Publications

Publications

Adebowale, K., Gong, Z., Hou, J. C., Wisdom, K. M., Garbett, D., Lee, H., Nam, S., Meyer, T., Odde, D., Shenoy, V. B., & Chaudhuri, O. (2021). Enhanced substrate stress relaxation promotes filopodia-mediated cell migration. NATURE MATERIALS, In Press. https://doi.org/10.5281/ZENODO.4562309

Adebowale, K., Gong, Z., Hou, J. C., Wisdom, K. M., Garbett, D., Lee, H., Nam, S., Meyer, T., Odde, D., Shenoy, V. B., & Chaudhuri, O. (2021). Enhanced substrate stress relaxation promotes filopodia-mediated cell migration. NATURE MATERIALS, https://doi.org/10.5281/ZENODO.4562309

Ahmadzadeh, H., Webster, M. R., Behera, R., Valencia, A. M. J., Wirtz, D., Weeraratna, A. T., & Shenoy, V. B. (2017). Modeling the two-way feedback between contractility and matrix realignment reveals a nonlinear mode of cancer cell invasion. Proceedings of the National Academy of Sciences of the United States of America, 114(9), E1617–E1626. https://doi.org/10.1073/pnas.1617037114

Ahmadzadeh, H., Webster, M. R., Behera, R., Valencia, A. M. J., Wirtz, D., Weeraratna, A. T., & Shenoy, V. B. (2017). Modeling the two-way feedback between contractility and matrix realignment reveals a nonlinear mode of cancer cell invasion. Proceedings of the National Academy of Sciences of the United States of America, 114(9), E1617–E1626. https://doi.org/10.1073/pnas.1617037114

Alisafaei, F., Gong, Z., Johnson, V. E., Dollé, J. P., Smith, D. H., & Shenoy, V. B. (2020). Mechanisms of local stress amplification in axons near the gray-white matter interface. Biophysical Journal, 119(7), 1290–1300. https://doi.org/10.1016/j.bpj.2020.08.024

Alisafaei, F., Gong, Z., Johnson, V. E., Dollé, J. P., Smith, D. H., & Shenoy, V. B. (2020). Mechanisms of local stress amplification in axons near the gray-white matter interface. Biophysical Journal, 119(7), 1290–1300. https://doi.org/10.1016/j.bpj.2020.08.024

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., Mandal, K., Saldanha, R., Swoger, M., Yang, H., Shi, X., Guo, M., Hehnly, H., Castañeda, C. A., Janmey, P. A., Patteson, A. E., & Shenoy, V. B. (2024). Vimentin is a key regulator of cell mechanosensing through opposite actions on actomyosin and microtubule networks. Communications Biology, 7(1), 658. https://doi.org/10.1038/s42003-024-06366-4

Alisafaei, F., Mandal, K., Saldanha, R., Swoger, M., Yang, H., Shi, X., Guo, M., Hehnly, H., Castañeda, C. A., Janmey, P. A., Patteson, A. E., & Shenoy, V. B. (2024). Vimentin is a key regulator of cell mechanosensing through opposite actions on actomyosin and microtubule networks. Communications Biology, 7(1), 658. https://doi.org/10.1038/s42003-024-06366-4

Alisafaei, F., Mandal, K., Swoger, M., Yang, H., Guo, M., Janmey, P. A., Patteson, A. E., & Shenoy, V. B. (2022). Vimentin Intermediate Filaments Can Enhance or Abate Active Cellular Forces in a Microenvironmental Stiffness-Dependent Manner. bioRxiv, 2022.2004.2002.486829-482022.486804.486802.486829. https://doi.org/10.1101/2022.04.02.486829 

Alisafaei, F., Mandal, K., Swoger, M., Yang, H., Guo, M., Janmey, P. A., Patteson, A. E., & Shenoy, V. B. (2022). Vimentin Intermediate Filaments Can Enhance or Abate Active Cellular Forces in a Microenvironmental Stiffness-Dependent Manner. bioRxiv, 2022.2004.2002.486829-482022.486804.486802.486829. https://doi.org/10.1101/2022.04.02.486829 

Alisafaei, F., Shakiba, D., Iannucci, L. E., Davidson, M. D., Pryse, K. M., Chao, P.-H. G., Burdick, J. A., Lake, S. P., Elson, E. L., Shenoy, V. B., Genin, G. M.(2022). Tension anisotropy drives phenotypic transitions of cells via two-way cell-ECM feedback. bioRxiv, 2022.2003.2013.484154-482022.484103.484113.484154. https://doi.org/10.1101/2022.03.13.484154 

