Daniel Andrew Beard, Ph.D. - Publications

Affiliations: 
Molecular and Integrative Physiology University of Michigan, Ann Arbor, Ann Arbor, MI 
Area:
Nonequilibrium thermodynamics in biochemical networks, Mass transport and microvascular exchange in physiological systems, Physiological and pathophysiological regulation of metabolism, Biophysics of supramolecular complexes

132 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Gu F, Randall EB, Whitesall S, Converso-Baran K, Carlson BE, Fink GD, Michele DE, Beard DA. Potential role of intermittent functioning of baroreflexes in the etiology of hypertension in spontaneously hypertensive rats. Jci Insight. 5. PMID 33004690 DOI: 10.1172/jci.insight.139789  0.48
2018 Allen LA, Schmidt JR, Thompson CT, Carlson BE, Beard DA, Lombard JH. High salt diet impairs cerebral blood flow regulation via salt-induced angiotensin ii suppression. Microcirculation (New York, N.Y. : 1994). e12518. PMID 30481399 DOI: 10.1111/micc.12518  0.48
2018 Kosinski SA, Carlson BE, Hummel SL, Brook RD, Beard DA. Computational Model-Based Assessment of Baroreflex Function from Response to Valsalva Maneuver. Journal of Applied Physiology (Bethesda, Md. : 1985). PMID 30236047 DOI: 10.1152/japplphysiol.00095.2018  0.48
2018 Bukowy JD, Dayton A, Cloutier D, Lombard JH, Solberg Woods LC, Beard DA, Cowley AW. Do computers dream of electric glomeruli? Kidney International. 94: 635. PMID 30143073 DOI: 10.1016/j.kint.2018.02.011  0.44
2018 Pewowaruk RJ, Philip JL, Tewari SG, Chen CS, Nyaeme MS, Wang Z, Tabima DM, Baker AJ, Beard DA, Chesler NC. Multiscale Computational Analysis of Right Ventricular Mechanoenergetics. Journal of Biomechanical Engineering. 140. PMID 30003251 DOI: 10.1115/1.4040044  0.72
2018 Philip JL, Pewowaruk RJ, Chen CS, Tabima DM, Beard DA, Baker AJ, Chesler NC. Impaired Myofilament Contraction Drives Right Ventricular Failure Secondary to Pressure Overload: Model Simulations, Experimental Validation, and Treatment Predictions. Frontiers in Physiology. 9: 731. PMID 29997518 DOI: 10.3389/fphys.2018.00731  0.48
2018 Bukowy JD, Dayton A, Cloutier D, Manis AD, Staruschenko A, Lombard JH, Solberg Woods LC, Beard DA, Cowley AW. Region-Based Convolutional Neural Nets for Localization of Glomeruli in Trichrome-Stained Whole Kidney Sections. Journal of the American Society of Nephrology : Jasn. PMID 29921718 DOI: 10.1681/ASN.2017111210  0.44
2018 Moxley MA, Vinnakota KC, Bazil JN, Qi NR, Beard DA. Systems-level computational modeling demonstrates fuel selection switching in high capacity running and low capacity running rats. Plos Computational Biology. 14: e1005982. PMID 29474500 DOI: 10.1371/journal.pcbi.1005982  0.4
2017 Bakermans AJ, Bazil JN, Nederveen AJ, Strijkers GJ, Boekholdt SM, Beard DA, Jeneson JAL. Human Cardiac 31P-MR Spectroscopy at 3 Tesla Cannot Detect Failing Myocardial Energy Homeostasis during Exercise. Frontiers in Physiology. 8: 939. PMID 29230178 DOI: 10.3389/fphys.2017.00939  0.4
2017 Thiagarajan R, Alavi A, Podichetty JT, Bazil JN, Beard DA. The feasibility of genome-scale biological network inference using Graphics Processing Units. Algorithms For Molecular Biology : Amb. 12: 8. PMID 28344638 DOI: 10.1186/s13015-017-0100-5  0.4
2017 Liu A, Philip J, Vinnakota KC, Van den Bergh F, Tabima DM, Hacker T, Beard DA, Chesler NC. Estrogen maintains mitochondrial content and function in the right ventricle of rats with pulmonary hypertension. Physiological Reports. 5. PMID 28320896 DOI: 10.14814/phy2.13157  0.48
2016 Tewari SG, Bugenhagen SM, Vinnakota KC, Rice JJ, Janssen PM, Beard DA. Influence of metabolic dysfunction on cardiac mechanics in decompensated hypertrophy and heart failure. Journal of Molecular and Cellular Cardiology. PMID 27085901 DOI: 10.1016/j.yjmcc.2016.04.003  1
