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Items: 12

1.

Bridging Mechanistic and Phenomenological Models of Complex Biological Systems.

Transtrum MK, Qiu P.

PLoS Comput Biol. 2016 May 17;12(5):e1004915. doi: 10.1371/journal.pcbi.1004915. eCollection 2016 May.

2.

Enzyme-catalyzed and binding reaction kinetics determined by titration calorimetry.

Hansen LD, Transtrum MK, Quinn C, Demarse N.

Biochim Biophys Acta. 2016 May;1860(5):957-66. doi: 10.1016/j.bbagen.2015.12.018. Epub 2015 Dec 22. Review.

PMID:
26721335
3.

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

Transtrum MK, Machta BB, Brown KS, Daniels BC, Myers CR, Sethna JP.

J Chem Phys. 2015 Jul 7;143(1):010901. doi: 10.1063/1.4923066. Review.

PMID:
26156455
4.

Enzyme kinetics determined by single-injection isothermal titration calorimetry.

Transtrum MK, Hansen LD, Quinn C.

Methods. 2015 Apr;76:194-200. doi: 10.1016/j.ymeth.2014.12.003. Epub 2014 Dec 10.

PMID:
25497059
5.

Model reduction by manifold boundaries.

Transtrum MK, Qiu P.

Phys Rev Lett. 2014 Aug 29;113(9):098701. Epub 2014 Aug 29.

6.

Parameter space compression underlies emergent theories and predictive models.

Machta BB, Chachra R, Transtrum MK, Sethna JP.

Science. 2013 Nov 1;342(6158):604-7. doi: 10.1126/science.1238723. Erratum in: Science. 2013 Nov 22;342(6161):931.

7.

Use of the LQ model with large fraction sizes results in underestimation of isoeffect doses.

Sheu T, Molkentine J, Transtrum MK, Buchholz TA, Withers HR, Thames HD, Mason KA.

Radiother Oncol. 2013 Oct;109(1):21-5. doi: 10.1016/j.radonc.2013.08.027. Epub 2013 Sep 20.

PMID:
24060173
8.

Structural susceptibility and separation of time scales in the van der Pol oscillator.

Chachra R, Transtrum MK, Sethna JP.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 2):026712. Epub 2012 Aug 31.

PMID:
23005887
9.

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

Transtrum MK, Qiu P.

BMC Bioinformatics. 2012 Jul 27;13:181. doi: 10.1186/1471-2105-13-181.

10.

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

Transtrum MK, Machta BB, Sethna JP.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Mar;83(3 Pt 2):036701. Epub 2011 Mar 3.

PMID:
21517619
11.

Comment on "Sloppy models, parameter uncertainty, and the role of experimental design".

Chachra R, Transtrum MK, Sethna JP.

Mol Biosyst. 2011 Aug;7(8):2522; author reply 2523-4. doi: 10.1039/c1mb05046j. Epub 2011 Apr 19.

PMID:
21503370
12.

Why are nonlinear fits to data so challenging?

Transtrum MK, Machta BB, Sethna JP.

Phys Rev Lett. 2010 Feb 12;104(6):060201. Epub 2010 Feb 10.

PMID:
20366807
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