2026
-
Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes
Cell Systems (2026).
-
A scalable approach to resolving variants of uncertain significance
[preprint] bioRxiv (2026).
-
Counting cells can accurately predict small-molecule bioactivity benchmarks
Nature Communications (2026).
2025
-
Identifying and targeting abnormal mitochondrial localization associated with psychosis
[preprint] bioRxiv (2025).
-
nELISA: a high-throughput, high-plex platform enables quantitative profiling of the inflammatory secretome
Nature Methods (2025).
-
cubic: CUDA-accelerated 3D BioImage Computing
Proceedings of the IEEE/CVF International Conference on Computer Vision Workshops (ICCVW) – BioImage Computing Workshop (2025).
-
The OASIS Consortium: Integrating Multi-Omics Technologies to Transform Chemical Safety Assessment
Toxicological Sciences (2025).
-
Alternate dyes for image-based profiling assays
SLAS Discovery (2025).
-
Morphological map of under- and overexpression of genes in human cells
Nature Methods (2025).
-
Combining phenomics with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion
Nature Communications (2025).
-
cp_measure: API‑first feature extraction for image‑based profiling workflows
Proceedings of The Championing Open-source DEvelopment in ML Workshop @ ICML25 (2025).
-
Live-cell painting: Image-based profiling in live cells using acridine orange
Molecular Biology of the Cell (2025).
-
A versatile information retrieval framework for evaluating profile strength and similarity
Nature Communications (2025).
-
Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World
Chemical Research in Toxicology (2025).
-
MorphoDiff: Cellular Morphology Painting with Diffusion Models.Proceedings of The
Thirteenth International Conference on Learning Representations (2025).
-
Learning Molecular Representation in a Cell. Proceedings of The
Thirteenth International Conference on Learning Representations (2025).
-
Reproducible image-based profiling with Pycytominer
Nature Methods (2025).
-
A genome-wide atlas of human cell morphology
Nature Methods (2025).
2024
-
MOTIVE: A Drug-Target Interaction Graph For Inductive Link Prediction
Proceedings of the Thirty-Eighth Annual Conference on Neural Information Processing Systems (2024).
-
Cell Painting: a decade of discovery and innovation in cellular imaging
Nature Methods (2024).
-
Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning
PLoS Computational Biology (2024).
-
Pervasive mislocalization of pathogenic coding variants underlying human disorders
Cell (2024).
-
Improved Detection of Drug-Induced Liver Injury by Integrating Predicted In Vivo and In Vitro Data
Chemical Research in Toxicology (2024).
-
Deciphering the impact of genomic variation on function
Nature (2024).
-
Cell Painting Gallery: an open resource for image-based profiling
Nature Methods (2024).
-
A postdoctoral training program in bioimage analysis
Molecular Biology of the Cell (2024).
-
Evaluating batch correction methods for image-based cell profiling
Nature Communications (2024).
-
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
Nature Methods (2024).
2023
-
FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity
Cell Metab (2023).
-
High-content microscopy reveals a morphological signature of bortezomib resistance
Elife (2023).
-
Assessing the performance of the Cell Painting assay across different imaging systems
Cytometry A (2023).
-
Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images
Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence (2023).
-
Deductive automated pollen classification in environmental samples via exploratory deep learning and imaging flow cytometry
New Phytol (2023).
-
Integrating inflammatory biomarker analysis and artificial intelligence-enabled image-based profiling to identify drug targets for intestinal fibrosis
Cell Chemical Biology (2023).
-
Smart microscopes of the future
Nature Methods (2023).
-
Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler
Cell Genomics (2023).
-
Optimizing the Cell Painting assay for image-based profiling
Nature Protocols (2023).
-
Predicting compound activity from phenotypic profiles and chemical structures
Nature Communications (2023).
-
A non-coding variant linked to metabolic obesity with normal weight affects actin remodeling in subcutaneous adipocytes
Nature Metabolism (2023).
-
High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly
Elife (2023).
-
Predicting reprogramming-related gene expression from cell morphology in human induced pluripotent stem cells
Molecular Biology of the Cell (2023).