2016 Holzem KM, Vinnakota KC, Ravikumar VK, Madden EJ, Ewald GA, Dikranian K, Beard DA, Efimov IR. Mitochondrial structure and function are not different between nonfailing donor and end-stage failing human hearts. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 30: 2698-707. PMID 27075244 DOI: 10.1096/fj.201500118R  0.4
2016 Vinnakota KC, Cha CY, Rorsman P, Balaban RS, La Gerche A, Wade-Martins R, Beard DA, Jeneson JA. Improving the physiological realism of experimental models. Interface Focus. 6: 20150076. PMID 27051507 DOI: 10.1098/rsfs.2015.0076  0.4
2016 Vinnakota KC, Bazil JN, Van den Bergh F, Wiseman RW, Beard DA. Feedback Regulation and Time Hierarchy of Oxidative Phosphorylation in Cardiac Mitochondria. Biophysical Journal. 110: 972-80. PMID 26910434 DOI: 10.1016/j.bpj.2016.01.003  1
2016 Bazil JN, Beard DA, Vinnakota KC. Catalytic Coupling of Oxidative Phosphorylation, ATP Demand, and Reactive Oxygen Species Generation. Biophysical Journal. 110: 962-71. PMID 26910433 DOI: 10.1016/j.bpj.2015.09.036  1
2016 Vinnakota KC, Singhal A, Van den Bergh F, Bagher-Oskouei M, Wiseman RW, Beard DA. Open-Loop Control of Oxidative Phosphorylation in Skeletal and Cardiac Muscle Mitochondria by Ca(2.). Biophysical Journal. 110: 954-61. PMID 26910432 DOI: 10.1016/j.bpj.2015.12.018  1
2016 Lee P, Carlson BE, Chesler N, Olufsen MS, Qureshi MU, Smith NP, Sochi T, Beard DA. Heterogeneous mechanics of the mouse pulmonary arterial network. Biomechanics and Modeling in Mechanobiology. PMID 26792789 DOI: 10.1007/s10237-015-0757-y  1
2016 Bassingthwaighte JB, Raymond GM, Dash RK, Beard DA, Nolan M. The Pathway for Oxygen: Tutorial Modelling on Oxygen Transport from Air to Mitochondrion : The Pathway for Oxygen. Advances in Experimental Medicine and Biology. 876: 103-10. PMID 26782201 DOI: 10.1007/978-1-4939-3023-4_13  0.52
2016 Vinnakota KC, Cha CY, Rorsman P, Balaban RS, Gerche AL, Wade-Martins R, Beard DA, Jeneson JAL. Improving the physiological realism of experimental models Interface Focus. 6. DOI: 10.1098/rsfs.2015.0076  0.52
2015 Moxley MA, Beard DA, Bazil JN. Global Kinetic Analysis of Mammalian E3 Reveals pH-dependent NAD+/NADH Regulation, Physiological Kinetic Reversibility, and Catalytic Optimum. The Journal of Biological Chemistry. PMID 26644471 DOI: 10.1074/jbc.M115.676619  0.52
2015 Bugenhagen SM, Beard DA. Computational analysis of the regulation of Ca(2+) dynamics in rat ventricular myocytes. Physical Biology. 12: 056008. PMID 26358004 DOI: 10.1088/1478-3975/12/5/056008  1
2015 Pannala VR, Beard DA, Dash RK. Letter to the Editor: Mitochondrial cytochrome c oxidase: mechanism of action and role in regulating oxidative phosphorylation. Journal of Applied Physiology (Bethesda, Md. : 1985). 119: 157. PMID 26177971 DOI: 10.1152/japplphysiol.00290.2015  1
2015 Tewari SG, Bugenhagen SM, Palmer BM, Beard DA. Dynamics of cross-bridge cycling, ATP hydrolysis, force generation, and deformation in cardiac muscle. Journal of Molecular and Cellular Cardiology. PMID 25681584 DOI: 10.1016/j.yjmcc.2015.02.006  1
2015 Dasika SK, Vinnakota KC, Beard DA. Characterization of the kinetics of cardiac cytosolic malate dehydrogenase and comparative analysis of cytosolic and mitochondrial isoforms. Biophysical Journal. 108: 420-30. PMID 25606689 DOI: 10.1016/j.bpj.2014.11.3466  1
2015 Dasika SK, Vinnakota KC, Beard DA. Determination of the catalytic mechanism for mitochondrial malate dehydrogenase. Biophysical Journal. 108: 408-19. PMID 25606688 DOI: 10.1016/j.bpj.2014.11.3467  1
2015 Belle A, Thiagarajan R, Soroushmehr SMR, Navidi F, Beard DA, Najarian K. Big data analytics in healthcare Biomed Research International. 2015. DOI: 10.1155/2015/370194  1
2014 Tewari SG, Zhou Y, Otto BJ, Dash RK, Kwok WM, Beard DA. Markov chain Monte Carlo based analysis of post-translationally modified VDAC gating kinetics. Frontiers in Physiology. 5: 513. PMID 25628567 DOI: 10.3389/fphys.2014.00513  1
