Van Valen, David

Combined from CaltechAUTHORS

• Laubscher, Emily and Wang, Xuefei (Julie), el al. (2024) Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning; Cell Systems; Vol. 15; No. 5; 475-482.e6; 10.1016/j.cels.2024.04.006
• Ma, Jun and Xie, Ronald, el al. (2024) The multimodality cell segmentation challenge: toward universal solutions; Nature Methods; 10.1038/s41592-024-02233-6
• Israel, Uriah and Marks, Markus, el al. (2024) A Foundation Model for Cell Segmentation; bioRvix; 2023.11.17.567630; PMCID PMC10690226; 10.1101/2023.11.17.567630
• Sockell, Alexandra and Wong, Wing, el al. (2023) A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids; Cell Systems; Vol. 14; No. 9; 764-776.e6; 10.1016/j.cels.2023.08.002
• Greenbaum, Shirley and Averbukh, Inna, el al. (2023) A spatially resolved timeline of the human maternal–fetal interface; Nature; Vol. 619; No. 7970; 595-605; PMCID PMC10356615; 10.1038/s41586-023-06298-9
• Scott, Ryan T. and Sanders, Lauren M., el al. (2023) Biomonitoring and precision health in deep space supported by artificial intelligence; Nature Machine Intelligence; Vol. 5; No. 3; 196-207; 10.1038/s42256-023-00617-5
• Sockell, Alexandra and Wong, Wing, el al. (2022) A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids; 10.1101/2022.11.01.514733
• Andrews, Brenda and Chang, Jae-Byum, el al. (2022) Imaging cell biology; Nature Cell Biology; Vol. 24; No. 8; 1180-1185; 10.1038/s41556-022-00960-6
• Miguel, Amanda and Zietek, Matylda, el al. (2022) Modulation of bacterial cell size and growth rate via activation of a cell envelope stress response; 10.1101/2022.07.26.501648
• Greenwald, Noah F. and Miller, Geneva, el al. (2022) Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning; Nature Biotechnology; Vol. 40; No. 4; 555-565; PMCID PMC9010346; 10.1038/s41587-021-01094-0
• McCaffrey, Erin F. and Donato, Michele, el al. (2022) The immunoregulatory landscape of human tuberculosis granulomas; Nature Immunology; Vol. 23; No. 2; 318-329; PMCID PMC8810384; 10.1038/s41590-021-01121-x
• Hartmann, Felix J. and Mrdjen, Dunja, el al. (2021) Single-cell metabolic profiling of human cytotoxic T cells; Nature Biotechnology; Vol. 39; No. 2; 186-197; 10.1038/s41587-020-0651-8
• Bannon, Dylan and Moen, Erick, el al. (2021) DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes; Nature Methods; Vol. 18; No. 1; 43-45; 10.1038/s41592-020-01023-0
• McCaffrey, Erin F. and Donato, Michele, el al. (2020) Multiplexed imaging of human tuberculosis granulomas uncovers immunoregulatory features conserved across tissue and blood; 10.1101/2020.06.08.140426
• Moen, Erick and Bannon, Dylan, el al. (2019) Deep learning for cellular image analysis; Nature Methods; Vol. 16; No. 12; 1233-1246; 10.1038/s41592-019-0403-1
• Greenwald, Noah and Keren, Leeat, el al. (2019) Combining Multiplexed Ion Beam Imaging (MIBI) with Convolutional Neural Networks to accurately segment cells in human tissue; Journal for ImmunoTherapy of Cancer; Vol. 7; No. S1; Art. No. P736; 10.1186/s40425-019-0764-0
• Moen, Erick and Borba, Enrico, el al. (2019) Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning; 10.1101/803205
• Anikeeva, Polina and Cissé, Ibrahim I., el al. (2019) Voices in methods development; Nature Methods; Vol. 16; No. 10; 945-951; PMCID PMC7075469; 10.1038/s41592-019-0585-6
• Bannon, Dylan and Moen, Erick, el al. (2018) DeepCell 2.0: Automated cloud deployment of deep learning models for large-scale cellular image analysis; 10.1101/505032
• Keren, Leeat and Bosse, Marc, el al. (2018) A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging; Cell; Vol. 174; No. 6; 1373-1387; PMCID PMC6132072; 10.1016/j.cell.2018.08.039
• Quach, N. T. and Bodner, K., el al. (2017) A forward genetic screen identifies host factors that influence the lysis-lysogeny decision in phage lambda; Molecular Biology of the Cell; Vol. 28; No. 26; Art. No. P1721; 10.1091/mbc.E17-10-0618
• Lane, Keara and Van Valen, David, el al. (2017) Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation; Cell Systems; Vol. 4; No. 4; 458-469.e5; 10.1016/j.cels.2017.03.010
• Van Valen, David A. and Kudo, Takamasa, el al. (2016) Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments; PLOS Computational Biology; Vol. 12; No. 11; Art. No. e1005177; PMCID PMC5096676; 10.1371/journal.pcbi.1005177
• Van Valen, David and Wu, David, el al. (2012) A Single-Molecule Hershey-Chase Experiment; Current Biology; Vol. 22; No. 14; 1339-1343; PMCID PMC3462812; 10.1016/j.cub.2012.05.023
• Wu, David and Van Valen, David, el al. (2010) Ion-Dependent Dynamics of DNA Ejections for Bacteriophage λ; Biophysical Journal; Vol. 99; No. 4; 1101-1109; PMCID PMC2920739; 10.1016/j.bpj.2010.06.024
• Van Valen, David and Haataja, Mikko, el al. (2009) Biochemistry on a Leash: The Roles of Tether Length and Geometry in Signal Integration Proteins; Biophysical Journal; Vol. 96; No. 4; 1275-1292; PMCID PMC2717227; 10.1016/j.bpj.2008.10.052