Alisafaei, F., Jokhun, D. S., Shivashankar, G. V., & Shenoy, V. B. (2019). Regulation of nuclear architecture, mechanics, and nucleocytoplasmic shuttling of epigenetic factors by cell geometric constraints. Proceedings of the National Academy of Sciences of the United States of America, 116(27), 13200–13209. https://doi.org/10.1073/pnas.1902035116
Alisafaei, F., Jokhun, D. S., Shivashankar, G. V., & Shenoy, V. B. (2019). Regulation of nuclear architecture, mechanics, and nucleocytoplasmic shuttling of epigenetic factors by cell geometric constraints. Proceedings of the National Academy of Sciences of the United States of America, 116(27), 13200–13209. https://doi.org/10.1073/pnas.1902035116
Alisafaei, F., Moheimani, H., Elson, E.L. and Genin, G.M. (2023). A nuclear basis for mechanointelligence in cells. Proceedings of the National Academy of Sciences, 120(19), p.e2303569120. https://doi.org/10.1073/pnas.2303569120
Alisafaei, F., Moheimani, H., Elson, E.L. and Genin, G.M. (2023). A nuclear basis for mechanointelligence in cells. Proceedings of the National Academy of Sciences, 120(19), p.e2303569120. https://doi.org/10.1073/pnas.2303569120
Almeida, J., Mathur, J., Lee, Y. L., Sarker, B., & Pathak, A. (2023). Mechanically primed cells transfer memory to fibrous matrices for invasion across environments of distinct stiffness and dimensionality. Molecular Biology of the Cell. https://doi.org/10.1091/MBC.E22-10-0469
Boyle, M. J., Goldman, Y. E., & Composto, R. J. (2023). Enhancing Nanoparticle Detection in Interferometric Scattering (iSCAT) Microscopy Using a Mask R-CNN. The Journal of Physical Chemistry B. https://doi.org/ 10.1021/acs.jpcb.3c00097
Boyle, M. J., Goldman, Y. E., & Composto, R. J. (2023). Enhancing Nanoparticle Detection in Interferometric Scattering (iSCAT) Microscopy Using a Mask R-CNN. The Journal of Physical Chemistry B. https://doi.org/ 10.1021/acs.jpcb.3c00097
Caporizzo, M. A., Chen, C. Y., Bedi, K., Margulies, K. B., & Prosser, B. L. (2020). Microtubules increase diastolic stiffness in failing human cardiomyocytes and myocardium. Circulation, 141(11), 902–915. https://doi.org/10.1161/CIRCULATIONAHA.119.043930
Caporizzo, M. A., Chen, C. Y., Bedi, K., Margulies, K. B., & Prosser, B. L. (2020). Microtubules increase diastolic stiffness in failing human cardiomyocytes and myocardium. Circulation, 141(11), 902–915. https://doi.org/10.1161/CIRCULATIONAHA.119.043930
Chen, C. Y., Salomon, A. K., Caporizzo, M. A., Curry, S., Kelly, N. A., Bedi, K. C., Bogush, A. I., Krämer, E., Schlossarek, S., Janiak, P., Moutin, M.-J., Carrier, L., Margulies, K. B., & Prosser, B. L. (2020). Depletion of vasohibin 1 speeds contraction and relaxation in failing human cardiomyocytes. Circulation Research, https://doi.org/10.1161/CIRCRESAHA.119.315947
Chen, C. Y., Salomon, A. K., Caporizzo, M. A., Curry, S., Kelly, N. A., Bedi, K. C., Bogush, A. I., Krämer, E., Schlossarek, S., Janiak, P., Moutin, M.-J., Carrier, L., Margulies, K. B., & Prosser, B. L. (2020). Depletion of vasohibin 1 speeds contraction and relaxation in failing human cardiomyocytes. Circulation Research, https://doi.org/10.1161/CIRCRESAHA.119.315947
Cho, S., Vashisth, M., Abbas, A., Majkut, S., Vogel, K., Xia, Y., Ivanovska, I. L., Irianto, J., Tewari, M., Zhu, K., Tichy, E. D., Mourkioti, F., Tang, H. Y., Greenberg, R. A., Prosser, B. L., & Discher, D. E. (2019). Mechanosensing by the lamina protects against nuclear rupture, DNA damage, and cell-cycle arrest. Developmental Cell, 49(6), 920-935.e5. https://doi.org/10.1016/j.devcel.2019.04.020
Cho, S., Vashisth, M., Abbas, A., Majkut, S., Vogel, K., Xia, Y., Ivanovska, I. L., Irianto, J., Tewari, M., Zhu, K., Tichy, E. D., Mourkioti, F., Tang, H. Y., Greenberg, R. A., Prosser, B. L., & Discher, D. E. (2019). Mechanosensing by the lamina protects against nuclear rupture, DNA damage, and cell-cycle arrest. Developmental Cell, 49(6), 920-935.e5. https://doi.org/10.1016/j.devcel.2019.04.020
Cosgrove, B. D., Loebel, C., Driscoll, T. P., Tsinman, T. K., Dai, E. N., Heo, S.-J., Dyment, N. A., Burdick, J. A., & Mauck, R. L. (2021). Nuclear envelope wrinkling predicts mesenchymal progenitor cell mechano-response in 2D and 3D microenvironments. Biomaterials, 270, 120662. https://doi.org/10.1016/j.biomaterials.2021.120662
Cosgrove, B. D., Loebel, C., Driscoll, T. P., Tsinman, T. K., Dai, E. N., Heo, S.-J., Dyment, N. A., Burdick, J. A., & Mauck, R. L. (2021). Nuclear envelope wrinkling predicts mesenchymal progenitor cell mechano-response in 2D and 3D microenvironments. Biomaterials, 270, 120662. https://doi.org/10.1016/j.biomaterials.2021.120662
Dai, E. N., Heo, S.-J., & Mauck, R. L. (2020). “Looping In” mechanics: Mechanobiologic regulation of the nucleus and the epigenome. Advanced Healthcare Materials, 2000030. https://doi.org/10.1002/adhm.202000030
