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For: Kohar V, Lu M. Role of noise and parametric variation in the dynamics of gene regulatory circuits. NPJ Syst Biol Appl 2018;4:40. [PMID: 30416751 DOI: 10.1038/s41540-018-0076-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 10/14/2018] [Accepted: 10/16/2018] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
1
Ramirez DA, Lu M. Dissecting reversible and irreversible single cell state transitions from gene regulatory networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.30.610498. [PMID: 39257745 PMCID: PMC11384016 DOI: 10.1101/2024.08.30.610498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
2
Park JH, Hothi P, de Lomana ALG, Pan M, Calder R, Turkarslan S, Wu WJ, Lee H, Patel AP, Cobbs C, Huang S, Baliga NS. Gene regulatory network topology governs resistance and treatment escape in glioma stem-like cells. SCIENCE ADVANCES 2024;10:eadj7706. [PMID: 38848360 PMCID: PMC11160475 DOI: 10.1126/sciadv.adj7706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
3
Katebi A, Chen X, Ramirez D, Li S, Lu M. Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML. NPJ Syst Biol Appl 2024;10:38. [PMID: 38594351 PMCID: PMC11003984 DOI: 10.1038/s41540-024-00366-0] [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: 10/16/2023] [Accepted: 03/29/2024] [Indexed: 04/11/2024]  Open
4
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
5
Park JH, Hothi P, Lopez Garcia de Lomana A, Pan M, Calder R, Turkarslan S, Wu WJ, Lee H, Patel AP, Cobbs C, Huang S, Baliga NS. Gene regulatory network topology governs resistance and treatment escape in glioma stem-like cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578510. [PMID: 38370784 PMCID: PMC10871280 DOI: 10.1101/2024.02.02.578510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
6
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: 3] [Impact Index Per Article: 3.0] [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]
7
Shin D, Cho KH. Critical transition and reversion of tumorigenesis. Exp Mol Med 2023;55:692-705. [PMID: 37009794 PMCID: PMC10167317 DOI: 10.1038/s12276-023-00969-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 04/04/2023]  Open
8
Clauss B, Lu M. A quantitative evaluation of topological motifs and their coupling in gene circuit state distributions. iScience 2023;26:106029. [PMID: 36824273 PMCID: PMC9941213 DOI: 10.1016/j.isci.2023.106029] [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: 08/11/2022] [Revised: 12/19/2022] [Accepted: 01/17/2023] [Indexed: 01/24/2023]  Open
9
Caranica C, Lu M. A data-driven optimization method for coarse-graining gene regulatory networks. iScience 2023;26:105927. [PMID: 36698721 PMCID: PMC9868542 DOI: 10.1016/j.isci.2023.105927] [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: 08/09/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]  Open
10
Su K, Katebi A, Kohar V, Clauss B, Gordin D, Qin ZS, Karuturi RKM, Li S, Lu M. NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity. Genome Biol 2022;23:270. [PMID: 36575445 PMCID: PMC9793520 DOI: 10.1186/s13059-022-02835-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/05/2022] [Indexed: 12/28/2022]  Open
11
Huang L, Clauss B, Lu M. What Makes a Functional Gene Regulatory Network? A Circuit Motif Analysis. J Phys Chem B 2022;126:10374-10383. [PMID: 36471236 PMCID: PMC9896654 DOI: 10.1021/acs.jpcb.2c05412] [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] [Indexed: 12/12/2022]
12
Dynamics of hepatocyte-cholangiocyte cell-fate decisions during liver development and regeneration. iScience 2022;25:104955. [PMID: 36060070 PMCID: PMC9437857 DOI: 10.1016/j.isci.2022.104955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/17/2022] [Accepted: 08/12/2022] [Indexed: 11/25/2022]  Open
13
Galbraith M, Bocci F, Onuchic JN. Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway. PLoS Comput Biol 2022;18:e1010306. [PMID: 35862460 PMCID: PMC9345490 DOI: 10.1371/journal.pcbi.1010306] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/02/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022]  Open
14
Uthaya Kumar DB, Motakis E, Yurieva M, Kohar V, Martinek J, Wu TC, Khoury J, Grassmann J, Lu M, Palucka K, Kaminski N, Koff JL, Williams A. Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro. Am J Physiol Lung Cell Mol Physiol 2022;322:L822-L841. [PMID: 35438006 PMCID: PMC9142163 DOI: 10.1152/ajplung.00254.2021] [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: 06/14/2021] [Revised: 04/03/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022]  Open
15
Yu C, Wang J. Data mining and mathematical models in cancer prognosis and prediction. MEDICAL REVIEW (BERLIN, GERMANY) 2022;2:285-307. [PMID: 37724193 PMCID: PMC10388766 DOI: 10.1515/mr-2021-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/29/2021] [Indexed: 09/20/2023]
16
