BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
POSITION TITLE
Beard, Daniel Andrew, Ph.D.
Professor
eRA COMMONS USER NAME
dbeard
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
Boston University, Boston, MA
University of Washington, Seattle, WA
University of Washington, Seattle, WA
New York University, New York, NY
DEGREE
(if applicable)
YEAR(s)
B.S.
M.S.
Ph.D.
Postdoctoral
1993
1997
1997
1997-2000
FIELD OF STUDY
Biomedical Engineering
Applied Mathematics
Bioengineering
Chemistry/Mathematics
A. Positions and Honors
Positions and Employment
1993-1997
Research Assistant (Graduate Student), Department of Bioengineering, University of
Washington, Seattle, WA
1998-2000
Howard Hughes Medical Institute Research Fellow, Computational Chemistry and Mathematics,
New York University, New York, NY
2001-2004
Research Assistant Professor, Department of Bioengineering, University of Washington,
Seattle, WA
2004-2005
Assistant Professor, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI
2005-2009
Associate Professor, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI
2009-Present Professor, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI
Professional Memberships
2007-present Member of American Society for Biochemistry and Molecular Biology
2004-present Member of Biophysical Society
2003-present Member American Physiological Society
2001-present Member Biomedical Engineering Society
1999-present Member Society for Industrial and Applied Mathematics
B. Selected peer-reviewed publications (of >70 total)
1. Bassingthwaighte JB, Beard DA. Fractal 15O-labeled water washout from the heart. Circ Res. 77:12121221, 1995.
2. Beard DA, Bassingthwaighte JB. Advection and diffusion of substances in biological tissues with complex
vascular networks. Ann Biomed Eng. 28:253-268, 2000.
3. Beard DA, Bassingthwaighte JB. The fractal nature of myocardial blood flow emerges from a whole-organ
model of arterial network. J Vasc Res. 37:282-296, 2000.
4. Beard DA, Schlick T. Inertial stochastic dynamics I. Long-timestep methods for Langevin dynamics. J.
Chem. Phys. 112:7323-7338, 2000.
5. Beard DA, Schlick T. Inertial stochastic dynamics II. Influence of inertia on slow kinetic processes of
supercoiled DNA. J. Chem. Phys. 112:7313-7322, 2000.
6. Schlick T, Beard DA, Huang J, Strahs D, Qian X. Computational challenges in simulating large DNA over
long times. IEEE Computing in Science and Engineering 2:38-51, 2000.
7. Beard DA, Schlick T. Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge
optimization algorithm and its application to the nucleosome. Biopolymers. 58:106-115, 2001.
8. Beard DA, Schlick T. Computational modeling predicts the structure and dynamics of chromatin fiber.
Structure. 9:105-114, 2001.
9. Beard DA, Bassingthwaighte JB. Modeling advection and diffusion of oxygen in complex vascular
networks. Ann Biomed Eng. 29:298-310, 2001.
10. Beard DA. Computational framework for generating transport models from databases of microvascular
anatomy. Ann Biomed Eng. 29:837-843, 2001.
11. Bassingthwaighte JB, Beard DA, Li Z. The mechanical and metabolic basis of myocardial blood flow
heterogeneity. Basic Res Cardiol. 2001 Nov;96(6):582-594.
12. Beard DA, Liang SD, Qian H. Energy balance for analysis of complex metabolic networks. Biophys J.
83:79-86, 2002.
13. Price ND, Famili I, Beard DA, Palsson BO. Extreme pathways and Kirchhoff's second law. Biophys J.
83:2879-2882, 2002.
14. Qian H, Beard DA, Liang SD. Stoichiometric network theory for nonequilibrium biochemical systems. Eur J
Biochem. 270:415-421, 2003.
15. Beard DA, Schlick T. Unbiased rotational moves for rigid-body dynamics. Biophys J. 85:2973-2976, 2003.
16. Schenkman KA, Beard DA, Ciesielski WA, Feigl EO. Comparison of buffer and red blood cell perfusion of
guinea pig heart oxygenation. Am J Physiol Heart Circ Physiol. 285:H1819-H1825, 2003.
17. Beard DA, Schenkman KA, Feigl EO. Myocardial oxygenation in isolated hearts predicted by an
anatomically realistic microvascular transport model. Am J Physiol Heart Circ Physiol. 285:H1826-H1836,
2003.
18. Zhang Q, Beard DA, Schlick T. Constructing irregular surfaces to enclose macromolecular complexes for
mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm. J Comput Chem.
24:2063-2074, 2003.
19. Beard DA, Babson E, Curtis E, Qian H. Thermodynamic constraints for biochemical networks. J Theor Biol.
228:327-333, 2004.
20. Beard DA, 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.
21. Beard DA, Qian H, Bassingthwaighte JB. Stoichiometric foundation of large-scale biochemical systems
analysis, in Modeling in Molecular Biology, edited by G. Ciobanu, Springer-Verlag, 2004.
