Cancer Systems Biology Laboratory

​*denotes equal contribution; Authors from the group are underlined

 

Preprints

1. Mohanty A, Nam A, Pozhiktov A, Bhattacharyya S, Yang L, Nathan A, Xiewei W, Srivastava S, Mambetsariev I, Nelson M, Pangeni R, Raz D, Cheng Y, He Y, Orban J, Subbalakshmi A R , Nasser MW, Batra SK, Jolly MK, Kulkarni P, Maserralli E, Salgia R (2019). A non-genetic mechanism for chemoresistance in lung cancer: the role of integrin β4/paxillin axis. bioRxiv: 781807

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2. Tripathi S, Levine H, Jolly MK (2019). A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells. bioRxiv: 592691

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3. Kumar S, Hari K, Jolly MK, Rangarajan A (2019). Feedback loops involving AMPK, ERK and TFEB in matrix detached leads to non-genetic heterogeneity. bioRxiv: 736546

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4. Murali M, Varghese BA, Karthikeyan N, Archana PT, Teo WS, McFarland A, Roden DL, Holliday H, Konrad C, Cazet A, Dodson E, George JT, Levine H, Jolly MK, Swarbick A, Nair R (2019). Targeting the Id1-Kif11-Aurka axis in triple negative breast cancer using combination therapy. bioRxiv: 760686

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5. Iyer A, Gupta K, Sharma S, Hari K, Lee YF, Ramalingam N, Yap Y-S, West J, Bhagat AA, Subramani BV, Sabuwala B, Jolly MK, Ramalingam N, Sengupta D (2019). Machine learning based identification and characterization of circulating tumor cells. bioRxiv: 867200

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6. Hari K, Sabuwala B, Subramani BV, La Porta C, Zapperi S, Font-Clos F, Jolly MK (2019). Identifying inhibitors of epithelial-mesenchymal plasticity using a network topology based approach. bioRxiv: 854307

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7. Archana PT*, Saxena K*, Murali R, Jolly MK, Nair R (2019). Cancer Stem Cell plasticity - a deadly deal. Preprints: 2019120388

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8. Chakraborty P, George JT, Tripathi S, Levine H, Jolly MK (2020). Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum. bioRxiv: 892414

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Peer-reviewed publications:

2019:

71. Sarkar S, Sinha SK, Levine H, Jolly MK, Dutta PS (2019). Anticipating critical transitions in epithelial-hybrid-mesenchymal cell fate determination. Proceedings of National Academy of Sciences USA (PNAS), in press

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70. Yang Y, Jolly MK, Levine H (2019). Computational modeling of collective cell migration: mechanical and biochemical aspects. Advances in Experimental Medicine and Biology, 1146: 1-11

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69. Kilinc AN, Kalathur RK, Sugiyama N, Antonaidis H, Birogul H, Ishay-Ronen D, George JT, Levine H, Jolly MK, Christofori G (2019). Histone deactylases, Mbd3/NuRD and Tet2 hydroxylase are crucial regulators of epithelial-mesenchymal plasticity and tumor metastasis. Oncogene, in press

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68. Celia-Terrassa T, Jolly MK (2019). Cancer Stem Cells and Epithelial-to-Mesenchymal Transition in Cancer Metastasis. Cold Spring Harb Perspect Med, in press

 

67. Jolly MK, Celia-Terrassa T. Dynamics of phenotypic heterogeneity associated with EMT and stemness during cancer progression (2019). Journal of Clinical Medicine, 8 (10): 1542

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66. Lourenco AR, Ban Y, Crowley MJP, Lee S, Ramchandani D, Du W, Elemento O, George JT, Jolly MK, Levine H, Sheng J, Wong ST, Altorki NK, Gao D (2019). Differential contributions of pre- and post-EMT tumor cells in the breast to lung metastasis. Cancer Research, in press

