selected publications academic article Wang, A., Lin, X., Chau, K. N., Onuchic, J. N., Levine, H., & George, J. T. (2024). RACER-m leverages structural features for sparse T cell specificity prediction. Science Advances. 10(20), eadl0161. Najafi, A., Jolly, M. K., & George, J. T. (2024). Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R. STAR Protocols. 5(1), 102819. George, J. T. (2023). Optimal phenotypic adaptation in fluctuating environments. Biophysical Journal. 122(22), 4414-4424. Najafi, A., Jolly, M. K., & George, J. T. (2023). Population dynamics of EMT elucidates the timing and distribution of phenotypic intra-tumoral heterogeneity. iScience. 26(7), 106964-106964. George, J. T., & Levine, H. (2023). Optimal cancer evasion in a dynamic immune microenvironment generates diverse post-escape tumor antigenicity profiles. eLife. 12, e82786. Najafi, A., Jolly, M. K., & George, J. T. (2023). Abstract 1231: A stochastic data-driven model predicts the timing and distribution of the epithelial-mesenchymal transition. Cancer Research. 83(7_Supplement), 1231-1231. Chau, K. N., George, J. T., Onuchic, J. N., Lin, X., & Levine, H. (2023). Contact map dependence of a T-cell receptor binding repertoire. 122(3), 271a-272a. Jain, P., Corbo, S., Mohammad, K., Sahoo, S., Ranganathan, S., George, J. T., ... Jolly, M. K. (2023). Epigenetic memory acquired during long-term EMT induction governs the recovery to the epithelial state. Journal of the Royal Society Interface. 20(198), 20220627. Ng Chau, K., George, J. T., Onuchic, J. N., Lin, X., & Levine, H. (2022). Contact map dependence of a T-cell receptor binding repertoire. Physical Review E. 106(1-1), 014406. Masuda, H., Harano, K., Miura, S., Wang, Y., Hirota, Y., Harada, O. i., ... Ueno, N. T. (2022). Changes in Triple-Negative Breast Cancer Molecular Subtypes in Patients Without Pathologic Complete Response After Neoadjuvant Systemic Chemotherapy. JCO Precision Oncology. 6(6), e2000368. Mandal, S., Tejaswi, T., Janivara, R., Srikrishnan, S., Thakur, P., Sahoo, S., ... Jolly, M. K. (2021). Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts. Biomolecules. 12(1), 29-29. Lin, X., George, J. T., Schafer, N. P., Chau, K. N., Birnbaum, M. E., Clementi, C., Onuchic, J. N., & Levine, H. (2021). Rapid Assessment of T-Cell Receptor Specificity of the Immune Repertoire. 1(5), 362-373. Chakraborty, P., George, J. T., Woodward, W. A., Levine, H., & Jolly, M. K. (2021). Gene expression profiles of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum. Transl Oncol. 14(4), 101026-101026. George, J. T., & Levine, H. (2021). Implications of Tumor-Immune Coevolution on Cancer Evasion and Optimized Immunotherapy. 7(4), 373-383. Thankamony, A. P., Murali, R., Karthikeyan, N., Varghese, B. A., Teo, W. S., McFarland, A., ... Nair, R. (2020). Targeting the Id1-Kif11 Axis in Triple-Negative Breast Cancer Using Combination Therapy. Biomolecules. 10(9), 1295-1295. George, J. T., Garber, H. R., Molldrem, J. J., & Levine, H. (2020). Abstract B59: Co-evolution between tumor cells and immune system in the setting of T-cell immunotherapy. CANCER IMMUNOLOGY RESEARCH. 8(4_Supplement), b59-b59. George, J. T., & Levine, H. (2020). Abstract A104: A stochastic model of tumor-immune evasion predicts sustained coevolution and tumor antigen downregulation. 8(3_Supplement), a104-a104. George, J. T., & Levine, H. (2020). Sustained Coevolution in a Stochastic Model of Cancer-Immune Interaction. 80(4), 811-819. Nihan Kilinc, A., Sugiyama, N., Reddy Kalathur, R. K., Antoniadis, H., Birogul, H., Ishay-Ronen, D., ... Christofori, G. (2020). Histone deacetylases, Mbd3/NuRD, and Tet2 hydroxylase are crucial regulators of epithelial-mesenchymal plasticity and tumor metastasis. Oncogene. 39(7), 1498-1513. Lourenco, A. R., Ban, Y. i., Crowley, M. J., Lee, S. B., Ramchandani, D., Du, W., ... Gao, D. (2020). Differential Contributions of Pre- and Post-EMT Tumor Cells in Breast Cancer Metastasis. Cancer Research. 80(2), 163-169. Chakraborty, P., George, J. T., Tripathi, S., Levine, H., & Jolly, M. K. (2020). Comparative Study of Transcriptomics-Based Scoring Metrics for the Epithelial-Hybrid-Mesenchymal Spectrum. Frontiers in Bioengineering and Biotechnology. 8, 220. Thangavel, H., De Angelis, C., Vasaikar, S., Bhat, R., Jolly, M. K., Nagi, C., ... Trivedi, M. V. (2019). A CTC-Cluster-Specific Signature Derived from OMICS Analysis of Patient-Derived Xenograft Tumors Predicts Outcomes in Basal-Like Breast Cancer. Journal of Clinical Medicine. 