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Sahoo, S and Hari, K and Jolly, MK (2025) Design principles of regulatory networks underlying epithelial mesenchymal plasticity in cancer cells. In: Current Opinion in Cell Biology, 92 .
Najafi, A and Jolly, MK and George, JT (2024) Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R. In: STAR Protocols, 5 (1).
Catalanotto, M and Vaz, JM and Abshire, C and Youngblood, R and Chu, M and Levine, H and Jolly, MK and Dragoi, A-M (2024) Dual role of CASP8AP2/FLASH in regulating epithelial-to-mesenchymal transition plasticity (EMP). In: Translational Oncology, 39 .
Jain, P and Kizhuttil, R and Nair, MB and Bhatia, S and Thompson, EW and George, JT and Jolly, MK (2024) Cell-state transitions and density-dependent interactions together explain the dynamics of spontaneous epithelial-mesenchymal heterogeneity. In: iScience, 27 (7).
Sehgal, M and Ramu, S and Vaz, JM and Ganapathy, YR and Muralidharan, S and Venkatraghavan, S and Jolly, MK (2024) Characterizing heterogeneity along EMT and metabolic axes in colorectal cancer reveals underlying consensus molecular subtype-specific trends. In: Translational Oncology, 40 .
Snijesh, VP and Nimbalkar, VP and Patil, S and Rajarajan, S and Anupama, CE and Mahalakshmi, S and Alexander, A and Soundharya, R and Ramesh, R and Srinath, BS and Jolly, MK and Prabhu, JS (2024) Differential role of glucocorticoid receptor based on its cell type specific expression on tumor cells and infiltrating lymphocytes. In: Translational Oncology, 45 .
El Meouche, I and Jain, P and Jolly, MK and Capp, J-P (2024) Drug tolerance and persistence in bacteria, fungi and cancer cells: Role of non-genetic heterogeneity. In: Translational Oncology, 49 .
Nair, MG and Mavatkar, AD and Naidu, CM and V P, S and C E, A and Rajarajan, S and Sahoo, S and Mohan, G and Jaikumar, VS and Ramesh, RS and B S, S and Jolly, MK and Maliekal, TT and Prabhu, JS (2024) Elucidating the Role of MicroRNA-18a in Propelling a Hybrid Epithelial�Mesenchymal Phenotype and Driving Malignant Progression in ER-Negative Breast Cancer. In: Cells, 13 (10).
Naik, HC and Chandel, D and Majumdar, S and Arava, M and Baro, R and BV, H and Hari, K and Ayyamperumal, P and Manhas, A and Jolly, MK and Gayen, S (2024) Lineage-specific dynamics of loss of X upregulation during inactive-X reactivation. In: Stem Cell Reports, 19 (11). pp. 1564-1582.
Sharma, S and Rani, H and Mahesh, Y and Jolly, MK and Dixit, J and Mahadevan, V (2024) Loss of p53 epigenetically modulates epithelial to mesenchymal transition in colorectal cancer. In: Translational Oncology, 43 .
BV, H and Jolly, MK (2024) Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma. In: iScience, 27 (3).
Cheng, Y-C and Zhang, Y and Tripathi, S and Harshavardhan, BV and Jolly, MK and Schiebinger, G and Levine, H and McDonald, TO and Michor, F (2024) Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to- mesenchymal transition. In: Proceedings of the National Academy of Sciences of the United States of America, 121 (32).
Prasanna, CVS and Jolly, MK and Bhat, R (2024) Spatial heterogeneity in tumor adhesion qualifies collective cell invasion. In: Biophysical Journal, 123 (12). pp. 1635-1647.
Sahu, S and Sahoo, S and Sullivan, T and O'Sullivan, TN and Turan, S and Albaugh, ME and Burkett, S and Tran, B and Salomon, DS and Kozlov, SV and Koehler, KR and Jolly, MK and Sharan, SK (2024) Spatiotemporal modulation of growth factors directs the generation of multilineage mouse embryonic stem cell-derived mammary organoids. In: Developmental Cell, 59 (2). 175-186.e8.
Solaimuthu, B and Khatib, A and Tanna, M and Karmi, A and Hayashi, A and Rmaileh, AA and Lichtenstein, M and Takoe, S and Jolly, MK and Shaul, YD (2024) The exostosin glycosyltransferase 1/STAT3 axis is a driver of breast cancer aggressiveness. In: Proceedings of the National Academy of Sciences of the United States of America, 121 (3).
