| Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging
Braunger, J. M., Cammarata, L. V., Sornapudi, T. R., Uhler, C., & Shivashankar, G. V. (2024). Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging. Aging cell, 23(3), e14056 (18 pp.). https://doi.org/10.1111/acel.14056 |
| Chromatin remodeling due to transient-link-and-pass activity enhances subnuclear dynamics
Das, R., Sakaue, T., Shivashankar, G. V., Prost, J., & Hiraiwa, T. (2024). Chromatin remodeling due to transient-link-and-pass activity enhances subnuclear dynamics. Physical Review Letters, 132(5), 058401 (6 pp.). https://doi.org/10.1103/PhysRevLett.132.058401 |
| Implanting mechanically reprogrammed fibroblasts for aged tissue regeneration and wound healing
Roy, B., Pekec, T., Yuan, L., & Shivashankar, G. V. (2024). Implanting mechanically reprogrammed fibroblasts for aged tissue regeneration and wound healing. Aging cell, 23(2), e14032 (14 pp.). https://doi.org/10.1111/acel.14032 |
| Unsupervised representation learning of chromatin images identifies changes in cell state and tissue organization in DCIS
Zhang, X., Venkatachalapathy, S., Paysan, D., Schaerer, P., Tripodo, C., Uhler, C., & Shivashankar, G. V. (2024). Unsupervised representation learning of chromatin images identifies changes in cell state and tissue organization in DCIS. Nature Communications, 15(1), 6112 (16 pp.). https://doi.org/10.1038/s41467-024-50285-1 |
| Imaging and AI based chromatin biomarkers for diagnosis and therapy evaluation from liquid biopsies
Challa, K., Paysan, D., Leiser, D., Sauder, N., Weber, D. C., & Shivashankar, G. V. (2023). Imaging and AI based chromatin biomarkers for diagnosis and therapy evaluation from liquid biopsies. npj Precision Oncology, 7, 135 (13 pp.). https://doi.org/10.1038/s41698-023-00484-8 |
| Deleterious mechanical deformation selects mechanoresilient cancer cells with enhanced proliferation and chemoresistance
Jiang, K., Lim, S. B., Xiao, J., Jokhun, D. S., Shang, M., Song, X., … Lim, C. T. (2023). Deleterious mechanical deformation selects mechanoresilient cancer cells with enhanced proliferation and chemoresistance. Advanced Science, 10(22), 2201663 (15 pp.). https://doi.org/10.1002/advs.202201663 |
| Detecting radio- and chemoresistant cells in 3D cancer co-cultures using chromatin biomarkers
Pekeč, T., Venkatachalapathy, S., Shim, A. R., Paysan, D., Grzmil, M., Schibli, R., … Shivashankar, G. V. (2023). Detecting radio- and chemoresistant cells in 3D cancer co-cultures using chromatin biomarkers. Scientific Reports, 13(1), 20662 (14 pp.). https://doi.org/10.1038/s41598-023-47287-2 |
| Mechanical forces and the 3D genome
Shivashankar, G. V. (2023). Mechanical forces and the 3D genome. Current Opinion in Structural Biology, 83, 102728 (7 pp.). https://doi.org/10.1016/j.sbi.2023.102728 |
| How enzymatic activity is involved in chromatin organization
Das, R., Sakaue, T., Shivashankar, G. V., Prost, J., & Hiraiwa, T. (2022). How enzymatic activity is involved in chromatin organization. eLife, 11, e79901 (18 pp.). https://doi.org/10.7554/eLife.79901 |
| Machine learning approaches to single-cell data integration and translation
Uhler, C., & Shivashankar, G. V. (2022). Machine learning approaches to single-cell data integration and translation. Proceedings of the IEEE, 110(5), 557-576. https://doi.org/10.1109/JPROC.2022.3166132 |
| Actomyosin contractility as a mechanical checkpoint for cell state transitions
