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*Equal contribution, #Corresponding author; Members from the group are underlined

Peer Reviewed Articles

A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.
Shyam S, Soundharya R, Sehgal M, Jolly MK (2023). Journal of the Royal Society Interface, 20: 20230389

Dynamical hallmarks of cancer: phenotypic switching in melanoma and epithelial-mesenchymal plasticity.
Jain P, Pillai M, Somarelli JA, Goyal Y, Jolly MK (2023). Seminars in Cancer Biology, 96: 48-63

Effects of microRNA-mediated negative feedback on gene expression noise.
Adhikary R, Roy A, Jolly MK, Das D (2023). Biophysical Journal, 122 (21): 4220-4240

Phenotypic heterogeneity drives differential disease outcome in triple negative breast cancer.
Thankamony AP, Murali R, Chakraborty P, Karthikeyan N, Vargheses BA, Jaikumar VS, Jolly MK, Nair R (2023). Frontiers in Oncology, 13: 1230647

Synthetic gene circuits combining CRISPR interference and CRISPR activation in E.coli: importance of equal guide RNA binding affinities to avoid context-dependent effects.
Barbier I, Kusumawadhani H*, Chauhan L*, Harlapur PV, Jolly MK, Schaerli Y (2023). ACS Synthetic Biology, 12 (10): 3064-71

Dynamical modelling of proliferative-invasive plasticity and IFNγ signaling reveals mechanisms of PD-L1 expression heterogeneity in melanoma.
Subhadarshini S*, Sahoo S*, Debnath S, Somarelli JA, Jolly MK# (2023). Journal for ImmunoTherapy of Cancer, 11: e006766

Androgen receptor driven gene score identified tumors with epithelial to mesenchymal transition features in triple negative breast cancer.
Rajarajan S, Snijesh VP, Anupama CE, Nair SJ, Mavetkar AD, Naidu CM, Patil S, Nimbalkar VP, Pillai M, Jolly MK, Radhakrishnan S, Ramesh RS, Srinath BS, Prabhu JS (2023). Translational Oncology, 37:101761

p53 amyloid pathology is correlated with cancer grades irrespective of the mutant or wildtype forms.
Sengupta S, Singh N, Paul A, Datta D, Chatterjee D, Mukherjee S, Gadhe L, Devi J, Yeshwanth M, Jolly MK, Maji S (2023). Journal of Cell Science, 136 (17): jcs261017

Theoretical and computational tools to model multistable gene regulatory networks.
Bocci F, Jia D, Nie Q, Jolly MK, Onuchic J (2023). Reports on Progress in Physics, 86 (10): 106601

Unraveling the dangerous duet between cancer stem cell plasticity and drug resistance.
Chatterjee N, Pulipaka B, Subbalakshmi AR, Jolly MK, Nair R (2023). Computational and Systems Oncology, 3 (3): e1051

Collective heterogeneity of mitochondrial potential in contact inhibition of proliferation.
Thurakkal B, Hari K, Marwaha R, Karki S, Jolly MK#, Das T# (2023). Biophysical Journal, 122 (19): 3909-3923

Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space.
Hari K, Duncan W, Ibrahim MA, Jolly MK#, Cummins B#, Gedeon T# (2023). NPJ Systems Biology & Applications, 9: 29

A synthetic lethal screen for Snail-induced enzalutamide resistance identifies JAK/STAT signaling as a therapeutic vulnerability in prostate cancer.
Ware KE, Thomas BC, Olawuni P, Sheth MU, Hawkey N, Yeshwanth M, Miller BC, Vietor KJ, Jolly MK, Kim SY, Armstrong AM, Somarelli JA (2023). Frontiers in Molecular Biosciences, 10: 1104505

Aberrations in ion channels interacting with lipid metabolism and epithelial mesenchymal transition in esophageal squamous cell carcinoma.
Parthasarathi KTS, Mandal S, George JP, Gaikwad KB, Sasidharan S, Gundimeda S, Jolly MK, Pandey A, Sharma J (2023). Frontiers in Molecular Biosciences, in press

Link updating strategies influence consensus decisions as a function of the direction of communication.
Kunjar S, Strandburg-Peshkin A, Giese H, Sarkar S, Jolly MK, Gradwohl N (2023). Royal Society Open Science, 10: 230215

Prognostic association of immunoproteasome expression in solid tumours is governed by the immediate immune environment.
Kumar R, Dhaka B, Sahoo S, Jolly MK, Radhakrishnan S (2023). Molecular Oncology, 17 (6): 1041-1059

Population dynamics of EMT elucidates the timing and distribution of intra-tumoral heterogeneity.
Najafi A, Jolly MK#, George JT# (2023). iScience, 26 (7): 106964