Dai, E. N., Heo, S.-J., & Mauck, R. L. (2020). “Looping In” mechanics: Mechanobiologic regulation of the nucleus and the epigenome. Advanced Healthcare Materials, 2000030. https://doi.org/10.1002/adhm.202000030
Discher, D. E. (2019). From DNA damage to epithelial integrity: New roles for cell forces. Molecular Biology of the Cell, 30 (16), 1879–1881. https://doi.org/10.1091/mbc.E19-06-0338
Discher, D. E. (2019). From DNA damage to epithelial integrity: New roles for cell forces. Molecular Biology of the Cell, 30 (16), 1879–1881. https://doi.org/10.1091/mbc.E19-06-0338
Galie, P. A., Pogoda, K., Tran, K. A., Cēbers, A., & Janmey, P. A. (2024). Magnetoelastic Elastomers and Hydrogels for Studies of Mechanobiology. In B. Doudin, M. Coey, & A. Cēbers (Eds.), Magnetic Microhydrodynamics: An Emerging Research Field (pp. 143-156). Springer International Publishing. https://doi.org/10.1007/978-3-031-58376-6_11
Galie, P. A., Pogoda, K., Tran, K. A., Cēbers, A., & Janmey, P. A. (2024). Magnetoelastic Elastomers and Hydrogels for Studies of Mechanobiology. In B. Doudin, M. Coey, & A. Cēbers (Eds.), Magnetic Microhydrodynamics: An Emerging Research Field (pp. 143-156). Springer International Publishing. https://doi.org/10.1007/978-3-031-58376-6_11
Gardini, L., Woody, M. S., Kashchuk, A. v., Goldman, Y. E., Ostap, E. M., & Capitanio, M. (2022). High-Speed Optical Traps Address Dynamics of Processive and Non-Processive Molecular Motors. Methods in Molecular Biology (Clifton, N.J.), 2478, 513–557. https://doi.org/10.1007/978-1-0716-2229-2_19
Hallström, G. F., Jones, D. L., Locke, R. C., Bonnevie, E. D., Kim, S. Y., Laforest, L., Garcia, D. C., & Mauck, R. L. (2023). Microenvironmental mechanoactivation through Yap/Taz suppresses chondrogenic gene expression. Molecular Biology of the Cell, mbc. E22-12-0543. https://doi.org/10.1091/mbc.E22-12-0543
Hallström, G. F., Jones, D. L., Locke, R. C., Bonnevie, E. D., Kim, S. Y., Laforest, L., Garcia, D. C., & Mauck, R. L. (2023). Microenvironmental mechanoactivation through Yap/Taz suppresses chondrogenic gene expression. Molecular Biology of the Cell, mbc. E22-12-0543. https://doi.org/10.1091/mbc.E22-12-0543
Hayes, B. H., Tsai, R. K., Dooling, L. J., Kadu, S., Lee, J. Y., Pantano, D., Rodriguez, P. L., Subramanian, S., Shin, J. W., & Discher, D. E. (2020). Macrophages show higher levels of engulfment after disruption of cis interactions between CD47 and the checkpoint receptor SIRPα. Journal of Cell Science, 133(5). https://doi.org/10.1242/jcs.237800
Hayes, B. H., Tsai, R. K., Dooling, L. J., Kadu, S., Lee, J. Y., Pantano, D., Rodriguez, P. L., Subramanian, S., Shin, J. W., & Discher, D. E. (2020). Macrophages show higher levels of engulfment after disruption of cis interactions between CD47 and the checkpoint receptor SIRPα. Journal of Cell Science, 133(5). https://doi.org/10.1242/jcs.237800
Hayes, B. H., Zhu, P. K., Wang, M., Pfeifer, C. R., Xia, Y., Phan, S., Andrechak, J. C., Du, J., Tobin, M. P., Anlas, A., Dooling, L. J., Vashisth, M., Irianto, J., Lampson, M. A., & Discher, D. E. (2023). Confinement plus Myosin-II suppression maximizes heritable loss of chromosomes, as revealed by live-cell ChReporters. Journal of Cell Science, jcs. 260753. https://doi.org/10.1242/jcs.260753
Hayes, B. H., Zhu, P. K., Wang, M., Pfeifer, C. R., Xia, Y., Phan, S., Andrechak, J. C., Du, J., Tobin, M. P., Anlas, A., Dooling, L. J., Vashisth, M., Irianto, J., Lampson, M. A., & Discher, D. E. (2023). Confinement plus Myosin-II suppression maximizes heritable loss of chromosomes, as revealed by live-cell ChReporters. Journal of Cell Science, jcs. 260753. https://doi.org/10.1242/jcs.260753
Heffler, J., Shah, P. P., Robison, P., Phyo, S., Veliz, K., Uchida, K., Bogush, A., Rhoades, J., Jain, R., & Prosser, B. L. (2020). A balance between intermediate filaments and microtubules maintains nuclear architecture in the cardiomyocyte. Circulation Research, 126(3), e10–e26. https://doi.org/10.1161/CIRCRESAHA.119.315582
Heffler, J., Shah, P. P., Robison, P., Phyo, S., Veliz, K., Uchida, K., Bogush, A., Rhoades, J., Jain, R., & Prosser, B. L. (2020). A balance between intermediate filaments and microtubules maintains nuclear architecture in the cardiomyocyte. Circulation Research, 126(3), e10–e26. https://doi.org/10.1161/CIRCRESAHA.119.315582
Heo, S.-J., Cosgrove, B. D., Dai, E. N., & Mauck, R. L. (2018). Mechano-adaptation of the stem cell nucleus. Nucleus, 9(1), 9–19. https://doi.org/10.1080/19491034.2017.1371398
Heo, S.-J., Cosgrove, B. D., Dai, E. N., & Mauck, R. L. (2018). Mechano-adaptation of the stem cell nucleus. Nucleus, 9(1), 9–19. https://doi.org/10.1080/19491034.2017.1371398