-
Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization
Current Protocols (2023).
-
Reference compounds for characterizing cellular injury in high-content cellular morphology assays
Nature Communications (2023).
2022
-
Morphology and gene expression profiling provide complementary information for mapping cell state
Cell Systems (2022).
-
High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations
Nature Methods (2022).
-
Imaging flow cytometry: a primer
Nature Reviews Methods Primers (2022).
-
PyImageJ: A library for integrating ImageJ and Python
Nature Methods (2022).
-
Why I shrank my lab by half
eLife (2022).
-
In vitro neutrophil migration is associated with inhaled corticosteroid treatment and serum cytokines in pediatric asthma
Front. Pharmacol (2022).
-
Virtual screening for small-molecule pathway regulators by image-profile matching
Cell Systems (2022).
-
Cell Painting predicts impact of lung cancer variants
Molecular Biology of the Cell (2022).
-
A New Image for Cell Sorting
The New England Journal of Medicine (2022).
-
Ask the Experts: The impact of artificial intelligence in drug discovery
BioTechniques (2022).
-
Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic
PLoS Computational Biology (2022).
-
The new era of quantitative cell imaging—challenges and opportunities
Molecular Cell (2022).
-
Image-based profiling: a powerful and challenging new data type
Pacific Symposium on Biocomputing (2022).
-
2021 BioImage Analysis Survey: Community experiences and needs for the future
Biological Imaging (2022).
2021
-
A Multiparametric Activity Profiling Platform for Neuron Disease Phenotyping and Drug Screening
Molecular Biology Cell (2021).
-
CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis
Bioinformatics (2021).
-
CellProfiler 4: improvements in speed, utility and usability
BMC Bioinformatics (2021).
-
A field guide to cultivating computational biology
PLoS Biology (2021).
-
Genes in human obesity loci are causal obesity genes in C. elegans
PLoS Genetics (2021).
-
Inter-laboratory automation of the in vitro micronucleus assay using imaging flow cytometry and deep learning
Archives of Toxicology (2021).
-
Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging
Communications Biology (2021).
-
Deepometry, a framework for applying supervised and weakly supervised deep learning to imaging cytometry
Nature Protocols (2021).
-
Which image-based phenotypes are most promising for using AI to understand cellular functions and why?
Cell Systems (2021).
-
ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis
Current Protocols (2021).
-
Developing open-source software for bioimage analysis: opportunities and challenges[version 1; peer review: 2 approved]
F1000Research (2021).
-
Open-source deep-learning software for bioimage segmentation
Molecular Biology of the Cell (2021).
-
Predicting cell health phenotypes using image-based morphology profiling
Molecular Biology of the Cell (2021).
2020
-
Molecular Diversity of Glutamatergic and GABAergic Synapses from Multiplexed Fluorescence Imaging
eNeuro (2020).
-
Image-based profiling for drug discovery: due for a machine-learning upgrade?
Nature Reviews Drug Discovery (2020).
-
A well-engineered path into cell biology and academia
Molecular Biology of the Cell (2020).
-
BIN1 protein isoforms are differentially expressed in astrocytes, neurons, and microglia: neuronal and astrocyte BIN1 are implicated in tau pathology
BMC Molecular Neurodegeneration (2020).
-
Keras R-CNN: library for cell detection in biological images using deep neural networks
BMC Bioinformatics (2020).
-
On the correlation between material-induced cell shape and phenotypical response of human mesenchymal stem cells
Scientific Reports (2020).
-
High‐content, label‐free analysis of proplatelet production from megakaryocytes
Journal of Thrombosis and Haemostasis (2020).
-
Objective assessment of stored blood quality by deep learning
PNAS (2020).
-
Bridging Domain and Data
Patterns (2020).
-
Harnessing the power of microscopy images to accelerate drug discovery: what are the possibilities?
Expert Opinion on Drug Discovery (2020).
-
nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer
Cell Systems (2020).
-
Label‐free leukemia monitoring by computer vision
Cytometry (2020).
