Daniel A. Beard

Peter J. Hunter, Andrew Miller, David P. Nickerson, 2009, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

Computational challenges in simulating large DNA over long times

Jing Huang, Tamar Schlick, Xiaoliang Qian, 2000, Comput. Sci. Eng..

A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation

Daniel A. Beard, D. Beard, 2005, PLoS Comput. Biol..

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm

Qing Zhang, Tamar Schlick, Daniel A. Beard, 2003, J. Comput. Chem..

Big Data Analytics in Healthcare

Kayvan Najarian, Ashwin Belle, Daniel A. Beard, 2015, BioMed research international.

Development of appropriate equations for physiologically based pharmacokinetic modeling of permeability-limited and flow-limited transport

Daniel A. Beard, Matthew D. Thompson, D. Beard, 2011, Journal of Pharmacokinetics and Pharmacodynamics.

Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart

Fan Wu, Daniel A. Beard, D. Beard, 2009, BMC Systems Biology.

Generating rate equations for complex enzyme systems by a computer-assisted systematic method

Feng Qi, Yu Han, Ranjan K. Dash, 2009, BMC Bioinformatics.

Systems-level computational modeling demonstrates fuel selection switching in high capacity running and low capacity running rats

Daniel A. Beard, Jason N. Bazil, Michael A. Moxley, 2018, PLoS Comput. Biol..

A database of thermodynamic properties of the reactions of glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway

Fan Wu, Xin Li, Feng Qi, 2011, Database J. Biol. Databases Curation.

Chemical Biophysics: Introduction

Hong Qian, Daniel A. Beard, 2008 .

Specification, Construction, and Exact Reduction of Finite State Transition System Models of Biochemical Processes

Daniel A. Beard, Scott M. Bugenhagen, 2012 .

The feasibility of genome-scale biological network inference using Graphics Processing Units

Amir Alavi, Jagdeep T. Podichetty, Daniel A. Beard, 2017, Algorithms for Molecular Biology.

BISEN: Biochemical Simulation Environment

Fan Wu, Feng Qi, Yu Han, 2009, Bioinform..

A Parallel Algorithm for Reverse Engineering Gene Regulatory Networks

Feng Qi, Daniel A. Beard, Jason N. Bazil, 2012 .

Strong Inference for Systems Biology

Daniel A. Beard, Martin J. Kushmerick, M. Kushmerick, 2009, PLoS Comput. Biol..

Minimum Information About a Simulation Experiment (MIASE)

Edmund J. Crampin, Olaf Wolkenhauer, Peter J. Hunter, 2011, PLoS Comput. Biol..

Chemical Biophysics: Bibliography

Hong Qian, Daniel A. Beard, 2008 .

Biosimulation: Appendices: mathematical and computational techniques

Daniel A. Beard, 2012 .

Metabolic Dynamics in Skeletal Muscle during Acute Reduction in Blood Flow and Oxygen Supply to Mitochondria: In-Silico Studies Using a Multi-Scale, Top-Down Integrated Model

Gerald M. Saidel, Ranjan K. Dash, Daniel A. Beard, 2008, PloS one.

The mechanical and metabolic basis of myocardial blood flow heterogeneity

James B. Bassingthwaighte, Daniel A. Beard, J. Bassingthwaighte, 2001, Basic Research in Cardiology.

The Fractal Nature of Myocardial Blood Flow Emerges from a Whole-Organ Model of Arterial Network

James B. Bassingthwaighte, Daniel A. Beard, J. Bassingthwaighte, 2000, Journal of Vascular Research.

Detailed Enzyme Kinetics in Terms of Biochemical Species: Study of Citrate Synthase

Daniel A. Beard, K. Vinnakota, D. Beard, 2008, PloS one.

Fractal structures and processes

Donald B. Percival, Gary M. Raymond, James B. Bassingthwaighte, 1996 .

A computational analysis of the long-term regulation of arterial pressure

Stig W. Omholt, Klas H. Pettersen, Brian E. Carlson, 2013, F1000Research.

Computational biology of cardiac myocytes: proposed standards for the physiome

Edmund J. Crampin, Nicolas P. Smith, James B. Bassingthwaighte, 2007, Journal of Experimental Biology.

Chemical Biophysics: Biochemical reaction networks

Hong Qian, Daniel A. Beard, 2008 .

Constraint‐based modeling of metabolomic systems

Hong Qian, Daniel A. Beard, H. Qian, 2005 .

The Inferred Cardiogenic Gene Regulatory Network in the Mammalian Heart

Xing Li, Daniel A. Beard, Jason N. Bazil, 2013, PloS one.

Chemical Biophysics: Conventions and calculations for biochemical systems

Hong Qian, Daniel A. Beard, 2008 .

Inertial stochastic dynamics. I. Long-time-step methods for Langevin dynamics

Tamar Schlick, Daniel A. Beard, T. Schlick, 2000 .

Modeling Advection and Diffusion of Oxygen in Complex Vascular Networks

James B. Bassingthwaighte, Daniel A. Beard, J. Bassingthwaighte, 2001, Annals of Biomedical Engineering.

Inertial stochastic dynamics. II. Influence of inertia on slow kinetic processes of supercoiled DNA

Tamar Schlick, Daniel A. Beard, T. Schlick, 2000 .

Taylor dispersion of a solute in a microfluidic channel

Daniel A. Beard, D. Beard, 2001 .

Heterogeneous mechanics of the mouse pulmonary arterial network

Taha Sochi, M. Umar Qureshi, Mette S. Olufsen, 2016, Biomechanics and modeling in mechanobiology.

Advection and Diffusion of Substances in Biological Tissues With Complex Vascular Networks

James B. Bassingthwaighte, Daniel A. Beard, J. Bassingthwaighte, 2000, Annals of Biomedical Engineering.