Modeling collective cell behavior in cancer: perspectives from an interdisciplinary conversation.
Adler FA, Anderson ARA, Bhushan A, Bogdan P, Bravo-Cordero JJ, Brock A, Chen Y, Cukierman E, DelGiorno KE, Denis GE, Ferrall-Fairbanks MC, Gartner ZC, Germain RN, Gordon DM, Hunter G, Jolly MK, Karacosta LG, Mythreye K, Katira P, Kulkarni RP, Kutys ML, Lander AD, Laughney AM, Levine H, Lou E, Lowenstein PR, Masters KL, Pe’er D, Peyton SR, Platt MO, Purvis JE, Quon G, Richer JK, Riddle NC, Rodriguez A, Snyder JC, Szeto GL, Tomlin CJ, Yanai I, Zervantonakis IK, Dueck H (2023). Cell Systems, 14 (4): 252-257

PRAME is a novel target of tumor-intrinsic Gas6/Axl activation and promotes cancer cell invasion in hepato-cellular carcinoma.
Hedrich V, Breitenecker K, Ortmayr G, Pupp F, Huber H, Chen D, Sahoo S, Jolly MK, Mikulits W (2023). Cancers, 15 (9): 2415

Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools.
Pillai M, Hojel E, Jolly MK#, Goyal Y# (2023). Nat Comput Sci, 3: 301-313

Dynamics of epithelial-mesenchymal plasticity: what have single-cell investigations elucidated so far?
Subhadarshini S, Sahoo S, Vaz JM, Jolly MK# (2023). ACS Omega, 8 (13): 11665-11673

Partial EMT and associated changes in cellular plasticity in oncovirus-positive samples.
Sehgal M*, Ray R*, Vaz JM, Kanikar S, Somarelli JA, Jolly MK# (2023). Advances in Cancer Biology – Metastasis, 7: 100091

The ELF3 transcription factor is associated with an epithelial phenotype and represses epithelial-mesenchymal transition.
Subbalakshmi AR*, Sahoo S*, Manjunatha P, Goyal S, Kasiviswanthan VA, Yeshwanth M, Soundharya R, McMullen I, Somarelli JA#, Jolly MK# (2023). Journal of Biological Engineering, 17: 17

Mapping spatiotemporal heterogeneity in tumor progression by integrating high-throughput imaging and omics analysis.
Patkulkar PA*, Subbalakshmi AR*, Jolly MK#, Sinharay S# (2023). ACS Omega, 8 (7):6126-6138

Coupled mutual inhibition and mutual activation motifs as tools for cell-fate control.
Sabuwala B*, Hari K*, Abhishek SV, Jolly MK# (2023). Cells Tissues Organs, in press (bioRxiv: 493756)

Unique sphingolipid signature identifies luminal and triple-negative breast cancer subtypes.
Kar A, Medatwal N, Rajput K, Mandal S, Pani T, Khan A, Shamra P, Oberoi A, Vishwakarma G, Deo S, Jolly MK, Bajaj A, Dasgupta U (2023). International Journal of Cancer, 152 (11): 2410-2423

Epigenetic memory acquired during long-term EMT induction governs the recovery to the epithelial state.
Jain P, Corbo S, Mohammad K, Sahoo S, Ranganathan S, George JT, Levine H, Taube J, Toneff M, Jolly MK# (2023). Journal of the Royal Society Interface, 20: 20220627

Spatio-temporal Pattern Formation due to Host-Circuit Interplay in Gene Expression Dynamics.
Chakraborty P, Roy U, Jolly MK, Ghosh S (2023). Chaos, Solitons & Fractals, 167: 112995

Spatiotemporal patterning enabled by gene regulatory networks.
Roy U*, Singh D*, Vincent N, Haritas CK, Jolly MK# (2023). ACS Omega, 8 (4): 3713-3725


Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.
Jindal R*, Nanda A*, Pillai M, Ware KE, Singh D, Sehgal M, Armstrong AJ, Somarelli JA#, Jolly MK# (2022). Computational & Structural Biotechnology Journal, 21: 1498-1509

Functional resilience of mutually repressing motifs embedded in larger networks.
Harlapur P, Duddu AS, Hari K, Kulkarni P, Jolly MK# (2022). Biomolecules, 12 (12): 1842

Network topology metrics explaining enrichment of hybrid epithelial mesenchymal phenotypes in metastasis.
Rashid M*, Hari K*, Thampi J, Santhosh KN, Jolly MK# (2022). PLoS Computational Biology, 18 (11): e1010687

PD-L1 activity is associated with partial EMT and metabolic reprogramming in carcinomas.
Muralidharan S*, Sehgal M*, Soundharya R*, Mandal S, Majumdar SS, Yeshwanth M, Saha A, Jolly MK# (2022). Current Oncology, 29 (11): 8285-8301

Landscape of epithelial-mesenchymal plasticity as an emergent property of coordinated modules in regulatory networks.
Hari K, Ullanat U, Balasubramanian A, Gopalan A, Jolly MK# (2022). eLife, 11: e76535

Spatiotemporal patterning enabled by gene regulatory networks.
Roy U*, Singh D*, Vincent N, Haritas CK, Jolly MK# (2022). ACS Omega, in press (bioRxiv: 488152)

Quantitative landscapes reveal trajectories of cell-state transitions associated with drug resistance in melanoma.
Pillai M*, Chen Z*, Jolly MK#, Li C# (2022). iScience, in press (bioRxiv: 488373)