-
Artificial intelligence and cancer
Nature Cancer (2020).
2019
-
Identification and local delivery of vasodilators for the reduction of ureteral contractions
Nature Biomedical Engineering (2019).
-
A High-Content Screen Identifies TPP1 and Aurora B as Regulators of Axonal Mitochondrial Transport
Cell Reports (2019).
-
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl
Nature Methods (2019).
-
Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning
Proceedings of Machine Learning Research (2019).
-
Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images
Cytometry (2019).
-
Scientific Community Image Forum: A discussion forum for scientific image software
PLoS Biology (2019).
-
Label‐Free Identification of White Blood Cells Using Machine Learning
Cytometry (2019).
-
DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images
PLoS Computational Biology (2019).
-
Capturing single-cell heterogeneity via data fusion improves image-based profiling
Nature Communications (2019).
-
Leveraging machine vision in cell-based diagnostics to do more with less
Nature Materials (2019).
2018
-
CellProfiler 3.0: Next-generation image processing for biology
PLoS Biol (2018).
-
Designed Surface Topographies Control ICAM-1 Expression in Tonsil-Derived Human Stromal Cells
Front Bioeng Biotechnol (2018).
-
Weakly Supervised Learning of Single-Cell Feature Embeddings
IEEE Conference on Computer Vision and Pattern Recognition (CVPR) (2018).
-
Opportunities and obstacles for deep learning in biology and medicine
J R Soc Interface (2018).
-
Combining morphological and migration profiles of in vitro time-lapse data
2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) (2018).
-
Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery
Cell Chem Biol (2018).
-
Diagnostic Potential of Imaging Flow Cytometry
Trends Biotechnol (2018).
-
Quality Control for High-Throughput Imaging Experiments Using Machine Learning in CellProfiler
Methods Mol Biol (2018).
2017
-
CytoGAN: Generative Modeling of Cell Images
Workshop on Machine Learning in Computational Biology, Neural Information Processing Systems (NeurIPS) (2017).
-
Applying Faster R-CNN for Object Detection on Malaria Images
2017 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) (2017).
-
Reconstructing cell cycle and disease progression using deep learning
Nat Commun (2017).
-
Data-analysis strategies for image-based cell profiling
Nat Methods (2017).
-
Mining for osteogenic surface topographies: In silico design to in vivo osseo-integration
Biomaterials (2017).
-
Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence
PLoS Pathog (2017).
-
Systematic morphological profiling of human gene and allele function via Cell Painting
Elife (2017).
-
A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay
Gigascience (2017).
2016
-
The antidepressant drug paroxetine as a new lead candidate in schistosome drug discovery
MedChemComm (2016).
-
Automating Morphological Profiling with Generic Deep Convolutional Networks
Neural Information Processing Systems (NeurIPS) MLCB Workshop 2016 Conference (2016).
-
Imagining the future of bioimage analysis
Nature Biotechnology (2016).
-
An open-source solution for advanced imaging flow cytometry data analysis using machine learning
Methods (2016).
-
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
Nature Protocols (2016).
-
High-Throughput, Automated Image Processing for Large-Scale Fluorescence Microscopy Experiments
Microscopy and Microanalysis (2016).
-
QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni
Journal of Chemical Information and Modeling (2016).
-
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets
Bioinformatics (2016).
-
High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro
Journal of Biomolecular Screening (2016).
-
Discovery of new anti-schistosomal hits by integration of QSAR-based virtual screening and high content screening
Journal of Medicinal Chemistry (2016).
-
An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells
Experimental Eye Research (2016).
-
Applications in image-based profiling of perturbations
Current Opinion in Biotechnology (2016).
-
CP-CHARM: segmentation-free image classification made accessible
BMC Bioinformatics (2016).
-
Label-free cell cycle analysis for high-throughput imaging flow cytometry
Nature Communications (2016).
-
A Genome-wide RNAi screen for microtubule network formation and lysosome motility regulation in Drosophila S2 cells
Cell Reports (2016).