Biswas, A and Sahoo, S and Riedlinger, GM and Ghodoussipour, S and Jolly, MK and De, S (2023) Transcriptional state dynamics lead to heterogeneity and adaptive tumor evolution in urothelial bladder carcinoma. In: Communications Biology, 6 (1).
Shyam, S and Ramu, S and Sehgal, M and Jolly, MK (2023) A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity. In: Journal of the Royal Society Interface, 20 (208).
Adhikary, R and Roy, A and Jolly, MK and Das, D (2023) Effects of microRNA-mediated negative feedback on gene expression noise. In: Biophysical Journal, 122 (21). pp. 4220-4240.
Rajarajan, S and Snijesh, VP and Anupama, CE and Nair, MG and Mavatkar, AD and Naidu, CM and Patil, S and Nimbalkar, VP and Alexander, A and Pillai, M and Jolly, MK and Sabarinathan, R and Ramesh, RS and BS, S and Prabhu, JS (2023) An androgen receptor regulated gene score is associated with epithelial to mesenchymal transition features in triple negative breast cancers. In: Translational Oncology, 37 .
Barbier, I and Kusumawardhani, H and Chauhan, L and Harlapur, PV and Jolly, MK and Schaerli, Y (2023) Synthetic Gene Circuits Combining CRISPR Interference and CRISPR Activation in E. coli: Importance of Equal Guide RNA Binding Affinities to Avoid Context-Dependent Effects. In: ACS Synthetic Biology, 12 (10). pp. 3064-3071.
Thurakkal, B and Hari, K and Marwaha, R and Karki, S and Jolly, MK and Das, T (2023) Collective heterogeneity of mitochondrial potential in contact inhibition of proliferation. In: Biophysical Journal, 122 (19). 3909 -3923.
Thankamony, AP and Ramkomuth, S and Ramesh, ST and Murali, R and Chakraborty, P and Karthikeyan, N and Varghese, BA and Jaikumar, VS and Jolly, MK and Swarbrick, A and Nair, R (2023) Phenotypic heterogeneity drives differential disease outcome in a mouse model of triple negative breast cancer. In: Frontiers in Oncology, 13 .
Chatterjee, N and Pulipaka, B and Subbalakshmi, AR and Jolly, MK and Nair, R (2023) Unraveling the dangerous duet between cancer cell plasticity and drug resistance. In: Computational and Systems Oncology, 3 (3).
Sengupta, S and Singh, N and Paul, A and Datta, D and Chatterjee, D and Mukherjee, S and Gadhe, L and Devi, J and Mahesh, Y and Jolly, MK and Maji, SK (2023) p53 amyloid pathology is correlated with higher cancer grade irrespective of the mutant or wild-type form. In: Journal of Cell Science, 136 (17).
Sehgal, M and Ray, R and Vaz, JM and Kanikar, S and Somarelli, JA and Jolly, MK (2023) Partial EMT and associated changes in cellular plasticity in oncovirus-positive samples. In: Advances in Cancer Biology - Metastasis, 7 .
Najafi, A and Jolly, MK and George, JT (2023) Population dynamics of EMT elucidates the timing and distribution of phenotypic intra-tumoral heterogeneity. In: iScience, 26 (7).
Kunjar, S and Strandburg-Peshkin, A and Giese, H and Minasandra, P and Sarkar, S and Jolly, MK and Gradwohl, N (2023) Link updating strategies influence consensus decisions as a function of the direction of communication. In: Royal Society Open Science, 10 (6).
Ware, KE and Thomas, BC and Olawuni, PD and Sheth, MU and Hawkey, N and Yeshwanth, M and Miller, BC and Vietor, KJ and Jolly, MK and Kim, SY and Armstrong, AJ and Somarelli, JA (2023) A synthetic lethal screen for Snail-induced enzalutamide resistance identifies JAK/STAT signaling as a therapeutic vulnerability in prostate cancer. In: Frontiers in Molecular Biosciences, 10 .
Hedrich, V and Breitenecker, K and Ortmayr, G and Pupp, F and Huber, H and Chen, D and Sahoo, S and Jolly, MK and Mikulits, W (2023) PRAME Is a Novel Target of Tumor-Intrinsic Gas6/Axl Activation and Promotes Cancer Cell Invasion in Hepatocellular Carcinoma. In: Cancers, 15 (9).
Kumar, R and Dhaka, B and Sahoo, S and Jolly, MK and Sabarinathan, R (2023) Prognostic association of immunoproteasome expression in solid tumours is governed by the immediate immune environment. In: Molecular Oncology .