Alisafaei, F., Shakiba, D., Iannucci, L. E., Davidson, M. D., Pryse, K. M., Chao, P.-H. G., Burdick, J. A., Lake, S. P., Elson, E. L., Shenoy, V. B., Genin, G. M.(2022). Tension anisotropy drives phenotypic transitions of cells via two-way cell-ECM feedback. bioRxiv, 2022.2003.2013.484154-482022.484103.484113.484154. https://doi.org/10.1101/2022.03.13.484154 

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

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 Cellhttps://doi.org/10.1091/MBC.E22-10-0469

Almeida, P., Janmey, P. A., & Kouwer, P. H. J. (2021). Fibrous hydrogels under multi‐axial deformation: Persistence length as the main determinant of compression softening. Advanced Functional Materials, 2010527. https://doi.org/10.1002/adfm.202010527

Almeida, P., Janmey, P. A., & Kouwer, P. H. J. (2021). Fibrous hydrogels under multi‐axial deformation: Persistence length as the main determinant of compression softening. Advanced Functional Materials, 2010527. https://doi.org/10.1002/adfm.202010527

Amiad Pavlov, D., Corredera, C. S., Dehghany, M., Heffler, J., Shen, K. M., Zuela-Sopilniak, N., Randell, R., Uchida, K., Jain, R., & Shenoy, V. (2024). Microtubule forces drive nuclear damage in LMNA cardiomyopathy. bioRxiv, 2024.2002. 2010.579774. https://doi.org/10.1101/2024.02.10.579774v1

Amiad Pavlov, D., Corredera, C. S., Dehghany, M., Heffler, J., Shen, K. M., Zuela-Sopilniak, N., Randell, R., Uchida, K., Jain, R., Shenoy, V., Lammerding, J., & Prosser, B. L. (2024). Microtubule forces drive nuclear damage in LMNA cardiomyopathy. bioRxiv, 2024.2002. 2010.579774. https://doi.org/10.1101/2024.02.10.579774v1

Avgoulas, E. I., Sutcliffe, M. P. F., Linderman, S. W., Birman, V., Thomopoulos, S., & Genin, G. M. (2019). Adhesive-based tendon-to-bone repair: failure modelling and materials selection. Journal of The Royal Society Interface, 16(153), 20180838. https://doi.org/10.1098/rsif.2018.0838

Avgoulas, E. I., Sutcliffe, M. P. F., Linderman, S. W., Birman, V., Thomopoulos, S., & Genin, G. M. (2019). Adhesive-based tendon-to-bone repair: failure modelling and materials selection. Journal of The Royal Society Interface, 16(153), 20180838. https://doi.org/10.1098/rsif.2018.0838

Ayariga, J. A., Dean, M., Nyairo, E., Thomas, V., & Dean, D. (2021). PLA/HA Multiscale nano-/micro-hybrid 3d scaffolds provide inductive cues to stems cells to differentiate into an osteogenic lineage. Additive Manufacturing for Medical Applications, 73(12), 3787–3797. https://doi.org/10.1007/S11837-021-04912-7

Ayariga, J. A., Dean, M., Nyairo, E., Thomas, V., & Dean, D. (2021). PLA/HA Multiscale nano-/micro-hybrid 3d scaffolds provide inductive cues to stem cells to differentiate into an osteogenic lineage. Additive Manufacturing for Medical Applications, 73(12), 3787–3797. https://doi.org/10.1007/S11837-021-04912-7

Babaei, B., Velasquez-Mao, A. J., Pryse, K. M., McConnaughey, W. B., Elson, E. L., & Genin, G. M. (2018). Energy dissipation in quasi-linear viscoelastic tissues, cells, and extracellular matrix. Journal of the Mechanical Behavior of Biomedical Materials, 84, 198–207. https://doi.org/10.1016/j.jmbbm.2018.05.011

Babaei, B., Velasquez-Mao, A. J., Pryse, K. M., McConnaughey, W. B., Elson, E. L., & Genin, G. M. (2018). Energy dissipation in quasi-linear viscoelastic tissues, cells, and extracellular matrix. Journal of the Mechanical Behavior of Biomedical Materials, 84, 198–207. https://doi.org/10.1016/j.jmbbm.2018.05.011