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65. Thangavel H, Angelis CD, 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, Obsorne K, Lewis MT, Levine H, Zhang B, Schiff R, Giuliano M, Trivedi MV (2019). A CTC-cluster-specific signature derived from OMICS analysis of patient-derived xenograft tumors predicts outcomes in basal-like breast cancers. Journal of Clinical Medicine, 8 (11): 1772

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64. Kalvala A, Wallet P, Yang L, Wang C, Li H, Nam A, Nathan A, Mambetsariev I, Poroyko V, Gao H, Chu P, Sattler M, Bild A, Manuel ER, Lee PP, Jolly MK, Kulkarni P, Salgia R (2019). Phenotypic Switching of Naïve T cells to Immune-suppressive Treg-like Cells by Mutant KRAS. Journal of Clinical Medicine, 8 (10): 1726

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63. Kang T, Bocci F, Jolly MK, Levine H, Onuchic JN, Levchenko A (2019). Pericytes enable effective angiogenesis in the presence of pro-inflammatory signals. Proceedings of National Academy of Sciences USA (PNAS), 116(47): 23551-23561

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62. Bocci F, Jolly MK, Onuchic JN (2019). A biophysical model uncovers the size distribution of migrating cell clusters across cancer types. Cancer Resarch, 79 (21): 5527-5535

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61. Nath B, Bidkar AP, Kumar V, Dalal A, Jolly MK, Ghosh SS, Biswas G (2019). Deciphering hydrodynamic and drug-resistant behaviors of metastatic EMT breast cancer cells moving in a constricted microcapillary. Journal of Clinical Medicine, 8 (8): 1194

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60. Saxena K, Subbalakshmi A R, Jolly MK (2019). Phenotypic heterogeneity in circulating tumor cells and its prognostic value in metastasis and overall survival. EBiomedicine, 46: 4-5

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59. Saxena K, Jolly MK (2019). Acute vs. chronic vs. cyclic hypoxia: their differential dynamics, molecular mechanisms, and effects on tumor progression. Biomolecules, 9 (8): 339

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58. Jia W, Deshmukh A, Mani SA, Jolly MK, Levine H (2019). A possible role for epigenetic feedback regulation in the dynamics of the Epithelial-Mesenchymal Transition (EMT). Physical Biology, 16 (6): 066004

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57. Mambetsariav I, Mirzapoiazova T, Lennon F, Jolly MK, Li H, Nasser MW, Vora L, Kulkarni P, Batra SK, Salgia R (2019). Small cell lung cancer therapeutic responses through fractal measurements: from radiology to mitochondrial biology. Journal of Clinical Medicine, 8 (7): 1038

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56. Bocci F*,Tripathi SC*, Vilchez S*, George JT, Casabar JC, Wong PK, Hanash SM, Levine H, Onuchic JN, Jolly MK (2019). NRF2 inhibits a complete epithelial-mesenchymal transition and is maximally expressed in a hybrid epithelial/mesenchymal phenotype. Integrative Biology, 11 (6): 251-263

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55. Varankar S, More M, Ancy A, Pansare K, Kumar B, Narayanan NJ, Jolly MK, Mali AM, Bapat SA (2019). Functional balance between Tcf21-Slug defines cellular plasticity and migratory modalities in high grade serous ovarian cancer cell lines. Carcinogenesis, in press

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54. Jia D, Li X, Bocci F, Tripathi S, Deng Y, Jolly MK, Onuchic JN, Levine H (2019). Quantifying cancer epithelial-mesenchymal plasticity and its association with stemness and immune response. Journal of Clinical Medicine, 8 (5): 725

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53. Lin X, Kulkarni P, Bocci F, Schafer N, Roy S, Tsai M-Y, He Y, Chen Y, Rajagopalan K, Mooney SM, Zeng Y, Weninger K, Grishaev A, Onuchic JN, Levine H, Wolynes PG, Salgia R, Rangarajan G, Uversky V, Orban J, Jolly MK (2019). Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level. Biomolecules, 9(2): E77