Emergent properties of coupled bistable switches.
Hari K*, Harlapur P*, Gopalan A, Ullanat V, Duddu AS, Jolly MK# (2022). Journal of BioSciences, in press (bioRxiv: 448553)

Stochastic population dynamics of cancer stemness and adaptive response to therapies.
Jain P, Duddu AS, Jolly MK# (2022). Essays in Biochemistry, 66 (4): 387-398

Dynamics of a hepatocyte-cholangiocyte decision-making gene regulatory network during liver development and regeneration.
Sahoo S, Mishra A, Diehl AM, Jolly MK# (2022). iScience, 25 (9): 104955

Mapping phenotypic heterogeneity in melanoma onto the epithelial-hybrid-mesenchymal axis.
Pillai M*, Rajaram G*, Thakur P, Agarwal N, Muralidharan S, Ray A, Somarelli JA, Jolly MK# (2022). Frontiers in Oncology, 12: 913803

Lack of correlation between landscape geometry and transition rates.
Jia W, Duddu AS, Jolly MK, Levine H# (2022). Journal of Physical Chemistry B, 126 (30): 5613-8

Robustness in phenotypic plasticity and heterogeneity patterns enabled by EMP networks.
Hebbar A*, Moger A*, Hari K, Jolly MK# (2022). Biophysical Journal, 121 (19): 3600-15

Cell geometry distinguishes migration-associated heterogeneity in two-dimensional systems.
Varankar S, Hari K, Kartika S, Bapat SA#, Jolly MK# (2022). Computational and Systems Oncology, 2 (3): e1041

P4HA2: a link between tumor-intrinsic hypoxia, partial EMT and collective migration.
Aggarwal V, Sahoo S, Donnenberg VS, Chakraborty P, Jolly MK, Sant S (2022). Advances in Cancer Biology – Metastasis, 5:100057

Oncogenic gain of cellular function by p53 amyloid due to aberrant alteration of cell cycle and proliferation.
Navalkar A, Pandey S, Paul A, Dey A, Saha S, Sahoo S, Jolly MK, Maiti TK, Maji SM (2022). Journal of Cell Science, 135 (15): jcs259500

A multistep growth model of high grade serous ovarian carcinoma identifies hypoxia driven signatures.
More MH, Varankar S, Naik RR, Dhake RD, Ray P, Bankar RM, Mali AM, Subbalakshmi AR, Chakraborty P, Jolly MK, Bapat SA (2022). Cells Tissues Organs, in press

Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer.
Brown MS, Abdollahi B, Wilkins OM, Lu H, Chakraborty P, Ognjenovic NB, Muller KE, Jolly MK, Christensen BC, Hassanpour S, Pattabiraman D (2022). Science Advances, 8 (31): abj8002

Single-cell analysis reveals X upregulation is not global in pre-gastrulation embryos.
Naik K, Hari K, Chandel C, Jolly MK, Gayen S (2022). iScience, 25 (6): 104465

Spontaneous differentiation leads to emergence of hybrid cell states related to poor prognosis in oral cancer.
Vipparthi K, Hari K, Chakraborty P, Ghosh S, Patel AK, Ghosh A, Biswas NK, Sharan R, Arun P, Jolly MK, Singh S (2022). iScience, 25(5): 104317

Analysis of Yes-associated protein 1 (YAP1) target gene signature to predict a progression subset of breast cancer.
Gomathi V, Kelkar DA, Mandal S, Jolly MK, Kulkarni M (2022). Journal of Clinical Medicine, 11 (7): 1947

Emergent dynamics of a three-node regulatory network explain phenotypic switching and heterogeneity: a case study of Th1/Th2/Th17 differentiation.
Duddu AS, Majumdar SS, Sahoo S, Jhunjhunwala S, Jolly MK# (2022). Molecular Biology of the Cell, 33 (6): ar46

Lhx2 in germ cells suppresses endothelial cell migration in the developing ovary.
Singh N, Singh D, Bhide A, Sharma R, Sahoo S, Jolly MK, Modi D (2022). Experimental Cell Research, 415: 113108

Emerging perspectives on growth factor metabolic relationships in the ovarian cancer ascites environment.
Monavarian M, Elhaw A, Tang P, Javed Z, Shonibare Z, Scalise CB, Arend R, Jolly MK, Sewell-Loftin MK, Hempel N, Mythreye K (2022). Seminars in Cancer Biology, 86(Pt 2):709-719

Population dynamics of epithelial-mesenchymal heterogeneity in cancer cells.
Jain P, Bhatia S, Thompson EW#, Jolly MK# (2022). Biomolecules, 12 (3): 348

In silico analysis of ion channels and its correlation with epithelial to mesenchymal transition in breast cancer.
Parthasarathy KTS, Mandal S, Singh S, Gundimeda S, Jolly MK, Pandey A, Sharma J (2022). Cancers, 14 (6): 1444

Nrf2 modulates the hybrid epithelial/mesenchymal phenotype and Notch signaling during collective cancer migration.
Mercedes SAV, Bocci F, Eder I, Ahmed M, Zhu N, Levine H#, Onuchic JN#, Jolly MK#, Wong PK# (2022). Frontiers in Molecular Biosciences, 9: 807324