Babaei, B., Velasquez-Mao, A. J., Thomopoulos, S., Elson, E. L., Abramowitch, S. D., & Genin, G. M. (2017). Discrete quasi-linear viscoelastic damping analysis of connective tissues, and the biomechanics of stretching. Journal of the Mechanical Behavior of Biomedical Materials, 69, 193–202. https://doi.org/10.1016/j.jmbbm.2016.12.013

Babaei, B., Velasquez-Mao, A. J., Thomopoulos, S., Elson, E. L., Abramowitch, S. D., & Genin, G. M. (2017). Discrete quasi-linear viscoelastic damping analysis of connective tissues, and the biomechanics of stretching. Journal of the Mechanical Behavior of Biomedical Materials, 69, 193–202. https://doi.org/10.1016/j.jmbbm.2016.12.013

Ban, E., Franklin, J. M., Nam, S., Smith, L. R., Wang, H., Wells, R. G., Chaudhuri, O., Liphardt, J. T., & Shenoy, V. B. (2018). Mechanisms of plastic deformation in collagen networks induced by cellular forces. Biophysical Journal, 114(2), 450–461. https://doi.org/10.1016/j.bpj.2017.11.3739

Ban, E., Franklin, J. M., Nam, S., Smith, L. R., Wang, H., Wells, R. G., Chaudhuri, O., Liphardt, J. T., & Shenoy, V. B. (2018). Mechanisms of plastic deformation in collagen networks induced by cellular forces. Biophysical Journal, 114(2), 450–461. https://doi.org/10.1016/j.bpj.2017.11.3739

Ban, E., Wang, H., Matthew Franklin, J., Liphardt, J. T., Janmey, P. A., & Shenoy, V. B. (2019). Strong triaxial coupling and anomalous Poisson effect in collagen networks. Proceedings of the National Academy of Sciences of the United States of America, 116(14), 6790–6799. https://doi.org/10.1073/pnas.1815659116

Ban, E., Wang, H., Matthew Franklin, J., Liphardt, J. T., Janmey, P. A., & Shenoy, V. B. (2019). Strong triaxial coupling and anomalous Poisson effect in collagen networks. Proceedings of the National Academy of Sciences of the United States of America, 116(14), 6790–6799. https://doi.org/10.1073/pnas.1815659116

Basu, D., Codjoe, J. M., Veley, K. M., & Haswell, E. S. (2022). The Mechanosensitive ion channel msl10 modulates susceptibility to Pseudomonas syringae in Arabidopsis thaliana. Molecular Plant-Microbe Interations. https://doi.org/10.1094/MPMI-08-21-0207-FI

Basu, D., Codjoe, J. M., Veley, K. M., & Haswell, E. S. (2022). The Mechanosensitive ion channel msl10 modulates susceptibility to Pseudomonas syringae in Arabidopsis thaliana. Molecular Plant-Microbe Interations. https://doi.org/10.1094/MPMI-08-21-0207-FI

Basu, D., Shoots, J. M., & Haswell, E. S. (2020). Interactions between the N- and C-termini of the mechanosensitive ion channel AtMSL10 are consistent with a three-step mechanism for activation. Journal of Experimental Botany, 71(14), 4020–4032. https://doi.org/10.1093/jxb/eraa192

Basu, D., Shoots, J. M., & Haswell, E. S. (2020). Interactions between the N- and C-termini of the mechanosensitive ion channel AtMSL10 are consistent with a three-step mechanism for activation. Journal of Experimental Botany, 71(14), 4020–4032. https://doi.org/10.1093/jxb/eraa192

Benias, P. C., Wells, R. G., Sackey-Aboagye, B., Klavan, H., Reidy, J., Buonocore, D., Miranda, M., Kornacki, S., Wayne, M., Carr-Locke, D. L., & Theise, N. D. (2018). Structure and distribution of an unrecognized interstitium in human tissues. Scientific Reports, 8(1), 1–8. https://doi.org/10.1038/s41598-018-23062-6

Benias, P. C., Wells, R. G., Sackey-Aboagye, B., Klavan, H., Reidy, J., Buonocore, D., Miranda, M., Kornacki, S., Wayne, M., Carr-Locke, D. L., & Theise, N. D. (2018). Structure and distribution of an unrecognized interstitium in human tissues. Scientific Reports, 8(1), 1–8. https://doi.org/10.1038/s41598-018-23062-6

