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For: Tiemann CA, Vanlier J, Hilbers PAJ, van Riel NAW. Parameter adaptations during phenotype transitions in progressive diseases. BMC Syst Biol 2011;5:174. [PMID: 22029623 PMCID: PMC3354367 DOI: 10.1186/1752-0509-5-174] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 10/26/2011] [Indexed: 12/22/2022]
Number Cited by Other Article(s)
1
Paalvast Y, Zhou E, Rozendaal YJW, Wang Y, Gerding A, van Dijk TH, de Boer JF, Rensen PCN, van Dijk KW, Kuivenhoven JA, Bakker BM, van Riel NAW, Groen AK. A Systems Analysis of Phenotype Heterogeneity in APOE*3Leiden.CETP Mice Induced by Long-Term High-Fat High-Cholesterol Diet Feeding. Nutrients 2022;14:nu14224936. [PMID: 36432620 PMCID: PMC9698005 DOI: 10.3390/nu14224936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]  Open
2
van Riel NAW, Tiemann CA, Hilbers PAJ, Groen AK. Metabolic Modeling Combined With Machine Learning Integrates Longitudinal Data and Identifies the Origin of LXR-Induced Hepatic Steatosis. Front Bioeng Biotechnol 2021;8:536957. [PMID: 33665185 PMCID: PMC7921164 DOI: 10.3389/fbioe.2020.536957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 12/16/2020] [Indexed: 11/23/2022]  Open
3
Kinetic analysis via mathematical modeling for ferrous iron oxidation in a class of SBR-type system. Chin J Chem Eng 2019. [DOI: 10.1016/j.cjche.2019.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
4
Rozendaal YJW, Wang Y, Hilbers PAJ, van Riel NAW. Computational modelling of energy balance in individuals with Metabolic Syndrome. BMC SYSTEMS BIOLOGY 2019;13:24. [PMID: 30808366 PMCID: PMC6390597 DOI: 10.1186/s12918-019-0705-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 02/14/2019] [Indexed: 02/07/2023]
5
Álvarez-Buylla Roces ME, Martínez-García JC, Dávila-Velderrain J, Domínguez-Hüttinger E, Martínez-Sánchez ME. Medical Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018;1069:1-33. [PMID: 30076565 DOI: 10.1007/978-3-319-89354-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
6
Modeling Procedures. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018;1069:35-134. [PMID: 30076566 DOI: 10.1007/978-3-319-89354-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
7
Rozendaal YJW, Wang Y, Paalvast Y, Tambyrajah LL, Li Z, Willems van Dijk K, Rensen PCN, Kuivenhoven JA, Groen AK, Hilbers PAJ, van Riel NAW. In vivo and in silico dynamics of the development of Metabolic Syndrome. PLoS Comput Biol 2018;14:e1006145. [PMID: 29879115 PMCID: PMC5991635 DOI: 10.1371/journal.pcbi.1006145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/13/2018] [Indexed: 12/16/2022]  Open
8
Oguz C, Watson LT, Baumann WT, Tyson JJ. Predicting network modules of cell cycle regulators using relative protein abundance statistics. BMC SYSTEMS BIOLOGY 2017;11:30. [PMID: 28241833 PMCID: PMC5329933 DOI: 10.1186/s12918-017-0409-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/17/2017] [Indexed: 11/10/2022]
9
Nyman E, Rozendaal YJW, Helmlinger G, Hamrén B, Kjellsson MC, Strålfors P, van Riel NAW, Gennemark P, Cedersund G. Requirements for multi-level systems pharmacology models to reach end-usage: the case of type 2 diabetes. Interface Focus 2016;6:20150075. [PMID: 27051506 DOI: 10.1098/rsfs.2015.0075] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
10
Evaluating computational models of cholesterol metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2015;1851:1360-76. [DOI: 10.1016/j.bbalip.2015.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 05/08/2015] [Accepted: 05/26/2015] [Indexed: 02/02/2023]
