Publications

Matthew R King, Andrew Z Lin, Kiersten M Ruff, Mina Farag, Wei Ouyang, Michael D Vahey, Emma Lundberg, Rohit V Pappu (2022). Uncovering molecular grammars of intrinsically disordered regions that organize nucleolar fibrillar centers. bioRxiv.

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Jayasankar Mohanakrishnan Kaimal, Marianna Tampere, Trang H Le, Ulrika Axelsson, Hao Xu, Hanna Axelsson, Anna Backstrom, Francesco Marabita, Elisabeth Moussaud-Lamodiere, Duncan Njenda, others (2022). Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing. bioRxiv.

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Wei Ouyang, Jiachuan Bai, Manish Kumar Singh, Christophe Leterrier, Paul Barthelemy, Samuel FH Barnett, Teresa Klein, Markus Sauer, Pakorn Kanchanawong, Nicolas Bourg, others (2022). ShareLoc-an open platform for sharing localization microscopy data. Nature Methods.

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Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller (2022). FISH-quant v2: a scalable and modular tool for smFISH image analysis. RNA.

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Wei Ouyang, Fynn Beuttenmueller, Estibaliz Gómez-de-Mariscal, Constantin Pape, Tom Burke, Carlos Garcia-López-de-Haro, Craig Russell, Lucı́a Moya-Sans, Cristina de-la-Torre-Gutiérrez, Deborah Schmidt, others (2022). BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis. bioRxiv.

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Trang Le, Casper F Winsnes, Ulrika Axelsson, Hao Xu, Jayasankar Mohanakrishnan Kaimal, Diana Mahdessian, Shubin Dai, Ilya S Makarov, Vladislav Ostankovich, Yang Xu, others (2022). Analysis of the human protein atlas weakly supervised single-cell classification competition. Nature Methods.

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Wei Ouyang, Richard W Bowman, Haoran Wang, Kaspar E Bumke, Joel T Collins, Ola Spjuth, Jordi Carreras-Puigvert, Benedict Diederich (2022). An Open-Source Modular Framework for Automated Pipetting and Imaging Applications. Advanced biology.

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Xian Hao, Jyotsana J Parmar, Benoı̂t Lelandais, Andrey Aristov, Wei Ouyang, Christian Weber, Christophe Zimmer (2021). Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures. Genome biology.

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Henry Pinkard, Nico Stuurman, Ivan E Ivanov, Nicholas M Anthony, Wei Ouyang, Bin Li, Bin Yang, Mark A Tsuchida, Bryant Chhun, Grace Zhang, others (2021). Pycro-Manager: open-source software for customized and reproducible microscope control. Nature methods.

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Wei Ouyang, Trang Le, Hao Xu, Emma Lundberg (2021). Interactive biomedical segmentation tool powered by deep learning and ImJoy. F1000Research.

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Estibaliz Gómez-de-Mariscal, Carlos Garcı́a-López-de-Haro, Wei Ouyang, Laurène Donati, Emma Lundberg, Michael Unser, Arrate Muñoz-Barrutia, Daniel Sage (2021). DeepImageJ: A user-friendly environment to run deep learning models in ImageJ. Nature Methods.

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Yue Qin, Edward L Huttlin, Casper F Winsnes, Maya L Gosztyla, Ludivine Wacheul, Marcus R Kelly, Steven M Blue, Fan Zheng, Michael Chen, Leah V Schaffer, others (2021). A multi-scale map of cell structure fusing protein images and interactions. Nature.

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Christophe Zimmer, Wei Ouyang (2020). Method, device, and computer program for improving the reconstruction of dense super-resolution images from diffraction-limited images acquired by single molecule localization microscopy.

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Lovisa Stenström, Diana Mahdessian, Christian Gnann, Anthony J Cesnik, Wei Ouyang, Manuel D Leonetti, Mathias Uhlén, Sara Cuylen-Haering, Peter J Thul, Emma Lundberg (2020). Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. Molecular systems biology.

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Wei Ouyang, Florian Mueller, Martin Hjelmare, Emma Lundberg, Christophe Zimmer (2019). ImJoy: an open-source computational platform for the deep learning era. Nature methods.

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Wei Ouyang, Casper F Winsnes, Martin Hjelmare, Anthony J Cesnik, Lovisa Åkesson, Hao Xu, Devin P Sullivan, Shubin Dai, Jun Lan, Park Jinmo, others (2019). Analysis of the human protein atlas image classification competition. Nature methods.

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Wei Ouyang, Andrey Aristov, Mickaël Lelek, Xian Hao, Christophe Zimmer (2018). Deep learning massively accelerates super-resolution localization microscopy. Nature biotechnology.

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Aubin Samacoits, Racha Chouaib, Adham Safieddine, Abdel-Meneem Traboulsi, Wei Ouyang, Christophe Zimmer, Marion Peter, Edouard Bertrand, Thomas Walter, Florian Mueller (2018). A computational framework to study sub-cellular RNA localization. Nature Communications.

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Wei Ouyang, Christophe Zimmer (2017). The imaging tsunami: computational opportunities and challenges. Current Opinion in Systems Biology.

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Geng Yang, Mingzhe Jiang, Wei Ouyang, Guangchao Ji, Haibo Xie, Amir M Rahmani, Pasi Liljeberg, Hannu Tenhunen (2017). IoT-based remote pain monitoring system: From device to cloud platform. IEEE journal of biomedical and health informatics.

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