Identifies Selectively Active Pharmacological Classes of Drugs for Repurposing and Chemical Starting Points for Novel Drug Discovery

(2020) Rebecca E. Hughes et al.   SLAS Discovery

Tales of 1,008 small molecules: phenomic profiling through live-cell imaging in a panel of reporter cell lines

(2020) Michael J. Cox et al.   Scientific Reports

Macrophage Cytological Profiling and Anti-Inflammatory Drug Discovery

(2019) Tannia A. Lau et al.   ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES

An assessment of the translational relevance of Drosophila in drug discovery

(2019) Katerina Papanikolopoulou et al.   Expert Opinion on Drug Discovery

Discovering metabolic disease gene interactions by correlated effects on cellular morphology

(2019) Yang Jiao et al.   Molecular Metabolism

The next generation blueprint of computational toxicology at the U.S. Environmental Protection Agency

(2019) Russell S Thomas et al.   TOXICOLOGICAL SCIENCES

Treating Rett syndrome: from mouse models to human therapies

(2019) Neeti Vashi et al.   MAMMALIAN GENOME

Accurate Prediction of Biological Assays with High-Throughput Microscopy Images and Convolutional Networks

(2019) Markus Hofmarcher et al.   Journal of Chemical Information and Modeling

Phenotypic Landscape of Schizophrenia-Associated Genes Defines Candidates and Their Shared Functions

(2019) Summer B. Thyme et al.   CELL

Leveraging machine vision in cell-based diagnostics to do more with less

(2019) Minh Doan et al.   NATURE MATERIALS

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

Morphological Deconvolution of Beta-Lactam Polyspecificity in E. coli

(2019) William J. Godinez et al.   ACS Chemical Biology

Design, Synthesis and Phenotypic Profiling of Pyrano-Furo-Pyridone Pseudo Natural Products

(2019) Herbert Waldmann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

From observing to predicting single-cell structure and function with high-throughput/high-content microscopy

(2019) Anatole Chessel et al.   Essays in Biochemistry

Three pitfalls to avoid in machine learning

(2019) Patrick Riley   NATURE

Daphne Koller

(2019) Asher Mullard   NATURE REVIEWS DRUG DISCOVERY

Capturing single-cell heterogeneity via data fusion improves image-based profiling

(2019) Mohammad H. Rohban et al.   Nature Communications

Multidimensional profiling of drug‐treated cells by Imaging Mass Cytometry

(2019) Alexandre Bouzekri et al.   FEBS Open Bio

A Scaffold Diversity Synthesis of Biologically Intriguing Cyclic Sulfonamides

(2019) Kamal Kumar et al.   CHEMISTRY-A EUROPEAN JOURNAL

GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation

(2019) T. Wollmann et al.   MEDICAL IMAGE ANALYSIS

Machine learning brings cell imaging promises into focus

(2019) Asher Mullard   NATURE REVIEWS DRUG DISCOVERY

Utility of In Vitro Bioactivity as a Lower Bound Estimate of In Vivo Adverse Effect Levels and in Risk-Based Prioritization

(2019) Katie Paul Friedman et al.   TOXICOLOGICAL SCIENCES

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting

(2019) Alex X. Lu et al.   PLoS Computational Biology

Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen

(2019) Joseph C Boyd et al.   BIOINFORMATICS

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl

(2019) Juan C. Caicedo et al.   NATURE METHODS

High-content image-based single cell phenotypic analysis for the testicular toxicity prediction induced by bisphenol A and its analogs bisphenol S, bisphenol AF, and tetrabromobisphenol A in a three-dimensional testicular cell co-culture model

(2019) Lei Yin et al.   TOXICOLOGICAL SCIENCES

Zebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation

(2019) Matthew N. McCarroll et al.   Nature Communications

Mapping the perturbome network of cellular perturbations

(2019) Michael Caldera et al.   Nature Communications

Applications of Deep-Learning in Exploiting Large-Scale and Heterogeneous Compound Data in Industrial Pharmaceutical Research