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52. Bocci F, Levine H, Onuchic JN, Jolly MK (2019). Deciphering the dynamics of epithelial-hybrid-mesenchymal transition and cancer stem cells in tumor progression. Current Stem Cell Reports, 5 (1): 11-21

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51. Jolly MK*, Ware KA*, Xu S, Gilja S, Shetler S, Yang Y, Wang X, Austin RG, Runyambo D, Hish AJ, Dewitt SB, George JT, Kruelen RT, Boss M-K,  Lazarides AL, Kerr DL, Gerber DG, Sivaraj D, Armstrong AJ, Dewhirst MW, Eward WC, Levine H, Somarelli JA (2019). E-cadherin represses anchorage-independent growth in sarcomas through both signaling and mechanical mechanisms. Molecular Cancer Research, 17 (6): 1391-1402

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50. 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 (2019). Spleen tyrosine kinase-mediated autophagy is required for epithelial-mesenchymal plasticity and metastasis in breast cancer. Cancer Research, 79 (8): 1832-1843 (Cover article)

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​​49. Xu S, Ware KE, Ding Y, Kim SY, Sheth M, Chan W, Townsend J, Armstrong AJ, Eward WC, Jolly MK, Somarelli JA (2019). An integrative systems biology and experimental approach identifies convergence of gene expression circuitry on alterations in epithelial plasticity, metabolism, and autophagy to promote chemoresistance. Journal of Clinical Medicine, 8 (2): 205 

(Cover article)

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​​48. Li X*, Jolly MK*, George JT, Pienta KJ, Levine H (2019). Computational modeling of the crosstalk between differently polarized macrophages and tumor cell plasticity in a tumor microenvironment. Frontiers in Oncology, 9:10

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47. Hewelt B, Li H, Jolly MK, Kulkarni P, Mambetsariev I, Salgia R (2019). The DNA walk and its demonstration of deterministic chaos – relevance to genomic alterations in lung cancer. Bioinformatics, in press

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46. Bocci F*, Gearhart-Serna L*, Boareto M, Riberio M, Ben-Jacob E, Devi GR, Levine H, Onuchic JN, Jolly MK (2019). Toward understanding cancer stem cell heterogeneity in the tumor microenvironment. Proceedings of National Academy of Sciences USA (PNAS), 116(1): 148-157

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45. Jia D*, George JT*, Tripathi SC, Kundnani D, Lu M, Hanash SM, Onuchic JN, Jolly MK, Levine H (2019). Testing the gene expression classification of the EMT spectrum. Physical Biology, 16 (2): 025002

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44. Biswas K, Jolly MK, Ghosh A (2019). Stability and mean residence times for hybrid epithelial/mesenchymal phenotype. Physical Biology, 16 (2): 025003

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43. Jolly MK, Somarelli JA, Sheth M, Biddle A, Tripathi SC, Hanash SM, Armstrong AJ, Bapat SA, Rangarajan A, Levine H (2019). Hybrid epithelial/mesenchymal phenotype promote metastasis and therapy resistance across carcinomas. Pharmacology & Therapeutics, 194: 161-184

 

2018:

42. Eapen MS, Hansbro PM, Callerfelt A-K L, Jolly MK, Myers S, Sharma P, Markos J, Chia C, Larby J, Haug G, Hardikar A, Weber HC, Mabeza G, Cavalheri V, Khor YH, McDonald CF, Sohal SS (2018). Chronic obstructive pulmonary disease (COPD) and lung cancer: underlying pathophysiology and new therapeutic modalities. Drugs, 78 (16): 1717-1740 

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41. Jolly MK*, Preca BT*, Tripathi SC*, Jia D, George JT, Hanash SM, Brabletz T, Stemmler MP, Maurer J, Levine H (2018). Regulation of epithelial-mesenchymal plasticity through interconnected feedback loops between ZEB1, ESRP1, HAS2, and CD44. APL Bioengineering, 2 (3): 031908​