2014 Moxley MA, Beard DA, Bazil JN. A pH-dependent kinetic model of dihydrolipoamide dehydrogenase from multiple organisms. Biophysical Journal. 107: 2993-3007. PMID 25517164 DOI: 10.1016/j.bpj.2014.09.025  1
2014 Bazil JN, Pannala VR, Dash RK, Beard DA. Determining the origins of superoxide and hydrogen peroxide in the mammalian NADH:ubiquinone oxidoreductase. Free Radical Biology & Medicine. 77: 121-9. PMID 25236739 DOI: 10.1016/j.freeradbiomed.2014.08.023  1
2014 Bazil JN, Stamm KD, Li X, Thiagarajan R, Nelson TJ, Tomita-Mitchell A, Beard DA. The inferred cardiogenic gene regulatory network in the mammalian heart. Plos One. 9: e100842. PMID 24971943 DOI: 10.1371/journal.pone.0100842  1
2014 Pettersen KH, Bugenhagen SM, Nauman J, Beard DA, Omholt SW. Arterial stiffening provides sufficient explanation for primary hypertension. Plos Computational Biology. 10: e1003634. PMID 24853828 DOI: 10.1371/journal.pcbi.1003634  1
2013 Beard DA, Pettersen KH, Carlson BE, Omholt SW, Bugenhagen SM. A computational analysis of the long-term regulation of arterial pressure. F1000research. 2: 208. PMID 24555102 DOI: 10.12688/f1000research.2-208.v1  1
2013 Tewari SG, Bugenhagen SM, Wang Z, Schreier DA, Carlson BE, Chesler NC, Beard DA. Analysis of cardiovascular dynamics in pulmonary hypertensive C57BL6/J mice. Frontiers in Physiology. 4: 355. PMID 24376421 DOI: 10.3389/fphys.2013.00355  1
2013 Beard DA, Feigl EO. Rebuttal from Daniel Beard and Eric Feigl. The Journal of Physiology. 591: 5801. PMID 24293528 DOI: 10.1113/jphysiol.2013.264663  1
2013 Beard DA, Feigl EO. CrossTalk opposing view: Guyton's venous return curves should not be taught. The Journal of Physiology. 591: 5795-7. PMID 24293526 DOI: 10.1113/jphysiol.2013.260034  1
2013 Menzies RI, Unwin RJ, Dash RK, Beard DA, Cowley AW, Carlson BE, Mullins JJ, Bailey MA. Effect of P2X4 and P2X7 receptor antagonism on the pressure diuresis relationship in rats. Frontiers in Physiology. 4: 305. PMID 24187541 DOI: 10.3389/fphys.2013.00305  0.52
2013 Beard DA. Tautology vs. physiology in the etiology of hypertension. Physiology (Bethesda, Md.). 28: 270-1. PMID 23997184 DOI: 10.1152/physiol.00038.2013  1
2013 Bazil JN, Vinnakota KC, Wu F, Beard DA. Analysis of the kinetics and bistability of ubiquinol:cytochrome c oxidoreductase. Biophysical Journal. 105: 343-55. PMID 23870256 DOI: 10.1016/j.bpj.2013.05.033  1
2013 Gjuvsland AB, Vik JO, Beard DA, Hunter PJ, Omholt SW. Bridging the genotype-phenotype gap: what does it take? The Journal of Physiology. 591: 2055-66. PMID 23401613 DOI: 10.1113/jphysiol.2012.248864  1
2013 Beard DA, Feigl EO. Reply to "letter to the editor: a return to the venous return controversy: a visual aid for combatants'". American Journal of Physiology. Heart and Circulatory Physiology. 304: H489. PMID 23377151 DOI: 10.1152/ajpheart.00886.2012  1
2013 Li X, Wu F, Beard DA. Identification of the kinetic mechanism of succinyl-CoA synthetase. Bioscience Reports. 33: 145-63. PMID 23088689 DOI: 10.1042/BSR20120069  1
2013 Pradhan RK, Vinnakota KC, Beard DA, Dash RK. Carrier-Mediated Transport Through Biomembranes Transport in Biological Media. 181-212. DOI: 10.1016/B978-0-12-415824-5.00005-9  1
2012 Bugenhagen SM, Beard DA. Specification, construction, and exact reduction of state transition system models of biochemical processes. The Journal of Chemical Physics. 137: 154108. PMID 23083149 DOI: 10.1063/1.4758074  1
2012 Tewari SG, Dash RK, Beard DA, Bazil JN. A biophysical model of the mitochondrial ATP-Mg/P(i) carrier. Biophysical Journal. 103: 1616-25. PMID 23062354 DOI: 10.1016/j.bpj.2012.08.050  1
2012 Bassingthwaighte JB, Beard DA, Carlson BE, Dash RK, Vinnakota K. Modeling to link regional myocardial work, metabolism and blood flows. Annals of Biomedical Engineering. 40: 2379-98. PMID 22915334 DOI: 10.1007/s10439-012-0613-5  1