Subhadarshini, S and Markus, J and Sahoo, S and Jolly, MK (2023) Dynamics of Epithelial-Mesenchymal Plasticity: What Have Single-Cell Investigations Elucidated So Far? In: ACS Omega, 8 (13). pp. 11665-11673.
Subbalakshmi, AR and Sahoo, S and Manjunatha, P and Goyal, S and Kasiviswanathan, VA and Mahesh, Y and Ramu, S and McMullen, I and Somarelli, JA and Jolly, MK (2023) The ELF3 transcription factor is associated with an epithelial phenotype and represses epithelial-mesenchymal transition. In: Journal of Biological Engineering, 17 (1).
Roy, U and Singh, D and Vincent, N and Haritas, CK and Jolly, MK (2023) Spatiotemporal Patterning Enabled by Gene Regulatory Networks. In: ACS Omega .
Kar, A and Medatwal, N and Rajput, K and Mandal, S and Pani, T and Khan, A and Sharma, P and Oberoi, AS and Vishwakarma, G and Deo, SVS and Jolly, MK and Bajaj, A and Dasgupta, U (2023) Unique sphingolipid signature identifies luminal and triple-negative breast cancer subtypes. In: International Journal of Cancer .
Hari, K and Duncan, W and Ibrahim, MA and Jolly, MK and Cummins, B and Gedeon, T (2023) Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space. In: npj Systems Biology and Applications, 9 (1).
Bocci, F and Jia, D and Nie, Q and Jolly, MK and Onuchic, J (2023) Theoretical and computational tools to model multistable gene regulatory networks. In: Reports on Progress in Physics, 86 (10).
Hari, K and Harlapur, P and Gopalan, A and Ullanat, V and Duddu, AS and Jolly, MK (2022) Emergent properties of coupled bistable switches. In: Journal of Biosciences, 47 (4).
Harlapur, P and Duddu, AS and Hari, K and Kulkarni, P and Jolly, MK (2022) Functional Resilience of Mutually Repressing Motifs Embedded in Larger Networks. In: Biomolecules, 12 (12).
Pillai, M and Chen, Z and Jolly, MK and Li, C (2022) Quantitative landscapes reveal trajectories of cell-state transitions associated with drug resistance in melanoma. In: iScience, 25 (12).
Aggarwal, V and Sahoo, S and Donnenberg, VS and Chakraborty, P and Jolly, MK and Sant, S (2022) P4HA2: A link between tumor-intrinsic hypoxia, partial EMT and collective migration. In: Advances in Cancer Biology - Metastasis, 5 .
Sahoo, S and Mishra, A and Diehl, AM and Jolly, MK (2022) Dynamics of hepatocyte-cholangiocyte cell-fate decisions during liver development and regeneration. In: iScience, 25 (9).
Jia, W and Duddu, AS and Jolly, MK and Levine, H (2022) Lack of Correlation between Landscape Geometry and Transition Rates. In: Journal of Physical Chemistry B, 126 (30). pp. 5613-5618.
Navalkar, A and Paul, A and Sakunthala, A and Pandey, S and Dey, AK and Saha, S and Sahoo, S and Jolly, MK and Maiti, TK and Maji, SK (2022) Oncogenic gain of function due to p53 amyloids occurs through aberrant alteration of cell cycle and proliferation. In: Journal of cell science, 135 (15).
Brown, MS and Abdollahi, B and Wilkins, OM and Lu, H and Chakraborty, P and Ognjenovic, NB and Muller, KE and Jolly, MK and Christensen, BC and Hassanpour, S and Pattabiraman, DR (2022) Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer. In: Science Advances, 8 (31).
Saxena, K and Subbalakshmi, AR and Kulkarni, P and Jolly, MK (2022) Cancer: More than a geneticist’s Pandora’s box. In: Journal of Biosciences, 47 (2).
Deb, S and Bhandary, S and Sinha, SK and Jolly, MK and Dutta, PS (2022) Identifying critical transitions in complex diseases. In: Journal of Biosciences, 47 (2).
Singh, N and Singh, D and Bhide, A and Sharma, R and Sahoo, S and Jolly, MK and Modi, D (2022) Lhx2 in germ cells suppresses endothelial cell migration in the developing ovary. In: Experimental Cell Research, 415 (1).
Biswas, K and Jolly, MK and Ghosh, A (2022) Mean residence times of TF-TF and TF-miRNA toggle switches. In: Journal of Biosciences, 47 (2).
Naik, HC and Hari, K and Chandel, D and Jolly, MK and Gayen, S (2022) Single-cell analysis reveals X upregulation is not global in pre-gastrulation embryos. In: iScience, 25 (6).
Foo, J and Basanta, D and Rockne, RC and Strelez, C and Shah, C and Ghaffarian, K and Mumenthaler, SM and Mitchell, K and Lathia, JD and Frankhouser, D and Branciamore, S and Kuo, Y-H and Marcucci, G and Velde, RV and Marusyk, A and Huang, S and Hari, K and Jolly, MK and Hatzikirou, H and Poels, KE and Spilker, ME and Shtylla, B and Robertson-Tessi, M and Anderson, ARA (2022) Roadmap on plasticity and epigenetics in cancer. In: Physical Biology, 19 (3).
Venkatasubramanian, G and Kelkar, DA and Mandal, S and Jolly, MK and Kulkarni, M (2022) Analysis of Yes-Associated Protein-1 (YAP1) Target Gene Signature to Predict Progressive Breast Cancer. In: Journal of Clinical Medicine, 11 (7).
Masuda, H and Harano, K and Miura, S and Wang, Y and Hirota, Y and Harada, O and Jolly, MK and Matsunaga, Y and Lim, B and Wood, AL and Parinyanitikul, N and Lee, HJ and Gong, G and George, JT and Levine, H and Lee, J and Wang, X and Lucci, A and Rao, A and Schweitzer, BL and Lawrence, OR and Seitz, RS and Morris, SW and Hout, DR and Nakamura, S and Krishnamurthy, S and Ueno, NT (2022) Changes in Triple-Negative Breast Cancer Molecular Subtypes in Patients Without Pathologic Complete Response After Neoadjuvant Systemic Chemotherapy. In: JCO Precision Oncology, 6 .
Vilchez Mercedes, SA and Bocci, F and Ahmed, M and Eder, I and Zhu, N and Levine, H and Onuchic, JN and Jolly, MK and Wong, PK (2022) Nrf2 Modulates the Hybrid Epithelial/Mesenchymal Phenotype and Notch Signaling During Collective Cancer Migration. In: Frontiers in Molecular Biosciences, 9 .
Subbalakshmi, AR and Ashraf, B and Jolly, MK (2022) Biophysical and biochemical attributes of hybrid epithelial/mesenchymal phenotypes. In: Physical Biology, 19 (2).
Monavarian, M and Elhaw, AT and Tang, PW and Javed, Z and Shonibare, Z and Scalise, CB and Arend, R and Jolly, MK and Sewell- Loftin, MK and Hempel, N and Mythreye, K (2022) Emerging perspectives on growth factor metabolic relationships in the ovarian cancer ascites environment. In: Seminars in Cancer Biology .
Parthasarathi, KTS and Mandal, S and Singh, S and Gundimeda, S and Jolly, MK and Pandey, A and Sharma, J (2022) In Silico Analysis of Ion Channels and Their Correlation with Epithelial to Mesenchymal Transition in Breast Cancer. In: Cancers, 14 (6).
Kulkarni, P and Bhattacharya, S and Achuthan, S and Behal, A and Jolly, MK and Kotnala, S and Mohanty, A and Rangarajan, G and Salgia, R and Uversky, V (2022) Intrinsically Disordered Proteins: Critical Components of the Wetware. In: Chemical Reviews, 122 (6). pp. 6614-6633.
Jolly, MK and Murphy, RJ and Bhatia, S and Whitfield, HJ and Redfern, A and Davis, MJ and Thompson, EW (2022) Measuring and Modelling the Epithelial- Mesenchymal Hybrid State in Cancer: Clinical Implications. In: Cells Tissues Organs, 211 (2). 110 -133.
Saxena, K and Srikrishnan, S and Celia-Terrassa, T and Jolly, MK (2022) OVOL1/2: Drivers of Epithelial Differentiation in Development, Disease, and Reprogramming. In: Cells Tissues Organs, 211 (2). 183 -192.
Patkulkar, PA and Subbalakshmi, AR and Jolly, MK and Sinharay, S (2022) Mapping Spatiotemporal Heterogeneity in Tumor Profiles by Integrating High-Throughput Imaging and Omics Analysis. In: ACS Omega .
Tretyakova, MS and Subbalakshmi, AR and Menyailo, ME and Jolly, MK and Denisov, EV (2022) Tumor Hybrid Cells: Nature and Biological Significance. In: Frontiers in Cell and Developmental Biology, 10 .
Mandal, S and Tejaswi, T and Janivara, R and Srikrishnan, S and Thakur, P and Sahoo, S and Chakraborty, P and Sohal, SS and Levine, H and George, JT and Jolly, MK (2022) Transcriptomic-based quantification of the epithelial-hybrid-mesenchymal spectrum across biological contexts. In: Biomolecules, 12 (1).
Sahoo, S and Ashraf, B and Duddu, AS and Biddle, A and Jolly, MK (2022) Interconnected high-dimensional landscapes of epithelial�mesenchymal plasticity and stemness in cancer. In: Clinical and Experimental Metastasis .
More, MH and Varankar, SS and Naik, RR and Dhake, RD and Ray, P and Bankar, RM and Mali, AM and Subbalakshmi, AR and Chakraborty, P and Jolly, MK and Bapat, SA (2022) A Multistep Tumor Growth Model of High-Grade Serous Ovarian Carcinoma Identifies Hypoxia-Associated Signatures. In: Cells Tissues Organs, 213 (2). pp. 79-95.
Jia, W and Jolly, MK and Levine, H (2022) NRF2-dependent Epigenetic Regulation can Promote the Hybrid Epithelial/Mesenchymal Phenotype. In: Frontiers in Cell and Developmental Biology, 9 .
Jain, P and Bhatia, S and Thompson, EW and Jolly, MK (2022) Population Dynamics of Epithelial�Mesenchymal Heterogeneity in Cancer Cells. In: Biomolecules, 12 (3).
Khumukcham, SS and Penugurti, V and Soni, A and Uppala, V and Hari, K and Jolly, MK and Dwivedi, A and Salam PK, A and Padala, C and Mukta, S and Bhopal, T and Manavathi, B (2022) A reciprocal feedback loop between HIF-1α and HPIP controls phenotypic plasticity in breast cancer cells. In: Cancer Letters, 526 . pp. 12-28.
Sahoo, S and Nayak, SP and Hari, K and Purkait, P and Mandal, S and Kishore, A and Levine, H and Jolly, MK (2021) Immunosuppressive Traits of the Hybrid Epithelial/Mesenchymal Phenotype. In: Frontiers in Immunology, 12 .
Pasani, S and Sahoo, S and Jolly, MK (2021) Hybrid E/M phenotype(S) and stemness: A mechanistic connection embedded in network topology. In: Journal of Clinical Medicine, 10 (1). pp. 1-19.
Biswas, K and Jolly, MK and Ghosh, A (2021) First passage time properties of miRNA-mediated protein translation. In: Journal of Theoretical Biology, 529 .
Subbalakshmi, AR and Sahoo, S and McMullen, I and Saxena, AN and Venugopal, SK and Somarelli, JA and Jolly, MK (2021) Klf4 induces mesenchymal�epithelial transition (Met) by suppressing multiple emt�inducing transcription factors. In: Cancers, 13 (20).
Pramanik, D and Jolly, MK and Bhat, R (2021) Matrix adhesion and remodeling diversifies modes of cancer invasion across spatial scales. In: Journal of Theoretical Biology, 524 .
Vilchez Mercedes, SA and Bocci, F and Levine, H and Onuchic, JN and Jolly, MK and Wong, PK (2021) Decoding leader cells in collective cancer invasion. In: Nature Reviews Cancer .
Sahoo, S and Mishra, A and Kaur, H and Hari, K and Muralidharan, S and Mandal, S and Jolly, MK (2021) A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells. In: NAR Cancer, 3 (3).
Roy, N and Kshattry, M and Mandal, S and Jolly, MK and Bhattacharyya, DK and Barah, P (2021) An integrative systems biology approach identifies molecular signatures associated with gallbladder cancer pathogenesis. In: Journal of Clinical Medicine, 10 (16).
Thankamony, AP and Subbalakshmi, AR and Jolly, MK and Nair, R (2021) Lineage plasticity in cancer: The tale of a skin-walker. In: Cancers, 13 (14).
Jia, D and Park, JH and Kaur, H and Jung, KH and Yang, S and Tripathi, S and Galbraith, M and Deng, Y and Jolly, MK and Kaipparettu, BA and Onuchic, JN and Levine, H (2021) Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer. In: British Journal of Cancer .
