2024
Wang A, Lin X, Ng Chau K, Onuchic JN, Levine H, George JT. RACER-m leverages structural features for sparse T cell specificity prediction. In press. Science Advances. BioRvix doi: 10.1101/2023.08.06.552190.
Najafi A, Jolly MK, George JT. Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R. STAR Protocols 2024;5(1):102819.
2023
George JT. Optimal phenotypic adaptation in fluctuating environments. Biophysical Journal 2023;122:4414-4424.
Ghoreyshi ZS, George JT. Quantitative approaches for decoding the specificity of the human T cell repertoire. Frontiers in Immunology 2023;14:1228873.
Najafi A, Jolly MK, George JT. Population dynamics of the epithelial to mesenchymal transition elucidates the timing and distribution of phenotypic intratumoral heterogeneity. iScience 2023;26:106964
George JT, Levine H. Optimal cancer evasion in a dynamic immune microenvironment generates diverse post-escape tumor antigenicity profiles. eLife 2023;12:e82786.
Jain P, Corbo S, Kulsoom M, George JT, Levine H, Toneff M, Jolly MK. Epigenetic memory acquired during long-term EMT induction governs the recovery to epithelial state. Journal of the Royal Society Interface 2023;20(198):20220627.
2022
Ng Chau K, George JT, Lin X, Onuchic, JN, Levine H. Contact map dependence of a T-cell receptor binding repertoire. Phys Rev E 2022;106(1):014406.
Mandal S, Tejaswi T, Janivara R, Srikrishnan S, Thakur P, Sahoo S, Chakraborty P, Singh Sohal S, Levine H, George JT, Jolly MK. Transcriptopmic-based quantification of the epithelial-hybrid-mesenchymal spectrum across biological contexts. Biomolecules 2022;12(1):29.
Masuda H, Harano K, Miura S, Wang Y, Hirota Y, Harada O, Jolly MK, Matsunaga Y, Lim B, Wood AL, Parinyanitikul N, Lee HJ, Gong G, George JT, Levine H, Lucci A, Rao A, Seitz RS, Lee J, Wang X, Morris SW, Hout DR, Nakamura S, Krishnamurthy S, Uneo NT. Changes in triple-negative breast cancer molecular subtype in patients without pathological complete response after neoadjuvant systemic therapy. JCO Precision Oncology 2022;6:e2000368.
2021
Lin X, George JT, Schafer NP, Ng Chau K, Birnbaum ME, Clementi C, Onuchic JN, Levine H. Rapid assessment of T-cell receptor specificity of the immune repertoire. Nature Computational Science 2021;1(5):362-373.
Chakraborty P, George JT, Woodward WA, Levine H, Jolly MK. Gene expression profiles of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum. Translational Oncology 2021;14(4):101026.
George JT, Levine H. Implications of tumor-immune co-evolution on cancer evasion and optimized immunotherapy. Trends in Cancer 2021;7(4):373-383.
2020
Thankamony AP, Murali R, Karthikeyan N, Varghese BA, Teo WS, McFarland A, Roden DL, Holliday H, Konrad CV, Cazet A, Dodson E, Yang J, Baker LA, George JT, Levine H, Jolly MK, Swarbrick A, Nair R. Targeting the Id1-Kif11 axis in triple-negative breast cancer using combination therapy. Biomolecules 2020;10(9):1295.
Chakraborty P, George JT, Tripathi SC, Levine H, Jolly MK. Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum. Frontiers in Bioengineering and Biotechnology 2020;8:220.
George JT, Levine H. Sustained co-evolution in a stochastic model of cancer-immune interaction. Cancer Research 2020;80(4):811-819.
Lourenco AR, Ban Y, Crowley MJ, Lee SB, Ramchandani D, Du W, Elemento O, George JT, Jolly MK, Levine H, Sheng J, Wong ST, Altorki NK, Gao D. Differential contributions of pre- and post- EMT tumor cells in breast cancer metastasis. Cancer Research 2020;80(2):163-169.
Nihan Kilinc A, Sugiyama N, Kalathur RKR, Antoniadis H, Birogul H, Ishay-Ronen D, George JT, Levine H, Jolly MK, Cristofori G. Histone deacetylases, Mbd3/NuRD, and Tet2 hydroxylase are crucial regulators of epithelial-mesenchymal plasticity and tumor metastasis. Oncogene 2020;39(7):1498-1513.
2019
Thangavel H, De Angelis C, Vasaikar S, Bhat R, Jolly MK, Nagi C, Creighton CJ, Chen F, Dobrolecki LE, George JT, Kumar T, Abdulkareem NM, Mao S, Nardone A, Rimawi M, Osborne CK, Lewis MT, Levine H, Zhang B, Schiff R, Giuliano M, Trivedi MV. 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 2019;8(11):1772.
Bocci F, Tripathi SC, Vilchez Mercedes SA, George JT, Casabar JP, Wong PK, Hanash SM, Levine H, Onuchic JN, Jolly MK. NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype. Integrative Biology 2019;11(6):251-263.
Shinde A, Hardy SD, Kim D, Akhand SS, Jolly MK, Wang WH, Anderson JC, Khodadadi RB, Brown WS, George JT, Liu S, Wan J, Levine H, Willey CD, Krusemark CJ, Geahlen RL, Wendt MK. Spleen tyrosine kinase-mediated autophagy is required for epithelial-mesenchymal plasticity and metastasis in breast cancer. Cancer Research 2019;79(8):1831-1843.
Jolly MK, Ware KE, Xu S, Gilja S, Shetler S, Yang Y, Wang X, Austin G, Runyambo D, Hish AJ, DeWitt SB, George JT, Kreulen RT, Boss MK, Lazarides AL, Kerr DL, Gerber DG, Sivaraj D, Armstrong AJ, Dewhirst MW, Eward WC, Levine H, Somarelli JA. E-cadherin represses anchorage-independent growth in sarcomas through both signaling and mechanical mechanisms. Molecular Cancer Research 2019;17(6):1391-1402.
Li X, Jolly MK, George JT, Pienta KJ, Levine H. Computational modeling of the crosstalk between macrophage polarization and tumor cell plasticity in the tumor microenvironment. Frontiers in Oncology 2019;9:10.
Jia D, George JT, Tripathi SC, Kundnani DL, Lu M, Hanash SM, Onuchic JN, Jolly MK, Levine H. Testing the gene expression classification of the EMT spectrum. Physical Biology 2019;16(2):025002.
2018
George JT, Levine H. Stochastic modeling of tumor progression and immune evasion. Journal of Theoretical Biology 2018;458:148-155.
Jolly MK, Preca BT, Tripathi SC, Jia D, George JT, Hanash SM, Brabletz T, Stemmler MP, Maurer J, Levine H. Interconnected feedback loops among ESRP1, HAS2, and CD44 regulate epithelial-mesenchymal plasticity in cancer. APL Bioengineering 2018;2(3):031908.
Bocci F, Jolly MK, George JT, Levine H, Onuchic JN. A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells, and Notch-Jagged signaling. Oncotarget 2018;9(52):29906-29920.
2017
George JT, Jolly MK, Xu S, Somarelli JA, Levine H. Survival outcomes in cancer patients predicted by a partial EMT gene expression scoring metric. Cancer Research 2017;77(22):6415-6428.
George JT, Kessler DA, Levine H. Effects of thymic selection on T cell recognition of foreign and tumor antigenic peptides. Proceedings of the National Academy of Sciences USA 2017;114(38):E7875-E7881.