2012 Beard DA, Neal ML, Tabesh-Saleki N, Thompson CT, Bassingthwaighte JB, Shimoyama M, Carlson BE. Multiscale modeling and data integration in the virtual physiological rat project. Annals of Biomedical Engineering. 40: 2365-78. PMID 22805979 DOI: 10.1007/s10439-012-0611-7  1
2012 Thompson MD, Beard DA, Wu F. Use of partition coefficients in flow-limited physiologically-based pharmacokinetic modeling. Journal of Pharmacokinetics and Pharmacodynamics. 39: 313-27. PMID 22639356 DOI: 10.1007/s10928-012-9252-6  1
2012 Beard DA, Mescam M. Mechanisms of pressure-diuresis and pressure-natriuresis in Dahl salt-resistant and Dahl salt-sensitive rats. Bmc Physiology. 12: 6. PMID 22583378 DOI: 10.1186/1472-6793-12-6  1
2012 Thompson MD, Beard DA. Physiologically based pharmacokinetic tissue compartment model selection in drug development and risk assessment. Journal of Pharmaceutical Sciences. 101: 424-35. PMID 21968734 DOI: 10.1002/jps.22768  1
2012 Beard DA. Biosimulation: Simulation of living systems Biosimulation: Simulation of Living Systems. 1-307. DOI: 10.1017/CBO9781139045582  1
2011 Bazil JN, Qi F, Beard DA. A parallel algorithm for reverse engineering of biological networks. Integrative Biology : Quantitative Biosciences From Nano to Macro. 3: 1215-23. PMID 22080176 DOI: 10.1039/c1ib00117e  1
2011 Pradhan RK, Qi F, Beard DA, Dash RK. Characterization of Mg2+ inhibition of mitochondrial Ca2+ uptake by a mechanistic model of mitochondrial Ca2+ uniporter. Biophysical Journal. 101: 2071-81. PMID 22067144 DOI: 10.1016/j.bpj.2011.09.029  1
2011 Qi F, Pradhan RK, Dash RK, Beard DA. Detailed kinetics and regulation of mammalian 2-oxoglutarate dehydrogenase. Bmc Biochemistry. 12: 53. PMID 21943256 DOI: 10.1186/1471-2091-12-53  1
2011 Wu F, Beard DA, Frisbee JC. Computational analyses of intravascular tracer washout reveal altered capillary-level flow distributions in obese Zucker rats. The Journal of Physiology. 589: 4527-43. PMID 21788350 DOI: 10.1113/jphysiol.2011.209775  1
2011 Frisbee JC, Wu F, Goodwill AG, Butcher JT, Beard DA. Spatial heterogeneity in skeletal muscle microvascular blood flow distribution is increased in the metabolic syndrome. American Journal of Physiology. Regulatory, Integrative and Comparative Physiology. 301: R975-86. PMID 21775645 DOI: 10.1152/ajpregu.00275.2011  1
2011 Vinnakota KC, Dash RK, Beard DA. Stimulatory effects of calcium on respiration and NAD(P)H synthesis in intact rat heart mitochondria utilizing physiological substrates cannot explain respiratory control in vivo. The Journal of Biological Chemistry. 286: 30816-22. PMID 21757763 DOI: 10.1074/jbc.M111.242529  1
2011 Beard DA, Feigl EO. Understanding Guyton's venous return curves. American Journal of Physiology. Heart and Circulatory Physiology. 301: H629-33. PMID 21666119 DOI: 10.1152/ajpheart.00228.2011  1
2011 Thompson MD, Beard DA. Development of appropriate equations for physiologically based pharmacokinetic modeling of permeability-limited and flow-limited transport. Journal of Pharmacokinetics and Pharmacodynamics. 38: 405-21. PMID 21584718 DOI: 10.1007/s10928-011-9200-x  1
2011 Carlson BE, Beard DA. Mechanical control of cation channels in the myogenic response. American Journal of Physiology. Heart and Circulatory Physiology. 301: H331-43. PMID 21572020 DOI: 10.1152/ajpheart.00131.2011  1
2011 Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, et al. Minimum Information About a Simulation Experiment (MIASE). Plos Computational Biology. 7: e1001122. PMID 21552546 DOI: 10.1371/journal.pcbi.1001122  1
2011 Mescam M, Vinnakota KC, Beard DA. Identification of the catalytic mechanism and estimation of kinetic parameters for fumarase. The Journal of Biological Chemistry. 286: 21100-9. PMID 21498518 DOI: 10.1074/jbc.M110.214452  1
