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Date of Document: January 23, 2017
1
CURRICULUM VITAE
Daniel A. Beard, Ph.D.
Professor, Department of Molecular and Integrative Physiology, Department of Medicine, De-
partment of Biomedical Engineering, Department of Emergency Medicine
Carl J. Wiggers Collegiate Professor of Cardiovascular Physiology
Home Address: 3521 Prestwick Court
Ann Arbor, MI 48105
(414) 736-6270
Office Address: North Campus Research Complex
University of Michigan
B10 – A122
2800 Plymouth Rd.
Ann Arbor, MI 48105
Phone: (414) 736-6270
Email: [email protected]
Education:
09/1989-06/1993 B.S., Biomedical Engineering
Boston University, Boston, MA
08/1993-07/1997 M.S., Applied Mathematics
University of Washington, Seattle, WA
08/1993-07/1997 Ph.D., Bioengineering
University of Washington, Seattle, WA
(Mentor: James B. Bassingthwaighte)
Postgraduate Training and Fellowship Appointments:
09/1997-11/2001 Postdoctoral Fellow
Howard Hughes Medical Institute and
Courant Institute of Mathematical Sciences
New York University
New York, NY
(Mentor: Tamar Schlick)
Primary Faculty Appointments:
01/2001-01/2004 Research Assistant Professor,
Department of Bioengineering
University of Washington
Seattle, WA
02/2004-06/2005 Assistant Professor, Department of Physiology
Date of Document: January 23, 2017
2
Biotechnology and Bioengineering Center
Medical College of Wisconsin
Milwaukee, WI
07/2005-06/2009 Associate Professor, Department of Physiology
Biotechnology and Bioengineering Center
Medical College of Wisconsin
Milwaukee, WI
07/2009-08/2013 Professor, Department of Physiology
Biotechnology and Bioengineering Center
Medical College of Wisconsin
Milwaukee, WI
09/2013-Present Professor, Department of Molecular and Integrative Physiology (primary)
Professor, Department of Medicine, Division of Cardiovascular
Medicine (joint)
Professor, Department of Biomedical Engineering (joint)
Professor, Department of Emergency Medicine (joint)
University of Michigan
Ann Arbor, MI
Affiliate Faculty Appointments:
02/2004-Present Affiliate Professor,
Department of Bioengineering
University of Washington
Seattle, WA
04/2006-Present Affiliate Professor,
Department of Biomedical Engineering
University of Wisconsin
Madison, WI
Awards and Honors:
09/1991 Barry M. Goldwater Scholar
06/1993 Tau Beta Pi
01/1998 Howard Hughes Postdoctoral Fellowship
2006 Top-10 Cited Paper in Journal of Theoretical Biology
07-08/2009 Visiting Fellow of the Isaac Newton Institute for Mathematical Sciences,
Cambridge, UK
2010 Fellow of the American Physiological Society, Cardiovascular Section
2014 Inaugural Carl J. Wiggers Collegiate Professor of Cardiovascular Physiology
2014 University of Michigan League of Research Excellence
2015 Fellow of the American Institute for Medical and Biological Engineering
Date of Document: January 23, 2017
3
Committees and Departmental Service (non-UMich):
Department Infrastructure Committee, University of Washington, 2001
Department Building Committee, University of Washington, 2001-2003
Department Advisory Committee, University of Washington, 2002-2003
Co-Director for joint MCW and Marquette University Bioinformatics Graduate Program,
2005-Present
MCW Information Technology Committee, 2008-2010
MCW Research Core Facilities Committee, 2010-2013
Committees and Departmental Service (UMich):
School of Medicine Sequence Director for M1 Cardiovascular Physiology and Renal Phys-
iology, 2015-Present
Cellular and Molecular Biology graduate program admission committee, 2016 cycle, 2017
cycle
M1 Scientific Trunk Lead for Cardiovascular Physiology, 2016-
Teaching Activities:
Fall 1993 Teaching Assistant for Biomedical Instrumentation Bioen 485, Department of
Bioengineering, University of Washington.
Spring 1996 Teaching Assistant for Mass Transport and Exchange in Biology Bioen 550,
University of Washington.
Summer 1997 Lecturer, Summer Workshop in Computer Simulation and Mathematical Mod-
eling, Marquette University, Department of Mathematics, Statistics, and Com-
puter Science.
Spring 2001;
Fall 2002;
Fall 2003
Methods in Molecular Modeling (New course developed), Bioen/Chem 575,
Departments of Bioengineering and Chemistry, University of Washington
(100% of course taught).
Spring 2002;
Spring 2003
Bioengineering Capstone Design, Bioen 480B, University of Washington (50%
of course taught).
Winter 2002;
Winter 2003
Computational Bioengineering, Bioen 485, Bioengineering, University of
Washington (50% of course taught).
Spring 2005 Instructor for basic probability and statistics for Physiological Genomics,
MCW
Spring 2005 Organizer and advisor for weekly Computational Biology Journal Club, MCW
Spring 2005,
2006, 2007
Co-Instructor and course organizer for Seminars in Bioinformatics and Com-
putational Biology, BIIN 17294, MCW (50% of course taught)
Summer 2006 Lecturer, Netherlands Organisation for Scientific Research Summer Pro-
gramme in Computational Life Sciences, Conferentiehotel Kapellerput, Heeze,
NL, 19-22 June, 2006.
Date of Document: January 23, 2017
4
Fall 2006 Theory and Simulation of Biochemical Systems (New course developed), BME
601, Departments of Biomedical Engineering and Chemical and Biological
Engineering, University of Wisconsin Madison (100% of course taught)
Fall 2007 Special Topics in Physiology: Chemical Biophysics of Cellular Processes
PHYS 8275, Department of Physiology, Medical College of Wisconsin (100%
of course taught)
Fall 2009 Computational Methods in Biomedical Research PHYS 8284, Department of
Physiology, Medical College of Wisconsin (3 credit course taught with Profes-
sor Ranjan Dash)
Spring 2011 Systems Biology Master Course (8C060), Department of Biomedical Engineer-
ing, Technical University of Eindhoven, NL (two lectures taught)
Fall 2011 Special Topics in Physiology: Classic Papers in Physiology Research, Depart-
ment of Physiology, Medical College of Wisconsin (100% of course taught)
Spring 2013 Special Topics in Physiology: Classic Papers in Physiology Research, Depart-
ment of Physiology, Medical College of Wisconsin (100% of course taught)
Winter 2015 Computational Systems Biology for Physiologists, Physiology/Bioinformatics
520, University of Michigan (2 lectures and 2 labs taught)
Fall 2015 Renal physiology sequence for M1 Students, University of Michigan (8 lec-
tures taught)
Winter 2016 STEM Inter-Professional Learning Community (STEM-IPLC) project, Educa-
tion 650, University of Michigan (6 hours of lecture/laboratory)
Membership in Professional and Honorary Societies:
Biomedical Engineering Society (BMES), 1999-Present
Society for Industrial and Applied Mathematics (SIAM), 1999- Present
American Physiological Society (APS), 2003- Present
Biophysical Society, 2005- Present
IEEE-EMBS, 2007-Present
Cardiac Physiome Society, 2012-Present
Editorial Boards and Related Experience:
Contributing Member of Faculty of 1000 Biology, Integrative Physiology Section
Volume Editor, Computational Biology and Theory, L. J. DeFelice, Editor-in-Chief, On-Line Bi-
ophysics Textbook, Biophysical Society, Bethesda, MD, 2001-2003
Editor of special issue—Systems Biology of the Mitochondrion—published in Am. J. Physiol.
