Transtrum MK - Search Results

1

The Spectrum of Mechanism-Oriented Models and Methods for Explanations of Biological Phenomena.

Hunt CA, Erdemir A, Lytton WW, Gabhann FM, Sander EA, Transtrum MK, Mulugeta L. Hunt CA, et al. Among authors: transtrum mk. Processes (Basel). 2018 May;6(5):56. doi: 10.3390/pr6050056. Epub 2018 May 14. Processes (Basel). 2018. PMID: 34262852 Free PMC article.

2

Bridging Mechanistic and Phenomenological Models of Complex Biological Systems.

Transtrum MK, Qiu P. Transtrum MK, et al. PLoS Comput Biol. 2016 May 17;12(5):e1004915. doi: 10.1371/journal.pcbi.1004915. eCollection 2016 May. PLoS Comput Biol. 2016. PMID: 27187545 Free PMC article.

3

Optimal experiment selection for parameter estimation in biological differential equation models.

Transtrum MK, Qiu P. Transtrum MK, et al. BMC Bioinformatics. 2012 Jul 27;13:181. doi: 10.1186/1471-2105-13-181. BMC Bioinformatics. 2012. PMID: 22838836 Free PMC article.

4

Model reduction by manifold boundaries.

Transtrum MK, Qiu P. Transtrum MK, et al. Phys Rev Lett. 2014 Aug 29;113(9):098701. doi: 10.1103/PhysRevLett.113.098701. Epub 2014 Aug 29. Phys Rev Lett. 2014. PMID: 25216014 Free PMC article.

5

Perspective: Sloppiness and emergent theories in physics, biology, and beyond.

Transtrum MK, Machta BB, Brown KS, Daniels BC, Myers CR, Sethna JP. Transtrum MK, et al. J Chem Phys. 2015 Jul 7;143(1):010901. doi: 10.1063/1.4923066. J Chem Phys. 2015. PMID: 26156455 Review.

6

The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems.

White A, Tolman M, Thames HD, Withers HR, Mason KA, Transtrum MK. White A, et al. Among authors: transtrum mk. PLoS Comput Biol. 2016 Dec 6;12(12):e1005227. doi: 10.1371/journal.pcbi.1005227. eCollection 2016 Dec. PLoS Comput Biol. 2016. PMID: 27923060 Free PMC article.

7

Unwinding the model manifold: Choosing similarity measures to remove local minima in sloppy dynamical systems.

Francis BL, Transtrum MK. Francis BL, et al. Among authors: transtrum mk. Phys Rev E. 2019 Jul;100(1-1):012206. doi: 10.1103/PhysRevE.100.012206. Phys Rev E. 2019. PMID: 31499860

8

Bayesian, frequentist, and information geometric approaches to parametric uncertainty quantification of classical empirical interatomic potentials.

Kurniawan Y, Petrie CL, Williams KJ Jr, Transtrum MK, Tadmor EB, Elliott RS, Karls DS, Wen M. Kurniawan Y, et al. Among authors: transtrum mk. J Chem Phys. 2022 Jun 7;156(21):214103. doi: 10.1063/5.0084988. J Chem Phys. 2022. PMID: 35676145

9

Why are nonlinear fits to data so challenging?

Transtrum MK, Machta BB, Sethna JP. Transtrum MK, et al. Phys Rev Lett. 2010 Feb 12;104(6):060201. doi: 10.1103/PhysRevLett.104.060201. Epub 2010 Feb 10. Phys Rev Lett. 2010. PMID: 20366807

10

Geometry of nonlinear least squares with applications to sloppy models and optimization.

Transtrum MK, Machta BB, Sethna JP. Transtrum MK, et al. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Mar;83(3 Pt 2):036701. doi: 10.1103/PhysRevE.83.036701. Epub 2011 Mar 3. Phys Rev E Stat Nonlin Soft Matter Phys. 2011. PMID: 21517619

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