CURRICULUM VITAEtraining.cvrc.virginia.edu/events/746resume.pdf · 2018-04-06 · Winter 2016 STEM Inter-Professional Learning Community (STEM-IPLC) project, ... Xuewen Chen Postdoctoral

Date of Document: April 6, 2018

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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


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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 2017 Berman-Zech Award of the Kinetics and Metabolism Society


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2018 Member of Michigan Academy of Medical Educators

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 Physiology, 2015-Present

• Cellular and Molecular Biology graduate program admission committee, 2016 cycle, 2017 cycle

• M1 Scientific Trunk Lead for Cardiovascular Physiology, 2016- • Taubman Institute Cardiovascular/Medicine Task Force, 2017 • Physiology MS Program Committee

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)


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Summer 2006 Lecturer, Netherlands Organisation for Scientific Research Summer Pro-gramme in Computational Life Sciences, Conferentiehotel Kapellerput, Heeze, NL, 19-22 June, 2006.

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, De-partment of Physiology, Medical College of Wisconsin (100% of course taught)

Spring 2013 Special Topics in Physiology: Classic Papers in Physiology Research, De-partment 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)

Fall 2016, 2017

Cardiovascular sequence for M1 Students, University of Michigan (8 lectures taught); Renal sequence for M1 Students, University of Michigan (1 lecture taught)

Winter 2018 Computational Systems Biology in Physiology (PHYSIOL 520)

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


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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 Biophysics 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- 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


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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 External Reviewer, New Eurasia Foundation, Government of the Russian Federa-

tion 2013-Present Chair, NIH Review Panel for PAR-11-203 Predictive Multiscale Models for Biomedical, Biological, Behavioral, Environmental and Clinical Research 2014 Ad Hoc Reviewer, NIH Review Panel, Modeling and Analysis of Biological Sys-

tems (MABS) 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 2017 Ad Hoc Reviewer, the European Research Council Consolidator Grant 2017 Call

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


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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 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


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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 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


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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

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.


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• 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.

• 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 Bioscienc-es, 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 in-teractions 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 in-teractions 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.


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• 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.

• 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 Symposi-um 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 Cardiovascular 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 Math-ematics Meeting, Mathematical Association of America, American Mathematical Associ-ation, Atlanta, GA. 5 January 2017.

• Multiscale Modeling of Cardiac Metabolism and Mechanics. Departmental Seminar, Physiology, Case Western Reserve University, 6 March 1017.

• The Mechanical-Energetic Basis of Heart Failure. 2nd Annual daVinci Convergence Symposium, Michelson Center for Conergent Bioscience, University of Southern Cali-fornia, 9 March 2017.

• The Control of Energetic Status and Mitochondrial Substrate Utilization in Health and Disease, KinMet Society Annual Meeting, Minneapolis, 3 May 2017.

• Graduate Commencement Address, Boston University College of Engineering, 20 May 2017.


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• Targeting myocardial mechanical-energetic coupling in heart failure, Pfizer Cambridge MA, 15 June 2017.

• Multiscale Modeling in Physiology. Mathworks Corporation, Natick MA, 23 August 2017.

• Targeting myocardial mechanical-energetic coupling in heart failure, Systems Pharma-cology Symposium, Mt. Sinai Icahn School of Medicine, New York, 29 September 2017.

• Myocardial Energy Transduction: From Substrates to Work, Cardiac Physiome Society, Toronto, 7 November 2017.

• Computational systems analysis to predict and analyze targets for improving mechanical-energetic coupling in the myocardium in heart failure, Multi-scale Systems Biology Methods for Studying Biomedical Processes in Patients Under Stress or with Chronic or Acute Diseases, UC Riverside, 15-16 November 2017.

• UC Davis meeting

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 Biolo-gy 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.

• Session Chair, Computational integration of organ physiology, Virtual Physiological Human Conference 2014, Trondheim, 9-12 September 20014.

• Scientific Advisory Committee, Cardiac Physiome 2015, Auckland, 8-10 April 2015. • Scientific Advisory Committee, Cardiac Physiome 2016, Seoul, 23-26 August 2016. • Program Committee/Scientific Advisory Committee, Cardiac Physiome 2017, Toronto 6-

9 November 2017.

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.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=7586234&query_hl=5&itool=pubmed_DocSum


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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 processes 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.

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.















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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-dephosphorylation 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 pharmaco-kinetic 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.

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.


















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35. Smith NP, Crampin EJ, Niederer SA, Bassingthwaighte JB, Beard DA. Computational biolo-gy 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 mito-chondrial 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.

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.



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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. Bi-ol. 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.

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-ubiquinone 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.


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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 estimation 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 explain 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. Pharmacokinet. 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.