(2019) Laurianne David et al.   Frontiers in Pharmacology

Mass Cytometry Imaging for the Study of Human Diseases—Applications and Data Analysis Strategies

(2019) Heeva Baharlou et al.   Frontiers in Immunology

High content phenotypic screening identifies serotonin receptor modulators with selective activity upon breast cancer cell cycle and cytokine signaling pathways

(2019) Scott J. Warchal et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Bioactivity screening of environmental chemicals using imaging-based high-throughput phenotypic profiling

(2019) Johanna Nyffeler et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Building predictive in vitro pulmonary toxicity assays using high-throughput imaging and artificial intelligence

(2018) Jia-Ying Joey Lee et al.   ARCHIVES OF TOXICOLOGY

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images

(2018) Eric M. Christiansen et al.   CELL

Filling the drug discovery gap: is high-content screening the missing link?

(2018) Thierry Dorval et al.   CURRENT OPINION IN PHARMACOLOGY

The rise of deep learning in drug discovery

(2018) Hongming Chen et al.   DRUG DISCOVERY TODAY

Systematic exploration of cell morphological phenotypes associated with a transcriptomic query

(2018) Isar Nassiri et al.   NUCLEIC ACIDS RESEARCH

Predicting cancer outcomes from histology and genomics using convolutional networks

(2018) Pooya Mobadersany et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

(2018) Jia-Ren Lin et al.   eLife

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

(2018) Lev Litichevskiy et al.   Cell Systems

Rapid Inhibition Profiling identifies a keystone target in the nucleotide biosynthesis pathway

(2018) Christine E. Peters et al.   ACS Chemical Biology

Target deconvolution from phenotype-based drug discovery by using chemical proteomics approaches

(2018) Kazuishi Kubota et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Polypharmacology by Design: A Medicinal Chemist’s Perspective on Multitargeting Compounds

(2018) Ewgenij Proschak et al.   JOURNAL OF MEDICINAL CHEMISTRY

Synergistic Effects of Stereochemistry and Appendages on the Performance Diversity of a Collection of Synthetic Compounds

(2018) Bruno Melillo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Patient-Derived Cellular Model for Huntington's Disease Reveals Phenotypes at Clinically Relevant CAG Lengths

(2018) Claudia Lin-Kar Hung et al.   MOLECULAR BIOLOGY OF THE CELL

Genetic and transcriptional evolution alters cancer cell line drug response

(2018) Uri Ben-David et al.   NATURE

Clinically applicable deep learning for diagnosis and referral in retinal disease

(2018) Jeffrey De Fauw et al.   NATURE MEDICINE

Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning

(2018) Nicolas Coudray et al.   NATURE MEDICINE

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy

(2018) Chawin Ounkomol et al.   NATURE METHODS

Avoiding common pitfalls in machine learning omic data science

(2018) Andrew E. Teschendorff   NATURE MATERIALS

A call for public archives for biological image data

(2018) Jan Ellenberg et al.   NATURE METHODS

DRUG-seq for miniaturized high-throughput transcriptome profiling in drug discovery

(2018) Chaoyang Ye et al.   Nature Communications

A phenotypic Caenorhabditis elegans screen identifies a selective suppressor of antipsychotic-induced hyperphagia

(2018) Anabel Perez-Gomez et al.   Nature Communications

High-throughput screening for selective appetite modulators: A multibehavioral and translational drug discovery strategy

(2018) Josua Jordi et al.   Science Advances

Multiplex Staining by Sequential Immunostaining and Antibody Removal on Routine Tissue Sections

(2017) Maddalena Maria Bolognesi et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Bioactive Potential of Marine Macroalgae from the Central Red Sea (Saudi Arabia) Assessed by High-Throughput Imaging-Based Phenotypic Profiling

(2017) Stephan Kremb et al.   Marine Drugs

Data-analysis strategies for image-based cell profiling

(2017) Juan C Caicedo et al.   NATURE METHODS

High-Throughput Imaging for the Discovery of Cellular Mechanisms of Disease

(2017) Gianluca Pegoraro et al.   TRENDS IN GENETICS

Reconstructing cell cycle and disease progression using deep learning

(2017) Philipp Eulenberg et al.   Nature Communications

Measuring drug absorption improves interpretation of behavioral responses in a larval zebrafish locomotor assay for predicting seizure liability

