PubMed

Strong inference for systems biology.

Beard DA, Kushmerick MJ.

PLoS Comput Biol. 2009 Aug;5(8):e1000459. Epub 2009 Aug 28. No abstract available. PMID: 19714210 [PubMed - indexed for MEDLINE]Related articlesFree article

Generating rate equations for complex enzyme systems by a computer-assisted systematic method.

Qi F, Dash RK, Han Y, Beard DA.

BMC Bioinformatics. 2009 Aug 4;10:238.PMID: 19653903 [PubMed - indexed for MEDLINE]Related articlesFree article

CellML metadata standards, associated tools and repositories.

Beard DA, Britten R, Cooling MT, Garny A, Halstead MD, Hunter PJ, Lawson J, Lloyd CM, Marsh J, Miller A, Nickerson DP, Nielsen PM, Nomura T, Subramanium S, Wimalaratne SM, Yu T.

Philos Transact A Math Phys Eng Sci. 2009 May 28;367(1895):1845-67.PMID: 19380315 [PubMed - in process]Related articlesFree article

Experimentally observed phenomena on cardiac energetics in heart failure emerge from simulations of cardiac metabolism.

Wu F, Zhang J, Beard DA.

Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):7143-8. Epub 2009 Apr 8.PMID: 19357309 [PubMed - indexed for MEDLINE]Related articlesFree article

BISEN: Biochemical Simulation Environment.

Vanlier J, Wu F, Qi F, Vinnakota KC, Han Y, Dash RK, Yang F, Beard DA.

Bioinformatics. 2009 Mar 15;25(6):836-7. Epub 2009 Feb 25.PMID: 19244386 [PubMed - indexed for MEDLINE]Related articles

Apparent diffusivity and Taylor dispersion of water and solutes in capillary beds.

Beard DA, Wu F.

Bull Math Biol. 2009 Aug;71(6):1366-77. Epub 2009 Feb 21.PMID: 19234745 [PubMed - indexed for MEDLINE]Related articles

Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart.

Wu F, Beard DA.

BMC Syst Biol. 2009 Feb 19;3:22.PMID: 19228404 [PubMed - indexed for MEDLINE]Related articlesFree article

A biophysically based mathematical model for the kinetics of mitochondrial calcium uniporter.

Dash RK, Qi F, Beard DA.

Biophys J. 2009 Feb 18;96(4):1318-32.PMID: 19217850 [PubMed - indexed for MEDLINE]Related articles

Multiple ion binding equilibria, reaction kinetics, and thermodynamics in dynamic models of biochemical pathways.

Vinnakota KC, Wu F, Kushmerick MJ, Beard DA.

Methods Enzymol. 2009;454:29-68.PMID: 19216922 [PubMed - indexed for MEDLINE]Related articles

The role of theoretical modeling in microcirculation research.

Secomb TW, Beard DA, Frisbee JC, Smith NP, Pries AR.

Microcirculation. 2008 Nov;15(8):693-8. Review.PMID: 18946803 [PubMed - indexed for MEDLINE]Related articles

Metabolic dynamics in skeletal muscle during acute reduction in blood flow and oxygen supply to mitochondria: in-silico studies using a multi-scale, top-down integrated model.

Dash RK, Li Y, Kim J, Beard DA, Saidel GM, Cabrera ME.

PLoS One. 2008 Sep 9;3(9):e3168.PMID: 18779864 [PubMed - indexed for MEDLINE]Related articlesFree article

Detailed kinetics and regulation of mammalian NAD-linked isocitrate dehydrogenase.

Qi F, Chen X, Beard DA.

Biochim Biophys Acta. 2008 Nov;1784(11):1641-51. Epub 2008 Jul 11.PMID: 18672100 [PubMed - indexed for MEDLINE]Related articlesFree article

Comment on 'Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions'.

Beard DA.

Mol Syst Biol. 2008;4:207; discussion 208. Epub 2008 Jul 15. No abstract available. PMID: 18628747 [PubMed - indexed for MEDLINE]Related articlesFree article

Phosphate metabolite concentrations and ATP hydrolysis potential in normal and ischaemic hearts.

Wu F, Zhang EY, Zhang J, Bache RJ, Beard DA.

J Physiol. 2008 Sep 1;586(Pt 17):4193-208. Epub 2008 Jul 10.PMID: 18617566 [PubMed - indexed for MEDLINE]Related articlesFree article

Modeling of cellular metabolism and microcirculatory transport.

Beard DA, Wu F, Cabrera ME, Dash RK.

Microcirculation. 2008 Nov;15(8):777-93. Review. Erratum in: Microcirculation. 2008 Nov;15(8):841. PMID: 18608987 [PubMed - indexed for MEDLINE]Related articles

The effects of reversibility and noise on stochastic phosphorylation cycles and cascades.

Miller CA, Beard DA.