8(11), 1772-1772. George, J. T., Molldrem, J. J., & Levine, H. (2019). Abstract 1195: Stochastic co-evolution of the adaptive immune system and an evading cancer population. Cancer Research. 79(13_Supplement), 1195-1195. Thangavel, H., Angelis, C. D., Vasaikar, S., Bhat, R., Jolly, M. K., Dobrolecki, L. E., ... Trivedi, M. V. (2019). Abstract 2783: OMICS analysis of breast cancer PDX tumors to determine CTC-cluster-specific signature in predicting breast cancer metastasis. Cancer Research. 79(13_Supplement), 2783-2783. Jolly, M. K., Ware, K. E., Xu, S., Gilja, S., Shetler, S., Yang, Y., ... Somarelli, J. A. (2019). E-Cadherin Represses Anchorage-Independent Growth in Sarcomas through Both Signaling and Mechanical Mechanisms. 17(6), 1391-1402. Bocci, F., Tripathi, S. C., Vilchez Mercedes, S. A., George, J. T., Casabar, J. P., Wong, P. K., ... Jolly, M. K. (2019). NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype. Integrative Biology: interdisciplinary approaches for molecular and cellular life sciences. 11(6), 251-263. George, J. T., Levine, H., Molldrem, J. J., & Garber, H. (2019). Stochastic cancer-immune coevolution: Implications for cancer incidence and immunotherapeutic efficacy. Journal of Clinical Oncology. 37(15_suppl), e14023-e14023. Shinde, A., Hardy, S. D., Kim, D., Akhand, S. S., Jolly, M. K., Wang, W., ... Wendt, M. K. (2019). Spleen Tyrosine Kinase-Mediated Autophagy Is Required for Epithelial-Mesenchymal Plasticity and Metastasis in Breast Cancer. Cancer Research. 79(8), 1831-1843. Li, X., Jolly, M. K., George, J. T., Pienta, K. J., & Levine, H. (2019). Computational Modeling of the Crosstalk Between Macrophage Polarization and Tumor Cell Plasticity in the Tumor Microenvironment. Frontiers in Oncology. 9, 10. Jia, D., George, J. T., Tripathi, S. C., Kundnani, D. L., Lu, M., Hanash, S. M., ... Levine, H. (2019). Testing the gene expression classification of the EMT spectrum. Physical Biology. 16(2), 025002-025002. George, J. T., & Levine, H. (2018). Stochastic modeling of tumor progression and immune evasion. Journal of Theoretical Biology. 458, 148-155. Jolly, M. K., Preca, B., Tripathi, S. C., Jia, D., George, J. T., Hanash, S. M., ... Levine, H. (2018). Interconnected feedback loops among ESRP1, HAS2, and CD44 regulate epithelial-mesenchymal plasticity in cancer. APL Bioengineering. 2(3), 031908-031908. Bocci, F., Jolly, M. K., George, J. T., Levine, H., & Onuchic, J. N. (2018). A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling. Oncotarget. 9(52), 29906-29920. George, J. T., Jolly, M. K., Xu, S., Somarelli, J. A., & Levine, H. (2017). Survival Outcomes in Cancer Patients Predicted by a Partial EMT Gene Expression Scoring Metric. 77(22), 6415-6428. George, J. T., Kessler, D. A., & Levine, H. (2017). Effects of thymic selection on T cell recognition of foreign and tumor antigenic peptides. Proceedings of the National Academy of Sciences of the United States of America. 114(38), E7875-E7881. George, J. T., Jolly, M. K., & Levine, H. (2017). Abstract 563: Quantitative EMT expression score for predicting survival outcome. Cancer Research. 77(13_Supplement), 563-563. Fei, R., George, J. T., Park, J., Means, A. K., & Grunlan, M. A. (2013). Ultra-strong thermoresponsive double network hydrogels. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 9(10), 2912-2919. Fei, R., George, J. T., Park, J., Means, A. K., & Grunlan, M. A. (2013). Ultra-strong thermoresponsive double network hydrogels. SOFT MATTER. 9(10), 2912-2919. Fei, R., George, J. T., Park, J., & Grunlan, M. A. (2012). Thermoresponsive nanocomposite double network hydrogels. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 8(2), 481-487. Fei, R., George, J. T., Park, J., & Grunlan, M. A. (2012). Thermoresponsive nanocomposite double network hydrogels. SOFT MATTER. 8(2), 481-487. Ghoreyshi, Z. S., Teimouri, H., Kolomeisky, A. B., & George, J. T. Integration of kinetic data into affinity-based models for improved Tcell specificity prediction. Biophysical Journal. S0006-3495(24)00711-2. conference paper George, J. T. (2022). Stochastic modeling uncovers the interplay between early cancer progression and adaptive immune-specific cancer escape. Cancer Research. Thangavel, H., Angelis, C. D., Vasaikar, S., Bhat, R., Jolly, M. K., Dobrolecki, L. E., ... Trivedi, M. V. (2019). Abstract 2783: OMICS analysis of breast cancer PDX tumors to determine CTC-cluster-specific signature in predicting breast cancer metastasis. 