Heo, S.-J., Thakur, S., Chen, X., Loebel, C., Xia, B., McBeath, R., Burdick, J. A., Shenoy, V. B., Mauck, R. L., & Lakadamyali, M. (2022). Aberrant chromatin reorganization in cells from diseased fibrous connective tissue in response to altered chemomechanical cues. Nature Biomedical Engineering 2022, 1–15. https://doi.org/10.1038/s41551-022-00910-5
Heo, S., Song, K., Thakur, S., Miller, L.M, Cao, X., Peredo, A., Seiber, B.N., Qu, F., Driscoll, T.P., Shenoy, V.B. and Lakadamyali, M., Burdick, J.A., Mauck, R.L. (2020) Nuclear softening expedites interstitial cell migration in fibrous networks and dense connective tissues. Science advances, 6(25), p.eaax5083. https://doi.org/10.1126/sciadv.aax5083
Heo, S., Song, K., Thakur, S., Miller, L.M, Cao, X., Peredo, A., Seiber, B.N., Qu, F., Driscoll, T.P., Shenoy, V.B. and Lakadamyali, M., Burdick, J.A., Mauck, R.L. (2020) Nuclear softening expedites interstitial cell migration in fibrous networks and dense connective tissues. Science advances, 6(25), p.eaax5083. https://doi.org/10.1126/sciadv.aax5083
Jing, H., Korasick, D. A., Emenecker, R. J., Morffy, N., Wilkinson, E. G., Powers, S. K., & Strader, L. C. (2022). Regulation of AUXIN RESPONSE FACTOR condensation and nucleo-cytoplasmic partitioning. Nature Communications, 13(4015). https://doi.org/10.1038/s41467-022-31628-2
Jones, D. L., Hallström, G. F., Jiang, X., Locke, R. C., Evans, M. K., Bonnevie, E. D., Srikumar, A., Leahy, T. P., Nijsure, M. P., & Boerckel, J. D. (2023). Mechanoepigenetic regulation of extracellular matrix homeostasis via Yap and Taz. Proceedings of the National Academy of Sciences, 120(22), e2211947120. https://doi.org/10.1073/pnas.2211947120
Jones, D. L., Hallström, G. F., Jiang, X., Locke, R. C., Evans, M. K., Bonnevie, E. D., Srikumar, A., Leahy, T. P., Nijsure, M. P., Boerckel, J. D., Mauck, R.L., Dyment, N.A. (2023). Mechanoepigenetic regulation of extracellular matrix homeostasis via Yap and Taz. Proceedings of the National Academy of Sciences, 120(22), e2211947120. https://doi.org/10.1073/pnas.2211947120
Jones, M. L., Dahl, K. N., Lele, T. P., Conway, D. E., Shenoy, V., Ghosh, S., & Szczesny, S. E. (2022). The Elephant in the Cell: Nuclear Mechanics and Mechanobiology. Journal of biomechanical engineering, 144(8). https://doi.org/10.1115/1.4053797
Jones, M. L., Dahl, K. N., Lele, T. P., Conway, D. E., Shenoy, V., Ghosh, S., & Szczesny, S. E. (2022). The Elephant in the Cell: Nuclear Mechanics and Mechanobiology. Journal of biomechanical engineering, 144(8). https://doi.org/10.1115/1.4053797
Kant, A., Guo, Z., Vinayak, V., Neguembor, M. V., Li, W. S., Agrawal, V., Pujadas, E., Almassalha, L., Backman, V., Lakadamyali, M., Cosma, M. P., & Shenoy, V. B. (2024). Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization. Nature Communications, 15(1), 4338. https://doi.org/10.1038/s41467-024-48698-z
Kant, A., Guo, Z., Vinayak, V., Neguembor, M. V., Li, W. S., Agrawal, V., Pujadas, E., Almassalha, L., Backman, V., Lakadamyali, M., Cosma, M. P., & Shenoy, V. B. (2024). Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization. Nature Communications, 15(1), 4338. https://doi.org/10.1038/s41467-024-48698-z
Kegelman, C. D., Collins, J. M., Nijsure, M. P., Eastburn, E. A., & Boerckel, J. D. (2020). Gone caving: Roles of the transcriptional regulators yap and taz in skeletal development. In Current Osteoporosis Reports (Vol. 18, Issue 5, pp. 526–540). Springer. https://doi.org/10.1007/s11914-020-00605-3
Kegelman, C. D., Collins, J. M., Nijsure, M. P., Eastburn, E. A., & Boerckel, J. D. (2020). Gone caving: Roles of the transcriptional regulators yap and taz in skeletal development. In Current Osteoporosis Reports (Vol. 18, Issue 5, pp. 526–540). Springer. https://doi.org/10.1007/s11914-020-00605-3
Kim, H. H.-S., & Lakadamyali, M. (2024). Microscopy methods to visualize nuclear organization in biomechanical studies. Current Opinion in Biomedical Engineering, 100528. https://doi.org/10.1016/j.cobme.2024.100528
Kim, H. H.-S., & Lakadamyali, M. (2024). Microscopy methods to visualize nuclear organization in biomechanical studies. Current Opinion in Biomedical Engineering, 100528. https://doi.org/10.1016/j.cobme.2024.100528
Lakadamyali, M. (2022). Single nucleosome tracking to study chromatin plasticity. Current Opinion in Cell Biology, 74, 23–28. https://doi.org/10.1016/J.CEB.2021.12.005
Lakadamyali, M. (2022). Single nucleosome tracking to study chromatin plasticity. Current Opinion in Cell Biology, 74, 23–28. https://doi.org/10.1016/J.CEB.2021.12.005
Lakadamyali, M. (2024). From feulgen to modern methods: marking a century of DNA imaging advances. Histochemistry and Cell Biology. https://doi.org/10.1007/s00418-024-02291-z
Lakadamyali, M. (2024). From feulgen to modern methods: marking a century of DNA imaging advances. Histochemistry and Cell Biology. https://doi.org/10.1007/s00418-024-02291-z [Review]