2015
-
Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification
Methods (2015).
-
CellProfiler Tracer: Exploring and Validating High-Throughput, Time-Lapse Microscopy Image Data
BMC Bioinformatics (2015).
-
Analysis of High-throughput Microscopy Videos: Catching Up with Cell Dynamics. Paper presented at
MICCAI 2015 (2015).
-
Morphological Profiles of RNAI-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects
PLoS One (2015).
-
Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images
Current Protocols in Molecular Biology (2015).
-
Pharmacological HIF2a inhibition improves VHL disease-associated phenotypes in zebrafish models
Journal of Clinical Investigation (2015).
-
Symmetry-Based Mitosis Detection in Time-Lapse Micoscopy. Paper presented at
ISBI 2015 (2015).
-
CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells
Chemistry and Biology (2015).
2014
-
Increased expression of the immune modulatory molecule PD-L1 (CD274) in anaplastic meningioma
Oncotarget (2014).
-
Pipeline for illumination correction of images for high-throughput microscopy
Journal of Microscopy (2014).
-
Nanoparticle vesicle encoding for imaging and tracking cell populations
Nature Methods (2014).
-
Automated image-based assay for evaluation of HIV neutralization and cell-to-cell fusion inhibition
BMC Infectious Diseases (2014).
-
ProtocolNavigator: emulation based software for the design, documentation and reproduction biological experiments
Bioinformatics (2014).
-
Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling
PNAS (2014).
-
High- and low-throughput scoring of fat mass and body fat distribution in
C. elegans (2014).
-
High Content Image Analysis Identifies Novel Regulators of Synaptogenesis in a High-Throughput RNAi Screen of Primary Neurons
PLoS ONE (2014).
-
Identification of host-targeted small molecules that restrict intracellular
mycobacterium tuberculosis (2014).
-
ZFHX4 is a master regulator of NuRD core member CHD4 and regulates the glioblastoma tumor initiating cell state
Cell Reports (2014).
-
Increasing the content of high-content screening: an overview
Journal of Biomolecular Screening (2014).
2013
-
Multiplex cytological profiling assay to measure diverse cellular states
PLoS ONE (2013).
-
Comparison of Methods for Image-Based Profiling of Cellular Morphological Responses to Small-Molecule Treatment
Journal of Biomolecular Screening (2013).
-
Niche-based screening identifies small-molecule inhibitors of leukemia stem cells
Nature Chemical Biology (2013).
-
A microscale human liver platform that supports the hepatic stages of
Plasmodium falciparum (2013).
-
Identification of small molecules for human hepatocyte expansion and iPS differentiation
Nature Chemical Biology (2013).
-
The bromodomain protein Brd4 insulates chromatin from DNA damage signalling
Nature (2013).
2012
-
Advanced Assay Development Guidelines for Image-Based High Content Screening and Analysis
Assay Guidance Manual (2012).
-
Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL
Cell (2012).
-
Biological imaging software tools
Nature Methods (2012).
-
A call for bioimaging software usability
Nature Methods (2012).
-
Annotated high-throughput microscopy image sets for validation
Nature Methods (2012).
-
An image analysis toolbox for high-throughput
C. elegans (2012).
-
An algorithm-based topographical biomaterials library to instruct cell fate
PNAS (2012).
-
A chemical screen probing the relationship between mitochondrial content and cell size
PLoS ONE (2012).
-
Workflow and metrics for image quality control in large-scale high-content screens
Journal of Biomolecular Screening (2012).
2011
-
Visualization of parameter space for image analysis
InfoVis 2011 (2011).
-
mTOR complex 1 regulates lipin 1 localization to control the SREBP pathway
Cell (2011).
-
Extracting biomedically important information from large, automated imaging experiments
ISBI 2011 (2011).
-
Improved structure, function, and compatibility for CellProfiler: modular high-throughput image analysis software
Bioinformatics (2011).
-
Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice
Journal of Clinical Investigation (2011).
-
Genome-scale RNAi on living-cell microarrays identifies novel regulators of
Drosophila melanogaster (2011).