Bensel, B. M., Woody, M. S., Pyrpassopoulos, S., Goldman, Y. E., Gilbert, S. P., & Ostap, E. M. (2020). The mechanochemistry of the kinesin-2 KIF3AC heterodimer is related to strain-dependent kinetic properties of KIF3A and KIF3C. Proceedings of the National Academy of Sciences of the United States of America, 117(27), 15632–15641. https://doi.org/10.1073/pnas.1916343117

Bensel, B. M., Woody, M. S., Pyrpassopoulos, S., Goldman, Y. E., Gilbert, S. P., & Ostap, E. M. (2020). The mechanochemistry of the kinesin-2 KIF3AC heterodimer is related to strain-dependent kinetic properties of KIF3A and KIF3C. Proceedings of the National Academy of Sciences of the United States of America, 117(27), 15632–15641. https://doi.org/10.1073/pnas.1916343117

Bilkey, N., Li, H., Borodinov, N., Ievlev, A. v., Ovchinnikova, O. S., Dixit, R., & Foston, M. (2022). Correlated mechanochemical maps of Arabidopsis thaliana primary cell walls using atomic force microscope infrared spectroscopy. Quantitative Plant Biology, 3, e31. https://doi.org/10.1017/QPB.2022.20

Bilkey, N., Li, H., Borodinov, N., Ievlev, A. v., Ovchinnikova, O. S., Dixit, R., & Foston, M. (2022). Correlated mechanochemical maps of Arabidopsis thaliana primary cell walls using atomic force microscope infrared spectroscopy. Quantitative Plant Biology, 3, e31. https://doi.org/10.1017/QPB.2022.20

Bonnevie, E. D., Gullbrand, S. E., Ashinsky, B. G., Tsinman, T. K., Elliott, D. M., Chao, P. Hsiu G., Smith, H. E., & Mauck, R. L. (2019). Aberrant mechanosensing in injured intervertebral discs as a result of boundary-constraint disruption and residual-strain loss. Nature Biomedical Engineering, 3(12), 998–1008. https://doi.org/10.1038/s41551-019-0458-4

Bonnevie, E. D., Gullbrand, S. E., Ashinsky, B. G., Tsinman, T. K., Elliott, D. M., Chao, P. Hsiu G., Smith, H. E., & Mauck, R. L. (2019). Aberrant mechanosensing in injured intervertebral discs as a result of boundary-constraint disruption and residual-strain loss. Nature Biomedical Engineering, 3(12), 998–1008. https://doi.org/10.1038/s41551-019-0458-4

Borodinov, N., Bilkey, N., Foston, M., Ievlev, A. V., Belianinov, A., Jesse, S., Vasudevan, R. K., Kalinin, S. V., & Ovchinnikova, O. S. (2019). Application of pan-sharpening algorithm for correlative multimodal imaging using AFM-IR. Npj Computational Materials, 5(1), 1–9. https://doi.org/10.1038/s41524-019-0186-z

Borodinov, N., Bilkey, N., Foston, M., Ievlev, A. V., Belianinov, A., Jesse, S., Vasudevan, R. K., Kalinin, S. V., & Ovchinnikova, O. S. (2019). Application of pan-sharpening algorithm for correlative multimodal imaging using AFM-IR. Npj Computational Materials, 5(1), 1–9. https://doi.org/10.1038/s41524-019-0186-z

Borodinov, N., Bilkey, N., Foston, M., Ievlev, A. V., Belianinov, A., Jesse, S., Vasudevan, R. K., Kalinin, S. V., & Ovchinnikova, O. S. (2019). Spectral map reconstruction using pan-sharpening algorithm: enhancing chemical imaging with AFM-IR. Microscopy and Microanalysis, 25(S2), 1024–1025. https://doi.org/10.1017/s1431927619005853

Borodinov, N., Bilkey, N., Foston, M., Ievlev, A. V., Belianinov, A., Jesse, S., Vasudevan, R. K., Kalinin, S. V., & Ovchinnikova, O. S. (2019). Spectral map reconstruction using pan-sharpening algorithm: enhancing chemical imaging with AFM-IR. Microscopy and Microanalysis, 25(S2), 1024–1025. https://doi.org/10.1017/s1431927619005853