Lakadamyali, M., & Cosma, M. P. (2020). Visualizing the genome in high resolution challenges our textbook understanding. Nature Methods, 17(4), 371–379. https://doi.org/10.1038/s41592-020-0758-3
Lakadamyali, M., & Cosma, M. P. (2020). Visualizing the genome in high resolution challenges our textbook understanding. Nature Methods, 17(4), 371–379. https://doi.org/10.1038/s41592-020-0758-3
Linares-Saldana, R., Kim, W., Bolar, N. A., Zhang, H., Koch-Bojalad, B. A., Yoon, S., Shah, P. P., Karnay, A., Park, D. S., Luppino, J. M., Nguyen, S. C., Padmanabhan, A., Smith, C. L., Poleshko, A., Wang, Q., Li, L., Srivastava, D., Vahedi, G., Eom, G. H., Blobel, G. A., Joyce, E. F., and Jain, R. (2021). BRD4 orchestrates genome folding to promote neural crest differentiation. Nature Genetics, 53(10), 1480–1492. https://doi.org/10.1038/s41588-021-00934-8
Linares-Saldana, R., Kim, W., Bolar, N. A., Zhang, H., Koch-Bojalad, B. A., Yoon, S., Shah, P. P., Karnay, A., Park, D. S., Luppino, J. M., Nguyen, S. C., Padmanabhan, A., Smith, C. L., Poleshko, A., Wang, Q., Li, L., Srivastava, D., Vahedi, G., Eom, G. H., Blobel, G. A., Joyce, E. F., and Jain, R. (2021). BRD4 orchestrates genome folding to promote neural crest differentiation. Nature Genetics, 53(10), 1480–1492. https://doi.org/10.1038/s41588-021-00934-8
Liu, S., Yang, H., Lu, T. J., Genin, G. M., & Xu, F. (2019). Electrostatic switching of nuclear basket conformations provides a potential mechanism for nuclear mechanotransduction. Journal of the Mechanics and Physics of Solids, 133, 103705. https://doi.org/10.1016/j.jmps.2019.103705
Liu, S., Yang, H., Lu, T. J., Genin, G. M., & Xu, F. (2019). Electrostatic switching of nuclear basket conformations provides a potential mechanism for nuclear mechanotransduction. Journal of the Mechanics and Physics of Solids, 133, 103705. https://doi.org/10.1016/j.jmps.2019.103705
Locke, R. C., Miller, L., Lemmon, E. A., Assi, S. S., Jones, D. L., Bonnevie, E. D., Burdick, J. A., Heo, S. J., & Mauck, R. L. (2022). Rapid Restoration of Cell Phenotype and Matrix Forming Capacity Following Transient Nuclear Softening. bioRxiv, 2022.2012.2005.519160-512022.519112.519105.519160. https://doi.org/10.1101/2022.12.05.519160
Locke, R. C., Miller, L., Lemmon, E. A., Assi, S. S., Jones, D. L., Bonnevie, E. D., Burdick, J. A., Heo, S. J., & Mauck, R. L. (2022). Rapid Restoration of Cell Phenotype and Matrix Forming Capacity Following Transient Nuclear Softening. bioRxiv, 2022.2012.2005.519160-512022.519112.519105.519160. https://doi.org/10.1101/2022.12.05.519160
Loneker, A. E., Alisafaei, F., Kant, A., Janmey, P. A., Shenoy, V. B., & Wells, R. G. (2022). Lipid droplets are intracellular mechanical stressors that promote hepatocyte dedifferentiation. bioRxiv, 2022.2008.2027.505524-502022.505508.505527.505524. https://doi.org/10.1101/2022.08.27.505524
Loneker, A. E., Alisafaei, F., Kant, A., Janmey, P. A., Shenoy, V. B., & Wells, R. G. (2022). Lipid droplets are intracellular mechanical stressors that promote hepatocyte dedifferentiation. bioRxiv, 2022.2008.2027.505524-502022.505508.505527.505524. https://doi.org/10.1101/2022.08.27.505524
Loneker, A. E., Alisafaei, F., Kant, A., Li, D., Janmey, P. A., Shenoy, V. B., & Wells, R. G. (2023). Lipid droplets are intracellular mechanical stressors that impair hepatocyte function. Proceedings of the National Academy of Sciences, 120(16), e2216811120. https://doi.org/10.1073/pnas.2216811120
Loneker, A. E., Alisafaei, F., Kant, A., Li, D., Janmey, P. A., Shenoy, V. B., & Wells, R. G. (2023). Lipid droplets are intracellular mechanical stressors that impair hepatocyte function. Proceedings of the National Academy of Sciences, 120(16), e2216811120. https://doi.org/10.1073/pnas.2216811120
Łysik, D., Deptuła, P., Chmielewska, S., Skłodowski, K., Pogoda, K., Chin, L., Song, D., Mystkowska, J., Janmey, P. A., & Bucki, R. (2022). Modulation of Biofilm Mechanics by DNA Structure and Cell Type. ACS Biomaterials Science & Engineering. https://doi.org/10.1021/ACSBIOMATERIALS.2C00777
Martinez-Sarmiento, J. A., Cosma, M. P., & Lakadamyali, M. (2024). Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming. Cell Reports, 43(5). https://doi.org/10.1016/j.celrep.2024.114170
Martinez-Sarmiento, J. A., Cosma, M. P., & Lakadamyali, M. (2024). Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming. Cell Reports, 43(5). https://doi.org/10.1016/j.celrep.2024.114170
Mason, D. E., Collins, J. M., Dawahare, J. H., Nguyen, T. D., Lin, Y., Voytik-Harbin, S. L., Zorlutuna, P., Yoder, M. C., & Boerckel, J. D. (2019). YAP and TAZ limit cytoskeletal and focal adhesion maturation to enable persistent cell motility. Journal of Cell Biology, 218(4), 1369–1389. https://doi.org/10.1083/jcb.201806065
