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Universally Sloppy Parameter Sensitivities in Systems Biology Models

Citations

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Cited by:

  1. Claudia Schillings & Mikael Sunnåker & Jörg Stelling & Christoph Schwab, 2015. "Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks," PLOS Computational Biology, Public Library of Science, vol. 11(8), pages 1-16, August.
  2. Elevitch, Craig R. & Johnson, C. Richard, 2020. "A procedure for ranking parameter importance for estimation in predictive mechanistic models," Ecological Modelling, Elsevier, vol. 419(C).
  3. Christian A Tiemann & Joep Vanlier & Maaike H Oosterveer & Albert K Groen & Peter A J Hilbers & Natal A W van Riel, 2013. "Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions," PLOS Computational Biology, Public Library of Science, vol. 9(8), pages 1-15, August.
  4. Alireza Yazdani & Lu Lu & Maziar Raissi & George Em Karniadakis, 2020. "Systems biology informed deep learning for inferring parameters and hidden dynamics," PLOS Computational Biology, Public Library of Science, vol. 16(11), pages 1-19, November.
  5. Samuel Bandara & Johannes P Schlöder & Roland Eils & Hans Georg Bock & Tobias Meyer, 2009. "Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model," PLOS Computational Biology, Public Library of Science, vol. 5(11), pages 1-12, November.
  6. Xinxian Shao & Andrew Mugler & Justin Kim & Ha Jun Jeong & Bruce R Levin & Ilya Nemenman, 2017. "Growth of bacteria in 3-d colonies," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-19, July.
  7. Fridtjof Brauns & Leila Iñigo de la Cruz & Werner K.-G. Daalman & Ilse Bruin & Jacob Halatek & Liedewij Laan & Erwin Frey, 2023. "Redundancy and the role of protein copy numbers in the cell polarization machinery of budding yeast," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  8. repec:plo:pcbi00:1003705 is not listed on IDEAS
  9. Andrew J K Conlan & Ellen Brooks Pollock & Trevelyan J McKinley & Andrew P Mitchell & Gareth J Jones & Martin Vordermeier & James L N Wood, 2015. "Potential Benefits of Cattle Vaccination as a Supplementary Control for Bovine Tuberculosis," PLOS Computational Biology, Public Library of Science, vol. 11(2), pages 1-27, February.
  10. repec:plo:pone00:0152316 is not listed on IDEAS
  11. Kirill Sechkar & Harrison Steel & Giansimone Perrino & Guy-Bart Stan, 2024. "A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  12. Bryan C Daniels & Ilya Nemenman, 2015. "Efficient Inference of Parsimonious Phenomenological Models of Cellular Dynamics Using S-Systems and Alternating Regression," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-14, March.
  13. Dominic M Dunstan & Mark P Richardson & Eugenio Abela & Ozgur E Akman & Marc Goodfellow, 2023. "Global nonlinear approach for mapping parameters of neural mass models," PLOS Computational Biology, Public Library of Science, vol. 19(3), pages 1-28, March.
  14. Sang O K Song & Justin Hogg & Zhi-Yong Peng & Robert Parker & John A Kellum & Gilles Clermont, 2012. "Ensemble Models of Neutrophil Trafficking in Severe Sepsis," PLOS Computational Biology, Public Library of Science, vol. 8(3), pages 1-16, March.
  15. Nathaniel J Linden & Boris Kramer & Padmini Rangamani, 2022. "Bayesian parameter estimation for dynamical models in systems biology," PLOS Computational Biology, Public Library of Science, vol. 18(10), pages 1-48, October.
  16. Giorgos Minas & David A Rand, 2017. "Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-23, July.
  17. Rodrigo P. Rocha & Loren Koçillari & Samir Suweis & Michele Filippo De Grazia & Michel Thiebaut Schotten & Marco Zorzi & Maurizio Corbetta, 2022. "Recovery of neural dynamics criticality in personalized whole-brain models of stroke," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  18. Eberhard O Voit & Harald A Martens & Stig W Omholt, 2015. "150 Years of the Mass Action Law," PLOS Computational Biology, Public Library of Science, vol. 11(1), pages 1-7, January.
