Computer Methods, Part C

<ol> <li>Predicting Fluorescence Lifetimes and Spectra of Biopolymers</li> <p>Patrik R. Callis</p> <p> <li>Modeling of Regulatory Networks: Theory and Applications in the study of the Drosophila Circadian Clock</li> <p>Elizabeth Y. Scribner, Hassan M. Fathallah-Shaykh</p> <p> <li>Strategies for articulated multibody-based adaptive coarse grain simulation of RNA</li> <p>Mohammad Poursina, Kishor D. Bhalerao, Samuel C. Flores , Kurt S. Anderson, Alain Laederach</p> <p> <li>Modeling Loop Entropy</li> <p>Gregory S. Chirikjian</p> <p> <li>Inferring Functional Relationships and Causal Network Structure from Gene Expression Profiles</li> <p>Radhakrishnan Nagarajan</p> <p> <li>Numerical solution of the chemical master equation: uniqueness and stability of the stationary distribution for chemical networks, and mRNA bursting in a gene network with negative feedback regulation</li> <p>E. S. Zeron, M. Santill_an</p> <p> <li>How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology</li> <p>Didier Gonze, Wassim Abou-Jaoud´e, Adama Ouattara, and Jos´e Halloy</p> <p> <li>Computational modelling of biological pathways by executable biology</li> <p>Maria Luisa Guerriero John K. Heath</p> <p> <li>Computing Molecular Fluctuations in Biochemical Reaction Systems Based on A Mechanistic, Statisitical Theory of Irreversible Processes </li> <p>Don Kulasiri</p> <p> <li>Probing the input-output behaviour of biochemical and genetic systems: system identification methods from control theory </li> <p>David McMillen, Brian Ingalls, Jordan Ang</p> <p> <li>Biochemical pathway modelling tools for drug target detection in cancer and other complex diseases</li> <p>Alberto Marin-Sanguino, Shailendra K. Gupta, Eberhard O. Voit and Julio Vera</p> <p> <li>Deterministic and Stochastic Simulation and Analysis of Biochemical Reaction Networks: The Lactose Operon Example</li> <p>Necmettin Yildirim, Caner Kazanci F</p> <p> <li>Multivariate Neighborhood Sample Entropy: A method for data reduction and prediction of complex data.</li> <p>Joshua S. Richman MD, PhD</p> <p> <li>Scaling differences of heartbeat excursions between wake and sleep periods</li> <p>L. Guzm´an-Vargas, I. Reyes-Ram´ırez, R. Hern´andez-P´erez, F. Angulo-Brown</p> <p> <li>Changepoint analysis for single-molecule polarized totalinternal reflection fluorescence microscopy experiments</li> <p>John F. Beausang, Yale E. Goldman, and Philip C. Nelson</p> <p> <li>Inferring mechanisms from dose-response curves</li> <p>Carson C. Chow, Karen M. Ong, Edward J. Dougherty, and S. Stoney Simons, Jr. </p> <p> <li>Spatial Aspects in Biological System Simulations</li> <p>Haluk Resat, Michelle N. Costa, and Harish Shankaran</p> <p> <li>Computational Approaches to Modeling Viral Structure and Assembly</li> <p>Stephen C. Harvey, Anton S. Petrov, Batsal Devkota and Mustafa Burak Boz</p> <p> <li>An Object-Oriented Software Suite for the Simulation and Design of Macromolecules</li> <p>Andrew Leaver-Fay, Michael Tyka, Steven M. Lewis, Oliver F. Lange, James Thompson, Ron Jacak, Kristian Kaufman, P. Douglas Renfrew, Colin A. Smith, Will Sheffler, Ian W. Davis, Seth Cooper, Adrien Treuille, Daniel J. Mandell, Florian Richter, Yih-En Andrew Ban, Sarel J. Fleishman, Jacob E. Corn, David E. Kim, Sergey Lyskov, Monica Berrondo, Stuart Mentzer, Zoran Popović, James J. Havranek, John Karanicolas, Rhiju Das, Jens Meiler, Tanja Kortemme, Jeffrey J. Gray, Brian Kuhlman<SUP>1</SUP>, David Baker, and Philip Bradley</p> <p> <li>Computational Design of Intermolecular Stability and Specificity in Protein Self-Assembly</li> </ol> <p>Vikas Nanda, Sohail Zahid, Fei Xu, Daniel Levine</p>