(2017) Steven Cassar et al.   JOURNAL OF PHARMACOLOGICAL AND TOXICOLOGICAL METHODS

Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map

(2017) Ian Smith et al.   PLOS BIOLOGY

Systematic morphological profiling of human gene and allele function via Cell Painting

(2017) Mohammad Hossein Rohban et al.   eLife

A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay

(2017) Mark-Anthony Bray et al.   GigaScience

Image-based ex-vivo drug screening for patients with aggressive haematological malignancies: interim results from a single-arm, open-label, pilot study

(2017) Berend Snijder et al.   Lancet Haematology

A brief introduction to weakly supervised learning

(2017) Zhi-Hua Zhou   National Science Review

Computer vision for high content screening

(2016) Oren Z. Kraus et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Applications in image-based profiling of perturbations

(2016) Juan C Caicedo et al.   CURRENT OPINION IN BIOTECHNOLOGY

Next-generation phenotypic screening

(2016) Scott J Warchal et al.   Future Medicinal Chemistry

Machine learning and computer vision approaches for phenotypic profiling

(2016) Ben T. Grys et al.   JOURNAL OF CELL BIOLOGY

Profiling Prediction of Kinase Inhibitors: Toward the Virtual Assay

(2016) Benjamin Merget et al.   JOURNAL OF MEDICINAL CHEMISTRY

A Grand Challenge. 2. Phenotypic Profiling of a Natural Product Library on Parkinson’s Patient-Derived Cells

(2016) Marie-Laure Vial et al.   JOURNAL OF NATURAL PRODUCTS

Real-Time Biological Annotation of Synthetic Compounds

(2016) Christopher J. Gerry et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Zebrafish behavioral profiling identifies multitarget antipsychotic-like compounds

(2016) Giancarlo Bruni et al.   Nature Chemical Biology

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

(2016) Mark-Anthony Bray et al.   Nature Protocols

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

Divergent Synthesis and Real-Time Biological Annotation of Optically Active Tetrahydrocyclopenta[c]pyranone Derivatives

(2016) Shawn D. Nelson et al.   ORGANIC LETTERS

Failure of Investigational Drugs in Late-Stage Clinical Development and Publication of Trial Results

(2016) Thomas J. Hwang et al.   JAMA Internal Medicine

Bacterial Cytological Profiling (BCP) as a Rapid and Accurate Antimicrobial Susceptibility Testing Method for Staphylococcus aureus

(2016) D.T. Quach et al.   EBioMedicine

High-throughput imaging-based nephrotoxicity prediction for xenobiotics with diverse chemical structures

(2015) Ran Su et al.   ARCHIVES OF TOXICOLOGY

Linking Phenotypes and Modes of Action Through High-Content Screen Fingerprints

(2015) Felix Reisen et al.   ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

(2015) Yolanda T. Chong et al.   CELL

Microscopy-Based High-Content Screening

(2015) Michael Boutros et al.   CELL

Phenotype-Guided Natural Products Discovery Using Cytological Profiling

(2015) Jessica L. Ochoa et al.   JOURNAL OF NATURAL PRODUCTS

Connecting Phenotype and Chemotype: High-Content Discovery Strategies for Natural Products Research

(2015) Kenji L. Kurita et al.   JOURNAL OF NATURAL PRODUCTS

Apolar and polar transitions drive the conversion between amoeboid and mesenchymal shapes in melanoma cells

(2015) Sam Cooper et al.   MOLECULAR BIOLOGY OF THE CELL

A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells

(2015) M. Breinig et al.   Molecular Systems Biology

Improving drug discovery with high-content phenotypic screens by systematic selection of reporter cell lines

(2015) Jungseog Kang et al.   NATURE BIOTECHNOLOGY

Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries

(2015) Kenji L. Kurita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant-derived antifungal agent poacic acid targets β-1,3-glucan

(2015) Jeff S. Piotrowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Developing predictive assays: The phenotypic screening “rule of 3”

