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Publications of Dr. Beard


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Journal Articles

 

  1. Haumann J, Dash RK, Stowe DF, Patel R, Beard DA, and Camara AKS. Mitochondrial free [Ca2+] increases during ATP/ADP antiport and ADP phosphorylation due to reduced matrix Ca2+ buffering. Biophys J, 2009 (submitted).
  2. Pradhan RK, Beard DA, and Dash RK. A biophysically-based mathematical model for the kinetics of mitochondrial Na+-Ca2+ antiporter. Biophys J, 2009 (in press).
  3. Qi F, Dash RK, Han Y and Beard DA, "Generating rate equations for complex enzyme systems by a computer-assisted systematic method", BMC Bioinformatics 2009, 10:238 doi:10.1186/1471-2105-10-238
  4. Wu F, Zhang J, and Beard DA., "Experimentally observed phenomena on cardiac energetics in heart failure emerge from simulations of cardiac metabolism". Proc Natl. Acad. Sci. USA (in press), 2009.
  5. Beard DA., Wu F.,"Apparent Diffusivity and Taylor Dispersion of Water and Solutes in Capillary Beds", Bull Math Biol. 2009 Feb 21.
  6. Wu F, Beard DA, "Roles of the Creatine Kinase System and Myoglobin in Maintaining Energetic State in the Working Heart.", BMC Syst Biol. 2009 Feb 19;3(1):22.
  7. Dash RK, Qi F, Beard DA,"A biophysically based mathematical model for the kinetics of mitochondrial calcium uniporter", Biophys J. 2009 Feb 18;96(4):1318-32.
  8. Vinnakota KC, Wu F, Kushmerick MJ, Beard DA, "Multiple ion binding equilibria, reaction kinetics, and thermodynamics in dynamic models of biochemical pathways",Methods Enzymol. 2009;454:29-68.
  9. Vanlier J, Wu F, Qi F, Vinnakota KC, Han Y, Dash RK, Yang F and Beard D,BISEN: Biochemical Simulation Environment,Bioinformatics 2009 (in press)
  10. Qi F, Chen X, and Beard DA, "Detailed kinetics and regulation of mammalian NAD-linked isocitrate dehydrogenase". Biochim Biophys Acta. 2008 Jul 11
  11. Deard DA, Wu F, Cabrera ME., and Dash Rk, " Modeling of Cellular Metabolism and Microcirculatory Transport", Microcirculation. 2008 Jun 26:1
  12. Heutte WJ, Beard DA, and Qian H. "Linear analysis near a steady state of biochemical networks: Control analysis, correlation metrics, and circuit theory". BMC Systems Biology (in press), 2008
  13. Xie D, Beard DA, and Dash RK. An efficient parallel algorithm for a general blood-tissue transport and metabolism model governed by a system of nonlinear hyperbolic equations. J Comp Phys 2008 (submitted).
  14. Dash RK, Li Y, Kim J, Beard DA, Saidel GM, and Cabrera ME. "Metabolic dynamics in skeletal muscle during acute reduction in blood flow and oxygen supply to mitochondria: In-silico studies using a multistale, top-down integrated model", PLoS ONE. 2008 Sep 9;3(9):e3168
  15. Miller CA and Beard DA, "The Effects of Reversibility and Noise on Stochastic Phosphorylation Cycles and Cascades", Biophys J. 2008 Sep;95(5):2183-92.
  16. Wu F, Zhang J, Bache RJ, and Beard DA, "Phosphate metabolite concentrations and ATP hydrolysis potential in normal and ischemic hearts", J Physiol. 2008 Sep 1;586(Pt 17):4193-208.
  17. Qi F, Yang F, Qian H, Kushmerick MJ, Bassingthwaighte JB and Beard DA, "Role of the purine nucleotide cycle in skeletal muscle energy metabolism". Ann Biomed Eng. (in review), 2008
  18. Beard DA, Vinnakota KC, and Wu F. "Detailed enzyme kinetics in terms of biochemical species: study of citrate synthase". PLoS ONE. 2008 Mar 19;3(3):e1825.
  19. Dash RK and Beard DA, "Analysis of Cardiac Mitochondrial Na+/Ca2+ Exchanger Kinetics with a Biophysical Model of Mitochondrial Ca2+ Handing Suggests a 3:1 Stoichiometry",J Physiol. 2008 Jul 1;586(13):3267-85. Epub 2008 May 8..
  20. Smith JR, Matus IR, Beard DA and Greene AS, "Differential expression of cardiac mitochondrial proteins". Proteomics 8:446-462, 2008.
  21. Wu F, Yang F, Vinnakota KC and Beard DA, "Computer Modeling of Mitochondral TCA Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electophysiology", and Supplemental Material, J Biol Chem. 282:24525-24537, 2007.
  22. Schenkman KA, Arakaki LSL, Ciesielski WA, Beard DA, "Optical spectroscopy demonstrates elevated intracellular oxygenation in an endotoxic model of sepsis in the perfused heart", Shock 27:695-700, 2007.
  23. Smith NP, Crampin EJ, Niederer SA, Bassingthwaighte JB, Beard DA,"Computational biol-ogy of cardiac myocytes: proposed standards for the physiome". J Exp Biol. 2007 210:1576-83, 2007
  24. Huang M, Camara AKS, Stowe DF, Qi F, and Beard DA, "Mitochondrial Inner Membrane Electrophysiology Assessed by Rhodamine-123 Transport and Fluorescence". Ann Biomed Eng. 35:1276-85, 2007
  25. Beard DA and Qian H, "Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processes", PLoS One, January 2007, Issue 1, e144
  26. Beard DA, "Modeling of Oxygen Transport and Cellular Energetics Explains Observations on In Vivo Cardiac Energy Metabolism", PLoS Computational Biology, Sep. 2006
  27. Wu F, Jeneson JA, Beard DA, "Oxidative ATP synthesis in skeletal muscle is controlled by substrate feedback". American Journal of Physiology – Cell Physiology, Vol. 292, No. 1, pp. C115-24, 2007