Biophys J. 2008 Sep;95(5):2183-92. Epub 2008 May 30.PMID: 18515389 [PubMed - indexed for MEDLINE]Related articlesFree article

Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory.

Heuett WJ, Beard DA, Qian H.

BMC Syst Biol. 2008 May 15;2:44.PMID: 18482450 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of cardiac mitochondrial Na+-Ca2+ exchanger kinetics with a biophysical model of mitochondrial Ca2+ handling suggests a 3:1 stoichiometry.

Dash RK, Beard DA.

J Physiol. 2008 Jul 1;586(13):3267-85. Epub 2008 May 8.PMID: 18467367 [PubMed - indexed for MEDLINE]Related articlesFree article

Detailed enzyme kinetics in terms of biochemical species: study of citrate synthase.

Beard DA, Vinnakota KC, Wu F.

PLoS One. 2008 Mar 19;3(3):e1825.PMID: 18350161 [PubMed - indexed for MEDLINE]Related articlesFree article

Differential expression of cardiac mitochondrial proteins.

Smith JR, Matus IR, Beard DA, Greene AS.

Proteomics. 2008 Feb;8(3):446-62.PMID: 18232060 [PubMed - indexed for MEDLINE]Related articles

Computer modeling of mitochondrial tricarboxylic acid cycle, oxidative phosphorylation, metabolite transport, and electrophysiology.

Wu F, Yang F, Vinnakota KC, Beard DA.

J Biol Chem. 2007 Aug 24;282(34):24525-37. Epub 2007 Jun 25.PMID: 17591785 [PubMed - indexed for MEDLINE]Related articlesFree article

Optical spectroscopy demonstrates elevated intracellular oxygenation in an endotoxic model of sepsis in the perfused heart.

Schenkman KA, Arakaki LS, Ciesielski WA, Beard DA.

Shock. 2007 Jun;27(6):695-700.PMID: 17505311 [PubMed - indexed for MEDLINE]Related articles

Computational biology of cardiac myocytes: proposed standards for the physiome.

Smith NP, Crampin EJ, Niederer SA, Bassingthwaighte JB, Beard DA.

J Exp Biol. 2007 May;210(Pt 9):1576-83.PMID: 17449822 [PubMed - indexed for MEDLINE]Related articlesFree article

Mitochondrial inner membrane electrophysiology assessed by rhodamine-123 transport and fluorescence.

Huang M, Camara AK, Stowe DF, Qi F, Beard DA.

Ann Biomed Eng. 2007 Jul;35(7):1276-85. Epub 2007 Mar 20.PMID: 17372838 [PubMed - indexed for MEDLINE]Related articles

Relationship between thermodynamic driving force and one-way fluxes in reversible processes.

Beard DA, Qian H.

PLoS One. 2007 Jan 3;2(1):e144.PMID: 17206279 [PubMed]Related articlesFree article

Systems biology of the mitochondrion.

Beard DA, Vendelin M.

Am J Physiol Cell Physiol. 2006 Dec;291(6):C1101-3. No abstract available. PMID: 17102034 [PubMed - indexed for MEDLINE]Related articlesFree article

Metabolic futile cycles and their functions: a systems analysis of energy and control.

Qian H, Beard DA.

Syst Biol (Stevenage). 2006 Jul;153(4):192-200.PMID: 16986621 [PubMed - indexed for MEDLINE]Related articles

Modeling of oxygen transport and cellular energetics explains observations on in vivo cardiac energy metabolism.

Beard DA.

PLoS Comput Biol. 2006 Sep 15;2(9):e107. Epub 2006 Jul 10.PMID: 16978045 [PubMed - indexed for MEDLINE]Related articlesFree article

Oxidative ATP synthesis in skeletal muscle is controlled by substrate feedback.

Wu F, Jeneson JA, Beard DA.

Am J Physiol Cell Physiol. 2007 Jan;292(1):C115-24. Epub 2006 Jul 12.PMID: 16837647 [PubMed - indexed for MEDLINE]Related articlesFree article

Effect of binding in cyclic phosphorylation-dephosphorylation process and in energy transformation.

Sarkar A, Beard DA, Franza BR.

Math Biosci. 2006 Jul;202(1):175-93. Epub 2006 Jun 13.PMID: 16774769 [PubMed - indexed for MEDLINE]Related articles

Population-based analysis of methadone distribution and metabolism using an age-dependent physiologically based pharmacokinetic model.

Yang F, Tong X, McCarver DG, Hines RN, Beard DA.

J Pharmacokinet Pharmacodyn. 2006 Aug;33(4):485-518. Epub 2006 Jun 7.PMID: 16758333 [PubMed - indexed for MEDLINE]Related articles

Thermodynamically based profiling of drug metabolism and drug-drug metabolic interactions: a case study of acetaminophen and ethanol toxic interaction.

Yang F, Beard DA.

