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For: Mendoza L, Pardo F. A robust model to describe the differentiation of T-helper cells. Theory Biosci 2010;129:283-93. [PMID: 20922578 DOI: 10.1007/s12064-010-0112-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 08/20/2010] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
1
Mendoza L, Vázquez-Ramírez R, Tzompantzi-de-Ita JM. The regulatory network that controls lymphopoiesis. Biosystems 2025;248:105399. [PMID: 39828207 DOI: 10.1016/j.biosystems.2025.105399] [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: 08/26/2024] [Revised: 01/08/2025] [Accepted: 01/10/2025] [Indexed: 01/22/2025]
2
Calzone L, Noël V, Barillot E, Kroemer G, Stoll G. Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells. Comput Struct Biotechnol J 2022;20:5661-5671. [PMID: 36284705 PMCID: PMC9582792 DOI: 10.1016/j.csbj.2022.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 11/24/2022]  Open
3
ROY PRITIKUMAR, ROY AMITKUMAR, KHAILOV EVGENIIN, AL BASIR FAHAD, GRIGORIEVA ELLINAV. A MODEL OF THE OPTIMAL IMMUNOTHERAPY OF PSORIASIS BY INTRODUCING IL-10 AND IL-22 INHIBITORS. J BIOL SYST 2020;28:609-639. [DOI: 10.1142/s0218339020500084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
4
Stalidzans E, Zanin M, Tieri P, Castiglione F, Polster A, Scheiner S, Pahle J, Stres B, List M, Baumbach J, Lautizi M, Van Steen K, Schmidt HH. Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice. NETWORK AND SYSTEMS MEDICINE 2020. [DOI: 10.1089/nsm.2020.0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
5
Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks. PLoS Comput Biol 2019;15:e1007075. [PMID: 31310618 PMCID: PMC6660093 DOI: 10.1371/journal.pcbi.1007075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 07/26/2019] [Accepted: 05/07/2019] [Indexed: 11/21/2022]  Open
6
Breitenbach T, Lorenz K, Dandekar T. How to Steer and Control ERK and the ERK Signaling Cascade Exemplified by Looking at Cardiac Insufficiency. Int J Mol Sci 2019;20:E2179. [PMID: 31052520 PMCID: PMC6539830 DOI: 10.3390/ijms20092179] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022]  Open
7
Figueiredo AS, Schumacher A. The T helper type 17/regulatory T cell paradigm in pregnancy. Immunology 2016;148:13-21. [PMID: 26855005 DOI: 10.1111/imm.12595] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 01/15/2016] [Accepted: 02/04/2016] [Indexed: 12/28/2022]  Open
8
Méndez A, Mendoza L. A Network Model to Describe the Terminal Differentiation of B Cells. PLoS Comput Biol 2016;12:e1004696. [PMID: 26751566 PMCID: PMC4720151 DOI: 10.1371/journal.pcbi.1004696] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 12/07/2015] [Indexed: 01/31/2023]  Open
9
Intosalmi J, Ahlfors H, Rautio S, Mannerstöm H, Chen ZJ, Lahesmaa R, Stockinger B, Lähdesmäki H. Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data. BMC SYSTEMS BIOLOGY 2015;9:81. [PMID: 26578352 PMCID: PMC4650136 DOI: 10.1186/s12918-015-0223-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/28/2015] [Indexed: 02/07/2023]
10
Mendoza L, Méndez A. A dynamical model of the regulatory network controlling lymphopoiesis. Biosystems 2015;137:26-33. [PMID: 26408858 DOI: 10.1016/j.biosystems.2015.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 08/22/2015] [Accepted: 09/21/2015] [Indexed: 12/22/2022]
11
Martinez-Sanchez ME, Mendoza L, Villarreal C, Alvarez-Buylla ER. A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity. PLoS Comput Biol 2015;11:e1004324. [PMID: 26090929 PMCID: PMC4475012 DOI: 10.1371/journal.pcbi.1004324] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 05/07/2015] [Indexed: 12/24/2022]  Open