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40. Jolly MK, Mani SA, Levine H (2018). Hybrid epithelial/mesenchymal phenotype(s): the ‘fittest’ phenotype(s) for metastasis? BBA Reviews on Cancer, 1870 (2): 151-157

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39. Bocci F, Jolly MK, George JT, Levine H, Onuchic JN (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 (Highlighted in News & Views)

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38. Tripathi S, Jolly MK, Woodward WA, Levine H, Deem MW (2018). Analysis of hierarchical organization in gene expression networks reveal underlying principles of collective tumor cell dissemination and metastatic aggressiveness of inflammatory breast cancer. Frontiers in Oncology, 8: 244

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37. Salgia R, Jolly MK, Dorff T, Lau C, Weninger K, Orban J, Kulkarni P (2018). Prostate-associated Gene 4 (PAGE4): leveraging the conformational dynamics of a dancing protein cloud as a therapeutic target. Journal of Clinical Medicine, 7 (6): 156

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36. Lin X, Roy S, Jolly MK, Bocci F, Schafer N, Tsai MY, Kulkarni P, Orban J, Grishaev A, Weninger K, Rangarajan G, Levine H, Onuchic JN (2018). PAGE4 and conformational switching: insights from molecular dynamics simulations and implications for prostate cancer. Journal of Molecular Biology, 430 (16): 2422-2438

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35. Jolly MK, Kulkarni P, Weninger K, Orban J, Levine H (2018). Phenotypic plasticity, bet-hedging, and androgen independence in prostate cancer: role of non-genetic heterogeneity. Frontiers in Oncology, 8: 50

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34. Evans MK, Brown M, Geradts J, Bao X, Robinson TJ, Jolly MK, Vermeulen PB, Palmer G, Gromeier M, Levine H, Morse MA, van Laere SJ, Devi GR (2018). Crosstalk between MNK and XIAP mediates NFkB activity to promote a hyperproliferative breast cancer phenotype. Cancer Research, 78 (7): 1726-1738

 

2017:

33. George JT*, Jolly MK*, Xu S, Somarelli JA, Levine H (2017). Survival outcome in cancer patients predicted by a partial EMT gene expression scoring metric. Cancer Research, 77 (22): 6415-6428

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32. Bocci F*, Jolly MK*, Tripathi SC*, Aguilar M, Hanash SM, Levine H, Onuchic JN (2017). Numb inhibits a complete epithelial-mesenchymal transition by modulating Notch signaling. Journal of the Royal Society Interface, 14 (136): 20170512

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31. Jolly MK, Boareto M, Debeb B, Aceto N, Farach-Carson MC, Woodward WA, Levine H (2017). Inflammatory Breast Cancer: a model for investigating cluster-based dissemination. NPJ Breast Cancer, 3: 21

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30. Kulkarni P, Jolly MK, Jia D, Mooney SM, Bhargava A, Kagohara LT, Chen Y, Hao P, He Y, Veltri RW, Grishaev A, Weninger K, Levine H, Orban J (2017). Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and its potential role in phenotypic heterogeneity. Proceedings of the National Academy of Sciences USA, 114 (13): E2644-E2653

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29. Jia D, Jolly MK, Harrison W, Boareto M, Ben-Jacob E, Levine H (2017). Operating principles of tristable circuits regulating cellular differentiation. Physical Biology, 14: 035007

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28. Jia D, Jolly MK, Tripathi SC, Hollander DP, Huang B, Lu M, Celiktas M, Ramirez-Pena E, Ben-Jacob E, Onuchic JN, Hanash SM, Mani SA, Levine H (2017). Distinguishing mechanisms underlying EMT tristability. Cancer Convergence, 1(1): 2