Boyle, J. J., Soepriatna, A., Damen, F., Rowe, R. A., Pless, R. B., Kovacs, A., Goergen, C. J., Thomopoulos, S., & Genin, G. M. (2019). Regularization-free strain mapping in three dimensions, with application to cardiac ultrasound. Journal of Biomechanical Engineering, 141(1). https://doi.org/10.1115/1.4041576

Boyle, J. J., Soepriatna, A., Damen, F., Rowe, R. A., Pless, R. B., Kovacs, A., Goergen, C. J., Thomopoulos, S., & Genin, G. M. (2019). Regularization-free strain mapping in three dimensions, with application to cardiac ultrasound. Journal of Biomechanical Engineering, 141(1). https://doi.org/10.1115/1.4041576

Boyle, M. J., Radhakrishnan, R., & Composto, R. J. (2024). Molecular Dynamics Study of the Effect of Grafting Density on Ion Diffusivity in a MARTINI Coarse-Grained Strong Polyelectrolyte Brush. Macromolecules. https://doi.org/10.1021/acs.macromol.4c01018

Boyle, M. J., Radhakrishnan, R., & Composto, R. J. (2024). Molecular Dynamics Study of the Effect of Grafting Density on Ion Diffusivity in a MARTINI Coarse-Grained Strong Polyelectrolyte Brush. Macromolecules. https://doi.org/10.1021/acs.macromol.4c01018

Calcutt, R., Vincent, R., Dean, D., Livingston Arinzeh, T., & Dixit, R. (2021). Plant cell adhesion and growth on artificial fibrous scaffolds as an in vitro model for plant development. Sci. Adv, 7, 1–11. https://www.science.org/doi/10.1126/sciadv.abj1469

Calcutt, R., Vincent, R., Dean, D., Livingston Arinzeh, T., & Dixit, R. (2021). Plant cell adhesion and growth on artificial fibrous scaffolds as an in vitro model for plant development. Sci. Adv, 7, 1–11. https://www.science.org/doi/10.1126/sciadv.abj1469

**  NOTE:  see press release for this publication HERE.

Cao, X., Ban, E., Baker, B. M., Lin, Y., Burdick, J. A., Chen, C. S., & Shenoy, V. B. (2017). Multiscale model predicts increasing focal adhesion size with decreasing stiffness in fibrous matrices. Proceedings of the National Academy of Sciences of the United States of America, 114(23), E4549–E4555. https://doi.org/10.1073/pnas.1620486114

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Cashin, J. L., Wirtz, A. J., Genin, G. M., & Zayed, M. (2022). A Fenestrated Balloon Expandable Stent System for the Treatment of Aortoiliac Occlusive Disease. Journal of Engineering and Science in Medical Diagnostics and Therapy, 6(1). https://doi.org/10.1115/1.4055877 

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Chang, J., Saraswathibhatla, A., Song, Z., Varma, S., Sanchez, C., Alyafei, N. H. K., Indana, D., Slyman, R., Srivastava, S., Liu, K., Bassik, M. C., Marinkovich, M. P., Hodgson, L., Shenoy, V., West, R. B., & Chaudhuri, O. (2023). Cell volume expansion and local contractility drive collective invasion of the basement membrane in breast cancer. Nature Materials, 1-12. https://doi.org/10.1038/s41563-023-01716-9

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Chang, J., Saraswathibhatla, A., Song, Z., Varma, S., Sanchez, C., Srivastava, S., Liu, K., Bassik, M. C., Marinkovich, M. P., Hodgson, L., Shenoy, V., West, R. B., & Chaudhuri, O. (2022). Collective invasion of the basement membrane in breast cancer driven by forces from cell volume expansion and local contractility. bioRxiv, 2022.2007.2028.501930-502022.501907.501928.501930. https://doi.org/10.1101/2022.07.28.501930 

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Charrier, E. E., Pogoda, K., Li, R., Park, C. Y., Fredberg, J. J., & Janmey, P. A. (2020). A novel method to make viscoelastic polyacrylamide gels for cell culture and traction force microscopy. APL Bioengineering, 4(3), 36104. https://doi.org/10.1063/5.0002750

Charrier, E. E., Pogoda, K., Li, R., Park, C. Y., Fredberg, J. J., & Janmey, P. A. (2020). A novel method to make viscoelastic polyacrylamide gels for cell culture and traction force microscopy. APL Bioengineering, 4(3), 36104. https://doi.org/10.1063/5.0002750

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