2011 Li X, Wu F, Qi F, Beard DA. A database of thermodynamic properties of the reactions of glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway. Database : the Journal of Biological Databases and Curation. 2011: bar005. PMID 21482578 DOI: 10.1093/database/bar005  1
2011 Beard DA. Comments on Point:Counterpoint: Muscle lactate and H⁺ production do/do not have a 1:1 association in skeletal muscle. Calculations of Robergs support the view of Vinnakota and Kushmerick. Journal of Applied Physiology (Bethesda, Md. : 1985). 110: 1493. PMID 21372102 DOI: 10.1152/japplphysiol.00242.2011  0.56
2011 Vinnakota KC, Beard DA. Kinetic analysis and design of experiments to identify the catalytic mechanism of the monocarboxylate transporter isoforms 4 and 1. Biophysical Journal. 100: 369-80. PMID 21244833 DOI: 10.1016/j.bpj.2010.11.079  1
2011 Beard DA. Simulation of cellular biochemical system kinetics. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 3: 136-46. PMID 21171044 DOI: 10.1002/wsbm.116  1
2011 Waters SL, Alastruey J, Beard DA, Bovendeerd PH, Davies PF, Jayaraman G, Jensen OE, Lee J, Parker KH, Popel AS, Secomb TW, Siebes M, Sherwin SJ, Shipley RJ, Smith NP, et al. Theoretical models for coronary vascular biomechanics: progress & challenges. Progress in Biophysics and Molecular Biology. 104: 49-76. PMID 21040741 DOI: 10.1016/j.pbiomolbio.2010.10.001  1
2011 Fink M, Niederer SA, Cherry EM, Fenton FH, Koivumäki JT, Seemann G, Thul R, Zhang H, Sachse FB, Beard D, Crampin EJ, Smith NP. Cardiac cell modelling: observations from the heart of the cardiac physiome project. Progress in Biophysics and Molecular Biology. 104: 2-21. PMID 20303361 DOI: 10.1016/j.pbiomolbio.2010.03.002  1
2010 Pradhan RK, Qi F, Beard DA, Dash RK. Characterization of membrane potential dependency of mitochondrial Ca2+ uptake by an improved biophysical model of mitochondrial Ca2+ uniporter. Plos One. 5: e13278. PMID 20949039 DOI: 10.1371/journal.pone.0013278  1
2010 Chen X, Qi F, Dash RK, Beard DA. Kinetics and regulation of mammalian NADH-ubiquinone oxidoreductase (Complex I). Biophysical Journal. 99: 1426-36. PMID 20816054 DOI: 10.1016/j.bpj.2010.06.063  1
2010 Haumann J, Dash RK, Stowe DF, Boelens AD, Beard DA, Camara AK. Mitochondrial free [Ca2+] increases during ATP/ADP antiport and ADP phosphorylation: exploration of mechanisms. Biophysical Journal. 99: 997-1006. PMID 20712982 DOI: 10.1016/j.bpj.2010.04.069  1
2010 Vinnakota KC, Mitchell DA, Deschenes RJ, Wakatsuki T, Beard DA. Analysis of the diffusion of Ras2 in Saccharomyces cerevisiae using fluorescence recovery after photobleaching. Physical Biology. 7: 026011. PMID 20526029 DOI: 10.1088/1478-3975/7/2/026011  1
2010 Li X, Dash RK, Pradhan RK, Qi F, Thompson M, Vinnakota KC, Wu F, Yang F, Beard DA. A database of thermodynamic quantities for the reactions of glycolysis and the tricarboxylic acid cycle. The Journal of Physical Chemistry. B. 114: 16068-82. PMID 20446702 DOI: 10.1021/jp911381p  1
2010 Bugenhagen SM, Cowley AW, Beard DA. Identifying physiological origins of baroreflex dysfunction in salt-sensitive hypertension in the Dahl SS rat. Physiological Genomics. 42: 23-41. PMID 20354102 DOI: 10.1152/physiolgenomics.00027.2010  1
2010 Pradhan RK, Beard DA, Dash RK. A biophysically based mathematical model for the kinetics of mitochondrial Na+-Ca2+ antiporter. Biophysical Journal. 98: 218-30. PMID 20338843 DOI: 10.1016/j.bpj.2009.10.005  1
2009 Xie D, Dash RK, Beard DA. An Improved Algorithm and Its Parallel Implementation for Solving a General Blood-Tissue Transport and Metabolism Model. Journal of Computational Physics. 228: 7850-7861. PMID 20161089 DOI: 10.1016/j.jcp.2009.07.024  1
2009 Vinnakota KC, Beard DA, Dash RK. Design of experiments for identification of complex biochemical systems with applications to mitochondrial bioenergetics. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 4171-4. PMID 19964622 DOI: 10.1109/IEMBS.2009.5333935  1