Biophys Chem. 2006 Mar 20;120(2):121-34. Epub 2005 Nov 28.PMID: 16314027 [PubMed - indexed for MEDLINE]Related articles

Computational modeling of physiological systems.

Beard DA, Bassingthwaighte JB, Greene AS.

Physiol Genomics. 2005 Sep 21;23(1):1-3; discussion 4. No abstract available. PMID: 16179418 [PubMed - indexed for MEDLINE]Related articlesFree article

A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation.

Beard DA.

PLoS Comput Biol. 2005 Sep;1(4):e36. Epub 2005 Sep 9. Erratum in: PLoS Comput Biol. 2006 Jan;2(1):e8. PMID: 16163394 [PubMed - indexed for MEDLINE]Related articlesFree article

Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry.

Yang F, Qian H, Beard DA.

Metab Eng. 2005 Jul;7(4):251-9.PMID: 16140239 [PubMed - indexed for MEDLINE]Related articles

Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium.

Qian H, Beard DA.

Biophys Chem. 2005 Apr 22;114(2-3):213-20. Epub 2004 Dec 22. Review.PMID: 15829355 [PubMed - indexed for MEDLINE]Related articles

Myocardial oxygenation and adenosine release in isolated guinea pig hearts during changes in contractility.

Ejike JC, Arakaki LS, Beard DA, Ciesielski WA, Feigl EO, Schenkman KA.

Am J Physiol Heart Circ Physiol. 2005 May;288(5):H2062-7. Epub 2004 Dec 9.PMID: 15591100 [PubMed - indexed for MEDLINE]Related articlesFree article

Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism.

Beard DA, Qian H.

Am J Physiol Endocrinol Metab. 2005 Mar;288(3):E633-44. Epub 2004 Oct 26.PMID: 15507536 [PubMed - indexed for MEDLINE]Related articlesFree article

Thermodynamic constraints for biochemical networks.

Beard DA, Babson E, Curtis E, Qian H.

J Theor Biol. 2004 Jun 7;228(3):327-33.PMID: 15135031 [PubMed - indexed for MEDLINE]Related articles

Unbiased rotational moves for rigid-body dynamics.

Beard DA, Schlick T.

Biophys J. 2003 Nov;85(5):2973-6.PMID: 14581199 [PubMed - indexed for MEDLINE]Related articlesFree article

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm.

Zhang Q, Beard DA, Schlick T.

J Comput Chem. 2003 Dec;24(16):2063-74.PMID: 14531059 [PubMed - indexed for MEDLINE]Related articles

Myocardial oxygenation in isolated hearts predicted by an anatomically realistic microvascular transport model.

Beard DA, Schenkman KA, Feigl EO.

Am J Physiol Heart Circ Physiol. 2003 Nov;285(5):H1826-36. Epub 2003 Jul 17.PMID: 12869375 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparison of buffer and red blood cell perfusion of guinea pig heart oxygenation.

Schenkman KA, Beard DA, Ciesielski WA, Feigl EO.

Am J Physiol Heart Circ Physiol. 2003 Nov;285(5):H1819-25. Epub 2003 Jul 17.PMID: 12869374 [PubMed - indexed for MEDLINE]Related articlesFree article

Stoichiometric network theory for nonequilibrium biochemical systems.

Qian H, Beard DA, Liang SD.

Eur J Biochem. 2003 Feb;270(3):415-21. Review.PMID: 12542691 [PubMed - indexed for MEDLINE]Related articlesFree article

Extreme pathways and Kirchhoff's second law.

Price ND, Famili I, Beard DA, Palsson BØ.

Biophys J. 2002 Nov;83(5):2879-82. No abstract available. PMID: 12425318 [PubMed - indexed for MEDLINE]Related articlesFree article

Energy balance for analysis of complex metabolic networks.

Beard DA, Liang SD, Qian H.

Biophys J. 2002 Jul;83(1):79-86.PMID: 12080101 [PubMed - indexed for MEDLINE]Related articlesFree article

The mechanical and metabolic basis of myocardial blood flow heterogeneity.

Bassingthwaighte JB, Beard DA, Li Z.

Basic Res Cardiol. 2001 Nov;96(6):582-94. Review.PMID: 11770077 [PubMed - indexed for MEDLINE]Related articles

Computational framework for generating transport models from databases of microvascular anatomy.

Beard DA.

Ann Biomed Eng. 2001 Oct;29(10):837-43.PMID: 11764314 [PubMed - indexed for MEDLINE]Related articles

Modeling advection and diffusion of oxygen in complex vascular networks.

Beard DA, Bassingthwaighte JB.

Ann Biomed Eng. 2001 Apr;29(4):298-310.PMID: 11339327 [PubMed - indexed for MEDLINE]Related articles

Computational modeling predicts the structure and dynamics of chromatin fiber.

Beard DA, Schlick T.

Structure. 2001 Feb 7;9(2):105-14.PMID: 11250195 [PubMed - indexed for MEDLINE]Related articles