12
Karl S, Dandekar T. Convergence behaviour and Control in Non-Linear Biological Networks. Sci Rep 2015;5:9746. [PMID: 26068060 PMCID: PMC4464179 DOI: 10.1038/srep09746] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 03/13/2015] [Indexed: 12/18/2022]  Open
13
Rodriguez A, Crespo I, Fournier A, del Sol A. Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET. PLoS One 2015;10:e0127216. [PMID: 26058016 PMCID: PMC4461287 DOI: 10.1371/journal.pone.0127216] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 04/13/2015] [Indexed: 01/09/2023]  Open
14
Albert R, Thakar J. Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015;6:353-69. [PMID: 25269159 DOI: 10.1002/wsbm.1273] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
15
Cappuccio A, Tieri P, Castiglione F. Multiscale modelling in immunology: a review. Brief Bioinform 2015;17:408-18. [PMID: 25810307 DOI: 10.1093/bib/bbv012] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/30/2015] [Indexed: 01/26/2023]  Open
16
Abou-Jaoudé W, Monteiro PT, Naldi A, Grandclaudon M, Soumelis V, Chaouiya C, Thieffry D. Model checking to assess T-helper cell plasticity. Front Bioeng Biotechnol 2015;2:86. [PMID: 25674559 PMCID: PMC4309205 DOI: 10.3389/fbioe.2014.00086] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/20/2014] [Indexed: 12/03/2022]  Open
17
Carbo A, Hontecillas R, Andrew T, Eden K, Mei Y, Hoops S, Bassaganya-Riera J. Computational modeling of heterogeneity and function of CD4+ T cells. Front Cell Dev Biol 2014;2:31. [PMID: 25364738 PMCID: PMC4207042 DOI: 10.3389/fcell.2014.00031] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 07/10/2014] [Indexed: 12/19/2022]  Open
18
Castiglione F, Pappalardo F, Bianca C, Russo G, Motta S. Modeling biology spanning different scales: an open challenge. BIOMED RESEARCH INTERNATIONAL 2014;2014:902545. [PMID: 25143952 PMCID: PMC4124842 DOI: 10.1155/2014/902545] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/25/2014] [Indexed: 02/03/2023]
19
Differentiation of Th subsets inhibited by nonstructural proteins of respiratory syncytial virus is mediated by ubiquitination. PLoS One 2014;9:e101469. [PMID: 24992002 PMCID: PMC4081659 DOI: 10.1371/journal.pone.0101469] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/05/2014] [Indexed: 12/02/2022]  Open
20
Li WZ, Wang J, Long R, Su GH, Bukhory DK, Dai J, Jin N, Huang SY, Jia P, Li T, Fan C, Liu K, Wang Z. Novel antibody against a glutamic acid-rich human fibrinogen-like protein 2-derived peptide near Ser91 inhibits hfgl2 prothrombinase activity. PLoS One 2014;9:e94551. [PMID: 24728278 PMCID: PMC3984148 DOI: 10.1371/journal.pone.0094551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 03/17/2014] [Indexed: 12/11/2022]  Open
21
Mbodj A, Junion G, Brun C, Furlong EEM, Thieffry D. Logical modelling of Drosophila signalling pathways. MOLECULAR BIOSYSTEMS 2014;9:2248-58. [PMID: 23868318 DOI: 10.1039/c3mb70187e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
22
Teku GN, Ortutay C, Vihinen M. Identification of core T cell network based on immunome interactome. BMC SYSTEMS BIOLOGY 2014;8:17. [PMID: 24528953 PMCID: PMC3937033 DOI: 10.1186/1752-0509-8-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 02/05/2014] [Indexed: 12/03/2022]
23