Mason, D. E., Collins, J. M., Dawahare, J. H., Nguyen, T. D., Lin, Y., Voytik-Harbin, S. L., Zorlutuna, P., Yoder, M. C., & Boerckel, J. D. (2019). YAP and TAZ limit cytoskeletal and focal adhesion maturation to enable persistent cell motility. Journal of Cell Biology, 218(4), 1369–1389. https://doi.org/10.1083/jcb.201806065
Mathur, J., Shenoy, V., & Pathak, A. (2020). Mechanical memory in cells emerges from mechanotransduction with transcriptional feedback and epigenetic plasticity. BioRxiv, 2020.03.20.000802. https://doi.org/10.1101/2020.03.20.000802
Mathur, J., Shenoy, V., & Pathak, A. (2020). Mechanical memory in cells emerges from mechanotransduction with transcriptional feedback and epigenetic plasticity. BioRxiv, 2020.03.20.000802. https://doi.org/10.1101/2020.03.20.000802
Mellis, I. A., Edelstein, H. I., Truitt, R., Goyal, Y., Beck, L. E., Symmons, O., Dunagin, M. C., Linares Saldana, R. A., Shah, P. P., Pérez-Bermejo, J. A., Padmanabhan, A., Yang, W., Jain, R., & Raj, A. (2021). Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. Cell Systems. https://doi.org/10.1016/J.CELS.2021.07.003
Mellis, I. A., Edelstein, H. I., Truitt, R., Goyal, Y., Beck, L. E., Symmons, O., Dunagin, M. C., Linares Saldana, R. A., Shah, P. P., Pérez-Bermejo, J. A., Padmanabhan, A., Yang, W., Jain, R., & Raj, A. (2021). Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. Cell Systems. https://doi.org/10.1016/J.CELS.2021.07.003
Neguembor, M. V., Martin, L., Castells-García, Á., Gómez-García, P. A., Vicario, C., Carnevali, D., AlHaj Abed, J., Granados, A., Sebastian-Perez, R., Sottile, F., Solon, J., Wu, C., Lakadamyali, M., & Cosma, M. P. (2021). Transcription-mediated supercoiling regulates genome folding and loop formation. Molecular Cell, 81(15), 3065-3081.e12. https://doi.org/10.1016/J.MOLCEL.2021.06.009
Neguembor, M. V., Martin, L., Castells-García, Á., Gómez-García, P. A., Vicario, C., Carnevali, D., AlHaj Abed, J., Granados, A., Sebastian-Perez, R., Sottile, F., Solon, J., Wu, C., Lakadamyali, M., & Cosma, M. P. (2021). Transcription-mediated supercoiling regulates genome folding and loop formation. Molecular Cell, 81(15), 3065-3081.e12. https://doi.org/10.1016/J.MOLCEL.2021.06.009
Pfeifer, C. R., Tobin, M. P., Cho, S., Vashisth, M., Dooling, L. J., Vazquez, L. L., Ricci-De Lucca, E. G., Simon, K. T., & Discher, D. E. (2022). Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate. Nucleus, 13(1), 129–143. https://www.tandfonline.com/doi/full/10.1080/19491034.2022.2045726
Pfeifer, C. R., Tobin, M. P., Cho, S., Vashisth, M., Dooling, L. J., Vazquez, L. L., Ricci-De Lucca, E. G., Simon, K. T., & Discher, D. E. (2022). Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate. Nucleus, 13(1), 129–143. https://www.tandfonline.com/doi/full/10.1080/19491034.2022.2045726
Pfeifer, C. R., Tobin, M. P., Cho, S., Vashisth, M., Dooling, L. J., Vazquez, L. L., Ricci-De Lucca, E. G., Simon, K. T., & Discher, D. E. (2022). Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate. Nucleus, 13(1), 129–143. https://doi.org/10.1080/19491034.2022.2045726
Pfeifer, C. R., Vashisth, M., Xia, Y., & Discher, D. E. (2019). Nuclear failure, DNA damage, and cell cycle disruption after migration through small pores: A brief review. Essays in Biochemistry 63(5), 569–577. https://doi.org/10.1042/EBC20190007
Pfeifer, C. R., Vashisth, M., Xia, Y., & Discher, D. E. (2019). Nuclear failure, DNA damage, and cell cycle disruption after migration through small pores: A brief review. Essays in Biochemistry 63(5), 569–577. https://doi.org/10.1042/EBC20190007
Phyo, S. A., Uchida, K., Chen, C. Y., Caporizzo, M. A., Bedi, K., Griffin, J., Margulies, K., & Prosser, B. L. (2022). Transcriptional, Post-Transcriptional, and Post-Translational Mechanisms Rewrite the Tubulin Code During Cardiac Hypertrophy and Failure. Frontiers in cell and developmental biology, 10. https://doi.org/10.3389/FCELL.2022.837486
Phyo, S. A., Uchida, K., Chen, C. Y., Caporizzo, M. A., Bedi, K., Griffin, J., Margulies, K., & Prosser, B. L. (2022). Transcriptional, Post-Transcriptional, and Post-Translational Mechanisms Rewrite the Tubulin Code During Cardiac Hypertrophy and Failure. Frontiers in cell and developmental biology, 10. https://doi.org/10.3389/FCELL.2022.837486
Poleshko, A., Shah, P. P., Gupta, M., Babu, A., Morley, M. P., Manderfield, L. J., Ifkovits, J. L., Calderon, D., Aghajanian, H., Sierra-Pagán, J. E., Sun, Z., Wang, Q., Li, L., Dubois, N. C., Morrisey, E. E., Lazar, M. A., Smith, C. L., Epstein, J. A., & Jain, R. (2017). Genome-nuclear lamina interactions regulate cardiac stem cell lineage restriction. Cell, 171(3), 573-587.e14. https://doi.org/10.1016/j.cell.2017.09.018
Poleshko, A., Shah, P. P., Gupta, M., Babu, A., Morley, M. P., Manderfield, L. J., Ifkovits, J. L., Calderon, D., Aghajanian, H., Sierra-Pagán, J. E., Sun, Z., Wang, Q., Li, L., Dubois, N. C., Morrisey, E. E., Lazar, M. A., Smith, C. L., Epstein, J. A., & Jain, R. (2017). Genome-nuclear lamina interactions regulate cardiac stem cell lineage restriction. Cell, 171(3), 573-587.e14. https://doi.org/10.1016/j.cell.2017.09.018
