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For: Renardy M, Joslyn LR, Millar JA, Kirschner DE. To Sobol or not to Sobol? The effects of sampling schemes in systems biology applications. Math Biosci 2021;337:108593. [PMID: 33865847 PMCID: PMC8184610 DOI: 10.1016/j.mbs.2021.108593] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022]
Number Cited by Other Article(s)
1
Whiteley JP, Brown CP, Gaffney EA. Sensitivity of cartilage mechanical behaviour to spatial variations in material properties. J Mech Behav Biomed Mater 2024;156:106575. [PMID: 38824865 DOI: 10.1016/j.jmbbm.2024.106575] [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: 09/25/2023] [Revised: 02/28/2024] [Accepted: 05/08/2024] [Indexed: 06/04/2024]
2
Saxton H, Xu X, Schenkel T, Clayton RH, Halliday I. Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis. PLoS Comput Biol 2024;20:e1011946. [PMID: 39018334 DOI: 10.1371/journal.pcbi.1011946] [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: 02/23/2024] [Revised: 07/29/2024] [Accepted: 06/13/2024] [Indexed: 07/19/2024]  Open
3
Jegatheesan T, Moorthy AS, Eberl HJ. A mathematical model of competition between fiber and mucin degraders in the gut provides a possible explanation for mucus thinning. J Theor Biol 2024;587:111824. [PMID: 38604595 DOI: 10.1016/j.jtbi.2024.111824] [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: 10/22/2023] [Revised: 03/14/2024] [Accepted: 04/06/2024] [Indexed: 04/13/2024]
4
Claes E, Heck T, Coddens K, Sonnaert M, Schrooten J, Verwaeren J. Bayesian cell therapy process optimization. Biotechnol Bioeng 2024;121:1569-1582. [PMID: 38372656 DOI: 10.1002/bit.28669] [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: 05/31/2023] [Revised: 11/17/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
5
Stadt MM, Layton AT. A modeling analysis of whole body potassium regulation on a high-potassium diet: proximal tubule and tubuloglomerular feedback effects. Am J Physiol Regul Integr Comp Physiol 2024;326:R401-R415. [PMID: 38465401 DOI: 10.1152/ajpregu.00283.2023] [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: 12/15/2023] [Revised: 02/15/2024] [Accepted: 03/05/2024] [Indexed: 03/12/2024]
6
Gasior KI, Cogan NG. Untangling the Molecular Interactions Underlying Intracellular Phase Separation Using Combined Global Sensitivity Analyses. Bull Math Biol 2024;86:60. [PMID: 38641666 DOI: 10.1007/s11538-024-01288-y] [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: 11/07/2023] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
7
Bisesi AT, Möbius W, Nadell CD, Hansen EG, Bowden SD, Harcombe WR. Bacteriophage specificity is impacted by interactions between bacteria. mSystems 2024;9:e0117723. [PMID: 38376179 PMCID: PMC11237722 DOI: 10.1128/msystems.01177-23] [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: 11/07/2023] [Accepted: 01/20/2024] [Indexed: 02/21/2024]  Open
8
Oliveira RHDM, Annex BH, Popel AS. Endothelial cells signaling and patterning under hypoxia: a mechanistic integrative computational model including the Notch-Dll4 pathway. Front Physiol 2024;15:1351753. [PMID: 38455844 PMCID: PMC10917925 DOI: 10.3389/fphys.2024.1351753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024]  Open
9
Day EC, Chittari SS, Bogen MP, Knight AS. Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows. ACS POLYMERS AU 2023;3:406-427. [PMID: 38107416 PMCID: PMC10722570 DOI: 10.1021/acspolymersau.3c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/19/2023]
10
Nanda P, Budak M, Michael CT, Krupinsky K, Kirschner DE. Development and Analysis of Multiscale Models for Tuberculosis: From Molecules to Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566861. [PMID: 38014103 PMCID: PMC10680629 DOI: 10.1101/2023.11.13.566861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
11
Nanda P, Kirschner DE. Calibration methods to fit parameters within complex biological models. FRONTIERS IN APPLIED MATHEMATICS AND STATISTICS 2023;9:1256443. [PMID: 38222943 PMCID: PMC10785782 DOI: 10.3389/fams.2023.1256443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
12
Gao G, Walter NG. Critical Assessment of Condensate Boundaries in Dual-Color Single Particle Tracking. J Phys Chem B 2023;127:7694-7707. [PMID: 37669232 DOI: 10.1021/acs.jpcb.3c03776] [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] [Indexed: 09/07/2023]
13
Budak M, Cicchese JM, Maiello P, Borish HJ, White AG, Chishti HB, Tomko J, Frye LJ, Fillmore D, Kracinovsky K, Sakal J, Scanga CA, Lin PL, Dartois V, Linderman JJ, Flynn JL, Kirschner DE. Optimizing tuberculosis treatment efficacy: Comparing the standard regimen with Moxifloxacin-containing regimens. PLoS Comput Biol 2023;19:e1010823. [PMID: 37319311 PMCID: PMC10306236 DOI: 10.1371/journal.pcbi.1010823] [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: 12/15/2022] [Revised: 06/28/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]  Open
14
Feng A, Xie Y, Sun Y, Wang X, Jiang B, Xiao J. Efficient Autonomous Exploration and Mapping in Unknown Environments. SENSORS (BASEL, SWITZERLAND) 2023;23:4766. [PMID: 37430680 DOI: 10.3390/s23104766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 07/12/2023]
15
Sorokin A, Goryanin I. FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models. Biomolecules 2023;13:biom13030500. [PMID: 36979435 PMCID: PMC10046323 DOI: 10.3390/biom13030500] [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: 12/31/2022] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023]  Open
16
dePillis L, Caffrey R, Chen G, Dela MD, Eldevik L, McConnell J, Shabahang S, Varvel SA. A mathematical model of the within-host kinetics of SARS-CoV-2 neutralizing antibodies following COVID-19 vaccination. J Theor Biol 2023;556:111280. [PMID: 36202234 PMCID: PMC9529354 DOI: 10.1016/j.jtbi.2022.111280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 08/22/2022] [Accepted: 09/14/2022] [Indexed: 10/25/2022]
17
Dela A, Shtylla B, Pillis L. Multi-method Global Sensitivity Analysis of Mathematical Models. J Theor Biol 2022;546:111159. [DOI: 10.1016/j.jtbi.2022.111159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/10/2022] [Accepted: 05/03/2022] [Indexed: 10/18/2022]
18
Hult C, Mattila JT, Gideon HP, Linderman JJ, Kirschner DE. Neutrophil Dynamics Affect Mycobacterium tuberculosis Granuloma Outcomes and Dissemination. Front Immunol 2021;12:712457. [PMID: 34675916 PMCID: PMC8525425 DOI: 10.3389/fimmu.2021.712457] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/18/2021] [Indexed: 01/01/2023]  Open
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