Singh, Shantanu

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

Bray, M.-A., Singh, S., Han, H., Davis, C. T., Borgeson, B., Hartland, C., Kost-Alimova, M., Gustafsdottir, S. M., Gibson, C. C., & Carpenter, A. E. (2016) · Nature Protocols

Cell Image Analysis TechniquesSingle-cell and spatial transcriptomics

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Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl

Caicedo, J. C., Goodman, A., Karhohs, K. W., Cimini, B. A., Ackerman, J., Haghighi, M., Heng, C., Becker, T., Doan, M., McQuin, C., et al. (2019) · Nature Methods

Cell Image Analysis TechniquesDigital Imaging for Blood Diseases

Cited by 809

Data-analysis strategies for image-based cell profiling

Caicedo, J. C., Cooper, S., Heigwer, F., Warchal, S., Qiu, P., Molnar, C., Vasilevich, A. S., Barry, J. D., Bansal, H. S., Kraus, O., et al. (2017) · Nature Methods

Cell Image Analysis TechniquesSingle-cell and spatial transcriptomics

Cited by 739

Optimizing the Cell Painting assay for image-based profiling

Cimini, B. A., Chandrasekaran, S. N., Kost-Alimova, M., Miller, L., Goodale, A., Fritchman, B., Byrne, P., Garg, S., Jamali, N., Logan, D. J., et al. (2023) · Nature Protocols

Cell Image Analysis TechniquesSingle-cell and spatial transcriptomics

Cited by 177

Canonical and atypical E2Fs regulate the mammalian endocycle

Chen, H.-Z., Ouseph, M. M., Li, J., Pécot, T., Chokshi, V., Kent, L., Bae, S., Byrne, M., Duran, C., Comstock, G., et al. (2012) · Nature Cell Biology

Cancer-related Molecular PathwaysDevelopmental Biology and Gene Regulation

Cited by 161

Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence

Barczak, A. K., Avraham, R., Singh, S., Luo, S. S., Zhang, W. R., Bray, M.-A., Hinman, A. E., Thompson, M., Nietupski, R. M., Golas, A., et al. (2017) · PLOS Pathogens

Tuberculosis Research and EpidemiologyMycobacterium research and diagnosis

Cited by 120

Evaluating batch correction methods for image-based cell profiling

Arevalo, J., Su, E., van Dijk, R., Carpenter, A. E., & Singh, S. (2023) · Nature Communications

Single-cell and spatial transcriptomicsCell Image Analysis Techniques

Cited by 89

TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41

Carey, K. L., Paulus, G. L. C., Wang, L., Balce, D. R., Luo, J. W., Bergman, P., Ferder, I. C., Kong, L., Renaud, N., Singh, S., et al. (2020) · Cell Reports

Autophagy in Disease and TherapyCalcium signaling and nucleotide metabolism

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