Quantifying the patterns of metabolic plasticity and heterogeneity along the epithelial-hybrid-mesenchymal spectrum in cancer.
Muralidharan S, Sahoo S, Saha A*, Chandran S*, Majumdar SS*, Levine H#, Jolly MK# (2022). Biomolecules, 12 (2): 297

Intrinsically disordered proteins: ensembles at the limits of Anfinsen’s dogma.
Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VU, Salgia R (2022). Biophysics Reviews, 3: 011306

Mean residence times of TF-TF and TF-miRNA toggle switches.
Biswas K, Jolly MK, Ghosh A (2022). Journal of Biosciences, 47: 26

Identifying critical transitions in complex diseases.
Deb S, Bhandary S, Sinha SK, Jolly MK, Dutta PS (2022). Journal of Biosciences, 47: 25

Roadmap on plasticity and epigenetic in cancer.
Foo J, Basanta D, Rockne R, Strelez C, Shah C, Ghaffarian K, Mumenthaler SM, Mitchell K, Lathia JD, Frankhouser D, Branciamore S, Kuo Y-H, Marcucci G, Velde RV, Marusyk A, Huang S, Hari K, Jolly MK, Hatzikirou H, Poels KE, Spilker ME, Shtylla B, Robertson-Tessi M, Anderson ARA (2022). Physical Biology, 19 (3): 031501

Tumor hybrid cells: nature and biological significance.
Tretyakova MS, Subbalakshmi AR, Menyailo ME, Jolly MK, Denisov EV (2022). Frontiers in Cell and Developmental Biology, 10: 814714

NRF2-dependent epigenetic regulation can promote the hybrid epithelial/ mesenchymal phenotype.
Jia W, Jolly MK#, Levine H# (2022). Frontiers in Cell and Developmental Biology, 9:828250

Biophysical and biochemical attributes of hybrid epithelial/ mesenchymal phenotypes.
Subbalakshmi AR, Ashraf B, Jolly MK# (2022). Physical Biology, 19(2):025001

Cancer: more than a geneticist’s Pandora’s box.
Saxena K, Subbalakshmi AR, Kulkarni P, Jolly MK# (2022). Journal of BioSciences,  47:21

Changes in triple-negative breast cancer molecular subtype in patients without pathological complete response after neoadjuvant systemic therapy.
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, Lee J, Wang X, Lucci A, Rao A, Schweitzer BL, Lawrence OR, Seitz RS, Morris SW, Hout DR, Nakamura S, Krishnamurthy S, Ueno NT (2022). JCO Precision Oncology, 6:e2000368

Interconnected high-dimensional landscapes of epithelial-mesenchymal plasticity and stemness.
Sahoo S, Ashraf B, Duddu AS, Biddle A#, Jolly MK# (2022). Clinical & Experimental Metastasis, 39(2):279-290

Quantitative systems pharmacology model-based investigation of adverse gastrointestinal events associated with prolonged treatment with PI3-kinase (PI3K) inhibitors.
Gadkar K, Friedrich C, Hurez V, Ruiz M-L, Dickman L, Jolly MK, Schutt L, Jin J, Ware JA, Ramanujan S (2022). CPT: Pharmacometrics & Systems Pharmacology, 11(5):616-627

Protein conformational dynamics and phenotypic switching.
Kulkarni P, Achuthan S, Bhattacharya S, Jolly MK, Kotnala S, Leite VBP, Mohanty A, Orban J, Roy S, Rangarajan G, Salgia R (2022).Biophysical Reviews, 13(6):1127-1138

CTCF expression and dynamic motif accessibility modulates epithelial-mesenchymal gene expression.
Johnson KS, Hussein S, Chakraborty P, Muruganantham A, Mikhail S, Gonzalez G, Song S, Jolly MK, Toneff M, Benton ML, Lin YC, Taube JH (2022).Cancers, 14(1):209

A reciprocal feedback loop between HIF1α and HPIP controls phenotypic plasticity in breast cancer cells.
Khumukcham SS, Penugruti V, Soni A, Uppala V, Hari K, Jolly MK, Dwivedi A, Salam PKA, Padala C, Mukta S, Triveni B, Bramanandam MB (2022). Cancer Letters, 526: 12-28

Transcriptomic-based quantification of epithelial-hybrid-mesenchymal spectrum across biological contexts.
Mandal S, Tejaswi T, Janivara R, Srikrishnan S, Thakur P, Sahoo S, Chakraborty P, Sohal SS, Levine H, George JT#, Jolly MK# (2022). Biomolecules, 12 (1): 29

Dynamic phenotype switching and group behavior help non-small cell lung cancer cells evade chemotherapy.
Nam A, Mohanty A, Bhattacharya S, Kotnala S, Achuthan S, Hari K, Srivastava S, Guo L, Nathan A, Chatterjee R, Jain M, Nasser MW, Batra S, Rangarajan G, Massarelli E, Levine H, Jolly MK, Kulkarni P, Salgia R (2022).Biomolecules, 12 (1): 8