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27. Jolly MK, Tripathi SC, Somarelli JA, Hanash SM, Levine H (2017). Epithelial-mesenchymal plasticity: how have quantitative mathematical models helped improve our understanding? Molecular Oncology, 11 (7): 739-754

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26. Jolly MK, Ware K, Gilja S, Somarelli JA, Levine H (2017). EMT and MET: necessary or permissive for metastasis? Molecular Oncology, 11 (7): 755-769 (Among top 20 downloaded articles in Jan 2017-Dec 2018 period)

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25. Jolly MK, Ward C, Eapen MS, Myers S, Hallgren O, Levine H, Sohal S (2017). Epithelial mesenchymal transition (EMT), a spectrum of states: role in both lung development and disease. Developmental Dynamics, 247 (3): 346-358 (Among top 20 downloaded articles in Jan 2017-Dec 2018 period)

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24. Jolly MK, Levine H. Computational systems biology of epithelial-hybrid-mesenchymal transitions (2017). Current Opinion in Systems Biology, 3: 1-6

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23. Jia D, Jolly MK, Kulkarni P, Levine H (2017). Phenotypic plasticity and cell-fate decisions in cancer: insights from dynamical systems theory. Cancers, 9 (7): 70

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22. Mooney SM*, Talebian V*, Jolly MK*, Jia D*, Gromala M, Levine H, McConkey BJ (2017). GRHL2/ZEB feedback loop – a key axis in the regulation of EMT in breast cancer. Journal of Cellular Biochemistry, 118 (9): 2559-2570

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21. Tripathi SC, Fahrmann JF, Celiktas M, Aguilar M, Marini KM, Jolly MK, Katayama H, Wang H, Murage EN, Dennison JB, Watkins N, Levine H, Ostrin EJ, Taguchi A, Hanash SM (2017). MCAM mediates chemoresistance in small cell lung cancer via PI3K/AKT/SOX2 Signaling Pathway. Cancer Research, 77 (16): 4414-4425

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20.Ware KE, Gilja S, Xu S, Shetler S, Jolly MK, Wang X, Bartholf-Dewitt S, Hish AJ, Jordan S, Eward W, Levine H, Armstrong AJ, Somarelli JA (2017). Induction of mesenchymal-epithelial transitions in sarcoma cells. Journal of Visualized Experiments, 112

 

2016:

19. Somarelli JA, Shelter S, Jolly MK, Wang S, Bartholf-Dewitt S, Hish A, Gilja S, Eward W, Ware K, Levine H, Armstrong AJ, Garcia-Blanco MA (2016). Mesenchymal-epithelial transition in sarcomas is controlled by the combinatorial expression of GRHL2 and miR-200s. Molecular and Cellular Biology, 36 (19): 2503-2513 (Cover article)

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18. Boareto M, Jolly MK, Goldman A, Pietila M, Mani SA, Sengupta S, Ben-Jacob E, Levine H, Onuchic JN (2016). Notch -Jagged signaling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype. Journal of the Royal Society Interface, 13 (118): 20151106

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17. Jolly MK, Tripathi SC, Jia D, Mooney SM, Celiktas M, Mani SA, Hanash S, Pienta KJ, Ben-Jacob E, Levine H (2016). Stability of the hybrid epithelial /mesenchymal phenotype. Oncotarget, 7 (19): 27067-27084

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16. Tripathi SC, Peters HL, Taguchi A, Katayama H, Wang H, Momin A, Jolly MK, Celiktas M, Rodriguez-Canales J, Liu H, Behrens C, Wistuba II, Ben-Jacob E, Levine H, Molldrem JJ, Hanash SM, Ostrin EJ (2016). Immuno-proteasome deficiency is a feature of non-small cell lung cancer with a mesenchymal phenotype and is associated with a poor outcome. Proceedings of the National Academy of Sciences USA, 113 (11): E1555-1564