Poleshko, A., Smith, C. L., Nguyen, S. C., Sivaramakrishnan, P., Wong, K. G., Murray, J. I., Lakadamyali, M., Joyce, E. F., Jain, R., & Epstein, J. A. (2019). H3k9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis. ELife, 8. https://doi.org/10.7554/eLife.49278
Poleshko, A., Smith, C. L., Nguyen, S. C., Sivaramakrishnan, P., Wong, K. G., Murray, J. I., Lakadamyali, M., Joyce, E. F., Jain, R., & Epstein, J. A. (2019). H3k9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis. ELife, 8. https://doi.org/10.7554/eLife.49278
Price, C. C., Mathur, J., Boerckel, J. D., Pathak, A., & Shenoy, V. B. (2021). Dynamic self-reinforcement of gene expression determines acquisition of cellular mechanical memory. Biophysical Journal, 120(22), 5074–5089. https://doi.org/10.1016/J.BPJ.2021.10.006
Price, C. C., Mathur, J., Boerckel, J. D., Pathak, A., & Shenoy, V. B. (2021). Dynamic self-reinforcement of gene expression determines acquisition of cellular mechanical memory. Biophysical Journal, 120(22), 5074–5089. https://doi.org/10.1016/J.BPJ.2021.10.006
Pyrpassopoulos, S., Shuman, H., & Ostap, E. M. (2022). Microtubule Dumbbells to Assess the Effect of Force Geometry on Single Kinesin Motors. Methods in Molecular Biology (Clifton, N.J.), 2478, 559–583. https://doi.org/10.1007/978-1-0716-2229-2_20
Santini, G. T., Shah, P. P., Karnay, A., & Jain, R. (2022). Aberrant chromatin organization at the nexus of laminopathy disease pathways. https://doi.org/10.1080/19491034.2022.2153564
See, K., Kiseleva, A. A., Smith, C. L., Liu, F., Li, J., Poleshko, A., & Epstein, J. A. (2020). Histone methyltransferase activity programs nuclear peripheral genome positioning. Developmental Biology, 466(1–2), 90–98. https://doi.org/10.1016/j.ydbio.2020.07.010
See, K., Kiseleva, A. A., Smith, C. L., Liu, F., Li, J., Poleshko, A., & Epstein, J. A. (2020). Histone methyltransferase activity programs nuclear peripheral genome positioning. Developmental Biology, 466(1–2), 90–98. https://doi.org/10.1016/j.ydbio.2020.07.010
See, K., Lan, Y., Rhoades, J., Jain, R., Smith, C. L., & Epstein, J. A. (2019). Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9Me2 domains. Development, 146(3). https://doi.org/10.1242/dev.174078
See, K., Lan, Y., Rhoades, J., Jain, R., Smith, C. L., & Epstein, J. A. (2019). Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9Me2 domains. Development, 146(3). https://doi.org/10.1242/dev.174078
Seo, J., Byun, W. Y., Alisafaei, F., Georgescu, A., Yi, Y. S., Massaro-Giordano, M., Shenoy, V. B., Lee, V., Bunya, V. Y., & Huh, D. (2019). Multiscale reverse engineering of the human ocular surface. Nature Medicine, 25(8), 1310–1318. https://doi.org/10.1038/s41591-019-0531-2
Seo, J., Byun, W. Y., Alisafaei, F., Georgescu, A., Yi, Y. S., Massaro-Giordano, M., Shenoy, V. B., Lee, V., Bunya, V. Y., & Huh, D. (2019). Multiscale reverse engineering of the human ocular surface. Nature Medicine, 25(8), 1310–1318. https://doi.org/10.1038/s41591-019-0531-2
Shah, P. P., Keough, K. C., Gjoni, K., Santini, G. T., Abdill, R. J., Wickramasinghe, N. M., Dundes, C. E., Karnay, A., Chen, A., Salomon, R. E. A., Walsh, P. J., Nguyen, S. C., Whalen, S., Joyce, E. F., Loh, K. M., Dubois, N., Pollard, K. S., & Jain, R. (2023). An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Genome Biology, 24(1), 1-35. https://doi.org/10.1186/S13059-023-02849-5
Shah, P. P., Keough, K. C., Gjoni, K., Santini, G. T., Abdill, R. J., Wickramasinghe, N. M., Dundes, C. E., Karnay, A., Chen, A., Salomon, R. E. A., Walsh, P. J., Nguyen, S. C., Whalen, S., Joyce, E. F., Loh, K. M., Dubois, N., Pollard, K. S., & Jain, R. (2023). An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Genome Biology, 24(1), 1-35. https://doi.org/10.1186/S13059-023-02849-5
Shah, P. P., Lv, W., Rhoades, J. H., Poleshko, A., Abbey, D., Caporizzo, M. A., Linares-Saldana, R., Heffler, J. G., Sayed, N., Thomas, D., Wang, Q., Stanton, L. J., Bedi, K., Morley, M. P., Cappola, T. P., Owens, A. T., Margulies, K. B., Frank, D. B., Wu, J. C., Rader, D.J., Yang, W., Prosser, B.L., Musunuru, K., Jain, R. (2021). Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. Cell Stem Cell, 28, 1–17. https://doi.org/10.1016/j.stem.2020.12.016
Shah, P. P., Lv, W., Rhoades, J. H., Poleshko, A., Abbey, D., Caporizzo, M. A., Linares-Saldana, R., Heffler, J. G., Sayed, N., Thomas, D., Wang, Q., Stanton, L. J., Bedi, K., Morley, M. P., Cappola, T. P., Owens, A. T., Margulies, K. B., Frank, D. B., Wu, J. C., Rader, D.J., Yang, W., Prosser, B.L., Musunuru, K., Jain, R. (2021). Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. Cell Stem Cell, 28, 1–17. https://doi.org/10.1016/j.stem.2020.12.016