Immunosuppressive traits of hybrid epithelial/mesenchymal phenotype.
Sahoo S*, Nayak SP*, Hari K, Purkait P, Mandal S, Kishore A, Levine H, Jolly MK# (2021). Frontiers in Immunology, 12: 797261

KLF4 induces mesenchymal-epithelial transition (MET) by suppressing multiple EMT-inducing transcription factors.
Subbalakshmi AR, Sahoo S, McMullen I, Saxena A, Venugopal SK, Somarelli JA#, Jolly MK# (2021). Cancers, 13 (20): 5135

Systems-level network modeling deciphers the master regulators of phenotypic plasticity and heterogeneity in melanoma.
Pillai M, Jolly MK# (2021). iScience, 24: 103111

First passage time properties of miRNA-mediated protein translation.
Biswas K, Jolly MK, Ghosh A (2021). Journal of Theoretical Biology, 529: 110863

Semi-coordinated allelic-bursting shape dynamic random monoallelic expression in pregastrulation embryos.
Naik HC, Hari K, Chandel D, Mandal S, Jolly MK, Gayen S (2021). iScience, 24 (9): 102954

Lineage plasticity in cancer: The tale of a skin-walker.
Thankamony AP, Subbalakshmi AR, Jolly MK#, Nair R# (2021). Cancers, 13 (14): 3602

Calcium signaling induces a partial EMT.
Norgard RJ, Pitaressi JR, Maddipati R, Aiello-Couzo NM, Balli D, Li J, Yamazoe T, Wengyn MD, Millstein ID, Folkert IW, Roasrio-Berrios DN, Kim I-K, Bassett JB, Payne R, Berry CT, Feng X, Sun K, Cioffi M, Chakraborty P, Jolly MK, Gutkind JS, Lyden D, Freedman BD, Foskett JK, Rustgi AK, Stanger BZ. EMBO Reports, 22 (9): e51872

A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.
Sahoo S, Mishra A, Kaur H, Hari K, Muralidharan S, Mandal S, Jolly MK# (2021). NAR Cancer, 3 (3): zcab027

Integrative systems biology approach identifies crucial genes and transcription factors associated with gallbladder cancer pathogenesis.
Roy N, Kshattry M, Mandal S, Jolly MK, Bhattacharyya DK, Barah P (2021). Journal of Clinical Medicine, 10 (16): 3520

First passage time properties of miRNA-mediated protein translation.
Biswas K, Jolly MK, Ghosh A (2021). Journal of Theoretical Biology, 110863

Systems-level network modeling deciphers the master regulators of phenotypic plasticity and heterogeneity in melanoma.
Pillai M, Jolly MK# (2021). iScience 24 :103111

Semi-coordinated allelic-bursting shape dynamic random monoallelic expression in pregastrulation embryos.
Naik HC, Hari K, Chandel D, Mandal S, Jolly MK, Gayen S (2021). iScience 24 (9): 102954

Lineage plasticity in cancer: The tale of a skin-walker.
Thankamony AP, Subbalakshmi AR, Jolly MK#, Nair R# (2021). Cancers, 13 (14): 3602

Calcium signaling induces a partial EMT.
Norgard RJ, Pitaressi JR, Maddipati R, Aiello-Couzo NM, Balli D, Li J, Yamazoe T, Wengyn MD, Millstein ID, Folkert IW, Roasrio-Berrios DN, Kim I-K, Bassett JB, Payne R, Berry CT, Feng X, Sun K, Cioffi M, Chakraborty P, Jolly MK, Gutkind JS, Lyden D, Freedman BD, Foskett JK, Rustgi AK, Stanger BZ. EMBO Reports, 7, 2021.

A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.
Sahoo S, Mishra A, Kaur H, Hari K, Muralidharan S, Mandal S, Jolly MK# (2021). NAR Cancer, 3 (3): zcab027

Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum.
Chakraborty P, Chen E, McMullen I, Armstrong A, Jolly MK#, Somarelli JA# (2021). Computational and Structural Biotechnology, 19: 3842-3851

Epithelial-to-mesenchymal transition enhances cancer cell sensitivity to cytotoxic effects of cold atmospheric plasmas in breast and bladder cancer systems.
Wang P, Zhou R, Thomas P, Zhao L, Zhou R, Mandal S, Jolly MK, Richard DJ, Rehm BHA, Ostrikov K, Dai X, Williams ED, Thompson EW (2021). Cancers, 13 (12): 2889

Phenotypic heterogeneity of triple-negative breast cancer mediated by epithelial-mesenchymal plasticity.
Kvokackova B, Remsik J, Jolly MK, Soucek K (2021). Cancers, 13 (9): 2188

Decoding leader cells in collective cancer invasion.
Mercedes SAV, Bocci, F, Levine H#, Onuchic JN#, Jolly MK#, Wong PK# (2021). Nature Reviews Cancer, 21, 592–604

Matrix adhesion and remodeling diversifies modes of cancer invasion across spatial scales.
Pramanik D, Jolly MK#, Bhat R# (2021). Journal of Theoretical Biology, 524: 110733