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.


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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.

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.


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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. 5:1245-61, 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 30(8):2698-707.

102. Pradhan RK, Feigl EO, Gorman MW, Brengelmann GL, Beard DA. Open-Loop (Feed-Forward) and Feedback Control of Coronary Blood Flow during Exercise Cardiac Pacing and Pressure Changes. Am J Physiol Heart Circ Physiol. 2016 310:H1683-94

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 94:162-75. doi: 10.1016/j.yjmcc.2016.04.003

104. Liu A. KC Vinnakota, T Hacker, J Phillips, D Tabima, F van den Bergh, DA Beard, NC Chesler. Estrogen maintains mitochondrial content and function in the right ventricle of rats with pulmonary hypertension. Physiol Rep. 2017 pii: e13157. doi: 10.14814/phy2.13157

105. Marshall-Colon A et al. Crops in silico: Generating virtual crops using an integrative and multi-scale modeling platform . Frontiers in Plant Science 2017 8:786. doi: 10.3389/fpls.2017.00786

106. Thiagarajan R, Alavi A, Podichetty JT, Bazil JN, Beard DA. The feasibility of genome-scale biological network inference using Graphics Processing Units. Algorithms Mol Biol. 2017 12:8 doi: 10.1186/s13015-017-0100-5


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Chapters & Reviews: 107. 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.

108. 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.

109. 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.

110. 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.

111. 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/society/btol/

112. 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, Spring-er-Verlag, 2004.

113. 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.

114. Beard DA, JB Bassingthwaighte, and AS Greene. Computational modeling of physiological systems. Physiological Genomics 23:1-3, 2005.

115. Beard DA and M Vendelin. Systems biology of the mitochondrion. Am J Physiol Cell Phys-iol. 29:C1101-3, 2006.

116. Beard DA, F Wu, ME Cabrera, and RK Dash. Modeling of cellular metabolism and micro-circulatory transport. Microcirculation 15:777-93, 2008.

117. 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.

118. Beard, DA. Comment on: ‘Dynamic analysis of optimality in myocardial energy metabo-lism under normal and ischemic conditions’. Mol. Sys. Biol. 4:207, 2008.

119. Beard DA, MJ Kushmerick. Strong inference for systems biology. PLoS Comp. Biol. 5: e1000459, 2009.

120. 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.


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121. 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.

122. 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 & challeng-es. Prog. Biophys. Mol. Biol. 104:49-76, 2011.

123. Beard DA, Simulation of cellular biochemical systems. Wiley Interdisciplinary Reviews in Systems Biology and Medicine 3:136-46, 2011.

124. Beard DA, and EO Feigl. Understanding Guyton’s venous return curves. Am. J. Physiol.. 301:H629-H633, 2011.

125. 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.

126. 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.

127. Gjuvsland AB, Vik JO, Beard DA, Hunter PJ, Omholt SW. Bridging the genotype-phenotype gap: what does it take? J Physiol. 591:2055-2066, 2013.

128. 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.

129. Beard DA, Tautology versus Physiology in the Etiology of Hypertension. Physiology 28:270-271, 2013.

130. 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.

131. Belle A, R Thiagarajan, SM Soroushmehr, F Navidi, DA Beard, and K Najarian. Big Data Analytics in Healthcare. Biomed Res Int. 2015:370194, 2015.

132. Bassingthwaighte JB, Raymond GM, Dash RK, Beard DA, Nolan M. The Pathway for Ox-ygen: 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

133. 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; 6:20150076. doi: 10.1098/rsfs.2015.0076

Books:


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134. Beard, DA and H Qian. Chemical Biophysics: Quantitative Analysis of Cellular Systems. Cambridge University Press, 2008.

135. Beard DA. Biosimulation: Simulation of Living Systems. Cambridge University Press, 2012.

Letters to the Editor: 136. 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. 137. Beard DA and EO Feigl. Reply to “Letter to the editor: A return to the venous return con-

troversy: a visual aid for combatants.” Am. J. Physiol. Heart Circ. Physiol. H489, 2013. 138. 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.

139. Beard DA. Tautological Nature of Guyton's Theory of Blood Pressure Control. Am J Hyper-tens. 2017 30:e5. doi: 10.1093/ajh/hpx038

Other: 140. Beard DA. PhD Thesis. Advection and diffusion of substances in tissues containing com-

plex vascular networks. University of Washington, Department of Bioengineering, 1997.

141. 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)

142. 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.

Documents

CURRICULUM VITAEtraining.cvrc.virginia.edu/events/746resume.pdf · 2018-04-06 · Winter 2016 STEM Inter-Professional Learning Community (STEM-IPLC) project, ... Xuewen Chen Postdoctoral