Cell Biology, January 2007
Associate Editor, PLoS Computational Biology, 2009-
Date of Document: January 23, 2017
5
Editorial Board, Physiological Genomics, 2006-
Editorial Board, Microcirculation, 2008-
Editorial Board, Journal of Biological Chemistry, 2008-
Editorial Board, Mathematical Biosciences, 2009-
Editorial Board, Frontiers in Computational Physiology and Medicine, 2011-
Editorial Board, Biophysical Journal, 2012-
Editorial Board, American Journal of Physiology, Heart and Circulatory Physiology, 2012-
National Elected/Appointed Leadership and Committee Positions:
2002 Ad Hoc Reviewer, NSF Review Panel, Biomedical Engineering
2004 Ad Hoc Reviewer, NIH RFA-ES-04-008
Metabolomics: Application to Environmental Health Research
2004-2008 Member, Mathworks Leadership Council for Computational Biology
2005-2010 Member, NIH Review Panel, Modeling and Analysis of Biological Systems
2006 Member, Level 1 Working Group, Cardiovascular Bioinformatics and
Computational Biology for NHLBI Strategic Planning
2006 Ad Hoc Member, NIH Technology Development Special Emphasis Panel, ZRG1
14A 20L, 29-30 June
2010 Member, Scientific Advisory Board, Coferon Inc.
2010 Member, NIH Review Panel for NIGMS GLUE grants, ZGM1 PPBC-0, 3
December 2010
2010-Present Member Biomedical Engineering Society IUPS (International Union of
Physiological Sciences) committee
2011-2015 Member, NIH Review Panel for NHLBI Systems Biology Systems Biology
Collaborations (PAR-09-214), ZRG1 VH-D
2012-2014 Technology Advisory Board, Milwaukee Institute
2012 Ad Hoc Member, Special Emphasis Panel for Gulf War Research, VHA CO
SPLD), 4 October 2012
2013 Chair, NIH Review Panel for PAR-11-203 Predictive Multiscale Models for
Biomedical, Biological, Behavioral, Environmental and Clinical Research, 26
February 2013
Date of Document: January 23, 2017
6
2014-Present Member, NIH Review Panel, Modeling and Analysis of Biological Systems
2014-Present Member, Advisory Board, National Biomedical Computation Resource
University of California, San Diego
2015 Member, NIH Review Panel for PAR-13-280 NIGMS Program Project Grants, 3
December 2015
2016 Chair, NIH Review Panel for PAR-11-203 Predictive Multiscale Models for
Biomedical, Biological, Behavioral, Environmental and Clinical Research, 11
March 2016
International Elected/Appointed Leadership and Committee Positions:
2005 Ad Hoc Reviewer, Austrian Science Fund
2010 Ad Hoc Reviewer, Estonian Science Foundation
2010-Present Member, Scientific Advisory Committee, Netherlands Consortium for Systems
Biology.
2011-Present Member, Scientific Advisory Board, European Framework Programme 6 Project,
Virtual Physiological Human: Sharing for Healthcare - A Research Environment.
2012-Present Member, Scientific Advisory Board, International Study Group for Systems
Biology
2012/2013 President and Annual Meeting Chair, Cardiac Physiome Society
2013 Panelist for Midterm Review of Federal Ministry of Education Research
(German) Virtual Liver Network
2015-Present External Advisory, University of North Dakota Integrative and Systems Biology
Cluster
Research Grants, Contracts, Awards, Projects (current):
Title: The Virtual Physiological Rat Project
Source: NIH-NIGMS (P50-GM094503)
Role: Principal Investigator
Dates: August 11, 2011-August 10, 2016
Direct Funds: $2,000,000 per year
Title: Mechanisms of Metabolic Dysfunction in Type 2 Diabetes
Date of Document: January 23, 2017
7
Source: NIH-NIDDK (R01-DK095210)
Role: Principal Investigator
Dates: April 15, 2012-March 31, 2017
Direct Funds: $425,000 per year
Title: Coronary Blood Flow: Integrated Theory and Experiments
Source: NIH-NHLBI (U01-HL118738)
Role: Principal Investigator
Dates: April 15, 2012-March 31, 2017
Direct Funds: $500,000 per year
Title: Integrated Modeling of Cardiac Metabolism and Transport
Source: NIH-NHLBI (R01-HL072011)
Role: Principal Investigator
Dates: April 1, 2004-June 30, 2018
Direct Funds: $450,000 per year
Research Grants, Contracts, Awards, Projects (completed):
Title: Mechanisms of Metabolic Disorder in Heart Disease
Source: NIH-NHLBI (R01-HL094317)
Role: Principal Investigator
Dates: December 1, 2008-November 30, 2013
Direct Funds: $200,000 per year
Title: Cations and ROS in Modulating Mitochondrial Function in Normal and
Ischemic Heart
Source: NIH-NHLBI (R01 HL095122)
Role Co-Investigator (PI: Dash/Camara)
Dates: May 1, 2010-April 30, 2014
Title: Genetic & Physiological Basis of Salt-induced Hypertension
Source: NIH-NHLBI (P01 HL82798)
Role: Co-Investigator (PI: Cowley)
Dates: August 1, 2006-July 31, 2011
Title: Regulating human embryonic stem cell differentiation via the mechanical
microenvironment
Source: NSF
Role: Co-Investigator (PI: Sean Palecek, U.W. Madison)
Dates: September 1, 2007-August 31, 2011
Direct Funds: $400,000 per year
Title: Computational Modeling of Mitochondrial Energetics
Source: American Heart Association
Date of Document: January 23, 2017
8
Role: Mentor (PI: Ranjan Dash, MCW)
Dates: July 1, 2007-June 30, 2011
Direct Funds: $60,000 per year
Title: Multiscale Modeling of the Heart in Metabolic Syndrome and
Cardiovascular Disease
Source: NIH-NIBIB (R01 EB005825)
Role: Principal Investigator
Dates: August 1, 2005-July 31, 2009
Direct Funds: $225,000 per year
Title: Constraint-Based Analysis of Large-Scale Biochemical Systems
Source: NIH-NIGMS (R01 GM068610)
Role: Principal Investigator
Dates: August 1, 2004-July 31, 2009
Direct Funds: $250,000 per year
Inventions, Discoveries, Patents:
Provisional patent application “Apparent Diffusivity and Anisotropic Dispersion of Water in Dif-
fusion Tensor Magnetic Resonance Imaging of Biological Tissues” #60/601,335 filed August 13,
2004.