Identification of EMT signaling crosstalk and gene regulatory networks by single-cell sequencing.
Deshmukh AP, Vasaikar S, Tomczak K, Tripathi S, den Hollander P, Arslan E, Chakraborty P, Soundararajan R, Jolly MK, Rai K, Levine H, Mani SA (2021). Proceedings of the National Academy of Sciences USA (PNAS), 118 (19): e2102050118

Countries with high deaths dye to flu and tuberculosis demonstrate lower COVID-19 mortality: roles of vaccinations.
Pathak S, Jolly MK, Nandi D (2021). Human Vaccines & Immunotherapeutics, 17(9):2851-2862

Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer.
Chauhan L*, Ram U*, Hari K, Jolly MK# (2021). eLife, 10: e64522

Identifying “more equal than others” edges in diverse biochemical networks.
Hari K, Ram U, Jolly MK# (2021). Proceedings of the National Academy of Sciences USA (PNAS), 118 (16): e2103698118

Towards decoding the coupled decision-making of metabolism and epithelial-mesenchymal transition in cancer.
Jia D, Park JH, Kaur H, Jung KH, Yang S, Tripathi S, Galbraith M, Deng Y, Jolly MK, Kaipparettu BA, Onuchic JN, Levine H (2021). British Journal of Cancer, 124, 1902–1911

Quantifying the epithelial /mesenchymal hybrid state in cancer: clinical implications.
Jolly MK#, Murphy RM, Bhatia S, Whitfield H, Davis MJ#, Thompson EW# (2021). Cells Tissues Organs, 2021

Multistability and consequent phenotypic plasticity in AMPK-Akt double negative feedback loop in cancer cells.
Chedere A, Hari K, Kumar S, Rangarajan A#, Jolly MK# (2021). Journal of Clinical Medicine, 10 (3): 472

Gene expression profiling of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum.
Chakraborty P, George JT, Woodward W, Levine H, Jolly MK# (2021).Translational Oncology, 14 (4): 101026

Hybrid E/M phenotype(s) and stemness: a mechanistic connection embedded in network topology.
Pasani S, Sahoo S, Jolly MK# (2021).Journal of Clinical Medicine, 10(1): 60

Group behavior and the emergence of cancer drug resistance.
Bhattacharya S, Mohanty A, Achuthan S, Kotnala S, Jolly MK, Kulkarni P, Salgia R (2021). Trends in Cancer, 7 (4): 323-334


A theoretical approach to coupling the epithelial-mesenchymal transition (EMT) to extracellular matrix (ECM) stiffness via LOXL2.
Deng Y, Chakraborty P, Jolly MK, Levine H (2020). Cancers 13 (7):1609.

Coupled feedback loops involving PAGE4, EMT and Notch signaling can give rise to non-genetic heterogeneity in prostate cancer cells.
Singh D, Bocci F, Kulkarni P, Jolly MK# (2020). Entropy 2021, 23 (3): 288

Operating principles of circular toggle polygons.
Hati S, Duddu AS, Jolly MK# (2020). Physical Biology 18 046003

Investigating epithelial-mesenchymal heterogeneity of tumors and circulating tumor cells with transcriptomic analysis and biophysical modeling.
Bocci F#, Mandal S, Tejaswi T, Jolly MK# (2020). Computational and Systems Oncology 2.1015

A computational systems biology approach identifies SLUG as a mediator of partial Epithelial-Mesenchymal Transition.
Subbalakshmi A R, Sahoo S, Biswas K, Jolly MK# (2020). Cells Tissues Organs

The Good, The Bad and The Ugly: A mathematical model investigates the differing outcomes among CoVID-19 patients.
Sahoo S, Jhunjhunwala S, Jolly MK#(2020). Journal of the Indian Institute of Science, 100 (4): 673-681

Multistability in cellular differentiation enabled by a network of three mutually repressing master regulators.
Duddu AS, Sahoo S, Hati S, Jhunjhunwala S, Jolly MK# (2020). Journal of the Royal Society Interface, 17 (170): 20200631

Targeting the Id1-Kif11 axis in triple negative breast cancer using combination therapy.
Archana PT*, Murali M*, 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, Swarbick A, Nair R (2020). Biomolecules, 10 (9): 1295

OVOL1/2: Drivers of epithelial differentiation in development, disease and reprogramming.
Saxena K, Srikrishnan S, Celia-Terrassa T, Jolly MK# (2020). Cells Tissues Organs, 211(2):183-192

NFATc acts as a non-canonical phenotypic stability factor for a hybrid epithelial/mesenchymal phenotype.
Subbalakshmi A R, Kundnani D, Biswas K, Hanash SM, Ghosh A, Tripathi SC#, Jolly MK# (2020). Frontiers in Oncology, 10: 553342

Anticipating the novel coronavirus disease (COVID-19) pandemic.
Kaur T, Sarkar S, Chowdhury S, Sinha SK, Jolly MK, Dutta PS (2020). Frontiers in Public Health, 89: 569669

Hypoxia, partial EMT and collective migration: emerging culprits in metastasis.
Saxena K, Jolly MK#, Balamurugan K# (2020). Translational Oncology, 13 (11): 100845