  19. Giorgos Minas & Dan J Woodcock & Louise Ashall & Claire V Harper & Michael R H White & David A Rand, 2020. "Multiplexing information flow through dynamic signalling systems," PLOS Computational Biology, Public Library of Science, vol. 16(8), pages 1-18, August.
  20. repec:plo:pcbi00:1004784 is not listed on IDEAS
  21. repec:plo:pone00:0027755 is not listed on IDEAS
  22. Neythen J Treloar & Nathan Braniff & Brian Ingalls & Chris P Barnes, 2022. "Deep reinforcement learning for optimal experimental design in biology," PLOS Computational Biology, Public Library of Science, vol. 18(11), pages 1-24, November.
  23. Port, Alexander & Bryan, Karin R. & Pilditch, Conrad A. & Hamilton, David P. & Bischof, Kai, 2015. "Algebraic equilibrium solution of tissue nitrogen quota in algae and the discrepancy between calibrated parameters and physiological properties," Ecological Modelling, Elsevier, vol. 312(C), pages 281-291.
  24. Céline Christiansen-Jucht & Kamil Erguler & Chee Yan Shek & María-Gloria Basáñez & Paul E. Parham, 2015. "Modelling Anopheles gambiae s.s. Population Dynamics with Temperature- and Age-Dependent Survival," IJERPH, MDPI, vol. 12(6), pages 1-31, May.
  25. Maksat Ashyraliyev & Ken Siggens & Hilde Janssens & Joke Blom & Michael Akam & Johannes Jaeger, 2009. "Gene Circuit Analysis of the Terminal Gap Gene huckebein," PLOS Computational Biology, Public Library of Science, vol. 5(10), pages 1-16, October.
  26. Zachary R Fox & Brian Munsky, 2019. "The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments," PLOS Computational Biology, Public Library of Science, vol. 15(1), pages 1-23, January.
  27. Yuncong Geng & Thu Vu Phuc Nguyen & Ehsan Homaee & Ido Golding, 2024. "Using bacterial population dynamics to count phages and their lysogens," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  28. Marc Hafner & Heinz Koeppl & Martin Hasler & Andreas Wagner, 2009. "‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators," PLOS Computational Biology, Public Library of Science, vol. 5(10), pages 1-10, October.
  29. Mark K Transtrum & Peng Qiu, 2016. "Bridging Mechanistic and Phenomenological Models of Complex Biological Systems," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-34, May.
  30. Nadin Haase & Wolf Holtkamp & Simon Christ & Dag Heinemann & Marina V Rodnina & Sophia Rudorf, 2024. "Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation," PLOS Computational Biology, Public Library of Science, vol. 20(3), pages 1-18, March.
  31. repec:plo:pcbi00:1005447 is not listed on IDEAS
  32. Juliane Liepe & Sarah Filippi & Michał Komorowski & Michael P H Stumpf, 2013. "Maximizing the Information Content of Experiments in Systems Biology," PLOS Computational Biology, Public Library of Science, vol. 9(1), pages 1-13, January.
  33. Gabriele Lillacci & Mustafa Khammash, 2010. "Parameter Estimation and Model Selection in Computational Biology," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-17, March.
  34. Andrew White & Malachi Tolman & Howard D Thames & Hubert Rodney Withers & Kathy A Mason & Mark K Transtrum, 2016. "The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems," PLOS Computational Biology, Public Library of Science, vol. 12(12), pages 1-26, December.
  35. Diego Fernández Slezak & Cecilia Suárez & Guillermo A Cecchi & Guillermo Marshall & Gustavo Stolovitzky, 2010. "When the Optimal Is Not the Best: Parameter Estimation in Complex Biological Models," PLOS ONE, Public Library of Science, vol. 5(10), pages 1-10, October.
  36. repec:plo:pcbi00:1007279 is not listed on IDEAS
  37. Adel Dayarian & Madalena Chaves & Eduardo D Sontag & Anirvan M Sengupta, 2009. "Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks," PLOS Computational Biology, Public Library of Science, vol. 5(1), pages 1-12, January.
  38. Joshua Russell-Buckland & Christopher P Barnes & Ilias Tachtsidis, 2019. "A Bayesian framework for the analysis of systems biology models of the brain," PLOS Computational Biology, Public Library of Science, vol. 15(4), pages 1-29, April.