Past Trainees:
Feng Yang Postdoctoral Fellow, 2004-2008 Senior Scientist, Eli Lilly and Comp-
any, Indianapolis, IN
Xuewen Chen Postdoctoral Fellow 2007-2008 Research Assistant Professor, Plant
Sciences Michigan State University
Samhita Rhodes Postdoctoral Fellow 2007 Chair, Biomedical Engineering, Grand
Valley State University
Ranjan Dash Postdoctoral Fellow 2006-2007 Associate Professor, Department of
Physiology, Medical College of Wis-
consin
Fan Wu Postdoctoral Fellow 2006-2011 Senior Scientist, Novartis Corporation,
Parsippany, NJ
Matthew D.
Thompson
Graduate student 2008-2012 NCI Cancer Prevention Fellow, Na-
tional Institutes of Health, Bethesda,
MD
Feng Qi Postdoctoral Fellow 2010-2012 Senior Scientist Lee Moffitt Cancer
Center
Date of Document: January 23, 2017
9
Muriel Mescam Postdoctoral Fellow 2010-2012 Assistant Professor of Biomedical En-
gineering, Université de Toulouse
Kalyan Vinnakota Postdoctoral Fellow 2007-2010
Research Scientist 2011-2013
Research Assistant Professor, Molecu-
lar and Integrative Physiology, Univer-
sity of Michigan
Scott Bugenhagen Graduate MSTP Student 2010-2014 Currently in medical school rotations
Jason Bazil Postdoctoral Fellow 2011-2015 Assistant Professor of Physiology,
Michigan State University
Recent Invited Lectures/Workshops/Presentations (last ten years):
Computational Modeling of Coronary Oxygen Transport and Cardiac Energy Metabo-
lism. Physiology Departmental Seminar, Mt. Sinai School of Medicine, 17 March 2008,
Analysis of coronary oxygen transport and mitochondrial cardiac energy metabolism.
Workshop on Multi-Scale Modelling of the Heart, Auckland, New Zealand, 27-29 March
2008.
Multi-Scale Modeling of Cardiac Energy Metabolism and Coronary Oxygen Transport in
Ischemia. Annual Meeting of the American Physiological Society, San Diego, 9 April
2008.
Integration of mitochondrial and cellular metabolism with tissue-level substrate
transport to explain emergent phenomena on phosphate metabolite concentations and
ATP hydrolysis potential in the heart and Merging Cellular Biochemical Models Using
Physicochemically Rigorous Rules. (two talks) SIAM Conference on the Life Sciences,
Montreal, 4-7 August 2008.
Emergent and Critical Phenomena in Cardiac Energy Metabolism in the Healthy Heart,
in Ischemia, and in the Development of Heart Failure. Distinguished Cardiovascular Lec-
ture Series. UCLA Medical Center. 17 November 2008.
Emergent and Critical Phenomena in Cardiac Energy Metabolism in the Healthy Heart,
in Ischemia, and in the Development of Heart Failure. Lillehei Heart Institute. UMinn
Medical Center. 17 December 2008.
BISEN: Biochemical Simulation Environment. CellML SBGN SBO BioPAX MIASE
Workshop, Auckland, New Zealand. 8 April 2009.
Merging Cellular Biochemical Models Using Physicochemically Rigorous Rules. The
Cardiac Physiome: Multi-scale and Multi-physics Mathematical Modelling Applied to
the Heart. Isaac Newton Institute for Mathematical Sciences, Cambridge, UK, 30 June
2009.
Clinically observed phenomena on cardiac energetics in heart failure emerge from simu-
lations of cardiac metabolism. The Cardiac Physiome: Multi-scale and Multi-physics
Mathematical Modelling Applied to the Heart. Isaac Newton Institute for Mathematical
Sciences, Cambridge, UK, 20 July 2009.
Creatine and Phosphate Pools Are Maintained at Energetically Optimal Levels in the
Heart During Hypertrophic Remodeling and Heart Failure. IEEE Engineering in Medi-
cine and Biology Society, Minneapolis, MN, 5 September 2009.
Date of Document: January 23, 2017
10
Systems Analysis of Metabolic Function in the Heart—from Molecules to Cells to Whole-
Organ Function. Biomathematics Lunchtime Seminar, New York University, New York,
NY, 28 September 2010.
Systems Analysis of Metabolic Function in the Heart—from Molecules to Cells to Whole-
Organ Function. Keynote Lecture, Netherlands Consortium for Systems Biology Annual
Meeting, Soesterberg, NL, 22 October 2010.
Systems Analysis of Metabolic Function in the Heart—Why You Don't Have a Heart At-
tack Every Time You Walk Up a Flight of Stairs. Frontiers in Interdisciplinary Biosci-
ences, Stanford University, 18 November 2010.
Design of Experiments to Probe Mitochondrial Energetics. Systems Biology Theory
Lunchtime Seminar. Department of Systems Biology, Harvard University, 11 February
2011.
Understanding the Genotype-to-Phenotype Map in Cardiovascular Disease. Biomedical
Engineering Departmental Colloquium. Department of Systems Biology, Technical Uni-
versity Eindhoven, 18 March 2011.
Influence of Molecular-Scale Remodeling on Whole-Body Phenotype in the Progression
of Cardiovascular Disease. 4th Cardiac Physiome Workshop, Merton College, Oxford, 8
July 2011.
Multiple-Scale Systems Modeling as a Tool to Probe and Predict Mechanisms of Com-
plex Disease. Keynote Address, Vasculata 2011, Atlanta, GA, 26 July, 2011.
A System Approach to Probe the Electrophysiological Basis of the Myogenic Response.