Calçada D, Vianello D, Giampieri E, Sala C, Castellani G, de Graaf A, Kremer B, van Ommen B, Feskens E, Santoro A, Franceschi C, Bouwman J. The role of low-grade inflammation and metabolic flexibility in aging and nutritional modulation thereof: a systems biology approach. Mech Ageing Dev 2014;136-137:138-47. [PMID: 24462698 DOI: 10.1016/j.mad.2014.01.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 02/07/2023]
24
Tieri P, Prana V, Colombo T, Santoni D, Castiglione F. Multi-scale Simulation of T Helper Lymphocyte Differentiation. ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2014. [DOI: 10.1007/978-3-319-12418-6_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
25
Castiglione F, Tieri P, De Graaf A, Franceschi C, Liò P, Van Ommen B, Mazzà C, Tuchel A, Bernaschi M, Samson C, Colombo T, Castellani GC, Capri M, Garagnani P, Salvioli S, Nguyen VA, Bobeldijk-Pastorova I, Krishnan S, Cappozzo A, Sacchetti M, Morettini M, Ernst M. The onset of type 2 diabetes: proposal for a multi-scale model. JMIR Res Protoc 2013;2:e44. [PMID: 24176906 PMCID: PMC3841357 DOI: 10.2196/resprot.2854] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/16/2013] [Indexed: 11/16/2022]  Open
26
Martínez-Sosa P, Mendoza L. The regulatory network that controls the differentiation of T lymphocytes. Biosystems 2013;113:96-103. [PMID: 23743337 DOI: 10.1016/j.biosystems.2013.05.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 02/13/2013] [Accepted: 05/21/2013] [Indexed: 12/22/2022]
27
Bérenguier D, Chaouiya C, Monteiro PT, Naldi A, Remy E, Thieffry D, Tichit L. Dynamical modeling and analysis of large cellular regulatory networks. CHAOS (WOODBURY, N.Y.) 2013;23:025114. [PMID: 23822512 DOI: 10.1063/1.4809783] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
28
Liao C, Lu T. A minimal transcriptional controlling network of regulatory T cell development. J Phys Chem B 2013;117:12995-3004. [PMID: 23642089 DOI: 10.1021/jp402306g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
29
Mendoza L. A Virtual Culture of CD4+ T Lymphocytes. Bull Math Biol 2013;75:1012-29. [DOI: 10.1007/s11538-013-9814-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 01/09/2013] [Indexed: 12/11/2022]
30
Saadatpour A, Albert R. Boolean modeling of biological regulatory networks: a methodology tutorial. Methods 2012;62:3-12. [PMID: 23142247 DOI: 10.1016/j.ymeth.2012.10.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 10/31/2012] [Indexed: 12/14/2022]  Open
31
Weinstein N, Mendoza L. Building Qualitative Models of Plant Regulatory Networks with SQUAD. FRONTIERS IN PLANT SCIENCE 2012;3:72. [PMID: 22639661 PMCID: PMC3355663 DOI: 10.3389/fpls.2012.00072] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 03/28/2012] [Indexed: 05/24/2023]
32
Rodríguez A, Sosa D, Torres L, Molina B, Frías S, Mendoza L. A Boolean network model of the FA/BRCA pathway. ACTA ACUST UNITED AC 2012;28:858-66. [PMID: 22267503 DOI: 10.1093/bioinformatics/bts036] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
33
Sankar M, Osmont KS, Rolcik J, Gujas B, Tarkowska D, Strnad M, Xenarios I, Hardtke CS. A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk. ACTA ACUST UNITED AC 2011;27:1404-12. [PMID: 21450717 DOI: 10.1093/bioinformatics/btr158] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
34
Demongeot J, Elena A, Noual M, Sené S, Thuderoz F. "Immunetworks", intersecting circuits and dynamics. J Theor Biol 2011;280:19-33. [PMID: 21439971 DOI: 10.1016/j.jtbi.2011.03.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 03/17/2011] [Accepted: 03/17/2011] [Indexed: 12/21/2022]
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