  28. Li P, Liang M, Beard DA, Greene AS. A parsimonious statistical method to identify differentially expressed genes in time course microarray experiments. (In Review), 2005.
  29. Yang F, Tong X, Gail McCarver D, Hines RN and Beard DA, "Population-Based Pharmacogenomic and Pharmacokinetic Analysis of Methadone Delivery, Distribution, and Metabolism in Children", J Pharmacokinet Pharmacodyn. 2006 Aug;33(4):485-518
  30. Qian H and Beard DA, "Metabolic Futile Cycles and Their Functions - A Systems Analysis of Energy and Control", IEE Proceedings - Systems Biology , Vol. 153, pp. 192-200 (2006)
  31. Yang F and Beard DA, "Thermodynamic Based Profiling Drug Metabolism and Drug-Drug Metabolic Interactions: A Case Study of Acetaminophen and Ethanol Toxic Interaction", Biophys Chem. 2006 Mar 20;120(2):121-34
  32. Beard DA, "A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation", PLoS Comput Biol. 2005 Sep 9;1(4):e36
  33. Yang F, Qian H, and Beard DA, "Ab Initio prediction of thermodynamically feasible reaction directions from network stoichiometry". Metab Eng. 2005 Jul;7(4):251-9.
  34. Okpechi-Ejike JC, Arakaki LSL, Beard DA, Ciesielski WA, Feigl EO and Schenkman KA, "Myocardial oxygenation and adenosine release in isolated guinea pig hearts during changes in contractility". Am J Physiol Heart Circ Physiol. 2005 May;288(5):H2062-7
  35. Sarkar A, Beard DA and Franza BR, "Effects of binding in the cyclic phophorylation-dephosphorylation process and in energy transformation". Math Biosci. 2006 Jul;202(1):175-93.
  36. Beard DA and Qian H, "Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism". Am J Physiol Endocrinol Metab. 2005 Mar;288(3):E633-44.
  37. Qian H and Beard DA, "Thermodynamics of Stoichiometric Biochemical Networks in Living Systems Far from Equilibrium". Biophysical Chemistry 114:213-220, 2005,
  38. Beard DA, Babson E, Curtis E and Qian H, "Thermodynamic constraints for biochemical networks",J. theor. Biol. 228:327-333, 2004.
  39. Zhang Q, Beard DA and Schlick T, "Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DiSCO) algorithm".
    J. Comp. Chem. 24:2063-2074, 2003.
  40. Beard DA and Schlick T, "Unbiased rotational moves for rigid-body dynamics". Biophys. J. 85:2973-2976, 2003.
  41. Beard DA, Schenkman KA, and Feigl EO, "Myocardial oxygenation in isolated hearts predicted by anatomically reasonable microvascular transport model". Am. J. Physiol. 285: H1826-H1836, 2003.
  42. Schenkman KA, Beard DA, Ciesielski WA and Feigl EO, "Comparison of buffer and red blood cell perfusion of guinea pig heart oxygenation". Am. J. Physiol. 285:H1819-H1825, 2003.
  43. Price ND, Famili I, Beard DA and Palsson BO, Letter to the editor: "Extreme pathways and Kirkhoff's second law". Biophys. J. 83:2879-2882, 2002.
  44. Qian H, Beard DA and Liang S.-D, "Stoichiometric network theory for nonequilibrium biochemical systems". Eur. J. Biochem. 270:415-421, 2003.
  45. Beard DA, Liang S.-D and Qian H., "Energy balance for analysis of complex metabolic networks". Biophys. J. 83: 79-86, 2002.
  46. Bassingthwaighte JB, Beard DA and Li Z, "The mechanical and metabolic basis of myocardial blood flow heterogeneity". Basic Res. Cardiol. 96:582-594, 2001.
  47. Beard DA, "Computational framework for generating transport models from databases of microvascular anatomy". Ann. Biomed. Eng. 29:837-843, 2001.
  48. Beard DA, "Taylor dispersion of a solute in a microfluidic channel". J Appl Phys 89:4667-4669, 2001; see comment by K. D. Dorfman and H. Brenner (J. Appl. Phys. 90: 6553-6554, 2001) and response by Beard DA (J. Appl. Phys. 90: 6555-6556, 2001).
  49. Beard DA and Bassingthwaighte JB, "Modeling oxygen transport in complex vascular networks", Ann. Biomed. Eng. 29:298-310, 2001.
  50. Beard DA, and Schlick T, "Computational modeling predicts the structure and dynamics of the chromatin fiber". Structure with Folding and Design. 9: 105-114, 2001.
  51. Beard DA, and Schlick T, "Modeling salt-mediated electrostatics of macromolecules: The discrete surface charge optimization algorithm and its application to the nucleosome". Biopolymers 58:106-115, 2001.
  52. Schlick T, Beard DA, Huang J, Strahs D, and Qian X.. "Computational challenges in simulating large DNA over long times". IEEE Computing in Science and Engineering 2(6):38-51, 2000.
  53. Beard DA and Schlick T, "Inertial stochastic dynamics I. Long-timestep methods for Langevin dynamics".
    J. Chem. Phys. 112:7323-7338, 2000.
  54. Beard DA and Schlick T, "Inertial stochastic dynamics II. Influence of inertia on slow kinetic processes of supercoiled DNA", J. Chem. Phys. 112:7313-7322, 2000.
  55. Beard DA and Bassingthwaighte JB, "Advection and diffusion of substances in biological tissues with complex vascular networks". Ann. Biomed. Eng. 28:253-268, 2000.
  56. Beard DA and Bassingthwaighte JB, "Fractal nature of myocardial blood flow described by a whole-organ model of the arterial network". J. Vasc. Res. 37:282-297, 2000.
  57. Beard DA and Bassingthwaighte JB, "Power-law kinetics of tracer washout from physiological systems". Ann. Biomed. Eng. 26:775-779, 1998.
  58. Bassingthwaighte JB and Beard DA, "Fractal 15O-water washout from the heart". Circ. Res. 77:1212-1221, 1995.