  39. Elba Raimúndez & Simone Keller & Gwen Zwingenberger & Karolin Ebert & Sabine Hug & Fabian J Theis & Dieter Maier & Birgit Luber & Jan Hasenauer, 2020. "Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines," PLOS Computational Biology, Public Library of Science, vol. 16(3), pages 1-21, March.
  40. Borut Kirn, 2019. "Visualization of Myocardial Strain Pattern Uniqueness with Respect to Activation Time and Contractility: A Computational Study," Data, MDPI, vol. 4(2), pages 1-7, May.
  41. Van Kinh Nguyen & Frank Klawonn & Rafael Mikolajczyk & Esteban A Hernandez-Vargas, 2016. "Analysis of Practical Identifiability of a Viral Infection Model," PLOS ONE, Public Library of Science, vol. 11(12), pages 1-16, December.
  42. repec:plo:pgen00:1006132 is not listed on IDEAS
  43. Chen, Yu & Yu, Hui & Liu, Chengjie & Xie, Jin & Han, Jun & Dai, Houde, 2024. "Synergistic fusion of physical modeling and data-driven approaches for parameter inference to enzymatic biodiesel production system," Applied Energy, Elsevier, vol. 373(C).
  44. repec:plo:pcbi00:1003471 is not listed on IDEAS
  45. Alejandro F. Villaverde, 2019. "Observability and Structural Identifiability of Nonlinear Biological Systems," Complexity, Hindawi, vol. 2019, pages 1-12, January.
  46. repec:plo:pone00:0024246 is not listed on IDEAS
  47. Filippi Sarah & Barnes Chris P. & Cornebise Julien & Stumpf Michael P.H., 2013. "On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(1), pages 87-107, March.
  48. Amrita X Sarkar & Eric A Sobie, 2010. "Regression Analysis for Constraining Free Parameters in Electrophysiological Models of Cardiac Cells," PLOS Computational Biology, Public Library of Science, vol. 6(9), pages 1-11, September.
  49. Hongwei Shao & Tao Peng & Zhiwei Ji & Jing Su & Xiaobo Zhou, 2013. "Systematically Studying Kinase Inhibitor Induced Signaling Network Signatures by Integrating Both Therapeutic and Side Effects," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-16, December.
  50. Farzaneh Khajouei & Saurabh Sinha, 2018. "An information theoretic treatment of sequence-to-expression modeling," PLOS Computational Biology, Public Library of Science, vol. 14(9), pages 1-24, September.
  51. Stephen J. Beckett & David Demory & Ashley R. Coenen & John R. Casey & Mathilde Dugenne & Christopher L. Follett & Paige Connell & Michael C. G. Carlson & Sarah K. Hu & Samuel T. Wilson & Daniel Murat, 2024. "Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  52. Agus Hartoyo & Peter J Cadusch & David T J Liley & Damien G Hicks, 2019. "Parameter estimation and identifiability in a neural population model for electro-cortical activity," PLOS Computational Biology, Public Library of Science, vol. 15(5), pages 1-27, May.
  53. Zack W Jones & Rachel Leander & Vito Quaranta & Leonard A Harris & Darren R Tyson, 2018. "A drift-diffusion checkpoint model predicts a highly variable and growth-factor-sensitive portion of the cell cycle G1 phase," PLOS ONE, Public Library of Science, vol. 13(2), pages 1-20, February.
  54. Jonathan R Karr & Alex H Williams & Jeremy D Zucker & Andreas Raue & Bernhard Steiert & Jens Timmer & Clemens Kreutz & DREAM8 Parameter Estimation Challenge Consortium & Simon Wilkinson & Brandon A Al, 2015. "Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models," PLOS Computational Biology, Public Library of Science, vol. 11(5), pages 1-21, May.
  55. Andreas Wagner, 2015. "Causal Drift, Robust Signaling, and Complex Disease," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-29, March.
  56. Joseph D Taylor & Samuel Winnall & Alain Nogaret, 2020. "Estimation of neuron parameters from imperfect observations," PLOS Computational Biology, Public Library of Science, vol. 16(7), pages 1-22, July.
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