Image-based cell phenotyping with deep learning Publication: Web Article Pratapa A, Doron M, Caicedo J. Image-based cell phenotyping with deep learning. 2021.
Cell Painting predicts impact of lung cancer variants Publication: Web Article Caicedo JC, Arevalo J, Piccioni F, Bray M-A, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter A, et al. Cell Painting predicts impact of lung cancer variants. Molecular Biology of the Cell. 2022;(6).
Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images Publication: Journal Article Caicedo J, Roth J, Goodman A, Becker T, Karhohs K, Broisin M, Molnar C, McQuin C, Sing S, Theis F, et al. Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images. Cytometry Part A. 2019;95(9):952–965.
Out of Distribution Generalization via Interventional Style Transfer in Single-Cell Microscopy Publication: Conference Paper Pernice WM, Doron M, Quach A, Pratapa A, Kenjeyev S, De Veaux N, Hirano M, Caicedo JC. Out of Distribution Generalization via Interventional Style Transfer in Single-Cell Microscopy. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops. 2023.
Learning representations for image-based profiling of perturbations Publication: Web Article Moshkov N, Bornholdt M, Benoit S, Smith M, McQuin C, Goodman A, Senft R, Han Y, Babadi M, Horvath P, et al. Learning representations for image-based profiling of perturbations. bioRxiv. 2022.
Data-analysis strategies for image-based cell profiling Publication: Journal Article Caicedo J, Cooper S, Heigwer F, Warchal S, Qiu P, Molnar C, Vasilevich A, Barry J, Bansal HS, Kraus O, et al. Data-analysis strategies for image-based cell profiling. Nature Methods. 2017;14(9):849–863.
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl Publication: Journal Article JC C, A G, KW K, BA C, J A, M H, C H, T B, M D, C M, et al. Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl. Nature Methods. 2019;16(12):1247–1253.
Applications in image-based profiling of perturbations Publication: Journal Article Caicedo J, Singh S, Carpenter A. Applications in image-based profiling of perturbations. Current Opinion in Biotechnology. 2016;39:134–142.
Deciphering causal genomic templates of complex molecular phenotypes Publication: Web Article Bhate SS, Seigal A, Caicedo J. Deciphering causal genomic templates of complex molecular phenotypes. bioRxiv. 2022.
Unbiased single-cell morphology with self-supervised vision transformers Publication: Unpublished Doron M, Moutakanni T, Chen ZS, Moshkov N, Caron M, Touvron H, Bojanowski P, Pernice WM, Caicedo JC. Unbiased single-cell morphology with self-supervised vision transformers. 2023.