Venkatachalapathy, S., Sreekumar, D., Ratna, P., & Shivashankar, G. V. (2022). Actomyosin contractility as a mechanical checkpoint for cell state transitions. Scientific Reports, 12(1), 16063 (13 pp.). https://doi.org/10.1038/s41598-022-20089-8 |
| Lateral confined growth of cells activates Lef1 dependent pathways to regulate cell-state transitions
Yuan, L., Roy, B., Ratna, P., Uhler, C., & Shivashankar, G. V. (2022). Lateral confined growth of cells activates Lef1 dependent pathways to regulate cell-state transitions. Scientific Reports, 12(1), 17318 (13 pp.). https://doi.org/10.1038/s41598-022-21596-4 |
| Guiding irregular nuclear morphology on nanopillar arrays for malignancy differentiation in tumor cells
Zeng, Y., Zhuang, Y., Vinod, B., Guo, X., Mitra, A., Chen, P., … Zhao, W. (2022). Guiding irregular nuclear morphology on nanopillar arrays for malignancy differentiation in tumor cells. Nano Letters, 22(18), 7724-7733. https://doi.org/10.1021/acs.nanolett.2c01849 |
| Graph-based autoencoder integrates spatial transcriptomics with chromatin images and identifies joint biomarkers for Alzheimer’s disease
Zhang, X., Wang, X., Shivashankar, G. V., & Uhler, C. (2022). Graph-based autoencoder integrates spatial transcriptomics with chromatin images and identifies joint biomarkers for Alzheimer’s disease. Nature Communications, 13(1), 7480 (17 pp.). https://doi.org/10.1038/s41467-022-35233-1 |
| Causal network models of SARS-CoV-2 expression and aging to identify candidates for drug repurposing
Belyaeva, A., Cammarata, L., Radhakrishnan, A., Squires, C., Yang, K. D., Shivashankar, G. V., & Uhler, C. (2021). Causal network models of SARS-CoV-2 expression and aging to identify candidates for drug repurposing. Nature Communications, 12(1), 1024 (13 pp.). https://doi.org/10.1038/s41467-021-21056-z |
| The characteristics of nuclear membrane fluctuations in stem cells
Ghanbarzadeh Nodehi, S., Shivashankar, G. V., Prost, J., & Mohammad-Rafiee, F. (2021). The characteristics of nuclear membrane fluctuations in stem cells. Journal of the Royal Society Interface, 18(176), 20201010 (9 pp.). https://doi.org/10.1098/rsif.2020.1010 |
| Mechanogenomic coupling of lung tissue stiffness, EMT and coronavirus pathogenicity
Uhler, C., & Shivashankar, G. V. (2021). Mechanogenomic coupling of lung tissue stiffness, EMT and coronavirus pathogenicity. Current Opinion in Solid State and Materials Science, 25(1), 100874 (4 pp.). https://doi.org/10.1016/j.cossms.2020.100874 |
| Single cell imaging-based chromatin biomarkers for tumor progression
Venkatachalapathy, S., Jokhun, D. S., Andhari, M., & Shivashankar, G. V. (2021). Single cell imaging-based chromatin biomarkers for tumor progression. Scientific Reports, 11(1), 23041 (14 pp.). https://doi.org/10.1038/s41598-021-02441-6 |
| Whole-body integration of gene expression and single-cell morphology
Vergara, H. M., Pape, C., Meechan, K. I., Zinchenko, V., Genoud, C., Wanner, A. A., … Arendt, D. (2021). Whole-body integration of gene expression and single-cell morphology. Cell, 184(18), 4819-4837. https://doi.org/10.1016/j.cell.2021.07.017 |
| Multi-domain translation between single-cell imaging and sequencing data using autoencoders
Yang, K. D., Belyaeva, A., Venkatachalapathy, S., Damodaran, K., Katcoff, A., Radhakrishnan, A., … Uhler, C. (2021). Multi-domain translation between single-cell imaging and sequencing data using autoencoders. Nature Communications, 12(1), 31 (10 pp.). https://doi.org/10.1038/s41467-020-20249-2 |