22. Beard DA, Qian H. Thermodynamic-based computational profiling of cellular regulatory control in
hepatocyte metabolism. Am J Physiol Endocrinol Metab. 288:E633-E644, 2005.
23. Qian H, Beard DA. Thermodynamics of stoichiometric biochemical networks in living systems far from
equilibrium. Biophys Chem. 114:213-220, 2005.
24. 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. Am J Physiol Heart Circ
Physiol. 288:H2062-H2067, 2005
25. Yang F, Qian H, Beard DA. Ab initio prediction of thermodynamically feasible reaction directions from
biochemical network stoichiometry. Metab Eng. 7:251-259, 2005.
26. Beard DA. A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation.
PLoS Comput Biol. 1(4):e36, 2005
27. Beard DA, Bassingthwaighte JB, Greene AS. Computational modeling of physiological systems. Physiol
Genomics. 23:1-3, 2005.
28. Yang F, Beard DA. Thermodynamically based profiling of drug metabolism and drug-drug metabolic
interactions: a case study of acetaminophen and ethanol toxic interaction. Biophys Chem. 120:121-134,
2006.
29. Qian H, Beard DA. Metabolic futile cycles and their functions: a systems analysis of energy and control.
Syst Biol (Stevenage).153:192-200, 2006.
30. Sarkar A, Beard DA, Franza BR. Effect of binding in cyclic phosphorylation-dephosphorylation process and
in energy transformation. Math Biosci. 202:175-193, 2006.
31. 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. J Pharmacokinet
Pharmacodyn. 33:485-518, 2006.
32. Beard DA. Modeling of oxygen transport and cellular energetics explains observations on in vivo cardiac
energy metabolism. PLoS Comput Biol. 2:e107, 2006.
33. Beard DA, Vendelin M. Systems biology of the mitochondrion. Am J Physiol Cell Physiol. 291:C1101C1103, 2006.
34. Wu F, Jeneson JA, Beard DA. Oxidative ATP synthesis in skeletal muscle is controlled by substrate
feedback. Am J Physiol Cell Physiol. 292:C115-C124, 2007.
35. Beard DA, Qian H. Relationship between Thermodynamic Driving Force and One-Way Fluxes in
Reversible Processes. PLoS ONE. 2:e144, 2007.
36. Smith NP, Crampin EJ, Niederer SA, Bassingthwaighte JB, Beard DA. Computational biology of cardiac
myocytes: proposed standards for the physiome. J Exp Biol. 210:1576-1583, 2007.
37. 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.
38. Huang M, Camara AK, Stowe DF, Qi F, Beard DA. Mitochondrial Inner Membrane Electrophysiology
Assessed by Rhodamine-123 Transport and Fluorescence. Ann Biomed Eng. 35:1276-1285, 2007.
39. Wu F, Yang F, Vinnakota KC, and Beard DA. Computer modeling of mitochondrial TCA cycle, oxidative
phosphorylation, metabolite transport, and electrophysiology. J Biol Chem. 282:24525-24537 2007.
40. Smith JR, Matus IR, Beard DA, and Greene AS. Differential expression of cardiac mitochondrial proteins.
Proteomics 8:446-462, 2008.
41. Beard, DA, Vinnakota KC, and Wu F. Detailed enzyme kinetics in terms of biochemical species: study of
citrate synthase. PLoS One. 3:e1825, 2008.
42. Beard, DA, F Wu, ME Cabrera, and RK Dash. Modeling cellular metabolism and microcirculatory transport.
Microcirculation 26:1 15:777-793, 2008.
43. Secomb, TW, DA Beard, JC Frisbee, NP Smith, and AR Pries. The role of theoretical modeling in
microcirculation research. Microcirculation 15:693-698, 2008.
44. Dash, RK, and DA Beard. Analysis of mitochondrial Na+/Ca2+ exchanger stoichiometry using an integrated
model of mitochondrial Ca2+ handling. J. Physiol. 586:3267-3285, 2008.
45. Heutte, WJ, DA Beard, and H Qian. Linear analysis near a steady state of biochemical networks: Control
analysis, correlation metrics, and circuit theory. BMC Systems Biology 2:44, 2008.
46. Miller, CA and DA Beard. The effects of reversibility and noise on stochastic phosphorylation cycles and
cascades. Biophys J. 95:2183-2192, 2008.
47. Wu, F, J Zhang, RJ Bache, and DA Beard. Phosphate metabolite concentrations and ATP hydrolysis
potential in normal and ischemic hearts. J Physiol. 586:4193-4208, 2008.
48. Qi, F, X Chen, and DA Beard. Detailed kinetics and regulation of mammalian NAD-linked isocitrate
dehydrogenase. Biochim Biophys Acta Proteins and Proteomics. 1784:1641-1651, 2008.