Invited Reviews and Editorials

  1. Beard DA, Bassingthwaighte JB and Greene AS, "Computational Modeling of Physiological Systems". Physiological Genomics 23:1-3, 2005.
  2. Beard DA and Vendelin M, "Systems biology of the mitochondrion", Am J Physiol Cell Physiol 291: C1101-C1103, 2006.

Chapters and Proceedings

  1. Beard DA and Qian H. Chemical Biophysics: Quantitative Analysis of Cellular Systems. Textbook published by Cambridge University Press
  2. Beard DA, Comment on: “Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions” by Luo et al. Mol. Syst. Biol. 2:0031 (2006). (in press), 2008.
  3. SecombTW, Beard DA, Frisbee JC, Smith NP and Pries AR. "The role of theoretical modeling in microcirculation research". Microcirculation (in press), 2008.
  4. Dash RK and Beard DA, "Cellular metabolism and microcirculatory transport. Microcir-culation" (in press), 2008.
  5. Beard DA, Vendelin M, "Systems biology of the mitochondrion". Am J Physiol Cell Physiol. 2006 Dec;291(6):C1101-3
  6. Beard DA, BassingthwaighteJB and Greene AS, "Computational modeling of physiological systems". Physiological Genomics 23:1-3, 2005
  7. Beard DA and Qian H, "Constraint-based modeling of metabolomic systems, in Encyclopedia of Genomics, Proteomics and Bioinformatics", edited by M. Dunn, L. Jorde, P. Little, and S. Subramaniam, John Wiley & Sons, Ltd., 2004.
  8. Beard DA, Qian H and Bassingthwaighte JB, "Stoichiometric foundation of large-scale biochemical systems analysis", in Modeling in Molecular Biology, edited by G. Ciobanu, Springer-Verlag, 2004.
  9. Beard DA, "A Molecular Modeler's Guide to Statistical Mechanics" (2001) in Beard DA editor, Computational Biology and Theory, L. J. DeFelice, editor-in-chief, On-Line Biophysics Textbook, Biophysical Society, Bethesda, MD
  10. Bassingthwaighte JB, Beard DA, Li Z and Yipintsoi T, "Is the fractal nature of intraorgan spatial flow distributions based on vascular network growth or on local metabolic needs? in Vascular Morphogenesis", edited by C. Little, V. Mironov, and E. H. Sage. Birkhauser, Basel 1998.
  11. Bassingthwaighte JB, Beard DA and King RB, "Fractal regional myocardial blood flows: the anatomical basis, in Fractals in Biology and Medicine", edited by G. Losa, E. Weibel, and T. Nonnenmacher. Birkhauser, Basel , 1997.
  12. Bassingthwaighte JB, Beard DA, Percival DB and Raymond GM, "Fractal structures and processes, in Chaos and the Changing Nature of Science and Medicine: An Introduction", edited by D. E. Herbert. AIP Press, Woodbury, NY, 1996.
  13. Bassingthwaighte JB and Beard DA, "Fractal organization of the coronary vasculature. Proceedings of the National Heart, Lung, and Blood Institute's Meeting on Coronary Vasculature", edited by W. Chilian. Bethesda, MD, 1995.