2010
-
Morphology-guided graph search for untangling objects:
C elegans (2010).
-
Resolving clustered worms via probabilistic shape models
ISBI 2010 (2010).
-
Abnormalities in Mitochondrial Structure in Cells of Patients with Bipolar Disorder
American Journal of Pathology (2010).
-
Screening Cellular Feature Measurements for Image-based Assay Development
Journal of Biomolecular Screening (2010).
-
Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis
Nature Chemical Biology (2010).
-
Visualization of image data from cells to organisms
Nature Methods (2010).
2009
-
Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening
PLoS Computational Biology (2009).
-
An intermittent live cell imaging screen for siRNA enhancers and suppressors of a kinesin-5 inhibitor
PLoS ONE (2009).
-
High throughput screen for novel antimicrobials using a whole animal infection model
ACS Chemical Biology (2009).
-
Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution
Bioinformatics (2009).
-
Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning
PNAS (2009).
2008
-
CellProfiler Analyst: data exploration and analysis software for complex image-based screens
BMC Bioinformatics (2008).
-
A novel small molecule regulator of guanine nucleotide exchange activity of ARF and Golgi membrane trafficking
Journal of Biological Chemistry (2008).
-
High-throughput screens for fluorescent dye discovery
Trends in Biotechnology (2008).
-
Using CellProfiler for automatic identification and measurement of biological objects in images
Current Protocols in Molecular Biology (2008).
2007
-
Image-based chemical screening
Nature Chemical Biology (2007).
-
Extracting rich information from images
Cell-Based Assays for High-Throughput Screening, Methods in Molecular Biology (2007).
-
CellProfiler: free, versatile software for automated biological image analysis
Biotechniques (2007).
2006
-
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
Genome Biology (2006).
-
The Spemann Organizer gene, Goosecoid, promotes tumor metastasis
PNAS (2006).
-
Genetic architecture of Hsp90-dependent drug resistance
Eukaryotic Cell (2006).
-
In germ cells of mouse embryonic ovaries, the decision to enter meiosis precedes premeiotic DNA replication
Nature Genetics (2006).
-
Methods for high-content, high throughput image-based cell screening
Proceedings of the Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB) (2006).
-
Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins
Nature Methods (2006).
-
Long-range directional movement of an interphase chromosome site
Current Biology (2006).
-
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen
Cell (2006).
-
Microarrays of lentiviruses for gene function screens in immortalized and primary cells
Nature Methods (2006).
2005
-
Voronoi-based segmentation of cells on image manifolds
Proceedings of the Workshop on Computer Vision for Biomedical Image Applications (CVBIA) (2005).
-
Cell microarrays and RNA interference chip away at gene function
Nature Genetics (2005).
-
In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation
Molecular and Cellular Biology (2005).
-
Distinctive actions of membrane-targeted versus nuclear localized estrogen receptors in breast cancer cells
Molecular Endocrinology (2005).
-
Common effects of acidic activators on large-scale chromatin structure and transcription
Molecular and Cellular Biology (2005).
2004
-
RNAi living-cell microarrays for loss-of-function screens in
Drosophila melanogaster (2004).
-
Automated microscopy identifies estrogen receptor subdomains with large-scale chromatin structure unfolding activity
Cytometry A (2004).
-
Systematic genome-wide screens of gene function
Nature Reviews Genetics (2004).
2003
-
Chromosomes and Chromatin
Nature Encyclopedia of the Human Genome (2003).
-
Regulation of nuclear receptor transcriptional activity by a novel DEAD box RNA helicase (DP97)
Journal of Biological Chemistry (2003).
2002
-
Alteration of large-scale chromatin structure by estrogen receptor
Molecular and Cellular Biology (2002).
2001
-
BRCA1-induced large-scale chromatin unfolding and allele-specific effects of cancer-predisposing mutations
Journal of Cell Biology (2001).
-
Ligand-mediated assembly and real-time cellular dynamics of estrogen receptor alpha-coactivator complexes in living cells
Molecular and Cellular Biology (2001).