(2015) Fabien Vincent et al.   Science Translational Medicine

Quantifying small molecule phenotypic effects using mitochondrial morpho-functional fingerprinting and machine learning

(2015) Lionel Blanchet et al.   Scientific Reports

A map of directional genetic interactions in a metazoan cell

(2015) Bernd Fischer et al.   eLife

Computational polypharmacology comes of age

(2015) Giulio Rastelli et al.   Frontiers in Pharmacology

Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects

(2015) Shantanu Singh et al.   PLoS One

Deducing the mechanism of action of compounds identified in phenotypic screens by integrating their multiparametric profiles with a reference genetic screen

(2014) Varadharajan Sundaramurthy et al.   Nature Protocols

The discovery of first-in-class drugs: origins and evolution

(2014) Jörg Eder et al.   NATURE REVIEWS DRUG DISCOVERY

Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

(2014) M. J. Wawer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integration of Chemical and RNAi Multiparametric Profiles Identifies Triggers of Intracellular Mycobacterial Killing

(2013) Varadharajan Sundaramurthy et al.   Cell Host & Microbe

“Function-First” Lead Discovery: Mode of Action Profiling of Natural Product Libraries Using Image-Based Screening

(2013) Christopher J. Schulze et al.   CHEMISTRY & BIOLOGY

Large-scale cytological profiling for functional analysis of bioactive compounds

(2013) Marcos H. Woehrmann et al.   Molecular BioSystems

A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes

(2013) Zheng Yin et al.   NATURE CELL BIOLOGY

Target identification and mechanism of action in chemical biology and drug discovery

(2013) Monica Schenone et al.   Nature Chemical Biology

A functional CFTR assay using primary cystic fibrosis intestinal organoids

(2013) Johanna F Dekkers et al.   NATURE MEDICINE

Vanillin Inhibits Translation and Induces Messenger Ribonucleoprotein (mRNP) Granule Formation in Saccharomyces cerevisiae: Application and Validation of High-Content, Image-Based Profiling

(2013) Aya Iwaki et al.   PLoS One

Multiplex Cytological Profiling Assay to Measure Diverse Cellular States

(2013) Sigrun M. Gustafsdottir et al.   PLoS One

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue

(2013) M. J. Gerdes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Morphobase, an Encyclopedic Cell Morphology Database, and Its Use for Drug Target Identification

(2012) Yushi Futamura et al.   CHEMISTRY & BIOLOGY

Chemical genetic discovery of targets and anti-targets for cancer polypharmacology

(2012) Arvin C. Dar et al.   NATURE

Reducing safety-related drug attrition: the use of in vitro pharmacological profiling

(2012) Joanne Bowes et al.   NATURE REVIEWS DRUG DISCOVERY

A Stem Cell-Based Approach to Cartilage Repair

(2012) K. Johnson et al.   SCIENCE

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

How were new medicines discovered?

(2011) David C. Swinney et al.   NATURE REVIEWS DRUG DISCOVERY

An algorithm-based topographical biomaterials library to instruct cell fate

(2011) H. V. Unadkat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Abnormalities in Mitochondrial Structure in Cells from Patients with Bipolar Disorder

(2010) Anne M. Cataldo et al.   AMERICAN JOURNAL OF PATHOLOGY

High-Content Phenotypic Profiling of Drug Response Signatures across Distinct Cancer Cells

(2010) P. D. Caie et al.   MOLECULAR CANCER THERAPEUTICS

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

(2010) Beate Neumann et al.   NATURE

Mechanism matters

(2010)   NATURE MEDICINE

High-Content, Image-Based Screening for Drug Targets in Yeast

(2010) Shinsuke Ohnuki et al.   PLoS One

Zebrafish Behavioral Profiling Links Drugs to Biological Targets and Rest/Wake Regulation

(2010) J. Rihel et al.   SCIENCE

Simple: A Sequential Immunoperoxidase Labeling and Erasing Method

(2009) George Glass et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Characterizing heterogeneous cellular responses to perturbations

(2008) M. D. Slack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA