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For: Lu M, Jolly MK, Levine H, Onuchic JN, Ben-Jacob E. MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination. Proc Natl Acad Sci U S A. 2013;110:18144-18149. [PMID: 24154725 DOI: 10.1073/pnas.1318192110] [Citation(s) in RCA: 366] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
Number Cited by Other Article(s)
1
Villela-Castrejon J, Levine H, Kaipparettu BA, Onuchic JN, George JT, Jia D. Computational modeling of cancer cell metabolism along the catabolic-anabolic axes. NPJ Syst Biol Appl 2025;11:46. [PMID: 40348758 PMCID: PMC12065808 DOI: 10.1038/s41540-025-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 04/19/2025] [Indexed: 05/14/2025]  Open
2
Janes KA, Lazzara MJ. Systems Biology of the Cancer Cell. Annu Rev Biomed Eng 2025;27:1-28. [PMID: 39689262 DOI: 10.1146/annurev-bioeng-103122-030552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2024]
3
Höpfl S, Özverin M, Nowack H, Tamas R, Clark AG, Radde N, Olayioye MA. Integrated mathematical and experimental modeling uncovers enhanced EMT plasticity upon loss of the DLC1 tumor suppressor. PLoS Comput Biol 2025;21:e1013076. [PMID: 40354489 PMCID: PMC12121911 DOI: 10.1371/journal.pcbi.1013076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 05/29/2025] [Accepted: 04/21/2025] [Indexed: 05/14/2025]  Open
4
McDermott M, Mehta R, Roussos Torres ET, MacLean AL. Modeling the dynamics of EMT reveals genes associated with pan-cancer intermediate states and plasticity. NPJ Syst Biol Appl 2025;11:31. [PMID: 40210876 PMCID: PMC11986130 DOI: 10.1038/s41540-025-00512-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 03/28/2025] [Indexed: 04/12/2025]  Open
5
Greene G, Zonfa I, Ravasz Regan E. A Boolean network model of hypoxia, mechanosensing and TGF-β signaling captures the role of phenotypic plasticity and mutations in tumor metastasis. PLoS Comput Biol 2025;21:e1012735. [PMID: 40238833 PMCID: PMC12061430 DOI: 10.1371/journal.pcbi.1012735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Revised: 05/08/2025] [Accepted: 03/26/2025] [Indexed: 04/18/2025]  Open
6
Robert C, Prista von Bonhorst F, Dupont G, Gonze D, De Decker Y. Role of tristability in the robustness of the differentiation mechanism. PLoS One 2025;20:e0316666. [PMID: 40106426 PMCID: PMC11922266 DOI: 10.1371/journal.pone.0316666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 12/14/2024] [Indexed: 03/22/2025]  Open
7
Guilberteau J, Jain P, Jolly MK, Pouchol C, Pouradier Duteil N. An integrative phenotype-structured partial differential equation model for the population dynamics of epithelial-mesenchymal transition. NPJ Syst Biol Appl 2025;11:24. [PMID: 40050291 PMCID: PMC11885588 DOI: 10.1038/s41540-025-00502-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 02/17/2025] [Indexed: 03/09/2025]  Open
8
Hu Q, Lu X, Xue Z, Wang R. Gene regulatory network inference during cell fate decisions by perturbation strategies. NPJ Syst Biol Appl 2025;11:23. [PMID: 40032872 PMCID: PMC11876352 DOI: 10.1038/s41540-025-00504-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Accepted: 02/21/2025] [Indexed: 03/05/2025]  Open
9
Kim KP, Lemmon CA. Fibrotic extracellular matrix preferentially induces a partial Epithelial-Mesenchymal Transition phenotype in a 3-D agent based model of fibrosis. Math Biosci 2025;381:109375. [PMID: 39832653 PMCID: PMC11925401 DOI: 10.1016/j.mbs.2025.109375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 12/10/2024] [Accepted: 01/02/2025] [Indexed: 01/22/2025]
10
Hari K, Harlapur P, Saxena A, Haldar K, Girish A, Malpani T, Levine H, Jolly MK. Low dimensionality of phenotypic space as an emergent property of coordinated teams in biological regulatory networks. iScience 2025;28:111730. [PMID: 39898023 PMCID: PMC11787609 DOI: 10.1016/j.isci.2024.111730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 09/14/2024] [Accepted: 12/30/2024] [Indexed: 02/04/2025]  Open
11
Sahoo S, Hari K, Jolly MK. Design principles of regulatory networks underlying epithelial mesenchymal plasticity in cancer cells. Curr Opin Cell Biol 2025;92:102445. [PMID: 39608060 DOI: 10.1016/j.ceb.2024.102445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 10/22/2024] [Accepted: 10/30/2024] [Indexed: 11/30/2024]
12
Tian XJ, Zhang R, Ferro MV, Goetz H. Modeling ncRNA-Mediated Circuits in Cell Fate Decision: From Systems Biology to Synthetic Biology. Methods Mol Biol 2025;2883:139-154. [PMID: 39702707 DOI: 10.1007/978-1-0716-4290-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
13
Prasad H, Bv H, Subbalakshmi AR, Mandal S, Jolly MK, Visweswariah SS. Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer. NPJ Syst Biol Appl 2024;10:149. [PMID: 39702657 DOI: 10.1038/s41540-024-00463-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 10/28/2024] [Indexed: 12/21/2024]  Open
14
Dey A, MacLean AL. Transition paths across the EMT landscape are dictated by network logic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.03.626660. [PMID: 39677780 PMCID: PMC11642844 DOI: 10.1101/2024.12.03.626660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
15
Hirway SU, Nairon KG, Skardal A, Weinberg SH. A Multicellular Mechanochemical Model to Investigate Tumor Microenvironment Remodeling and Pre-Metastatic Niche Formation. Cell Mol Bioeng 2024;17:573-596. [PMID: 39926379 PMCID: PMC11799507 DOI: 10.1007/s12195-024-00831-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 10/27/2024] [Indexed: 02/11/2025]  Open
16
Hu Q, Tang R, He X, Wang R. General relationship of local topologies, global dynamics, and bifurcation in cellular networks. NPJ Syst Biol Appl 2024;10:135. [PMID: 39557967 PMCID: PMC11573990 DOI: 10.1038/s41540-024-00470-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Accepted: 11/07/2024] [Indexed: 11/20/2024]  Open
17
Chen Z, Lu J, Zhao X, Yu H, Li C. Energy Landscape Reveals the Underlying Mechanism of Cancer-Adipose Conversion in Gene Network Models. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2404854. [PMID: 39258786 PMCID: PMC11538663 DOI: 10.1002/advs.202404854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Indexed: 09/12/2024]
18
Barcenas M, Bocci F, Nie Q. Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data. Biophys J 2024;123:2849-2859. [PMID: 38504523 PMCID: PMC11393678 DOI: 10.1016/j.bpj.2024.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/09/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]  Open
19
Hernández-Magaña A, Bensussen A, Martínez-García JC, Álvarez-Buylla ER. A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence. NPJ Syst Biol Appl 2024;10:99. [PMID: 39223160 PMCID: PMC11369243 DOI: 10.1038/s41540-024-00422-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]  Open
20
Cheng YC, Zhang Y, Tripathi S, Harshavardhan BV, Jolly MK, Schiebinger G, Levine H, McDonald TO, Michor F. Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition. Proc Natl Acad Sci U S A 2024;121:e2406842121. [PMID: 39093947 PMCID: PMC11317558 DOI: 10.1073/pnas.2406842121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024]  Open
21
Subbalakshmi AR, Ramisetty S, Mohanty A, Pareek S, Do D, Shrestha S, Khan A, Talwar N, Tan T, Vishnubhotla P, Singhal SS, Salgia R, Kulkarni P. Phenotypic Plasticity and Cancer: A System Biology Perspective. J Clin Med 2024;13:4302. [PMID: 39124569 PMCID: PMC11313222 DOI: 10.3390/jcm13154302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/01/2024] [Accepted: 07/18/2024] [Indexed: 08/12/2024]  Open
22
Jain P, Kizhuttil R, Nair MB, Bhatia S, Thompson EW, George JT, Jolly MK. Cell-state transitions and density-dependent interactions together explain the dynamics of spontaneous epithelial-mesenchymal heterogeneity. iScience 2024;27:110310. [PMID: 39055927 PMCID: PMC11269952 DOI: 10.1016/j.isci.2024.110310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/21/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024]  Open
23
Skibba ME, Brasier AR. NF-κB/RelA signaling in secretoglobin progenitors mediates plasticity and MMP-induced barrier disruption in house dust mite-induced allergic asthma. Am J Physiol Lung Cell Mol Physiol 2024;327:L86-L101. [PMID: 38713619 PMCID: PMC11380976 DOI: 10.1152/ajplung.00066.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024]  Open