2783-2783. Grunlan, M. A., Fei, R., George, J. T., & Means, A. K. (2013). High strength thermoresponsive double network hydrogels. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. George, J. T., Fei, R., Park, J. T., & Grunlan, M. A. (2012). Thermoresponsive double network hydrogels with improved mechanical properties. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. institutional repository document Fan, Y., & George, J. T. (2024). Distinct evolutionary patterns of tumor immune escape and elimination determined by ECM architectures Wang, A., Lin, X., Chau, K. N., Onuchic, J. N., Levine, H., & George, J. T. (2023). RACER-m Leverages Structural Features for Sparse T Cell Specificity Prediction George, J. T. (2023). Optimal Cellular Phenotypic Adaptation in Fluctuating Environments Najafi, A., Jolly, M. K., & George, J. T. (2023). Population Dynamics of EMT Elucidates the Timing and Distribution of Phenotypic Intra-tumoral Heterogeneity Jain, P., Corbo, S., Mohammad, K., George, J. T., Levine, H., Toneff, M., & Jolly, M. K. (2022). Epigenetic memory acquired during long-term EMT induction governs the recovery to the epithelial state George, J. T., & Levine, H. (2022). Optimal Cancer Evasion in a Dynamic Immune Microenvironment Chau, K. N., George, J. T., Onuchic, J. N., Lin, X., & Levine, H. (2021). Contact map dependence of a T cell receptor binding repertoire Mandal, S., Tejaswi, T., Janivara, R., Srikrishnan, S., Thakur, P., Sahoo, S., ... Jolly, M. K. (2021). Transcriptomic-based quantification of the epithelial-hybrid-mesenchymal spectrum across biological contexts Chakraborty, P., George, J. T., Woodward, W. A., Levine, H., & Jolly, M. K. (2020). Gene expression profiles of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum Lin, X., George, J. T., Schafer, N. P., Chau, K. N., Birnbaum, M. E., Clementi, C., Onuchic, J. N., & Levine, H. (2020). Rapid Assessment of T-Cell Receptor Specificity of the Immune Repertoire Chakraborty, P., George, J. T., Tripathi, S., Levine, H., & Jolly, M. K. (2020). Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum Murali, R., Varghese, B. A., Karthikeyan, N., Archana, P. T., Teo, W. S., McFarland, A., ... Nair, R. (2019). Targeting the Id1-Kif11-Aurka axis in triple negative breast cancer using combination therapy George, J. T., & Levine, H. (2019). Sustained Co-evolution in a Stochastic Model of the Cancer-Immune Interaction Jia, D., George, J. T., Tripathi, S. C., Kundnani, D. L., Lu, M., Hanash, S. M., ... Levine, H. (2018). Testing the Gene Expression Classification of the EMT Spectrum Li, X., Jolly, M. K., George, J. T., Pienta, K. J., & Levine, H. (2018). Computational modeling of the crosstalk between macrophage polarization and tumor cell plasticity in the tumor microenvironment Bocci, F., Tripathi, S. C., Mercedes, S., George, J. T., Casabar, J. P., Wong, P. K., ... Jolly, M. K. (2018). NRF2 activates a partial Epithelial-Mesenchymal Transition and is maximally present in a hybrid Epithelial/Mesenchymal phenotype Jolly, M. K., Ware, K. E., Xu, S., Gilja, S., Shetler, S., Yang, Y., ... Somarelli, J. A. (2018). E-cadherin represses anchorage-independent growth in sarcomas through both signaling and mechanical mechanisms Bocci, F., Jolly, M. K., George, J., Levine, H., & Onuchic, J. N. (2018). A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling Villela-Castrejon, J., Levine, H., Onuchic, J. N., George, J. T., & Jia, D. Computational modeling of cancer cell metabolism along the catabolic-anabolic axes Teimouri, H., Ghoreyshi, Z. S., Kolomeisky, A. B., & George, J. T. Feature Selection Enhances Peptide Binding Predictions for TCR-Specific Interactions Shrestha, P., Ghoreyshi, Z. S., & George, J. T. How Modulation of the Tumor Microenvironment Drives Cancer Immune Escape Dynamics Ghoreyshi, Z. S., Teimouri, H., Kolomeisky, A. B., & George, J. T. Integration of Kinetic Data into Affinity-Driven Models for Improved T Cell-Antigen Specificity Prediction
teaching activities BMEN341 Biofluid Mechanics Instructor BMEN341 Biotransport Instructor BMEN491 Hnr-research Instructor BMEN689 Sptp: Stochastic Model & Math Instructor BMEN691 Research Instructor