Publications

Overview

All VPR publications can be found below ordered by year of publication. You may sort by type of publication, keywords, associated research project or search by abstract, title or author.

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Search Title, Authors, Abstract, Year

2013

Validation of an axially-distributed model for quantification of myocardial blood flow using 13N-ammonia PET
Alession AM, Bassingthwaighte JB, Glenny R, Caldwell JH
J Nucl Cardiol. 2013 Feb; 20(1):64-75. PMCID: PMC4165648
A computational analysis of the long-term regulation of arterial pressure
Beard DA, Pettersen KH, Carlson BE, Omholt SW, Bugenhagen SM
F1000 Research. 2013 Dec; 2:208. PMCID: PMC3886803
Modeling the Afferent Dynamics of the Baroreflex Control System
Mahdi A, Sturdy J, Ottesen JT, Olufsen MS
PLoS Comput Biol. 2013; 9(12)e1003384. PMCID: PMC3861044
Defects in connexin signaling underlie arrhythmogenic right ventricular cardiomyopathy in a novel mouse model
Lyon RC, Mezzano V, Wright A, Pfeiffer E, Chuang J, Banares K, Castaneda A, Ouyang K, Cui L, Gu Y, Evans SM, Omens JH, Peterson KL, McCulloch AD, Sheikh F
Hum Mol Gen. 2013 Oct; 23(5):1134-50. PMCID: PMC3919010
Left ventricular finite element model bounded by a systemic circulation model
Veress AI, Raymond GM, Gullberg GT, Bassingthwaighte JB
J Biomech Eng. 2013 May;135(5):54502. PMCID: PMC3705858
Molecular and sub cellular-scale modeling of nucleotide diffusion in the cardiac myofilament lattice
Kekenes-Huskey PM, Liao T, Gillette AK, Hake JE, Zhang Y, Michailova AP, McCulloch AD, McCammon JA
Biophysical Journal. 2013 Nov; 105(9): 2130-40. PMCID: PMC3835335
A biophysically based mathematical model for the catalytic mechanism of glutathione reductase
Pannala VR, Bazil JN, Camara AKS, Dash RK
Free Radic Biol Med. 2013 Dec; 65: 1385-97. PMCID: PMC3870161
Functional tissue units and their primary tissue motifs in multi-scale physiology
de Bono B, Grenon P, Baldock R, Hunter P
J Biomed Semantics. 2013 Oct;4(1):22. PMCID: PMC4126067
Progression of glomerular filtration rate reduction determined in conscious Dahl salt-sensitive rats
Cowley AJ Jr, Ryan RP, Kurth T, Skelton MM, Schock-Kusch D, Gretz N
Hypertension. 2013 Jul; 62(1):85-90. PMCID: PMC3806646
Ontology of physics for biology: representing physical dependencies as a basis for biological processes
Cook DL, Neal ML, Bookstein FL, Gennari JH
J Biomed Semantics. 2013 Dec;4(1):41. PMCID: PMC3904761
Effect of P2X4 and P2X7 receptor antagonism on the pressure diuresis relationship in rats
Menzies RI, Unwin RJ, Dash RK, Beard DA, Cowley AW Jr., Carlson BE, Mullins JJ, Bailey MA
Front Physiol. 2013 Oct; 4:305. PMCID: PMC3807716
Analysis of cardiovascular dynamics in pulmonary hypertensive C57BL6/J mice
Tewari SG, Bugenhagen SM, Wang Z, Schreieir DA, Carlson BE, Chesler NC, Beard DA
Front. Physiol. 2013 Dec; 4:355. PMCID: PMC3858724
JSim, an open-source modeling system for data analysis
Butterworth E, Jardine BE, Raymond GM, Neal ML, Bassingthwaighte JB
F1000 Research. 2013 Dec, 2: 288. PMCID: PMC3901508.
SBML and CellML translation in antimony and JSim
Smith LP, Butterworth E, Bassingthwaighte JB, Sauro HM
Bioinformatics. Apr 2013; 30(7): 903-7. PMCID: PMC3967103
Tautology vs Physiology in the Etiology of Hypertension.
Beard DA
Physiology. 2013 Sep;28(5): 270-1. PMCID: PMC3768096

2012

Optimization and parameter estimation: Genetic algorithms
Vinnakota KC, Bugenhagen SM
In W Dubitzky et al. (Ed.),  Encyclopedia of systems biology (Volume 1). Springer-Verlag New York, LLC.
Carrier-Mediated Transport through Biomembranes. Transport in Biological Media
Pradhan RK, Vinnakota KC, Beard DA, Dash RK
Elsevier, 2012.
Qualitative features of a new baroreceptor model
Mahdi A, Ottesen JT, Olufsen MS
Proc The 1st international workshop on innovative simulation for healthcare, I-WISH. W. Backfrieder, A. Bruzzone, F. Longo, V. Novak, J. Rosen (eds), Rende (CS), Italy, 75-80, 2012.
Dahl Salt-Sensitive Rats are Protected Against Vascular Defects Related to Diet-Induced Obesity.
Beyer AM, Raffai G, Weinberg B, Fredrich K, Lombard JH
Hypertension 60: 404-10, 2012. PMID: 22710645, PMCID: PMC3444144
A Biophysical Model of the Mitochondrial ATP-Mg/P(i) Carrier
Tewari SG, Dash RK, Beard DA, Bazil JN
Biophys J. 103(7): 1616-2, 2012. PMID: 23062354, PMCID: PMC3471468
Interpreting genetic effects through models of cardiac electromechanics.
Niederer SA, Land S, Omholt SW, Smith NP
AJP – Heart 303(11): H1294-H1303, 2012. PMID: 23042948, PMCID: PMC3532540
Modelling cell function
Bassingthwaighte JB, Boyle C, Pichardo C, Diaz V
Personalized Computational Biomedicine: A Guide to the Virtual Physiological Human pp 001-0NN, edited by Coveney P and Noble D. London, UK: Royal Society of London, 2012.
An atlas-based geometry pipeline for cardiac hermite model construction and diffusion tensor reorientation
Zhang Y, Liang X, Ma J, Jing Y, Gonzales MJ, Villongco C, Krishnamurthy A, Frank LR, Nigam V, Stark P, Narayan SM, McCulloch AD
Med Imag Anal 16: 1130-41, 2012. PMID: 22841777, PMCID: PMC3443263
Increase of sodium delivery stimulates the mitochondrial respiratory chain H2O2 production in rat renal medullary thick ascending limb
Ohsaki Y, O’Connor P, Mori T, Ryan RP, Dickinson BC, Chang CJ, Lu Y, Ito S, Cowley AW Jr
Am J Physiol Renal Physiol. 302:F95-F102. 2012 PMCID: PMC3251339
Compartmental modeling in the analysis of biological systems
Bassingthwaighte JB, Butterworth E, Jardine B, Raymond G
Computational Toxicology: Volume 1 929: 391-438, edited by Brad Reisfeld and Arthur N Mayeno. Methods in Molecular Biology, 2012.

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