Single cell RNAseq identifies subsets of cells in the feto-maternal interface that highly express factors that drive pathogenesis of SARS-CoV-2.
Ashray N, Bhide A, Chakraborty P, Mishra A, Chhabria K, Jolly MK, Modi D (2020). Frontiers in Cell and Developmental Biology, 8: 783

A non-genetic mechanism for chemoresistance in lung cancer: the role of integrin β4/paxillin axis.
Mohanty A, Nam A, Pozhiktov A, Bhattacharyya S, Yang L, Nathan A, Xiewei W, Srivastava S, Mambetsariev I, Nelson M, Subbalakshmi A R, Guo L, Nasser MW, Batra SK, Orban J, Jolly MK, Maserralli E, Kulkarni P, Salgia R (2020). iScience, 23 (9): 101496

Understanding the principles of pattern formation driven by Notch signaling through integratingexperiments and theoretical models.
Bocci F, Onuchic JN#, Jolly MK# (2020). Frontiers in Physiology, 11: 929

Epigenetic feedback and stochastic cell division can drive resistance to EMT.
Jia D, Tripathi S, Chakraborty P, Chedere A, Rangarajan A, Levine H#, Jolly MK# (2020). Oncotarget, 11 (27): 2611-2624

A complex polycyclic aromatic hydrocarbon environmental chemical mixture promotes aggressive phenotype and survival signaling with hormone receptor selectivity in breast cancer cells.
Gearhart-Serna LM, Davis JB, Jolly MK, Jayasundara N, Saeur SJ, Giulio RD, Devi GR (2020). Carcinogenesis, 41(12):1648-1659

Cellular plasticity in matrix-attached and -detached cells: implications in metastasis.
Ranganathan S, Kumar S, Mohanty SS, Jolly MK, Rangarajan A (2020). Journal of the Indian Institute of Science, 100 (3): 525-536

Twist1 induces chromosomal instability (CIN) in colorectal cancer cells.
Khot M, Sreekumar D, Jahagirdar S, Kulkarni A, Hari K, Faseela EE, Radhakrishnan S, Jolly MK, Sengupta K. Human Molecular Genetics, 29 (10): 1673-88

Integrative analysis and machine learning based characterization of single circulating tumor cells.
Iyer A, Gupta K, Sharma S, Hari K, Lee YF, Ramalingam N, Yap YS, West J Bhagat AA, Subramani BV, Sabuwala B, Tan TZ, Thiery JP, Jolly MK, Ramalingam N, Sengupta D (2020). Journal of Clinical Medicine, 9 (4): 1206

Identifying inhibitors of epithelial-mesenchymal plasticity using a network topology based approach.
Hari K, Sabuwala B, Subramani BV, La Porta C, Zapperi S, Font-Clos F, Jolly MK# (2020). NPJ Systems Biology & Applications, 6: 15

Cancer Stem Cell plasticity – a deadly deal.
Archana PT*, Saxena K*, Murali R, Jolly MK#, Nair R# (2020). Frontiers in Molecular Biosciences, 7:79

Emergent properties of the HNF4α-PPARγ network may drive consequent phenotypic plasticity in NAFLD.
Sahoo S*, Singh D*, Chakraborty P, Jolly MK# (2020). Journal of Clinical Medicine, 9 (3): 870

Decoding molecular interplay underlies the pulsatile IGF1R expression during acquisition of chemoresistance.
Dhadve AC, Hari K, Rekhi B, Jolly MK, De A, Ray P (2020). BBA – Molecular Basis of Disease, 1866 (1): 165754

Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum.
Chakraborty P, George JT, Tripathi S, Levine H, Jolly MK# (2020). Frontiers in Bioengineering and Biotechnology, 8: 220

ZEB1: a critical regulator of cell plasticity, DNA damage response and therapy resistance.
Drapela S, Bouchal J, Jolly MK, Culig Z, Soucek K (2020). Frontiers in Molecular BioSciences, 10:3389

A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells.
Tripathi S, Chakraborty P, Levine H#, Jolly MK# (2020). PLoS Computational Biology, 16 (2): e1007619

The Physics of Cellular Decision-Making during Epithelial-Mesenchymal Transition.
Tripathi S, Levine H#, Jolly MK# (2020). Annual Reviews of Biophysics, 49: 1-18

Differential contributions of pre- and post-EMT tumor cells in the breast to lung metastasis.
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 (2020). Cancer Research, 80 (2): 163-169 (Featured in Cancer Research Highlights)

Histone deactylases, Mbd3/NuRD and Tet2 hydroxylase are crucial regulators of epithelial-mesenchymal plasticity and tumor metastasis.
Kilinc AN, Kalathur RK, Sugiyama N, Antonaidis H, Birogul H, Ishay-Ronen D, George JT, Levine H, Jolly MK, Christofori G (2020). Oncogene, 39: 1498-1513


Anticipating critical transitions in epithelial-hybrid-mesenchymal cell fate determination.
Sarkar S, Sinha SK#, Levine H#, Jolly MK#, Dutta PS# (2019). Proceedings of the National Academy of Sciences USA (PNAS), 116 (52): 26343-26352