Vasculata 2011, Atlanta, GA, 28 July, 2011.
Regulation of the ATP hydrolysis potential in cardiac and skeletal muscle. Center for
Systems Biology and Bioenergetics, Nijmegen, Netherlands, 13 February 2012.
The Virtual Physiological Rat project: A National Center for Systems Biology to study
interactions between genes, environmental factors, and physiological systems. Keynote
Address, Bioinformatics and Systems Biology, Lorentz Center, Leiden, Netherlands, 17
February 2012.
The Virtual Physiological Rat project: A National Center for Systems Biology to study
interactions between genes, environmental factors, and physiological systems. Annual
Meeting of National Centers of Systems Biology, University of Chicago, 19 July 2012.
Multi-scale modular modeling of cardiovascular function to probe the etiology of com-
plex cardiovascular disease. Mathematical Biosciences Institute, Molecular to Systems
Physiology, The Ohio State University, Columbus Ohio, 9 May 2014.
Modular multiscale modelling of cardiovascular function to probe the etiology of com-
plex cardiovascular disease, Plenary Talk, Virtual Physiological Human Conference
2014, Trondheim, 9-12 September.
Modular multi-scale modeling of cardiovascular function to probe the etiology of com-
plex cardiovascular disease. Georgia Tech Integrative BioSystems Institute, Distin-
guished Seminar Series, 27 October 2014.
The emergence of heart failure as a consequence of myocardial metabolic dysfunction.
Annual meeting of Biophysical Society, Baltimore, MD, 8 February 2015.
Mechano-energetic link in myocardial dysfunction in heart failure. UW Madison, 9
March 2015.
Date of Document: January 23, 2017
11
Quantitative Systems Physiology and Pharmacology. Pfizer Research Technology Center,
Cambridge, MA, 24 March 2015.
The metabolic contribution to whole-organ mechanical dysfunction in heart failure. In-
ternational Society for Heart Research, Seattle, WA, 8 June 2015.
How to: Computational Modeling of the Cardiovascular System. AHA Council on Hy-
pertension, Washington DC, 17 September 2015.
Two keynote lectures: Introduction to Quantitative Systems Pharmacology and Quantita-
tive Systems Physiology and Pharmacology and Drug Development. Novartis Sympo-
sium on Quantitative and Systems Pharmacology. 16 October 2015.
Modular Multi-Scale Modeling of Cardiovascular Function to Probe the Etiology of
Complex Cardiovascular Disease. Rice University Department of Bioengineering Semi-
nar 24 November 2015.
Systems Biology of Complex Cardiovascular Disease. Keynote Address, Integrative Sys-
tems Biology Seminar, University of North Dakota, 20 April 2016.
The Virtual Physiological Rat Project. Public Lecture, Plants in Silico, University of Illi-
nois Campaign-Urbana, 18 May 2016.
Multi-Scale Modeling of Cardiac Energy Metabolism and Coronary Flow. Cardiac Regu-
latory Mechanisms--Gordon Research Conference. New London NH, 6 June 2016.
Multi-Scale Modeling of Cardiovascular Function to Probe the Etiology of Complex Car-
diovascular Disease. Systems Biology of Complex Disease, Cambridge MA, 14 June
2016.
Multi-Scale Regulation of Coronary Blood Flow. European Society for Mathematical and
Theoretical Biology, Nottingham, UK. 11 July 2016.
Mechanical-Energetic Coupling in Cardiac Contraction and Heart Failure. Joint Mathe-
matics Meeting, Mathematical Association of America, American Mathematical Associa-
tion, Atlanta, GA. 5 January 2017.
Recent Conference Organization:
Organizing Chair, Systems Biology and Bioinformatics Track, 2008 meeting of the Bio-
medical Engineering Society.
Co-Chair, Computational Physiology and the Physiome Project, IEEE Engineering in
Medicine and Biology Society, Minneapolis, MN, 2-6 September 2009.
Co-Chair, Emerging Topics in Computational Bioinformatics and Systems Biology, IEEE
Engineering in Medicine and Biology Society, Minneapolis, MN, 2-6 September 2009.
Chair, Probing Mechanisms of Complex Cardiovascular Disease Using Computational
Modeling, IEEE Engineering in Medicine and Biology Society, San Diego, CA, 28 Au-
gust – 1 September, 2012.
Organizing Committee and Session Chair, International Study Group for Systems Biol-
ogy 2012. Ameland, The Netherlands, September 25-28, 2012.
Meeting Chair, 2013 Cardiac Physiome Workshop, Bar Harbor, Maine, October 17-19,
2013.
Organizer of Current Topics Workshop, Mathematical Biosciences Institute, Molecular
to Systems Physiology, The Ohio State University, Columbus Ohio, May 5-9, 2014.
Date of Document: January 23, 2017
12
Session Chair, Computational integration of organ physiology, Virtual Physiological Hu-
man Conference 2014, Trondheim, 9-12 September 20014.
BIBLIOGRAPHY
Refereed Journal Publications/Original Papers:
1. Bassingthwaighte JB, Beard DA. Fractal 15O-labeled water washout from the heart. Circ Res.
77:1212-21, 1995.
2. Beard DA, Bassingthwaighte JB. Power-law kinetics of tracer washout from physiological
systems. Ann Biomed Eng. 26:775-9, 1998.
3. Beard DA, Bassingthwaighte JB. Advection and diffusion of substances in biological tissues
with complex vascular networks. Ann Biomed Eng. 28:253-68, 2000.
4. Beard DA, Bassingthwaighte JB. The fractal nature of myocardial blood flow emerges from
a whole-organ model of arterial network. J Vasc Res. 37:282-96, 2000.
5. Beard DA, Schlick T. Inertial stochastic dynamics I. Long-timestep methods for Langevin
dynamics. J Chem Phys. 112:7323-7338, 2000.
6. Beard DA, Schlick T. Inertial stochastic dynamics II. Influence of inertia on slow kinetic pro-
cesses of supercoiled DNA. J Chem Phys. 112:7313-7322, 2000.
7. 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.
8. 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, 2001.
9. Beard DA, Schlick T. Computational modeling predicts the structure and dynamics of the
chromatin fiber. Structure. 9:105-14, 2001.
10. Beard DA, Bassingthwaighte JB. Modeling advection and diffusion of oxygen in complex
vascular networks. Ann Biomed Eng. 29:298-310, 2001.
