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Select item 94917191.

Analysis of sloppiness in model simulations: Unveiling parameter uncertainty when mathematical models are fitted to data

Gloria M. Monsalve-Bravo, Brodie A. J. Lawson, Christopher Drovandi, Kevin Burrage, Kevin S. Brown, Christopher M. Baker, Sarah A. Vollert, Kerrie Mengersen, Eve McDonald-Madden, Matthew P. Adams

Sci Adv. 2022 Sep; 8(38): eabm5952. Published online 2022 Sep 21. doi: 10.1126/sciadv.abm5952

PMCID:: PMC9491719

Article PDF–2.9M

Select item 59933242.

Parameter uncertainty quantification using surrogate models applied to a spatial model of yeast mating polarization

Marissa Renardy, Tau-Mu Yi, Dongbin Xiu, Ching-Shan Chou

PLoS Comput Biol. 2018 May; 14(5): e1006181. Published online 2018 May 29. doi: 10.1371/journal.pcbi.1006181

PMCID:: PMC5993324

Article PDF–5.9M

Select item 79026383.

Automating parameter selection to avoid implausible biological pathway models

Chris S. Magnano, Anthony Gitter

NPJ Syst Biol Appl. 2021; 7: 12. Published online 2021 Feb 23. doi: 10.1038/s41540-020-00167-1

PMCID:: PMC7902638

Article PDF–4.9M

Select item 109473024.

Visual Parameter Space Exploration in Time and Space

Nikolaus Piccolotto, Markus Bögl, Silvia Miksch

Comput Graph Forum. 2023 Sep; 42(6): e14785. Published online 2023 Apr 3. doi: 10.1111/cgf.14785

PMCID:: PMC10947302

Article PDF–4.0M

Select item 96296505.

Bayesian parameter estimation for dynamical models in systems biology

Nathaniel J. Linden, Boris Kramer, Padmini Rangamani

PLoS Comput Biol. 2022 Oct; 18(10): e1010651. Published online 2022 Oct 21. doi: 10.1371/journal.pcbi.1010651

Correction in:: PLoS Comput Biol. 2023 Apr; 19(4): e1011041.

PMCID:: PMC9629650

Article PDF–4.1M

Select item 63328396.

Assessing parameter identifiability in compartmental dynamic models using a computational approach: application to infectious disease transmission models

Kimberlyn Roosa, Gerardo Chowell

Theor Biol Med Model. 2019; 16: 1. Published online 2019 Jan 14. doi: 10.1186/s12976-018-0097-6

PMCID:: PMC6332839

Article PDF–1.7M

Select item 94916127.

Utility of constraints reflecting system stability on analyses for biological models

Yoshiaki Kariya, Masashi Honma, Keita Tokuda, Akihiko Konagaya, Hiroshi Suzuki

PLoS Comput Biol. 2022 Sep; 18(9): e1010441. Published online 2022 Sep 9. doi: 10.1371/journal.pcbi.1010441

PMCID:: PMC9491612

Article PDF–4.3M

Select item 44564898.

Interplay between order-parameter and system parameter dynamics: considerations on perceptual-cognitive-behavioral mode-mode transitions exhibiting positive and negative hysteresis and on response times

T. D. Frank, V. L. S. Profeta, H. S. Harrison

J Biol Phys. 2015 Jun; 41(3): 257–292. Published online 2015 Mar 3. doi: 10.1007/s10867-015-9378-z

PMCID:: PMC4456489

Article PDF–1.4M

Select item 103180169.

Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space

Kishore Hari, William Duncan, Mohammed Adil Ibrahim, Mohit Kumar Jolly, Breschine Cummins, Tomas Gedeon

NPJ Syst Biol Appl. 2023; 9: 29. Published online 2023 Jul 3. doi: 10.1038/s41540-023-00289-2

PMCID:: PMC10318016

Article PDF–1.6M

Select item 1052101210.