Duddu AS, Majumdar SS, Sahoo S, Jhunjhunwala S, Jolly MK. Emergent dynamics of a three-node regulatory network explain phenotypic switching and heterogeneity: a case study of Th1/Th2/Th17 cell differentiation. Mol Biol Cell 2022;33:ar46. [PMID: 35353012 PMCID: PMC9265159 DOI: 10.1091/mbc.e21-10-0521] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]  Open
17
Yu C, Liu Q, Wang J. A physical mechanism of heterogeneity and micro-metastasis in stem cell, cancer and cancer stem cell. J Chem Phys 2022;156:075103. [DOI: 10.1063/5.0078196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
18
Sahoo S, Nayak SP, Hari K, Purkait P, Mandal S, Kishore A, Levine H, Jolly MK. Immunosuppressive Traits of the Hybrid Epithelial/Mesenchymal Phenotype. Front Immunol 2022;12:797261. [PMID: 34975907 PMCID: PMC8714906 DOI: 10.3389/fimmu.2021.797261] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022]  Open
19
Wu Y, Jiao Y, Zhao Y, Jia H, Xu L. Noise-induced quasiperiod and period switching. Phys Rev E 2022;105:014419. [PMID: 35193235 DOI: 10.1103/physreve.105.014419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
20
Paredes O, Morales JA, Mendizabal AP, Romo-Vázquez R. Metacode: One code to rule them all. Biosystems 2021;208:104486. [PMID: 34274462 DOI: 10.1016/j.biosystems.2021.104486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022]
21
Kohar V, Gordin D, Katebi A, Levine H, Onuchic JN, Lu M. Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. Bioinformatics 2021;37:1327-1329. [PMID: 33279968 PMCID: PMC8599779 DOI: 10.1093/bioinformatics/btaa785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/08/2020] [Accepted: 09/04/2020] [Indexed: 11/12/2022]  Open
22
Katebi A, Ramirez D, Lu M. Computational systems-biology approaches for modeling gene networks driving epithelial-mesenchymal transitions. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2021;1:e1021. [PMID: 34164628 PMCID: PMC8219219 DOI: 10.1002/cso2.1021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
23
Hati S, Duddu AS, Jolly MK. Operating principles of circular toggle polygons. Phys Biol 2021;18. [PMID: 33730700 DOI: 10.1088/1478-3975/abef79] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/17/2021] [Indexed: 11/12/2022]
24
Shumilov AV, Gotovtsev PM. Modeling the activity of the dopamine signaling pathway by combination of analog electrical circuit and mathematical approaches. Heliyon 2021;7:e05879. [PMID: 33553717 PMCID: PMC7855338 DOI: 10.1016/j.heliyon.2020.e05879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 12/22/2019] [Accepted: 12/24/2020] [Indexed: 11/24/2022]  Open
25
Duddu AS, Sahoo S, Hati S, Jhunjhunwala S, Jolly MK. Multi-stability in cellular differentiation enabled by a network of three mutually repressing master regulators. J R Soc Interface 2020;17:20200631. [PMID: 32993428 DOI: 10.1098/rsif.2020.0631] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
26
Huang B, Lu M, Galbraith M, Levine H, Onuchic JN, Jia D. Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation. J R Soc Interface 2020;17:20200500. [PMID: 32781932 PMCID: PMC7482558 DOI: 10.1098/rsif.2020.0500] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022]  Open
27
Katebi A, Kohar V, Lu M. Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle. iScience 2020;23:101150. [PMID: 32450514 PMCID: PMC7251928 DOI: 10.1016/j.isci.2020.101150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/05/2020] [Accepted: 05/05/2020] [Indexed: 02/03/2023]  Open
28
Ramirez D, Kohar V, Lu M. Toward Modeling Context-Specific EMT Regulatory Networks Using Temporal Single Cell RNA-Seq Data. Front Mol Biosci 2020;7:54. [PMID: 32391378 PMCID: PMC7190801 DOI: 10.3389/fmolb.2020.00054] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/17/2020] [Indexed: 01/02/2023]  Open
29
Computational study of parameter sensitivity in DevR regulated gene expression. PLoS One 2020;15:e0228967. [PMID: 32053690 PMCID: PMC7018068 DOI: 10.1371/journal.pone.0228967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/27/2020] [Indexed: 11/26/2022]  Open
30
Yu C, Liu Q, Chen C, Yu J, Wang J. Landscape perspectives of tumor, EMT, and development. Phys Biol 2019;16:051003. [PMID: 31067516 DOI: 10.1088/1478-3975/ab2029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
31
Jia D, Li X, Bocci F, Tripathi S, Deng Y, Jolly MK, Onuchic JN, Levine H. Quantifying Cancer Epithelial-Mesenchymal Plasticity and its Association with Stemness and Immune Response. J Clin Med 2019;8:E725. [PMID: 31121840 PMCID: PMC6572429 DOI: 10.3390/jcm8050725] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/14/2019] [Accepted: 05/20/2019] [Indexed: 12/19/2022]  Open
32
Deciphering the Dynamics of Epithelial-Mesenchymal Transition and Cancer Stem Cells in Tumor Progression. CURRENT STEM CELL REPORTS 2019. [DOI: 10.1007/s40778-019-0150-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
33
Sha Y, Haensel D, Gutierrez G, Du H, Dai X, Nie Q. Intermediate cell states in epithelial-to-mesenchymal transition. Phys Biol 2019;16:021001. [PMID: 30560804 PMCID: PMC6602058 DOI: 10.1088/1478-3975/aaf928] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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