11. Beard DA. Taylor dispersion of a solute in a microfluidic T-Sensor. J. Appl. Phys. 89:4667-
4669, 2001; see comment by KD Dorfman and H Brenner (J. Appl. Phys. 90: 6553-6554,
2001) and response by DA Beard (J. Appl. Phys. 90: 6555-6556, 2001).
12. Beard DA. Computational framework for generating transport models from databases of mi-
crovascular anatomy. Ann Biomed Eng. 29:837-43, 2001.
13. Bassingthwaighte JB, Beard DA, Li Z. The mechanical and metabolic basis of myocardial
blood flow heterogeneity. Basic Res Cardiol. 96:582-94, 2001.
14. Beard DA, Liang SD, Qian H. Energy balance for analysis of complex metabolic networks.
Biophys J. 83:79-86, 2002.
15. Price ND, Famili I, Beard DA, Palsson BO. Extreme pathways and Kirchhoff's second law.
Biophys J. 83:2879-82, 2002.
Date of Document: January 23, 2017
13
16. Qian H, Beard DA, Liang SD. Stoichiometric network theory for nonequilibrium biochemi-
cal systems. Eur J Biochem. 270:415-21, 2003.
17. Beard DA, Schlick T. Unbiased rotational moves for rigid-body dynamics. Biophys J.
85:2973-6, 2003.
18. 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. 2003
Nov;285(5):H1819-25.
19. 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:H1826-36, 2003.
20. 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. 24:2063-74, 2003.
21. Beard DA, Babson E, Curtis E, Qian H. Thermodynamic constraints for biochemical net-
works. J Theor Biol. 228:327-33, 2004.
22. Beard DA, Qian H. Thermodynamic-based computational profiling of cellular regulatory
control in hepatocyte metabolism. Am J Physiol Endocrinol Metab. 288:E633-44, 2005.
23. Qian H, Beard DA. Thermodynamics of stoichiometric biochemical networks in living sys-
tems far from equilibrium. Biophys Chem. 114:213-20, 2005.
24. Ejike JC, Arakaki LS, Beard DA, Ciesielski WA, Feigl EO, Schenkman KA. Myocardial ox-
ygenation and adenosine release in isolated guinea pig hearts during changes in contractility.
Am J Physiol Heart Circ Physiol. 288:H2062-7, 2005.
25. Yang F, Qian H, Beard DA. Ab initio prediction of thermodynamically feasible reaction di-
rections from biochemical network stoichiometry. Metab Eng. 7:251-9, 2005.
26. Beard DA. A biophysical model of the mitochondrial respiratory system and oxidative phos-
phorylation. PLoS Comput Biol. 1:e36, 2005.
27. 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. 120:121-34, 2006.
28. Qian H, Beard DA. Metabolic futile cycles and their functions: a systems analysis of energy
and control. Syst Biol (Stevenage). 153:192-200, 2006.
29. Sarkar A, Beard DA, Franza BR. Effect of binding in cyclic phosphorylation-dephosphoryla-
tion process and in energy transformation. Math Biosci. 202:175-93, 2006.
30. Yang F, Tong X, McCarver DG, Hines RN, Beard DA. Population-based analysis of metha-
done distribution and metabolism using an age-dependent physiologically based pharmacoki-
netic model. J Pharmacokinet Pharmacodyn. 33:485-518, 2006.
31. Beard DA. Modeling of oxygen transport and cellular energetics explains observations on in
vivo cardiac energy metabolism. PLoS Comput Biol. 2:e107, 2006.
Date of Document: January 23, 2017
14
32. Wu F, Jeneson JA, Beard DA. Oxidative ATP synthesis in skeletal muscle is controlled by
substrate feedback. Am J Physiol Cell Physiol. 292:C115-24, 2007.
33. Beard DA, Qian H. Relationship between Thermodynamic Driving Force and One-Way
Fluxes in Reversible Processes. PLoS ONE. 2:e144, 2007.
34. Huang M, Camara AK, Stowe DF, Qi F, Beard DA. Mitochondrial inner membrane electro-
physiology assessed by rhodamine-123 transport and fluorescence. Ann Biomed Eng.
35:1276-85, 2007.
35. 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.
36. 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.
37. Wu, F., F Yang, KC Vinnakota, and D. Beard, Computer modeling of mitochondrial TCA
cycle, oxidative phosphorylation, metabolite transport, and electrophysiology. J Biol Chem.
282:24525-24537, 2007.
38. Smith JR, IR Matus, DA Beard, and AS Greene. Differential expression of cardiac mitochon-
drial proteins. Proteomics 8:446-462, 2008.
39. Beard DA, KC Vinnakota, and F Wu. Detailed enzyme kinetics in terms of biochemical spe-
cies: study of citrate synthase. PLoS One. 3:e1825, 2008.
40. Dash, RK, and DA Beard. Analysis of cardiac mitochondrial Na+-Ca2+ exchanger kinetics
with a biophysical model of mitochondrial Ca2+ handing suggests a 3:1 stoichiometry. J.
Physiol. 586:3267-3285, 2008.
41. Heutte, WJ, DA Beard, and H Qian. Linear analysis near a steady state of biochemical net-
works: Control analysis, correlation metrics, and circuit theory. BMC Systems Biology 2:44,
2008.
42. Miller, CA and DA Beard. The effects of reversibility and noise on stochastic phosphoryla-
tion cycles and cascades. Biophys J. 95:2183-2192, 2008.
43. Wu, F, EY Zhang, 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.
44. 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.
45. 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.
Date of Document: January 23, 2017
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46. Vinnakota, KC, F Wu., MJ Kushmerick, and DA Beard. Multiple ion binding equilibria, re-
action kinetics, and thermodynamics in dynamic models of biochemical pathways. Methods
in Enzymology. 454:29-68, 2009.
47. 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.
48. Wu, F, and DA Beard. Roles of the creatine kinase system and myoglobin in maintaining en-
ergetic state in the working heart. BMC Systems Biology 3:22, 2009.
49. Vanlier, J, F Wu, F Qi, K C Vinnakota, Y Han, RK Dash, and DA Beard. BISEN: Biochemi-
cal simulation environment. Bioinformatics 25:836-837, 2009.
50. 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.
51. Beard, DA and F Wu. Apparent diffusivity and anisotropic dispersion of water in diffusion
tensor magnetic resonance imaging of biological tissues. Bull. Math. Biol. 71:1366-1377,
2009.
52. 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.
53. Qi, F, RK Dash, Y Han, and DA Beard. Generating rate equations for complex enzyme sys-
tems by a computer-assisted systematic method. BMC Bioinformatics 10:238, 2009.
54. 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.