24
Bracken CP, Goodall GJ, Gregory PA. RNA regulatory mechanisms controlling TGF-β signaling and EMT in cancer. Semin Cancer Biol 2024;102-103:4-16. [PMID: 38917876 DOI: 10.1016/j.semcancer.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024]
25
Gottumukkala SB, Ganesan TS, Palanisamy A. Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer. NPJ Syst Biol Appl 2024;10:53. [PMID: 38760412 PMCID: PMC11101644 DOI: 10.1038/s41540-024-00378-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024]  Open
26
Lee J, Kim N, Cho KH. Decoding the principle of cell-fate determination for its reverse control. NPJ Syst Biol Appl 2024;10:47. [PMID: 38710700 PMCID: PMC11074314 DOI: 10.1038/s41540-024-00372-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/16/2024] [Indexed: 05/08/2024]  Open
27
Wu S, Qin X, Huang L. The role of alternative polyadenylation in epithelial-mesenchymal transition of non-small cell lung cancer. Hum Mol Genet 2024;33:677-686. [PMID: 38224682 DOI: 10.1093/hmg/ddae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/17/2024]  Open
28
Hong T, Xing J. Data- and theory-driven approaches for understanding paths of epithelial-mesenchymal transition. Genesis 2024;62:e23591. [PMID: 38553870 PMCID: PMC11017362 DOI: 10.1002/dvg.23591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/16/2024] [Accepted: 03/16/2024] [Indexed: 04/02/2024]
29
Rashid M, Devi BM, Banerjee M. Combinatorial Cooperativity in miR200-Zeb Feedback Network can Control Epithelial-Mesenchymal Transition. Bull Math Biol 2024;86:48. [PMID: 38555331 DOI: 10.1007/s11538-024-01277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/27/2024] [Indexed: 04/02/2024]
30
Bose A, Datta S, Mandal R, Ray U, Dhar R. Increased heterogeneity in expression of genes associated with cancer progression and drug resistance. Transl Oncol 2024;41:101879. [PMID: 38262110 PMCID: PMC10832509 DOI: 10.1016/j.tranon.2024.101879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/16/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]  Open
31
Celià-Terrassa T, Kang Y. How important is EMT for cancer metastasis? PLoS Biol 2024;22:e3002487. [PMID: 38324529 PMCID: PMC10849258 DOI: 10.1371/journal.pbio.3002487] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]  Open
32
Hu Q, Luo M, Wang R. Identifying critical regulatory interactions in cell fate decision and transition by systematic perturbation analysis. J Theor Biol 2024;577:111673. [PMID: 37984586 DOI: 10.1016/j.jtbi.2023.111673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
33
Chen Y, Chen Y, Yu XQ, Feng Q, Wang X, Liu L. Expression profiles of lncRNAs, miRNAs, and mRNAs and interaction analysis indicate their potential involvement during testicular fusion in Spodoptera litura. Genomics 2024;116:110758. [PMID: 38065236 DOI: 10.1016/j.ygeno.2023.110758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024]
34
Golconda P, Andrade-Medina M, Oberstein A. Subconfluent ARPE-19 Cells Display Mesenchymal Cell-State Characteristics and Behave like Fibroblasts, Rather Than Epithelial Cells, in Experimental HCMV Infection Studies. Viruses 2023;16:49. [PMID: 38257749 PMCID: PMC10821009 DOI: 10.3390/v16010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024]  Open
35
Nurmagambetova A, Mustyatsa V, Saidova A, Vorobjev I. Morphological and cytoskeleton changes in cells after EMT. Sci Rep 2023;13:22164. [PMID: 38092761 PMCID: PMC10719275 DOI: 10.1038/s41598-023-48279-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023]  Open
36
Merckens A, Sieler M, Keil S, Dittmar T. Altered Phenotypes of Breast Epithelial × Breast Cancer Hybrids after ZEB1 Knock-Out. Int J Mol Sci 2023;24:17310. [PMID: 38139138 PMCID: PMC10744253 DOI: 10.3390/ijms242417310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023]  Open
37
He X, Tang R, Lou J, Wang R. Identifying key factors in cell fate decisions by machine learning interpretable strategies. J Biol Phys 2023;49:443-462. [PMID: 37458834 PMCID: PMC10651582 DOI: 10.1007/s10867-023-09640-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/15/2023] [Indexed: 11/16/2023]  Open
38