** NOTE: new video for this publication HERE.
Shah, P. P., Santini, G. T., Shen, K. M., & Jain, R. (2023). InterLINCing Chromatin Organization and Mechanobiology in Laminopathies. Current Cardiology Reports, 1-8. https://doi.org/10.1007/s11886-023-01853-2
Shah, P. P., Santini, G. T., Shen, K. M., & Jain, R. (2023). InterLINCing Chromatin Organization and Mechanobiology in Laminopathies. Current Cardiology Reports, 1-8. https://doi.org/10.1007/s11886-023-01853-2
Smith, C. L., Lan, Y., Jain, R., Epstein, J. A., & Poleshko, A. (2021). Global chromatin relabeling accompanies spatial inversion of chromatin in rod photoreceptors. Science Advances, 7(39), 3035–3059. https://doi.org/10.1126/SCIADV.ABJ3035
Smith, C. L., Lan, Y., Jain, R., Epstein, J. A., & Poleshko, A. (2021). Global chromatin relabeling accompanies spatial inversion of chromatin in rod photoreceptors. Science Advances, 7(39), 3035–3059. https://doi.org/10.1126/SCIADV.ABJ3035
Smith, L. R., Irianto, J., Xia, Y., Pfeifer, C. R., & Discher, D. E. (2019). Constricted migration modulates stem cell differentiation. Molecular Biology of the Cell, 30(16), 1985–1999. https://doi.org/10.1091/mbc.E19-02-0090
Smith, L. R., Irianto, J., Xia, Y., Pfeifer, C. R., & Discher, D. E. (2019). Constricted migration modulates stem cell differentiation. Molecular Biology of the Cell, 30(16), 1985–1999. https://doi.org/10.1091/mbc.E19-02-0090
Tang, Q., Sensale, S., Bond, C., Xing, J., Qiao, A., Hugelier, S., Arab, A., Arya, G., & Lakadamyali, M. (2023). Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets. Current Biology. https://doi.org/10.1016/j.cub.2023.10.068
Tang, Q., Sensale, S., Bond, C., Xing, J., Qiao, A., Hugelier, S., Arab, A., Arya, G., & Lakadamyali, M. (2023). Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets. Current Biology. https://doi.org/10.1016/j.cub.2023.10.068
Tobin, M. P., Pfeifer, C. R., Zhu, P. K., Hayes, B. H., Wang, M., Vashisth, M., Xia, Y., Phan, S. H., Belt, S. A., Irianto, J. & Discher, D. (2023). Differences in cell shape, motility, and growth reflect chromosomal number variations that can be visualized with live-cell ChReporters. Molecular Biology of the Cell, mbc. E23-06-0207. https://doi.org/10.1091/mbc.E23-06-0207
Tobin, M. P., Pfeifer, C. R., Zhu, P. K., Hayes, B. H., Wang, M., Vashisth, M., Xia, Y., Phan, S. H., Belt, S. A., Irianto, J. & Discher, D. (2023). Differences in cell shape, motility, and growth reflect chromosomal number variations that can be visualized with live-cell ChReporters. Molecular Biology of the Cell, mbc. E23-06-0207. https://doi.org/10.1091/mbc.E23-06-0207
Tobin, M. P., Pfeifer, C. R., Zhu, P. K., Hayes, B. H., Wang, M., Vashisth, M., Xia, Y., Phan, S. H., Belt, S. A., Irianto, J., & Discher, D. E. (2023). Differences in cell shape, motility, and growth reflect chromosomal number variations that can be visualized with live-cell ChReporters. Molecular Biology of the Cell, 34(13), br19. https://doi.org/10.1091/mbc.E23-06-0207
Tobin, M. P., Pfeifer, C. R., Zhu, P. K., Hayes, B. H., Wang, M., Vashisth, M., Xia, Y., Phan, S. H., Belt, S. A., Irianto, J., & Discher, D. E. (2023). Differences in cell shape, motility, and growth reflect chromosomal number variations that can be visualized with live-cell ChReporters. Molecular Biology of the Cell, 34(13), br19. https://doi.org/10.1091/mbc.E23-06-0207
Vashisth, M., Cho, S., Irianto, J., Xia, Y., Wang, M., Hayes, B., Wieland, D., Wells, R., Jafarpour, F., Liu, A., & Discher, D. E. (2021). Scaling concepts in ’omics: Nuclear lamin-B scales with tumor growth and often predicts poor prognosis, unlike fibrosis. Proceedings of the National Academy of Sciences of the United States of America, 118(48). https://doi.org/10.1073/PNAS.2112940118/-/DCSUPPLEMENTAL
Vashisth, M., Cho, S., Irianto, J., Xia, Y., Wang, M., Hayes, B., Wieland, D., Wells, R., Jafarpour, F., Liu, A., & Discher, D. E. (2021). Scaling concepts in ’omics: Nuclear lamin-B scales with tumor growth and often predicts poor prognosis, unlike fibrosis. Proceedings of the National Academy of Sciences of the United States of America, 118(48). https://doi.org/10.1073/PNAS.2112940118