Wang, P and Zhou, R and Thomas, P and Zhao, L and Zhou, R and Mandal, S and Jolly, MK and Richard, DJ and Rehm, BHA and Ostrikov, K and Dai, X and Williams, ED and Thompson, EW (2021) Epithelial-to-mesenchymal transition enhances cancer cell sensitivity to cytotoxic effects of zcold atmospheric plasmas in breast and bladder cancer systems. In: Cancers, 13 (12).
Hati, S and Duddu, AS and Jolly, MK (2021) Operating principles of circular toggle polygons. In: Physical Biology, 18 (4).
Deng, Y and Chakraborty, P and Jolly, MK and Levine, H (2021) A theoretical approach to coupling the epithelial-mesenchymal transition (Emt) to extracellular matrix (ecm) stiffness via loxl2. In: Cancers, 13 (7).
Chakraborty, P and George, JT and Woodward, WA and Levine, H and Jolly, MK (2021) Gene expression profiles of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum. In: Translational Oncology, 14 (4).
Singh, D and Bocci, F and Kulkarni, P and Jolly, MK (2021) Coupled feedback loops involving PAGE4, EMT and notch signaling can give rise to non-genetic heterogeneity in prostate cancer cells. In: Entropy, 23 (3). pp. 1-16.
Chauhan, L and Ram, U and Hari, K and Jolly, MK (2021) Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer. In: eLife, 10 .
Chedere, A and Hari, K and Kumar, S and Rangarajan, A and Jolly, MK (2021) Multi-stability and consequent phenotypic plasticity in AMPK-Akt double negative feedback loop in cancer cells. In: Journal of Clinical Medicine, 10 (3). pp. 1-16.
Norgard, RJ and Pitarresi, JR and Maddipati, R and Aiello-Couzo, NM and Balli, D and Li, J and Yamazoe, T and Wengyn, MD and Millstein, ID and Folkert, IW and Rosario-Berrios, DN and Kim, I-K and Bassett, JB and Payne, R and Berry, CT and Feng, X and Sun, K and Cioffi, M and Chakraborty, P and Jolly, MK and Gutkind, JS and Lyden, D and Freedman, BD and Foskett, JK and Rustgi, AK and Stanger, BZ (2021) Calcium signaling induces a partial EMT. In: EMBO Reports .
Subbalakshmi, AR and Sahoo, S and Biswas, K and Jolly, MK (2021) A Computational Systems Biology Approach Identifies SLUG as a Mediator of Partial Epithelial-Mesenchymal Transition (EMT). In: Cells Tissues Organs .
Pathak, S and Jolly, MK and Nandi, D (2021) Countries with high deaths due to flu and tuberculosis demonstrate lower COVID-19 mortality: roles of vaccinations. In: Human Vaccines and Immunotherapeutics .
Kulkarni, P and Achuthan, S and Bhattacharya, S and Jolly, MK and Kotnala, S and Leite, VBP and Mohanty, A and Orban, J and Roy, S and Rangarajan, G and Salgia, R (2021) Protein conformational dynamics and phenotypic switching. In: Biophysical Reviews .
Naik, HC and Hari, K and Chandel, D and Mandal, S and Jolly, MK and Gayen, S (2021) Semicoordinated allelic-bursting shape dynamic random monoallelic expression in pregastrulation embryos. In: iScience, 24 (9).
Pillai, M and Jolly, MK (2021) Systems-level network modeling deciphers the master regulators of phenotypic plasticity and heterogeneity in melanoma. In: iScience, 24 (10).
Hari, K and Sabuwala, B and Subramani, BV and La Porta, CAM and Zapperi, S and Font-Clos, F and Jolly, MK (2020) Identifying inhibitors of epithelial–mesenchymal plasticity using a network topology-based approach. In: npj Systems Biology and Applications, 6 (1).
Saxena, K and Jolly, MK and Balamurugan, K (2020) Hypoxia, partial EMT and collective migration: Emerging culprits in metastasis. In: Translational Oncology, 13 (11).
Sahoo, S and Jhunjhunwala, S and Jolly, MK (2020) The Good, The Bad and The Ugly: A Mathematical Model Investigates the Differing Outcomes Among CoVID-19 Patients. In: Journal of the Indian Institute of Science . (In Press)
Thankamony, AP and Murali, R and Karthikeyan, N and Varghese, BA and Teo, WS and McFarland, A and Roden, DL and Holliday, H and Konrad, CV and Cazet, A and Dodson, E and Yang, J and Baker, LA and George, JT and Levine, H and Jolly, MK and Swarbrick, A and Nair, R (2020) Targeting the id1-kif11 axis in triple-negative breast cancer using combination therapy. In: Biomolecules, 10 (9). pp. 1-15.