A CTC-cluster-specific signature derived from OMICS analysis of patient-derived xenograft tumors predicts outcomes in basal-like breast cancers.
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). Journal of Clinical Medicine, 8 (11): 1772

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

Phenotypic Switching of Naïve T cells to Immune-suppressive Treg-like Cells by Mutant KRAS
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). Journal of Clinical Medicine, 8 (10): 1726

Cancer Stem Cells and Epithelial-to-Mesenchymal Transition in Cancer Metastasis.
Celia-Terrassa T#, Jolly MK# (2019). Cold Spring Harb Perspect Med, 10(7):a036905

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

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

Deciphering hydrodynamic and drug-resistant behaviors of metastatic EMT breast cancer cells moving in a constricted microcapillary.
Nath B, Bidkar AP, Kumar V, Dalal A, Jolly MK, Ghosh SS, Biswas G (2019). Journal of Clinical Medicine, 8 (8): E1194

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

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

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

Small cell lung cancer therapeutic responses through fractal measurements: from radiology to mitochondrial biology.
Mambetsariav I, Mirzapoiazova T, Lennon F, Jolly MK, Li H, Nasser MW, Vora L, Kulkarni P, Batra SK, Salgia R (2019). Journal of Clinical Medicine, 8 (7): E1038

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

Functional balance between Tcf21-Slug defines cellular plasticity and migratory modalities in high grade serous ovarian cancer cell lines.
Varankar S, More M, Ancy A, Pansare K, Kumar B, Narayanan NJ, Jolly MK, Mali AM, Bapat SA (2019). Carcinogenesis, 41(4):515-526

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

Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level.
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). Biomolecules, 9(2): E77

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

E-cadherin represses anchorage-independent growth in sarcomas through both signaling and mechanical mechanisms.
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). Molecular Cancer Research, 17 (6): 1391-1402

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

The DNA walk and its demonstration of deterministic chaos – relevance to genomic alterations in lung cancer.
Hewelt B, Li H, Jolly MK, Kulkarni P, Mambetsariev I, Salgia R (2019). Bioinformatics, 35 (16): 2738-2748

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

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

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

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

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

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


Chronic obstructive pulmonary disease (COPD) and lung cancer: underlying pathophysiology and new therapeutic modalities.
Eapen MS, Hansbro PM, CallerfeltA-K L, Jolly MK, MyersS, 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). Drugs, 78 (16): 1717-1740

Regulation of epithelial-mesenchymal plasticity through interconnected feedback loops between ZEB1, ESRP1, HAS2, and CD44.
Jolly MK*, Preca BT*, Tripathi SC*, Jia D, George JT, Hanash SM, Brabletz T, Stemmler MP, Maurer J, Levine H (2018). APL Bioengineering, 2 (3): 031908 (Among the ‘Top cited articles in 2019’)

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

A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells, and Notch-Jagged signaling.
Bocci F, Jolly MK, George JT, Levine H, Onuchic JN (2018). Oncotarget, 9 (52): 29906-29920 (Highlighted in News & Views)

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

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

PAGE4 and conformational switching: insights from molecular dynamics simulations and implications for prostate cancer.
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). Journal of Molecular Biology, 430 (16): 2422-2438

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

Crosstalk between MNK and XIAP mediates NFkB activity to promote a hyperproliferative breast cancer phenotype.
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). Cancer Research, 78 (7): 1726-1738


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

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

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

Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and its potential role in phenotypic heterogeneity.
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). Proceedings of the National Academy of Sciences USA (PNAS), 114(13): E2644-E2653

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

Distinguishing mechanisms underlying EMT Tristability.
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). Cancer Convergence, 1:2

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

EMT and MET: necessary or permissive for metastasis?
Jolly MK, Ware K, Gilja S, Somarelli JA, Levine H (2017). Molecular Oncology, 11 (7): 755-769

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

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

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

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

MCAM mediates chemoresistance in small cell lung cancer via PI3K/AKT/SOX2 Signaling Pathway.
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). Cancer Research, 77 (16): 4414-4425

Induction of mesenchymal-epithelial transitions in sarcoma cells.
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). Journal of Visualized Experiments, 112


Mesenchymal-epithelial transition in sarcomas is controlled by the combinatorial expression of GRHL2 and miR-200s.
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). Molecular and Cellular Biology, 36 (19): 2503-2513 (Cover article)

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

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

Immuno-proteasome deficiency is a feature of non-small cell lung cancer with a mesenchymal phenotype and is associated with a poor outcome.
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). Proceedings of the National Academy of Sciences USA (PNAS), 113 (11): E1555-1564

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

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


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

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

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

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

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

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

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


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

The three-way switch operation of Rac1/ RhoA GTPase-based circuit controlling amoeboid-hybrid-mesenchymal transition.
Huang B, Lu M, Jolly MK, Tsarfaty I, Onuchic JN, Ben-Jacob E (2014). Scientific Reports4: 6449

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

Mathematical modeling of sub-cellular asymmetry of Fat-Dachsous Heterodimer for generation of Planar Cell Polarity.
Jolly MK*,#, Rizvi MS*, Kumar A, Sinha P (2014). PLoS ONE9(5): e97641


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

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