49. Dash, RK, Y Li, J. Kim, DA Beard, GM Saidel, and ME Cabrera. Metabolic dynamics in skeletal muscle
during acute reduction in blood flow and oxygen supply to mitochondria: in-silico studies using a multiscale, top-down integrated model. PLoS ONE. 3:e3168, 2008.
50. Vinnakota, KC, F Wu., MJ Kushmerick, and DA Beard. Multiple ion binding equilibria, reaction kinetics, and
thermodynamics in dynamic models of biochemical pathways. Methods in Enzymology. 454:29-68, 2009.
51. Dash, RK, F. Qi and DA Beard. A biophysically-based mathematical model for the kinetics of mitochondrial
calcium uniporter. Biophys. J. 96:1318-1332, 2009.
52. Vanlier, J, F Wu, F Qi, K C Vinnakota, Y Han, RK Dash, and DA Beard. BISEN: Biochemical simulation
environment. Bioinformatics 25:836-837, 2009.
53. Wu, F, and DA Beard. Roles of the creatine kinase system and myoglobin in maintaining energetic data in
the working heart. BMC Syst Biol. 3:22, 2009.
54. Beard, DA, R Britten, MT Cooling, A Garny, MD Halstead, PJ Hunter, J Lawson, CM Lloyd, J Marsh, A
Miller, D Nickerson, PM Nielsen, T Nomura, S Subramanium, SM Wimalaratne, and T Yu. CellML
metadata: Standards, tools and repositories. Phil. Transact A Math Phys Eng Sci. 367:1845-1867, 2009.
55. Beard, DA and F Wu. Apparent diffusivity and anisotropic dispersion of water in diffusion tensor magnetic
resonance imaging of biological tissues. Bull. Math. Biol. 71:1366-77, 2009.
56. Wu, F, J. Zhang, and DA Beard. Experimentally observed phenomena on cardiac energetics in heart failure
emerge from simulations of cardiac metabolism. Proc Natl Acad Sci USA.106:7143-7148, 2009.
57. Qi, F, RK Dash, Y Han, and DA Beard. Generating rate equations for complex enzyme systems by a
computer-assisted systematic method. BMC Bioinformatics. 10:238, 2009.
58. Xie, D, RK Dash, and DA Beard. An improved algorithm and its parallel implementation for solving a
general blood-tissue transport and metabolism model. J. Comp. Physics. 228: 7850-7861, 2009.
59. Beard, DA, MJ Kushmerick. Strong inference for systems biology. PLoS Comp. Biol. 5: e1000459, 2009.
Research Support
Ongoing Research Support
1 R01 HL72011-06A1 Beard (PI)
9/1/08-6/30/2012
NIH-NHLBI
Title: Integrated Modeling of Cardiac Metabolism and Transport
The major goals of this project are to develop models of cardiac tissue oxygen transport and metabolism and
to analyze experimental data on cardiac oxygen transport, oxidative metabolism, and cellular energetics.
Role: PI
HL82798 – Project 1 - Allen W. Cowley, Jr. (PI)
08/01/2006-7/31/2011
NIH/NHLBI
Title: Genetic & Physiological Basis of Salt-induced Hypertension
Role: Co-Investigator
EFRI-0735903 Sean Palecek (PI)
09/01/2007-8/31/2011
NSF
Title: Regulating human embryonic stem cell differentiation via the mechanical microenvironment
This project will elucidate the mechanisms by which embryonic stem cells (ESCs) integrate
microenvironmental cues and decide whether to self-renew or differentiate along specific developmental
pathways.
Role: Co-Investigator
2 P01GM066730-06 Bosnjak (PI)
08/01/2008-7/31/2013
NIH
Title: Anesthetic-Induced Cardiac Preconditioning; Project II: Mitochondrial Function in Anesthetic Pre
conditioning
The overall objective of this Project is to directly investigate the specific effects of volatile anesthetics on
mitochondrial function that leads to APC.
Role: Co-Investigator
1 RO1 HL094317-01 Beard (PI)
01/01/2009-12/31/2012
NHLBI
Title: Mechanisms of Metabolic Dysfunction in Heart Disease
This project is focused on determining how molecular-level changes in mitochondrial enzymes and
transporters that occur in heart disease affect overall cardiac function and determining how therapies may be
targeted at the molecular level to improve function at the whole-organ level.
Completed
1 R01 GM068610-01 Beard (PI)
8/01/04-7/31/09
NIH-NHLBI
Title: Constraint-Based Analysis of Large-Scale Biochemical Systems
The major goals are to develop computational technology and tools for profiling metabolic regulation in healthy
and disease states.
Role: PI
1 R01 EB005825-01 Beard (PI)8/01/05-7/31/09
NIH-NIBIB
Title: MSM Multiscale Modeling of Heart in Cardiovascular Disease
The major goals of this project are to develop a multi-scale model of cardiac metabolism, linking (1) cellular
and subcellular processes including metabolism and excitation-contraction coupling; (2) coronary blood flow
and blood-tissue exchange of substrates; and (3) tissue mechanics and whole-heart function.
Role: PI