2009 Beard DA, Wu F. Creatine and phosphate pools are maintained at energetically optimal levels in the heart during hypertrophic remodeling and heart failure. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 4487-90. PMID 19964369 DOI: 10.1109/IEMBS.2009.5333680  1
2009 Beard DA, Kushmerick MJ. Strong inference for systems biology. Plos Computational Biology. 5: e1000459. PMID 19714210 DOI: 10.1371/journal.pcbi.1000459  1
2009 Qi F, Dash RK, Han Y, Beard DA. Generating rate equations for complex enzyme systems by a computer-assisted systematic method. Bmc Bioinformatics. 10: 238. PMID 19653903 DOI: 10.1186/1471-2105-10-238  1
2009 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, et al. CellML metadata standards, associated tools and repositories. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 367: 1845-67. PMID 19380315 DOI: 10.1098/rsta.2008.0310  1
2009 Wu F, Zhang J, Beard DA. Experimentally observed phenomena on cardiac energetics in heart failure emerge from simulations of cardiac metabolism. Proceedings of the National Academy of Sciences of the United States of America. 106: 7143-8. PMID 19357309 DOI: 10.1073/pnas.0812768106  1
2009 Vanlier J, Wu F, Qi F, Vinnakota KC, Han Y, Dash RK, Yang F, Beard DA. BISEN: Biochemical Simulation Environment. Bioinformatics (Oxford, England). 25: 836-7. PMID 19244386 DOI: 10.1093/bioinformatics/btp069  1
2009 Beard DA, Wu F. Apparent diffusivity and Taylor dispersion of water and solutes in capillary beds. Bulletin of Mathematical Biology. 71: 1366-77. PMID 19234745 DOI: 10.1007/s11538-009-9405-y  1
2009 Wu F, Beard DA. Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart. Bmc Systems Biology. 3: 22. PMID 19228404 DOI: 10.1186/1752-0509-3-22  1
2009 Dash RK, Qi F, Beard DA. A biophysically based mathematical model for the kinetics of mitochondrial calcium uniporter. Biophysical Journal. 96: 1318-32. PMID 19217850 DOI: 10.1016/j.bpj.2008.11.005  1
2009 Vinnakota KC, Wu F, Kushmerick MJ, Beard DA. Multiple ion binding equilibria, reaction kinetics, and thermodynamics in dynamic models of biochemical pathways. Methods in Enzymology. 454: 29-68. PMID 19216922 DOI: 10.1016/S0076-6879(08)03802-0  1
2008 Secomb TW, Beard DA, Frisbee JC, Smith NP, Pries AR. The role of theoretical modeling in microcirculation research. Microcirculation (New York, N.Y. : 1994). 15: 693-8. PMID 18946803 DOI: 10.1080/10739680802349734  1
2008 Dash RK, Li Y, Kim J, Beard DA, Saidel GM, Cabrera ME. 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. Plos One. 3: e3168. PMID 18779864 DOI: 10.1371/journal.pone.0003168  1
2008 Qi F, Chen X, Beard DA. Detailed kinetics and regulation of mammalian NAD-linked isocitrate dehydrogenase. Biochimica Et Biophysica Acta. 1784: 1641-51. PMID 18672100 DOI: 10.1016/j.bbapap.2008.07.001  1
2008 Beard DA. Comment on 'Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions'. Molecular Systems Biology. 4: 207; discussion 208. PMID 18628747 DOI: 10.1038/msb.2008.37  1
2008 Wu F, Zhang EY, Zhang J, Bache RJ, Beard DA. Phosphate metabolite concentrations and ATP hydrolysis potential in normal and ischaemic hearts. The Journal of Physiology. 586: 4193-208. PMID 18617566 DOI: 10.1113/jphysiol.2008.154732  1
2008 Beard DA, Wu F, Cabrera ME, Dash RK. Modeling of cellular metabolism and microcirculatory transport. Microcirculation (New York, N.Y. : 1994). 15: 777-93. PMID 18608987 DOI: 10.1080/10739680802019709  1
2008 Miller CA, Beard DA. The effects of reversibility and noise on stochastic phosphorylation cycles and cascades. Biophysical Journal. 95: 2183-92. PMID 18515389 DOI: 10.1529/biophysj.107.126185  1
2008 Heuett WJ, Beard DA, Qian H. Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory. Bmc Systems Biology. 2: 44. PMID 18482450 DOI: 10.1186/1752-0509-2-44  1
