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<html>
<head>
<title>Bibliography</title>
</head>
<body>
<h1>Bibliography</h1>
<b>Books.</b><br>
<ul>
<li>
<a href="http://www.math.ttu.edu/~lallen/stochasticbook.html">
An Introduction to Stochastic Models with Applications to Biology</a>
by
<a href="http://www.math.ttu.edu/~lallen/">Linda Allen</a>
<li>
<a name="cormen2001" href="http://projects.csail.mit.edu/clrs/">
Introduction to Algorithms, Second Edition.</a> by
Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest, and Clifford Stein.
<li>
<a name="devroye1986" href="http://cg.scs.carleton.ca/~luc/rnbookindex.html">
Non-Uniform Random Variate Generation</a> by
<a href="http://cg.scs.carleton.ca/~luc/index.html">Luc Devroye</a>.
<li>
<a name="gillespie1992">Markov Processes: An Introduction for
Physical Scientists</a> by Daniel T. Gillespie. Academic Press,
Boston, 1992.
<li>
<a name="ullah2011"
href="http://www.sbi.uni-rostock.de/publications/books/stochasticapproaches/"</a>Stochastic Approaches for Systems Biology</a> by
<a href="http://www.sbi.uni-rostock.de/team/single/dr-mukhtar-ullah/">Mukhtar
Ullah</a> and
<a href="http://www.sbi.uni-rostock.de/team/single/prof-olaf-wolkenhauer/">Olaf Wolkenhauer</a>.
<li>
<a name="wilkinson2006"
href="http://www.staff.ncl.ac.uk/d.j.wilkinson/smfsb/">
Stochastic Modelling for Systems Biology</a> by
<a href="http://www.staff.ncl.ac.uk/d.j.wilkinson/">Darren Wilkinson</a>.
</ul>
<b>Articles.</b><br>
<ul>
<li>
<a name="cao2004">Yang Cao, Hong Li, and Linda Petzold</a>
"Efficient formulation of the stochastic simulation algorithm for
chemically reacting systems."
Journal of Chemical Physics,
Vol. 121, No. 9, 2004.
<li>
<a name="cao2006a">Yang Cao, Daniel T. Gillespie, and Linda Petzold</a>
"Efficient step size selection for the tau-leaping simulation
method"
Journal of Chemical Physics,
Vol. 124, 2006.
<li>
<a name="cao2006b">Yang Cao and Linda Petzold</a>
"Accuracy limitations and the measurement of errors in the stochastic
simulation of chemically reacting systems."
Journal of Computational Physics,
Vol. 212, 2006, 6-24.
<li>
<a name="gibson2000">Michael A. Gibson and Jehoshua Bruck.</a>
"Efficient Exact Stochastic Simulation of Chemical Systems with
Many Species and Many Channels."
Journal of Physical Chemistry A, Vol. 104, No. 9, 1876-1889, 2000.
<li>
<a name="gillespie1976">Daniel T. Gillespie</a>
"A General Method for Numerically Simulating the Stochastic Time
Evolution of Coupled Chemical Reactions",
Journal of Computational Physics, Vol. 22, No. 4, 1976, 403-434.
<li>
<a name="gillespie1977">Daniel T. Gillespie</a>
"Exact Stochastic Simulation of Coupled Chemical Reactions."
Journal of Physical Chemistry, Vol. 81, No. 25, 1977.
<li>
<a name="gillespie2007">Daniel T. Gillespie</a>
"Stochastic Simulation of Chemical Kinetics"
Annu. Rev. Phys. Chem.,
Vol. 58, 2007, 35-55.
<li>
<a name="kierzek2002">Andrzej M. Kierzek</a>
"STOCKS: STOChastic Kinetic Simulations of biochemical systems with
the Gillespie algorithm"
Bioinformatics, Vol. 18, No. 3, 2002, 470-481.
<li>
<a name="li2006">Hong Li and Linda Petzold</a>
<a href="http://www.engr.ucsb.edu/~cse">"Logarithmic Direct Method for
Discrete Stochastic Simulation of Chemically Reacting Systems"</a>.
Department of Computer Science, University of California, Santa Barbara,
2006.
<li>
<a name="lipshtat2007">Azi Lipshtat</a>
""All possible steps" approach to the accelerated use of
Gillespie's algorithm"
Journal of Chemical Physics,
Vol. 126, No. 18, 2007.
<li>
<a name="matsumoto1998">M. Matsumoto and T. Nishimura</a>
<a href="http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html">
"Mersenne Twister: A 623-dimensionally equidistributed
uniform pseudorandom number generator."</a>
ACM Trans. on Modelling and Computer Simulation,
Vol. 8, No. 1, Jan. 1998, 3-30.
<li>
<a name="marsaglia2000">George Marsaglia and Wai Wan Tsang.</a>
"The ziggurat method for generating random variables."
Journal of Statistical Software,
Vol. 5, 2000, Issue 8.
http://www.jstatsoft.org/v05/i08/
<li>
<a name="mauch2010">Sean Mauch and Mark Stalzer</a>,
<a href="http://link.aip.org/link/?JCPSA6/133/144108/1">
"An efficient method for computing steady state solutions with
Gillespie's direct method,"</a> Journal of Chemical Physics,
Vol. 133, Iss. 14, Num. 144108, Oct. 14, 2010.
<li>
<a name="mauch2011">Sean Mauch and Mark Stalzer</a>,
<a href="http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.47">
"Efficient Formulations for Exact Stochastic Simulation of Chemical
Systems,"</a> IEEE/ACM Transactions on Computational Biology and
Bioinformatics, pp. 27-35, January-February, 2011.
<li>
<a name="mccollum2005">James M. McCollum, Gregory D. Peterson, Chris D. Cox,
Michael L. Simpson, and Nagiza F. Samatova</a>
"The sorting direct method for stochastic simulation of biochemical
systems with varying reaction execution behavior."
Computational Biology and Chemistry,
Vol. 30, No. 1, Feb. 2006, 39-49.
<li>
<a name="proctor2005">C. J. Proctor, C. Soti, R. J. Boys, C. S. Gillespie,
D. P. Shanley, D. J. Wilkinson, and T. B. L. Kirkwood</a>
"Modelling the actions of chaperones and their role in ageing"
Mechanisms of Ageing and Development,
Vol. 126, No. 1, Jan. 2005, 119-131.
<li>
<a name="rubin2006">Herman Rubin and Brad Johnson.</a>
"Efficient generation of exponential and normal deviates."
Journal of Statistical Computation and Simulation, Vol. 76, No. 6,
509-518, 2006.
<li>
<a name="Sehl2009">M. Sehl, A. V. Alekseyenko, K. L. Lange</a>
"Accurate Stochastic Simulation via the Step Anticipation
tau-Leaping (SAL) Algorithm"
Journal of Computational Biology, Vol. 16, Iss. 9, 1195-1208, Sep. 2009.
<li>
<a name="slepoy2008">Alexander Slepoy, Aidan P. Thompson,
and Steven J. Plimpton</a>
"A constant-time kinetic Monte Carlo algorithm for simulation of large
biochemical reaction networks"
Journal of Chemical Physics,
Vol. 128, No. 20, 2008.
</ul>
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