55. Beard, DA and F Wu. Creatine and phosphate pools are maintained at energetically opti-
mallevels in the heart during hypertrophic remodeling and heart failure. IEEE Eng. Med.
Biol. Soc. 2009:4487-4490, 2009.
56. Vinnakota KC, DA Beard, and RK Dash. Design of experiments for identification of com-
plex biochemical systems with applications to mitochondrial bioenergetics. IEEE Eng. Med.
Biol. Soc. 2009: 4171-4174, 2009.
57. Pradhan RK, DA Beard DA, and RK Dash. A biophysically based mathematical model for
the kinetics of mitochondrial Na+-Ca2+ antiporter. Biophys J. 98:218-30, 2010.
58. Li, X, RK Dash, RK Pradhan, F Qi, MD Thompson, KC Vinnakota, F Wu, F Yang, and DA
Beard. A database of thermodynamic quantities for the reactions of glycolysis and the tricar-
boxylic acid cycle. J. Phys. Chem. B 114:16068-82, 2010.
59. Vinnakota, KC, DA Mitchell, RJ Deschenes, T Wakatsuki, and DA Beard. Single and dually
lipidated Ras2 show diffusion-dominant mobility in Saccharomyces cerevisiae plasma mem-
brane. Phys. Biol. 7:026044, 2010.
Date of Document: January 23, 2017
16
60. Bugenhagen, SB, AW Cowley Jr., and DA Beard. Identifying physiological origins of baro-
reflex dysfunction in salt-sensitive hypertension in the Dahl SS rat. Physiol. Genomics 42:23-
41, 2010.
61. Haumann, J, RK Dash, DF Stowe, AD Boelens, DA Beard, and AK Camara. Mitochondrial
free [Ca2+] increases during ATP/ADP antiport and ADP phosphorylation: Exploration of
mechanisms. Biophys. J. 99:997-1006, 2010.
62. Chen X, F Qi, RK Dash, and DA Beard. Kinetics and regulation of mammalian NADH-ubiq-
uinone oxidoreductase (Complex I). Biophys. J. 5: 1426-1436, 2010.
63. Pradhan RK, F Qi F, DA Beard, and RK Dash. Characterization of membrane potential de-
pendency of mitochondrial Ca2+ uptake by an improved biophysical model of mitochondrial
Ca2+ uniporter. PLoS One. 5:e13278, 2010.
64. Vinnakota, KC, and DA Beard. Kinetic analysis and design of experiments to identify the
catalytic mechanism monocarboxylate transporter isoforms 4 and 1. Biophys J. 100:369-380,
2011.
65. Mescam, M, KC Vinnakota, and DA Beard. Identification of the catalytic mechanism and es-
timation of kinetic parameters for fumarase. J. Biol. Chem. 286:21100-21109, 2011.
66. Vinnakota, KC, and DA Beard. Stimulatory effect of calcium on respiration or NADH syn-
thesis in intact rat heart mitochondria utilizing physiological substrates is not sufficient to ex-
plain respiratory control in vivo. J. Biol. Chem. 286:30816-30822, 2011.
67. Carlson, BE, and DA Beard. Mechanical control of cation channels in the myogenic re-
sponse. Am. J. Physiol. 301:H331-H343, 2011.
68. Li, X, and DA Beard. A database of thermodynamic properties of the reactions of glycolysis,
the tricarboxylic acid cycle, and the pentose phosphate pathway. Database (Oxford)
2011:bar005.
69. Frisbee, JC, F Wu, and DA Beard. Spatial heterogeneity in skeletal muscle microvascular
perfusion distribution is increased in the metabolic syndrome. Am J Physiol Regul Integr
Comp Physiol. 301:R975-86, 2011.
70. Wu, F, DA Beard, and JC Frisbee. Computational analyses of intravascular tracer washout
reveal altered capillary-level flow distributions in obese Zucker rats. J. Physiol. 589:4527-43,
2011.
71. Thompson, MD and DA Beard. Development of appropriate equations for physiologically-
based pharmacokinetic modeling of permeability-limited and flow-limited transport. J. Phar-
macokinet. Pharmacodyn. 38:405-421, 2011.
72. Qi, F, RK Pradhan, RK Dash, and DA Beard. Detailed kinetics and regulation of mammalian
2-oxoglutarate dehydrogenase. BMC Biochemistry 12:53, 2011.
73. Pradhan, RK, F Qi, DA Beard, and RK Dash. Characterization of Mg2+ inhibition of mito-
chondrial Ca2+ uptake by a mechanistic model of mitochondrial Ca2+ uniporter. Biophys. J.
101:2071-2081, 2011.
Date of Document: January 23, 2017
17
74. Bazil, JN, F Qi, and DA Beard. A parallel algorithm for reverse engineering of biological
networks. Integrative Biology 3:1215-1223, 2011.
75. Thompson, MD and DA Beard. Physiologically based pharmacokinetic tissue compartment
model selection in drug development and risk assessment. J. Pharm. Sci. 101:424-35, 2012.
76. Thompson, MD, DA Beard, and F Wu. Use of partition coefficients in flow-limited physio-
logically based pharmacokinetic modeling. J. Pharmacokinet. Pharmacodyn. 39:313-327,
2012.
77. Beard DA, and M Mescam. Mechanisms of pressure-diuresis and pressure-natriuresis in Dahl
salt-resistant and Dahl salt-sensitive rats. BMC Physiol. 12:6, 2012.
78. Bugenhagen, SM, and DA Beard. Specification, construction, and exact reduction of state
transition system models of biochemical processes. J. Chem. Phys. 137:154108, 2012.
79. Beard DA, ML Neal, N Tabesh-Saleki, CT Thompson, JB Bassingthwaighte, M Shimoyama,
and BE Carlson. Multiscale modeling and data integration in the Virtual Physiological Rat
Project. Ann. Biomed. Eng. 40:2379-2398, 2012.
80. Tewari, SG, RK Dash, DA Beard, and JN Bazil. A biophysical model of the mitochondrial
ATP-Mg/Pi carrier. Biophys. J. 103:1616-1625 2012.
81. Li, X, F Wu, and DA Beard. Identification of the kinetic mechanism of succinyl-CoA synthe-
tase. Bioscience Reports 33 / art:e00014 / BSR20120069, 2013.
82. Bazil JN, KC Vinnakota, F Wu, and DA Beard. Analysis of the kinetics and bistability of
ubiquinol:cytochrome c oxidoreductase. Biophys. J. 105:343-55, 2013.