Adhikary R, Roy A, Jolly MK, Das D. Effects of microRNA-mediated negative feedback on gene expression noise. Biophys J 2023;122:4220-4240. [PMID: 37803829 PMCID: PMC10645566 DOI: 10.1016/j.bpj.2023.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/19/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023]  Open
39
Delamonica B, Balázsi G, Shub M. Cusp bifurcation in a metastatic regulatory network. J Theor Biol 2023;575:111630. [PMID: 37804940 PMCID: PMC11132523 DOI: 10.1016/j.jtbi.2023.111630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/28/2023] [Accepted: 10/01/2023] [Indexed: 10/09/2023]
40
Jain P, Pillai M, Duddu AS, Somarelli JA, Goyal Y, Jolly MK. Dynamical hallmarks of cancer: Phenotypic switching in melanoma and epithelial-mesenchymal plasticity. Semin Cancer Biol 2023;96:48-63. [PMID: 37788736 DOI: 10.1016/j.semcancer.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023]
41
Zhang N, Yong EH. Dynamics, statistics, and task allocation of foraging ants. Phys Rev E 2023;108:054306. [PMID: 38115539 DOI: 10.1103/physreve.108.054306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 10/11/2023] [Indexed: 12/21/2023]
42
Shah S, Philipp LM, Giaimo S, Sebens S, Traulsen A, Raatz M. Understanding and leveraging phenotypic plasticity during metastasis formation. NPJ Syst Biol Appl 2023;9:48. [PMID: 37803056 PMCID: PMC10558468 DOI: 10.1038/s41540-023-00309-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023]  Open
43
Clarkson-Paredes C, Karl MT, Popratiloff A, Miller RH. A unique cell population expressing the Epithelial-Mesenchymal Transition-transcription factor Snail moderates microglial and astrocyte injury responses. PNAS NEXUS 2023;2:pgad334. [PMID: 37901440 PMCID: PMC10612478 DOI: 10.1093/pnasnexus/pgad334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023]
44
Haerinck J, Goossens S, Berx G. The epithelial-mesenchymal plasticity landscape: principles of design and mechanisms of regulation. Nat Rev Genet 2023;24:590-609. [PMID: 37169858 DOI: 10.1038/s41576-023-00601-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/13/2023]
45
Bocci F, Jia D, Nie Q, Jolly MK, Onuchic J. Theoretical and computational tools to model multistable gene regulatory networks. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2023;86:10.1088/1361-6633/acec88. [PMID: 37531952 PMCID: PMC10521208 DOI: 10.1088/1361-6633/acec88] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/02/2023] [Indexed: 08/04/2023]
46
Najafi A, Jolly MK, George JT. Population dynamics of EMT elucidates the timing and distribution of phenotypic intra-tumoral heterogeneity. iScience 2023;26:106964. [PMID: 37426354 PMCID: PMC10329148 DOI: 10.1016/j.isci.2023.106964] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/24/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023]  Open
47
He Y, Zhang Q, Chen Y, Wu Y, Quan Y, Chen W, Yao J, Zhang P. ZHX2 deficiency enriches hybrid MET cells through regulating E-cadherin expression. Cell Death Dis 2023;14:444. [PMID: 37460540 DOI: 10.1038/s41419-023-05974-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/18/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
48
Qiao D, Skibba M, Xu X, Brasier AR. Genomic targets of the IRE1-XBP1s pathway in mediating metabolic adaptation in epithelial plasticity. Nucleic Acids Res 2023;51:3650-3670. [PMID: 36772828 PMCID: PMC10164557 DOI: 10.1093/nar/gkad077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/19/2023] [Accepted: 02/09/2023] [Indexed: 02/12/2023]  Open
49
Subhadarshini S, Markus J, Sahoo S, Jolly MK. Dynamics of Epithelial-Mesenchymal Plasticity: What Have Single-Cell Investigations Elucidated So Far? ACS OMEGA 2023;8:11665-11673. [PMID: 37033874 PMCID: PMC10077445 DOI: 10.1021/acsomega.2c07989] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
50
Pillai M, Hojel E, Jolly MK, Goyal Y. Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools. NATURE COMPUTATIONAL SCIENCE 2023;3:301-313. [PMID: 38177938 DOI: 10.1038/s43588-023-00427-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/03/2023] [Indexed: 01/06/2024]
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