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15. Mooney SM, Jolly MK, Levine H, Kulkarni P (2016). Phenotypic plasticity in prostate cancer: the role of intrinsically disordered proteins. Asian Journal of Andrology, 18 (5): 704-710

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14. Grigore AD*, Jolly MK*, Jia D, Farach-Carson MC, Levine H (2016). Tumor budding: the name is EMT. Partial EMT. Journal of Clinical Medicine, 5(5): E51

 

2015:

13. Huang B, Jolly MK, Lu M, Tsarfaty I, Ben-Jacob E, Onuchic JN (2015). Modeling the transitions between collective and solitary migration phenotypes in cancer metastasis. Scientific Reports, 5: 17379 (Recommended by F1000 faculty)

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12. Boareto M, Jolly MK, Ben-Jacob E, Onuchic JN (2015). Jagged mediates differences in normal and tumor angio-genesis by affecting tip-stalk fate decision. Proceedings of the National Academy of Sciences USA, 112 (29): E3836-E3844

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11. Jolly MK*, Jia D*, Boareto M, Mani SA, Pienta KJ, Ben-Jacob E, Levine H (2015). Coupling the modules of EMT and stemness: A tunable 'stemness window' model. Oncotarget, 6(28): 25161-25174

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10. Jolly MK*, Boareto M*, Lu M, Clementi C, Onuchic JN, Ben-Jacob E (2015). Operating principles of Notch-Delta-Jagged module of cell-cell communication. New Journal of Physics, 17: 055021

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9. Jia D*, Jolly MK*, Boareto M, Parsana P, Mooney SM, Pienta KJ, Levine H, Ben-Jacob E (2015). OVOL guides the epithelial-hybrid-mesenchymal transition. Oncotarget, 6 (17): 15436-15448

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8. Jolly MK, Boareto M, Huang B, Jia D, Lu M, Onuchic JN, Ben-Jacob E, Levine H (2015). Implications of the hybrid epithelial/mesenchymal phenotype in metastasis.  Frontiers in Oncology,5: 155

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7. Boareto M, Jolly MK, Lu M, Onuchic JN, Clementi C, Ben-Jacob E (2015). Jagged-Delta Asymmetry in Notch Signaling can give rise to a Sender/Receiver hybrid phenotype, Proceedings of the National Academy of Sciences USA, 112 (5): E402-E409

 

2014:

6. ​Jolly MK, Huang B, Lu M, Mani SA, Levine H, Ben-Jacob E (2014). Towards elucidating the connection between epithelial-mesenchymal transitions and stemness, Journal of the Royal Society Interface, 11 (101): 20140962 (Highlighted in National Science Foundation (NSF) News)

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5. Huang B, Lu M, Jolly MK, Tsarfaty I, Onuchic JN, Ben-Jacob E (2014). The three-way switch operation of Rac1/ RhoA GTPase-based circuit controlling amoeboid-hybrid-mesenchymal transition, Scientific Reports 4: 6449

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4. Lu M*, Jolly MK*, Onuchic JN, Ben-Jacob E (2014). Toward Decoding the Principles of Cancer Metastasis Circuits. Cancer Research, 74 (17): 4574-4587

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3. Jolly MK*, Rizvi MS*, Kumar A, Sinha P (2014). Mathematical modeling of sub-cellular asymmetry of Fat-Dachsous Heterodimer for generation of Planar Cell Polarity, PLoS ONE 9(5): e97641

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2013:

2. Lu M*, Jolly MK*, Levine H, Onuchic JN, Ben-Jacob E (2013). MicroRNA-based regulation of epithelial-hybrid-mesenchymal    cell fate determination. Proceedings of the National Academy of Sciences USA, 110 (45): 18144-18149

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1. Lu M, Jolly MK, Gomoto R, Huang B, Onuchic JN, Ben-Jacob E (2013). Tristability in Cancer Associated miRNA-TF Chimera Toggle Switch. Journal of Physical Chemistry B, 117 (42): 13164-13174​