Artificial neural networks for model identification and parameter estimation in computational cognitive models

Milena Rmus, Ti-Fen Pan, Liyu Xia, Anne G. E. Collins

Version 2. bioRxiv. Preprint. 2023 Sep 15 [revised 2024 Apr 2]. doi: 10.1101/2023.09.14.557793

PMCID:: PMC10521012

Article PDF–15M

Select item 1051188511.

Parameter estimation and identifiability analysis for a bivalent analyte model of monoclonal antibody-antigen binding

Kyle Nguyen, Kan Li, Kevin Flores, Georgia D. Tomaras, S. Moses Dennison, Janice M. McCarthy

Anal Biochem. 2023 Oct 15; 679: 115263. doi: 10.1016/j.ab.2023.115263

PMCID:: PMC10511885

Article PDF–21M

Select item 787862612.

CaliPro: A Calibration Protocol That Utilizes Parameter Density Estimation to Explore Parameter Space and Calibrate Complex Biological Models

Louis R. Joslyn, Denise E. Kirschner, Jennifer J. Linderman

Cell Mol Bioeng. 2021 Feb; 14(1): 31–47. Published online 2020 Sep 15. doi: 10.1007/s12195-020-00650-z

PMCID:: PMC7878626

Article PDF–5.0M

Select item 1075770613.

Connecting Agent-Based Models with High-Dimensional Parameter Spaces to Multidimensional Data Using SMoRe ParS: A Surrogate Modeling Approach

Daniel R. Bergman, Kerri-Ann Norton, Harsh Vardhan Jain, Trachette Jackson

Bull Math Biol. 2024; 86(1): 11. Published online 2023 Dec 30. doi: 10.1007/s11538-023-01240-6

PMCID:: PMC10757706

Article PDF–2.8M

Select item 1035379114.

Biological complexity facilitates tuning of the neuronal parameter space

Marius Schneider, Alexander D. Bird, Albert Gidon, Jochen Triesch, Peter Jedlicka, Hermann Cuntz

PLoS Comput Biol. 2023 Jul; 19(7): e1011212. Published online 2023 Jul 3. doi: 10.1371/journal.pcbi.1011212

PMCID:: PMC10353791

Article PDF–3.7M

Select item 909782515.

GAMES: A dynamic model development workflow for rigorous characterization of synthetic genetic systems

Kate E. Dray, Joseph J. Muldoon, Niall M. Mangan, Neda Bagheri, Joshua N. Leonard

ACS Synth Biol. Author manuscript; available in PMC 2023 Feb 18.

Published in final edited form as: ACS Synth Biol. 2022 Feb 18; 11(2): 1009–1029. Published online 2022 Jan 13. doi: 10.1021/acssynbio.1c00528

Correction in:: ACS Synth Biol. 2022 Apr 15; 11(4): 1699–1704.

PMCID:: PMC9097825

Article PDF–3.5M

Select item 646573816.

Parameter Identification for a Model of Neonatal Fc Receptor-Mediated Recycling of Endogenous Immunoglobulin G in Humans

Felicity Kendrick, Neil D. Evans, Oscar Berlanga, Stephen J. Harding, Michael J. Chappell

Front Immunol. 2019; 10: 674. Published online 2019 Apr 8. doi: 10.3389/fimmu.2019.00674

PMCID:: PMC6465738

Article PDF–1.8M

Select item 1093377917.

Identifying microstructural changes in diffusion MRI; How to circumvent parameter degeneracy

Hossein Rafipoor, Ying-Qiu Zheng, Ludovica Griffanti, Saad Jbabdi, Michiel Cottaar

Neuroimage. 2022 Oct 15; 260: 119452. doi: 10.1016/j.neuroimage.2022.119452

PMCID:: PMC10933779

Article PDF–6.1M

Select item 1032215618.

A genetic and linguistic analysis of the admixture histories of the islands of Cabo Verde

Romain Laurent, Zachary A Szpiech, Sergio S da Costa, Valentin Thouzeau, Cesar A Fortes-Lima, Françoise Dessarps-Freichey, Laure Lémée, José Utgé, Noah A Rosenberg, Marlyse Baptista, Paul Verdu

eLife. 2023; 12: e79827. Published online 2023 Apr 25. doi: 10.7554/eLife.79827