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Imaging Platform

Predicting reprogramming-related gene expression from cell morphology in human induced pluripotent stem cells.

Wakui T, Negishi M, Murakami Y, et al. Predicting reprogramming-related gene expression from cell morphology in human induced pluripotent stem cells. Molecular biology of the cell. 2023;34(5):ar45. doi:10.1091/mbc.E22-06-0215

Predicting compound activity from phenotypic profiles and chemical structures.

Moshkov N, Becker T, Yang K, et al. Predicting compound activity from phenotypic profiles and chemical structures. Nature communications. 2023;14(1):1967. doi:10.1038/s41467-023-37570-1

Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization.

Garcia-Fossa F, Cruz MC, Haghighi M, et al. Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization. Current protocols. 2023;3(3):e713. doi:10.1002/cpz1.713

A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes.

Glunk V, Laber S, Sinnott-Armstrong N, et al. A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes. Nature metabolism. 2023;5(5):861-879. doi:10.1038/s42255-023-00807-w

Distributed-Something: scripts to leverage AWS storage and computing for distributed workflows at scale.

Weisbart E, Cimini BA. Distributed-Something: scripts to leverage AWS storage and computing for distributed workflows at scale. Nature methods. 2023. doi:10.1038/s41592-023-01918-8

Optimizing the Cell Painting assay for image-based profiling.

Cimini BA, Chandrasekaran SN, Kost-Alimova M, et al. Optimizing the Cell Painting assay for image-based profiling. Nature protocols. 2023. doi:10.1038/s41596-023-00840-9

Moving beyond the desktop: prospects for practical bioimage analysis via the web.

Ouyang W, Eliceiri KW, Cimini BA. Moving beyond the desktop: prospects for practical bioimage analysis via the web. Frontiers in bioinformatics. 2023;3:1233748. doi:10.3389/fbinf.2023.1233748

Integrating inflammatory biomarker analysis and artificial intelligence-enabled image-based profiling to identify drug targets for intestinal fibrosis.

Yu S, Kalinin AA, Paraskevopoulou MD, et al. Integrating inflammatory biomarker analysis and artificial intelligence-enabled image-based profiling to identify drug targets for intestinal fibrosis. Cell chemical biology. 2023. doi:10.1016/j.chembiol.2023.06.014

Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler.

Laber S, Strobel S, Mercader JM, et al. Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler. Cell genomics. 2023;3(7):100346. doi:10.1016/j.xgen.2023.100346

OME-Zarr: a cloud-optimized bioimaging file format with international community support.

Moore J, Basurto-Lozada D, Besson S, et al. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochemistry and cell biology. 2023. doi:10.1007/s00418-023-02209-1