2008 Dash RK, Beard DA. Analysis of cardiac mitochondrial Na+-Ca2+ exchanger kinetics with a biophysical model of mitochondrial Ca2+ handling suggests a 3:1 stoichiometry. The Journal of Physiology. 586: 3267-85. PMID 18467367 DOI: 10.1113/jphysiol.2008.151977  1
2008 Beard DA, Vinnakota KC, Wu F. Detailed enzyme kinetics in terms of biochemical species: study of citrate synthase. Plos One. 3: e1825. PMID 18350161 DOI: 10.1371/journal.pone.0001825  1
2008 Smith JR, Matus IR, Beard DA, Greene AS. Differential expression of cardiac mitochondrial proteins. Proteomics. 8: 446-62. PMID 18232060 DOI: 10.1002/pmic.200701009  1
2008 Beard DA, Qian H. Chemical biophysics: Quantitative analysis of cellular systems Chemical Biophysics: Quantitative Analysis of Cellular Systems. 1-311. DOI: 10.5860/choice.46-2643  1
2007 Wu F, Yang F, Vinnakota KC, Beard DA. Computer modeling of mitochondrial tricarboxylic acid cycle, oxidative phosphorylation, metabolite transport, and electrophysiology. The Journal of Biological Chemistry. 282: 24525-37. PMID 17591785 DOI: 10.1074/jbc.M701024200  1
2007 Schenkman KA, Arakaki LS, Ciesielski WA, Beard DA. Optical spectroscopy demonstrates elevated intracellular oxygenation in an endotoxic model of sepsis in the perfused heart. Shock (Augusta, Ga.). 27: 695-700. PMID 17505311 DOI: 10.1097/SHK.0b013e31802e44e7  1
2007 Smith NP, Crampin EJ, Niederer SA, Bassingthwaighte JB, Beard DA. Computational biology of cardiac myocytes: proposed standards for the physiome. The Journal of Experimental Biology. 210: 1576-83. PMID 17449822 DOI: 10.1242/jeb.000133  1
2007 Huang M, Camara AK, Stowe DF, Qi F, Beard DA. Mitochondrial inner membrane electrophysiology assessed by rhodamine-123 transport and fluorescence. Annals of Biomedical Engineering. 35: 1276-85. PMID 17372838 DOI: 10.1007/s10439-007-9265-2  1
2007 Beard DA, Qian H. Relationship between thermodynamic driving force and one-way fluxes in reversible processes. Plos One. 2: e144. PMID 17206279 DOI: 10.1371/journal.pone.0000144  1
2007 Wu F, Jeneson JA, Beard DA. Oxidative ATP synthesis in skeletal muscle is controlled by substrate feedback. American Journal of Physiology. Cell Physiology. 292: C115-24. PMID 16837647 DOI: 10.1152/ajpcell.00237.2006  1
2006 Beard DA, Vendelin M. Systems biology of the mitochondrion. American Journal of Physiology. Cell Physiology. 291: C1101-3. PMID 17102034 DOI: 10.1152/ajpcell.00481.2006  1
2006 Qian H, Beard DA. Metabolic futile cycles and their functions: a systems analysis of energy and control. Systems Biology. 153: 192-200. PMID 16986621 DOI: 10.1049/ip-syb:20050086  1
2006 Beard DA. Modeling of oxygen transport and cellular energetics explains observations on in vivo cardiac energy metabolism. Plos Computational Biology. 2: e107. PMID 16978045 DOI: 10.1371/journal.pcbi.0020107  1
2006 Sarkar A, Beard DA, Franza BR. Effect of binding in cyclic phosphorylation-dephosphorylation process and in energy transformation. Mathematical Biosciences. 202: 175-93. PMID 16774769 DOI: 10.1016/j.mbs.2006.03.011  1
2006 Yang F, Tong X, McCarver DG, Hines RN, Beard DA. Population-based analysis of methadone distribution and metabolism using an age-dependent physiologically based pharmacokinetic model. Journal of Pharmacokinetics and Pharmacodynamics. 33: 485-518. PMID 16758333 DOI: 10.1007/s10928-006-9018-0  1
2006 Yang F, Beard DA. Thermodynamically based profiling of drug metabolism and drug-drug metabolic interactions: a case study of acetaminophen and ethanol toxic interaction. Biophysical Chemistry. 120: 121-34. PMID 16314027 DOI: 10.1016/j.bpc.2005.10.013  1
2005 Beard DA, Bassingthwaighte JB, Greene AS. Computational modeling of physiological systems. Physiological Genomics. 23: 1-3; discussion 4. PMID 16179418 DOI: 10.1152/physiolgenomics.00117.2005  1