Wang, M., Ivanovska, I., Vashisth, M., & Discher, D. E. (2022). Nuclear mechanoprotection: From tissue atlases as blueprints to distinctive regulation of nuclear lamins. APL Bioengineering, 6(2), 021504. https://doi.org/10.1063/5.0080392
Wang, M., Phan, S., Hayes, B. H., & Discher, D. E. (2023). Genetic heterogeneity in p53-null leukemia increases transiently with spindle assembly checkpoint inhibition and is not rescued by p53. Chromosoma, 1-16. https://doi.org/10.1007/s00412-023-00800-y
Wang, M., Phan, S., Hayes, B. H., & Discher, D. E. (2023). Genetic heterogeneity in p53-null leukemia increases transiently with spindle assembly checkpoint inhibition and is not rescued by p53. Chromosoma, 1-16. https://doi.org/10.1007/s00412-023-00800-y
Woodworth, M. A., & Lakadamyali, M. (2024). Toward a comprehensive view of gene architecture during transcription. Current Opinion in Genetics & Development, 85, 102154. https://doi.org/10.1016/j.gde.2024.102154
Woodworth, M. A., & Lakadamyali, M. (2024). Toward a comprehensive view of gene architecture during transcription. Current Opinion in Genetics & Development, 85, 102154. https://doi.org/10.1016/j.gde.2024.102154
Xia, Y., Cho, S., Vashisth, M., Ivanovska, I. L., Dingal, P. C. D. P., & Discher, D. E. (2019). Manipulating the mechanics of extracellular matrix to study effects on the nucleus and its structure. Methods, 157, 3–14. https://doi.org/10.1016/j.ymeth.2018.12.009
Xia, Y., Cho, S., Vashisth, M., Ivanovska, I. L., Dingal, P. C. D. P., & Discher, D. E. (2019). Manipulating the mechanics of extracellular matrix to study effects on the nucleus and its structure. Methods, 157, 3–14. https://doi.org/10.1016/j.ymeth.2018.12.009
Xia, Y., Ivanovska, I. L., Zhu, K., Smith, L., Irianto, J., Pfeifer, C. R., Alvey, C. M., Ji, J., Liu, D., Cho, S., Bennett, R. R., Liu, A. J., Greenberg, R. A., & Discher, D. E. (2018). Nuclear rupture at sites of high curvature compromises retention of DNA repair factors. Journal of Cell Biology, 217(11), 3796–3808. https://doi.org/10.1083/jcb.201711161
Xia, Y., Ivanovska, I. L., Zhu, K., Smith, L., Irianto, J., Pfeifer, C. R., Alvey, C. M., Ji, J., Liu, D., Cho, S., Bennett, R. R., Liu, A. J., Greenberg, R. A., & Discher, D. E. (2018). Nuclear rupture at sites of high curvature compromises retention of DNA repair factors. Journal of Cell Biology, 217(11), 3796–3808. https://doi.org/10.1083/jcb.201711161
Xia, Y., Pfeifer, C. R., & Discher, D. E. (2019). Nuclear mechanics during and after constricted migration. Acta Mechanica Sinica/Lixue Xuebao, 35(2), 299–308. https://doi.org/10.1007/s10409-018-00836-9
Xia, Y., Pfeifer, C. R., & Discher, D. E. (2019). Nuclear mechanics during and after constricted migration. Acta Mechanica Sinica/Lixue Xuebao, 35(2), 299–308. https://doi.org/10.1007/s10409-018-00836-9
Xia, Y., Pfeifer, C. R., Zhu, K., Irianto, J., Liu, D., Pannell, K., Chen, E. J., Dooling, L. J., Tobin, M. P., Wang, M., Ivanovska, I. L., Smith, L. R., Greenberg, R. A., & Discher, D. E. (2019). Rescue of DNA damage after constricted migration reveals a mechano-regulated threshold for cell cycle. The Journal of Cell Biology, 218(8), 2545–2563. https://doi.org/10.1083/jcb.201811100
Xia, Y., Pfeifer, C. R., Zhu, K., Irianto, J., Liu, D., Pannell, K., Chen, E. J., Dooling, L. J., Tobin, M. P., Wang, M., Ivanovska, I. L., Smith, L. R., Greenberg, R. A., & Discher, D. E. (2019). Rescue of DNA damage after constricted migration reveals a mechano-regulated threshold for cell cycle. The Journal of Cell Biology, 218(8), 2545–2563. https://doi.org/10.1083/jcb.201811100
Zhang, J., Alisafaei, F., Nikolić, M., Nou, X. A., Kim, H., Shenoy, V. B., & Scarcelli, G. (2020). Nuclear mechanics within intact cells is regulated by cytoskeletal network and internal nanostructures. Small, 1907688. https://doi.org/10.1002/smll.201907688
Zhang, J., Alisafaei, F., Nikolić, M., Nou, X. A., Kim, H., Shenoy, V. B., & Scarcelli, G. (2020). Nuclear mechanics within intact cells is regulated by cytoskeletal network and internal nanostructures. Small, 1907688. https://doi.org/10.1002/smll.201907688