Kaur, T and Sarkar, S and Chowdhury, S and Sinha, SK and Jolly, MK and Dutta, PS (2020) Anticipating the Novel Coronavirus Disease (COVID-19) Pandemic. In: Frontiers in Public Health, 8 .
Duddu, AS and Sahoo, S and Hati, S and Jhunjhunwala, S and Jolly, MK (2020) Multi-stability in cellular differentiation enabled by a network of three mutually repressing master regulators: Multi-stability in cellular differentiation enabled by a network of three mutually repressing master regulators. In: Journal of the Royal Society Interface, 17 (170).
Subbalakshmi, AR and Kundnani, D and Biswas, K and Ghosh, A and Hanash, SM and Tripathi, SC and Jolly, MK (2020) NFATc Acts as a Non-Canonical Phenotypic Stability Factor for a Hybrid Epithelial/Mesenchymal Phenotype. In: Frontiers in Oncology, 10 .
Mohanty, A and Nam, A and Pozhitkov, A and Yang, L and Srivastava, S and Nathan, A and Wu, X and Mambetsariev, I and Nelson, M and Subbalakshmi, AR and Guo, L and Nasser, MW and Batra, SK and Orban, J and Jolly, MK and Massarelli, E and Kulkarni, P and Salgia, R (2020) A Non-genetic Mechanism Involving the Integrin β4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer. In: iScience, 23 (9).
Bocci, F and Onuchic, JN and Jolly, MK (2020) Understanding the Principles of Pattern Formation Driven by Notch Signaling by Integrating Experiments and Theoretical Models. In: Frontiers in Physiology, 11 .
Ranganathan, S and Kumar, S and Mohanty, SS and Jolly, MK and Rangarajan, A (2020) Cellular Plasticity in Matrix-attached and -Detached Cells: Implications in Metastasis. In: Journal of the Indian Institute of Science, 100 (3). pp. 525-536.
Khot, M and Sreekumar, D and Jahagirdar, S and Kulkarni, A and Hari, K and Faseela, EE and Sabarinathan, R and Jolly, MK and Sengupta, K (2020) Twist1 induces chromosomal instability (CIN) in colorectal cancer cells. In: Human molecular genetics, 29 (10). pp. 1673-1688.
Dhadve, AC and Hari, K and Rekhi, B and Jolly, MK and De, A and Ray, P (2020) Decoding molecular interplay between RUNX1 and FOXO3a underlying the pulsatile IGF1R expression during acquirement of chemoresistance. In: Biochimica et Biophysica Acta - Molecular Basis of Disease, 1866 (6).
Jolly, MK and Celia-Terrassa, T (2020) Insights into the multi-dimensional dynamic landscape of epithelial-mesenchymal plasticity through inter-disciplinary approaches. In: Journal of Clinical Medicine, 9 (6).
Thankamony, AP and Saxena, K and Murali, R and Jolly, MK and Nair, R (2020) Cancer Stem Cell Plasticity � A Deadly Deal. In: Frontiers in Molecular Biosciences, 7 .
Chakraborty, P and George, JT and Tripathi, S and Levine, H and Jolly, MK (2020) Comparative Study of Transcriptomics-Based Scoring Metrics for the Epithelial-Hybrid-Mesenchymal Spectrum. In: Frontiers in Bioengineering and Biotechnology, 8 .
Sahoo, S and Singh, D and Chakraborty, P and Jolly, MK (2020) Emergent properties of the HNF4Α-pparγ network may drive consequent phenotypic plasticity in NAFLD. In: Journal of Clinical Medicine, 9 (3).
Drapela, S and Bouchal, J and Jolly, MK and Culig, Z and SouÄek, K (2020) ZEB1: A Critical Regulator of Cell Plasticity, DNA Damage Response, and Therapy Resistance. In: Frontiers in Molecular Biosciences, 7 .
Tripathi, S and Chakraborty, P and Levine, H and Jolly, MK (2020) A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells. In: PLoS Computational Biology, 16 (2).
Lourenco, AR and Ban, Y and Crowley, MJ and Lee, SB and Ramchandani, D and Du, W and Elemento, O and George, JT and Jolly, MK and Levine, H and Sheng, J and Wong, ST and Altorki, NK and Gao, D (2020) Differential contributions of pre- And post-EMT tumor cells in breast cancer metastasis. In: Cancer Research, 80 (2). pp. 163-169.
