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For: Macklin P. When Seeing Isn't Believing: How Math Can Guide Our Interpretation of Measurements and Experiments. Cell Syst 2019;5:92-94. [PMID: 28837815 DOI: 10.1016/j.cels.2017.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Number Cited by Other Article(s)
1
L Rocha H, Aguilar B, Getz M, Shmulevich I, Macklin P. A multiscale model of immune surveillance in micrometastases gives insights on cancer patient digital twins. NPJ Syst Biol Appl 2024;10:144. [PMID: 39627216 PMCID: PMC11614875 DOI: 10.1038/s41540-024-00472-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 11/15/2024] [Indexed: 12/06/2024]  Open
2
Luque LM, Carlevaro CM, Rodriguez-Lomba E, Lomba E. In silico study of heterogeneous tumour-derived organoid response to CAR T-cell therapy. Sci Rep 2024;14:12307. [PMID: 38811838 PMCID: PMC11137006 DOI: 10.1038/s41598-024-63125-5] [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: 02/19/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024]  Open
3
Metzcar J, Jutzeler CR, Macklin P, Köhn-Luque A, Brüningk SC. A review of mechanistic learning in mathematical oncology. Front Immunol 2024;15:1363144. [PMID: 38533513 PMCID: PMC10963621 DOI: 10.3389/fimmu.2024.1363144] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/20/2024] [Indexed: 03/28/2024]  Open
4
Coulier A, Singh P, Sturrock M, Hellander A. Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation. PLoS Comput Biol 2022;18:e1010683. [PMID: 36520957 PMCID: PMC9799300 DOI: 10.1371/journal.pcbi.1010683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 12/29/2022] [Accepted: 10/25/2022] [Indexed: 12/23/2022]  Open
5
Shojaee P, Mornata F, Deutsch A, Locati M, Hatzikirou H. The impact of tumor associated macrophages on tumor biology under the lens of mathematical modelling: A review. Front Immunol 2022;13:1050067. [PMID: 36439180 PMCID: PMC9685623 DOI: 10.3389/fimmu.2022.1050067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/18/2022] [Indexed: 09/10/2023]  Open
6
Madamanchi A, Thomas M, Magana A, Heiland R, Macklin P. Supporting Computational Apprenticeship Through Educational and Software Infrastructure: A Case Study in a Mathematical Oncology Research Lab. PRIMUS 2022;32:446-467. [PMID: 35197716 PMCID: PMC8863170 DOI: 10.1080/10511970.2021.1881849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
7
Getz M, Wang Y, An G, Asthana M, Becker A, Cockrell C, Collier N, Craig M, Davis CL, Faeder JR, Ford Versypt AN, Mapder T, Gianlupi JF, Glazier JA, Hamis S, Heiland R, Hillen T, Hou D, Islam MA, Jenner AL, Kurtoglu F, Larkin CI, Liu B, Macfarlane F, Maygrundter P, Morel PA, Narayanan A, Ozik J, Pienaar E, Rangamani P, Saglam AS, Shoemaker JE, Smith AM, Weaver JJA, Macklin P. Iterative community-driven development of a SARS-CoV-2 tissue simulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.04.02.019075. [PMID: 32511322 PMCID: PMC7239052 DOI: 10.1101/2020.04.02.019075] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
8
Rocha HL, Godet I, Kurtoglu F, Metzcar J, Konstantinopoulos K, Bhoyar S, Gilkes DM, Macklin P. A persistent invasive phenotype in post-hypoxic tumor cells is revealed by fate mapping and computational modeling. iScience 2021;24:102935. [PMID: 34568781 PMCID: PMC8449249 DOI: 10.1016/j.isci.2021.102935] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/23/2021] [Accepted: 07/29/2021] [Indexed: 12/03/2022]  Open
9
Bustamante DJ, Basile EJ, Hildreth BM, Browning NW, Jensen SA, Moldovan L, Petrache HI, Moldovan NI. Biofabrication of spheroids fusion-based tumor models: computational simulation of glucose effects. Biofabrication 2021;13. [PMID: 33498017 DOI: 10.1088/1758-5090/abe025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/26/2021] [Indexed: 01/04/2023]
10
Perrillat-Mercerot A, Guillevin C, Miranville A, Guillevin R. Using mathematics in MRI data management for glioma assesment. J Neuroradiol 2019;48:282-290. [PMID: 31811826 DOI: 10.1016/j.neurad.2019.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/01/2022]
11
Macklin P. Key challenges facing data-driven multicellular systems biology. Gigascience 2019;8:giz127. [PMID: 31648301 PMCID: PMC6812467 DOI: 10.1093/gigascience/giz127] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022]  Open
12
Ozik J, Collier N, Heiland R, An G, Macklin P. Learning-accelerated discovery of immune-tumour interactions. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2019;4:747-760. [PMID: 31497314 PMCID: PMC6690424 DOI: 10.1039/c9me00036d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/18/2019] [Indexed: 05/04/2023]
13
Metzcar J, Wang Y, Heiland R, Macklin P. A Review of Cell-Based Computational Modeling in Cancer Biology. JCO Clin Cancer Inform 2019;3:1-13. [PMID: 30715927 PMCID: PMC6584763 DOI: 10.1200/cci.18.00069] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 12/14/2022]  Open
14
Schumacher LJ. Neural crest migration with continuous cell states. J Theor Biol 2019;481:84-90. [PMID: 30707976 DOI: 10.1016/j.jtbi.2019.01.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 01/09/2023]
15
Ghaffarizadeh A, Heiland R, Friedman SH, Mumenthaler SM, Macklin P. PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems. PLoS Comput Biol 2018;14:e1005991. [PMID: 29474446 PMCID: PMC5841829 DOI: 10.1371/journal.pcbi.1005991] [Citation(s) in RCA: 233] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/07/2018] [Accepted: 01/19/2018] [Indexed: 02/07/2023]  Open
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