11
Haanstra JR, Bakker BM. Drug target identification through systems biology. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015;15:17-22. [PMID: 26464086 DOI: 10.1016/j.ddtec.2015.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 05/18/2015] [Accepted: 06/12/2015] [Indexed: 06/05/2023]
12
Hijmans BS, Tiemann CA, Grefhorst A, Boesjes M, van Dijk TH, Tietge UJF, Kuipers F, van Riel NAW, Groen AK, Oosterveer MH. A systems biology approach reveals the physiological origin of hepatic steatosis induced by liver X receptor activation. FASEB J 2014;29:1153-64. [PMID: 25477282 DOI: 10.1096/fj.14-254656] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 11/05/2014] [Indexed: 12/12/2022]
13
Sips FLP, Tiemann CA, Oosterveer MH, Groen AK, Hilbers PAJ, van Riel NAW. A computational model for the analysis of lipoprotein distributions in the mouse: translating FPLC profiles to lipoprotein metabolism. PLoS Comput Biol 2014;10:e1003579. [PMID: 24784354 PMCID: PMC4006703 DOI: 10.1371/journal.pcbi.1003579] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 03/11/2014] [Indexed: 12/27/2022]  Open
14
Vanlier J, Tiemann CA, Hilbers PAJ, van Riel NAW. Optimal experiment design for model selection in biochemical networks. BMC SYSTEMS BIOLOGY 2014;8:20. [PMID: 24555498 PMCID: PMC3946009 DOI: 10.1186/1752-0509-8-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 02/13/2014] [Indexed: 01/06/2023]
15
Parameter trajectory analysis to identify treatment effects of pharmacological interventions. PLoS Comput Biol 2013;9:e1003166. [PMID: 23935478 PMCID: PMC3731221 DOI: 10.1371/journal.pcbi.1003166] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 06/18/2013] [Indexed: 11/29/2022]  Open
16
van der Wulp MYM, Verkade HJ, Groen AK. Regulation of cholesterol homeostasis. Mol Cell Endocrinol 2013;368:1-16. [PMID: 22721653 DOI: 10.1016/j.mce.2012.06.007] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 05/17/2012] [Accepted: 06/11/2012] [Indexed: 12/28/2022]
17
van Riel NAW, Tiemann CA, Vanlier J, Hilbers PAJ. Applications of analysis of dynamic adaptations in parameter trajectories. Interface Focus 2013;3:20120084. [PMID: 23853705 PMCID: PMC3638482 DOI: 10.1098/rsfs.2012.0084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]  Open
18
Vanlier J, Tiemann CA, Hilbers PAJ, van Riel NAW. Parameter uncertainty in biochemical models described by ordinary differential equations. Math Biosci 2013;246:305-14. [PMID: 23535194 DOI: 10.1016/j.mbs.2013.03.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 03/07/2013] [Accepted: 03/12/2013] [Indexed: 12/21/2022]
19
Randolph-Gips M, Srinivasan P. Modeling autism: a systems biology approach. J Clin Bioinforma 2012;2:17. [PMID: 23043674 PMCID: PMC3507704 DOI: 10.1186/2043-9113-2-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 08/09/2012] [Indexed: 12/13/2022]  Open
20
van de Pas NCA, Woutersen RA, van Ommen B, Rietjens IMCM, de Graaf AA. A physiologically based in silico kinetic model predicting plasma cholesterol concentrations in humans. J Lipid Res 2012;53:2734-46. [PMID: 23024287 DOI: 10.1194/jlr.m031930] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
21
Vanlier J, Tiemann CA, Hilbers PAJ, van Riel NAW. A Bayesian approach to targeted experiment design. Bioinformatics 2012;28:1136-42. [PMID: 22368245 PMCID: PMC3324513 DOI: 10.1093/bioinformatics/bts092] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
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