Lourenco, AR and Ban, Y and Crowley, MJ and Lee, SB and Ramchandani, D and Du, W and Elemento, O and George, JT and Jolly, MK and Levine, H and Sheng, J and Wong, ST and Altorki, NK and Gao, D (2020) Differential contributions of pre- And post-EMT tumor cells in breast cancer metastasis. In: Cancer Research, 80 (2). pp. 163-169.
Sarkar, S and Sinha, SK and Levine, H and Jolly, MK and Dutta, PS (2019) Anticipating critical transitions in epithelial-hybrid-mesenchymal cell-fate determination. In: Proceedings of the National Academy of Sciences of the United States of America, 116 (52). pp. 26343-26352.
Jolly, MK and Ware, KE and Xu, S and Gilja, S and Shetler, S and Yang, Y and Wang, X and Austin, RG and Runyambo, D and Hish, AJ and DeWitt, SB and George, JT and Kreulen, RT and Boss, M-K and Lazarides, AL and Kerr, DL and Gerber, DG and Sivaraj, D and Armstrong, AJ and Dewhirst, MW and Eward, WC and Levine, H and Somarelli, JA (2019) E-cadherin represses anchorage-independent growth in sarcomas through both signaling and mechanical mechanisms. In: Molecular Cancer Research, 17 (6). pp. 1391-1402.
Lin, X and Kulkarni, P and Bocci, F and Schafer, NP and Roy, S and Tsai, MY and He, Y and Chen, Y and Rajagopalan, K and Mooney, SM and Zeng, Y and Weninger, K and Grishaev, A and Onuchic, JN and Levine, H and Wolynes, PG and Salgia, R and Rangarajan, G and Uversky, V and Orban, J and Jolly, MK (2019) Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level. In: Biomolecules, 9 (2).
Xu, S and Ware, KE and Ding, Y and Kim, SY and Sheth, MU and Rao, S and Chan, W and Armstrong, AJ and Eward, WC and Jolly, MK and Somarelli, JA (2019) An integrative systems biology and experimental approach identifies convergence of epithelial plasticity, metabolism, and autophagy to promote chemoresistance. In: Journal of Clinical Medicine, 8 (2).
Biswas, K and Jolly, MK and Ghosh, A (2019) Stability and mean residence times for hybrid epithelial/mesenchymal phenotype. In: Physical Biology, 16 (2).
Culig, Z and Jolly, MK and Souček, K (2023) Editorial: Heterogeneity and plasticity of prostate cancer. In: Frontiers in Molecular Biosciences, 10 .
Mattei, F and Jolly, MK (2023) Interdisciplinary research in cancer and immunity employing biophysical approaches. In: iScience, 26 (5).
Adler, FR and Anderson, ARA and Bhushan, A and Bogdan, P and Bravo-Cordero, JJ and Brock, A and Chen, Y and Cukierman, E and DelGiorno, KE and Denis, GV and Ferrall-Fairbanks, MC and Gartner, ZJ and Germain, RN and Gordon, DM and Hunter, G and Jolly, MK and Karacosta, LG and Mythreye, K and Katira, P and Kulkarni, RP and Kutys, ML and Lander, AD and Laughney, AM and Levine, H and Lou, E and Lowenstein, PR and Masters, KS and Pe'er, D and Peyton, SR and Platt, MO and Purvis, JE and Quon, G and Richer, JK and Riddle, NC and Rodriguez, A and Snyder, JC and Lee Szeto, G and Tomlin, CJ and Yanai, I and Zervantonakis, IK and Dueck, H (2023) Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation. In: Cell Systems, 14 (4). pp. 252-257.
Jolly, MK and Roy, S (2022) Editorial: Topical Collection on Emergent Dynamics of Biological Networks. In: Journal of Biosciences, 47 (4).
Capp, J-P and Jolly, MK and Sharma, A (2021) Editorial: Non-Genetic Heterogeneity in Development and Disease. In: Frontiers in Genetics, 12 .
Tripathi, SC and Jolly, MK and Mani, SA and Levine, H (2021) Editorial: Characterizing the Multi-Faceted Dynamics of Tumor Cell Plasticity. In: Frontiers in Molecular Biosciences, 7 .
Saxena, K and Subbalakshmi, AR and Jolly, MK (2019) Phenotypic heterogeneity in circulating tumor cells and its prognostic value in metastasis and overall survival. In: EBioMedicine, 46 . pp. 4-5.