83. Tewari SG, Bugenhagen SM, Wang Z, Schreier DA, Carlson BE, Chesler NC, and Beard
DA. Analysis of cardiovascular dynamics in pulmonary hypertensive C57BL6/J mice. Fron-
tiers in Physiology 2013; 4:355. doi: 10.3389/fphys.2013.00355
84. Menzies RI, RJ Unwin, K Dash, DA Beard, AW Cowley, BE Carlson, JJ Mullins, MA Bai-
ley. Effect of P2X4 and P2X7 receptor antagonism on the pressure diuresis relationship in
rats, Frontiers in Renal and Epithelial Physiology. 4:305. doi: 10.3389/fphys.2013.00305
85. Beard DA, KH Pettersen, BE Carlson, SW Omholt, and SM Bugenhagen. A Computational
Analysis of the Long-Term Regulation of Arterial Pressure. F1000 Research 2013, 2:208
doi: 10.12688/f1000research.2-208.v1 http://f1000r.es/1xq
86. Pettersen KH, SM Bugenhagen, J Nauman, DA Beard, and SW Omholt. Arterial stiffening
provides sufficient explanation for primary hypertension. PLoS Comput Biol. 2014
10:e1003634.
87. Bazil JN, Stamm KD, Li X, Nelson TJ, Tomita-Mitchell A, Beard, DA. The Inferred Cardio-
genic Gene Regulatory Network in the Mammalian Heart. PLoS One. 2014 9:e100842.
88. Bazil JN, Pannala VR, Dash RK, Beard DA. Determining the origins of superoxide and hy-
drogen peroxide in the mammalian NADH:ubiquinone oxidoreductase. Free Radic Biol Med.
77:121-9, 2014.
89. Moxley MA, DA Beard, JN Bazil. A pH-dependent Kinetic Model of Dihydrolipoamide De-
hydrogenase from Multiple Organisms. Biophys. J. 107:2984-98, 2014.
Date of Document: January 23, 2017
18
90. Dasika SK, KC Vinnakota, DA Beard. Determination of the Catalytic Mechanism for Mito-
chondrial Malate Dehydrogenase. Biophys. J. 108:408-19, 2015
91. Dasika SK, KC Vinnakota, DA Beard. Characterization of the Kinetics of Cardiac Cytosolic
Malate Dehydrogenase and Comparative Analysis of Cytosolic and Mitochondrial Isoforms.
Biophys J. 108:420-30, 2015
92. Tewari S, Y Zho, B Otto, RK Dash, W Kwok, and DA Beard. Markov chain Monte Carlo
based analysis of post-translationally modified VDAC1 gating kinetics. Frontiers in Physiol-
ogy 5:513, 2015; doi: 10.3389/fphys.2014.00513
93. Tewari SG, SM Bugenhagen, BM Palmer, and DA Beard. Dynamics of cross-bridge cycling,
ATP hydrolysis, force generation, and deformation in cardiac muscle. J. Mol. Cell. Cardiol.
96:11-25, 2015.
94. Bugenhagen, SM, and DA Beard. Computational analysis of the regulation of Ca2+ dynamics
in rat ventricular myocytes. Physical Biol. 12:056008 2015.
95. Fan F, Chen CC, Zhang J, Schreck CM, Roman EA, Williams JM, Hirata T, Sharma M,
Beard DA, Savin VJ, Roman RJ. Fluorescence dilution technique for measurement of albu-
min reflection coefficient in isolated glomeruli. Am J Physiol Renal Physiol. 309:F1049-59.,
2015.
96. Moxley MA, DA Beard, JN Bazil. Global Kinetic Analysis of Mammalian E3 Reveals pH-
dependent NAD+/NADH Regulation, Physiological Kinetic Reversibility, and Catalytic Op-
timum. J Biol Chem. 291:2712-30, 2016.
97. Lee P, Carlson BE, Chesler N, Olufsen MS, Qureshi MU, Smith NP, Sochi T, Beard DA.
Heterogeneous mechanics of the mouse pulmonary arterial network. Biomech Model Mecha-
nobiol. (in press) 2016.
98. Vinnakota KC, A Singhal, F Van den Bergh, M Oskouei, RW Wiseman DA Beard. Open-
Loop Stimulation by Calcium Contributes to Control of Oxidative Phosphorylation in Skele-
tal Muscle Mitochondria but not in Cardiac Mitochondria. Biophys J. 110:954-61, 2016.
99. Vinnakota KC, JN Bazil, DA Beard. Feedback Regulation and Time Hierarchy of Oxidative
Phosphorylation in Cardiac Mitochondria. Biophys J. 110:972-80, 2016.
100. Bazil JN, KC Vinnakota, DA Beard. Catalytic Coupling of Oxidative Phosphorylation, ATP
Demand, and Mitochondrial Reactive Oxygen Species Generation. Biophys J. 110:962-71,
2016.
101. 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 J. 2016 Apr 13. pii: fj.201500118R. [Epub
ahead of print]
102. Pradhan RK, Feigl EO, Gorman MW, Brengelmann GL, Beard DA. Open-Loop (Feed-For-
ward) and Feedback Control of Coronary Blood Flow during Exercise Cardiac Pacing and
Pressure Changes. Am J Physiol Heart Circ Physiol. 2016 Apr 1:ajpheart.00663.2015. doi:
10.1152/ajpheart.00663.2015. [Epub ahead of print]
Date of Document: January 23, 2017
19
103. 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.
J Mol Cell Cardiol. 2016 Apr 13. pii: S0022-2828(16)30069-4. doi:
10.1016/j.yjmcc.2016.04.003. [Epub ahead of print]
Chapters & Reviews:
104. Bassingthwaighte, JB, and DA Beard. Fractal organization of the coronary vasculature. Pro-
ceedings of the National Heart, Lung, and Blood Institute's Meeting on Coronary Vascula-
ture, edited by W. Chilian. Bethesda, MD, 1995.
105. Bassingthwaighte, JB, DA Beard, DB Percival, and GM Raymond. Fractal structures and
processes, in Chaos and the Changing Nature of Science and Medicine: An Introduction, ed-
ited by D. E. Herbert. AIP Press, Woodbury, NY, 1996.
106. Bassingthwaighte, JB, DA Beard, and RB King. 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.
107. Bassingthwaighte, JB, DA Beard, Z Li, and T Yipintsoi. 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.
108. Beard DA, A Molecular Modeler's Guide to Statistical Mechanics (2001) in D. A. Beard,
editor, Computational Biology and Theory, L. J. DeFelice, editor-in-chief, On-Line Biophys-
ics Textbook, Biophysical Society, Bethesda, MD http://www.biophysics.org/biophys/soci-
ety/btol/
109. Beard DA, H Qian, and JB Bassingthwaighte. Stoichiometric foundation of large-scale bio-
chemical systems analysis, in Modeling in Molecular Biology, edited by G. Ciobanu,
Springer-Verlag, 2004.