2005 Beard DA. A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation. Plos Computational Biology. 1: e36. PMID 16163394 DOI: 10.1371/journal.pcbi.0010036  1
2005 Yang F, Qian H, Beard DA. Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry. Metabolic Engineering. 7: 251-9. PMID 16140239 DOI: 10.1016/j.ymben.2005.03.002  1
2005 Qian H, Beard DA. Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. Biophysical Chemistry. 114: 213-20. PMID 15829355 DOI: 10.1016/j.bpc.2004.12.001  1
2005 Ejike JC, Arakaki LS, Beard DA, Ciesielski WA, Feigl EO, Schenkman KA. Myocardial oxygenation and adenosine release in isolated guinea pig hearts during changes in contractility. American Journal of Physiology. Heart and Circulatory Physiology. 288: H2062-7. PMID 15591100 DOI: 10.1152/ajpheart.00777.2004  1
2005 Beard DA, Qian H. Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism. American Journal of Physiology. Endocrinology and Metabolism. 288: E633-44. PMID 15507536 DOI: 10.1152/ajpendo.00239.2004  1
2004 Beard DA, Babson E, Curtis E, Qian H. Thermodynamic constraints for biochemical networks. Journal of Theoretical Biology. 228: 327-33. PMID 15135031 DOI: 10.1016/j.jtbi.2004.01.008  1
2003 Beard DA, Schlick T. Unbiased rotational moves for rigid-body dynamics. Biophysical Journal. 85: 2973-6. PMID 14581199 DOI: 10.1016/S0006-3495(03)74717-1  1
2003 Zhang Q, Beard DA, Schlick T. Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm. Journal of Computational Chemistry. 24: 2063-74. PMID 14531059 DOI: 10.1002/jcc.10337  1
2003 Qian H, Beard DA, Liang SD. Stoichiometric network theory for nonequilibrium biochemical systems. European Journal of Biochemistry / Febs. 270: 415-21. PMID 12542691 DOI: 10.1046/j.1432-1033.2003.03357.x  1
2002 Price ND, Famili I, Beard DA, Palsson BØ. Extreme pathways and Kirchhoff's second law. Biophysical Journal. 83: 2879-82. PMID 12425318 DOI: 10.1016/S0006-3495(02)75297-1  1
2002 Beard DA, Liang SD, Qian H. Energy balance for analysis of complex metabolic networks. Biophysical Journal. 83: 79-86. PMID 12080101 DOI: 10.1016/S0006-3495(02)75150-3  1
2001 Bassingthwaighte JB, Beard DA, Li Z. The mechanical and metabolic basis of myocardial blood flow heterogeneity. Basic Research in Cardiology. 96: 582-94. PMID 11770077 DOI: 10.1007/s003950170010  1
2001 Beard DA, Bassingthwaighte JB. Modeling advection and diffusion of oxygen in complex vascular networks. Annals of Biomedical Engineering. 29: 298-310. PMID 11339327 DOI: 10.1114/1.1359450  1
2001 Beard DA, Schlick T. Computational modeling predicts the structure and dynamics of chromatin fiber. Structure (London, England : 1993). 9: 105-14. PMID 11250195 DOI: 10.1016/S0969-2126(01)00572-X  1
2001 Beard DA, Schlick T. Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome. Biopolymers. 58: 106-15. PMID 11072233 DOI: 10.1002/1097-0282(200101)58:1<106::AID-BIP100>3.0.CO;2-#  1
2000 Beard DA, Bassingthwaighte JB. The fractal nature of myocardial blood flow emerges from a whole-organ model of arterial network. Journal of Vascular Research. 37: 282-96. PMID 10965227 DOI: 10.1159/000025742  1
2000 Beard DA, Bassingthwaighte JB. Advection and diffusion of substances in biological tissues with complex vascular networks. Annals of Biomedical Engineering. 28: 253-68. PMID 10784090 DOI: 10.1114/1.273  1
2000 Schlick T, Beard DA, Huang J, Strahs DA, Qian X. Computational challenges in simulating large DNA over long times Computing in Science and Engineering. 2: 38-51.  1
1998 Beard DA, Bassingthwaighte JB. Power-law kinetics of tracer washout from physiological systems. Annals of Biomedical Engineering. 26: 775-9. PMID 9779949 DOI: 10.1114/1.105  1
1995 Bassingthwaighte JB, Beard DA. Fractal 15O-labeled water washout from the heart. Circulation Research. 77: 1212-21. PMID 7586234 DOI: 10.1161/01.RES.77.6.1212  1
Show low-probability matches.