110. Beard DA, and H Qian. Constraint-based modeling of metabolomic systems, in Encyclope-
dia of Genomics, Proteomics and Bioinformatics, edited by M. Dunn, L. Jorde, P. Little, and
S. Subramaniam, John Wiley & Sons, Ltd., 2004.
111. Beard DA, JB Bassingthwaighte, and AS Greene. Computational modeling of physiological
systems. Physiological Genomics 23:1-3, 2005.
112. Beard DA and M Vendelin. Systems biology of the mitochondrion. Am J Physiol Cell Phys-
iol. 29:C1101-3, 2006.
113. Beard DA, F Wu, ME Cabrera, and RK Dash. Modeling of cellular metabolism and micro-
circulatory transport. Microcirculation 15:777-93, 2008.
114. Secomb, TW, DA Beard, JC Frisbee, NP Smith, and AR Pries. The role of theoretical mod-
eling in microcirculation research. Microcirculation 15:963-698, 2008.
115. Beard, DA. Comment on: ‘Dynamic analysis of optimality in myocardial energy metabo-
lism under normal and ischemic conditions’. Mol. Sys. Biol. 4:207, 2008.
Date of Document: January 23, 2017
20
116. Beard DA, MJ Kushmerick. Strong inference for systems biology. PLoS Comp. Biol. 5:
e1000459, 2009.
117. Jol, S, A Kümmel, V Hatzimanikatis, DA Beard, M Heinemann. Thermodynamic calcula-
tion for biochemical transport and reaction processes. Biophys. J. 99:3139-3144, 2010.
118. Fink, M, SA Niederer, EM Cherry, FH Fenton, JT Koivumäki, G Seemann, R Thulf, H
Zhangg, FB Sachse, DA Beard, EJ Crampin, NP Smith. Cardiac cell modelling: Observations
from the heart of the cardiac physiome project. Prog. Biophys. Mol. Biol. 104:2-21, 2011.
119. Waters, SL, J Alastruey-Arimon, DA Beard, PHM Bovendeerd, PF Davies, G Jayaraman,
OE Jensen, J Lee, KH Parker, AS Popel, TW Secomb, SJ Sherwin, RJ Shipley, NP Smith, F
van de Vosse. Theoretical models for coronary vascular biomechanics: progress & chal-
lenges. Prog. Biophys. Mol. Biol. 104:49-76, 2011.
120. Beard DA, Simulation of cellular biochemical systems. Wiley Interdisciplinary Reviews in
Systems Biology and Medicine 3:136-46, 2011.
121. Beard DA, and EO Feigl. Understanding Guyton’s venous return curves. Am. J. Physiol..
301:H629-H633, 2011.
122. Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cool-
ing MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C,
Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H,
Snoep JL, Tolle D, Wolkenhauer O, Le Novère N. Minimum Information About a Simula-
tion Experiment (MIASE). PLoS Comput. Biol. 7:e1001122, 2011.
123. Bassingthwaighte JB, DA Beard, BE Carlson, RK Dash, KC Vinnakota. Modeling to link
regional myocardial work, metabolism, and blood flows. Ann. Biomed. Eng. 40:2365-2378,
2012.
124. Gjuvsland AB, Vik JO, Beard DA, Hunter PJ, Omholt SW. Bridging the genotype-pheno-
type gap: what does it take? J Physiol. 591:2055-2066, 2013.
125. Pradhan, RK, KC Vinnakota, DA Beard, and RK Dash. Carrier-mediated transport through
biomembranes, in Transport in Biological Media, edited by SM Becker and AV Kuznetsov.
Academic Press, Oxford UK, 2013.
126. Beard DA, Tautology versus Physiology in the Etiology of Hypertension. Physiology
28:270-271, 2013.
127. Beard DA and EO Feigl. CrossTalk opposing view: Guyton's venous return curves should
not be taught. J. Physiol. 191:5795-5797. Rebuttal from Beard and Feigl, J Physiol 191:5801,
2013.
128. Belle A, R Thiagarajan, SM Soroushmehr, F Navidi, DA Beard, and K Najarian. Big Data
Analytics in Healthcare. Biomed Res Int. 2015:370194 2015.
129. Bassingthwaighte JB, Raymond GM, Dash RK, Beard DA, Nolan M. The Pathway for Oxy-
gen: Tutorial Modelling on Oxygen Transport from Air to Mitochondrion : The Pathway for
Oxygen. Adv Exp Med Biol. 2016;876:103-10. doi: 10.1007/978-1-4939-3023-4_13
Date of Document: January 23, 2017
21
130. 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 Fo-
cus. 2016 Apr 6;6(2):20150076. doi: 10.1098/rsfs.2015.0076
Books:
131. Beard, DA and H Qian. Chemical Biophysics: Quantitative Analysis of Cellular Systems.
Cambridge University Press, 2008.
132. Beard DA. Biosimulation: Simulation of Living Systems. Cambridge University Press, 2012.
Letters to the Editor:
133. Beard DA. Point:Counterpoint Muscle lactate and H+ production do / do not have a 1:1 as-
sociation in skeletal muscle. J. Appl Physiol. 110:1493, 2011.
134. Beard DA and EO Feigl. Reply to “Letter to the editor: A return to the venous return contro-
versy: a visual aid for combatants.” Am. J. Physiol. Heart Circ. Physiol. H489, 2013.
135. Pannala V, DA Beard, and RK Dash: Letter to the Editor: "Mitochondrial cytochrome c oxi-
dase: mechanism of action and role in regulating oxidative phosphorylation” J Appl Phys-
iol. 119:157, 2015.
Other:
136. Beard DA. PhD Thesis. Advection and diffusion of substances in tissues containing com-
plex vascular networks. University of Washington, Department of Bioengineering, 1997.
137. Levchenko, VV, R Fleming, H Qian, and DA Beard. An annotated English translation of
‘Kinetics of stationary reactions’ [M. I. Temkin, Dokl. Akad. Nauk SSSR. 152, 156 (1963)].
arXiv:1001.2861v1 (http://arxiv.org/abs/1001.2861)
138. Beard DA, Review of ‘Physiology, Biophysics, and Biomedical Engineering’ Wood et al.
Florida, USA: CRC Press Talyor & Francis Group (2012), The Physiologist 55: 209, 2012.