Algorithmic Systems Biology - Computer Science Propels Systems Biology

[1]  L. Hood,et al.  The digital code of DNA , 2003, Nature.

[2]  Corrado Priami,et al.  Snazer: the simulations and networks analyzer , 2010, BMC Systems Biology.

[3]  Corrado Priami,et al.  Process Calculi Abstractions for Biology , 2009, Algorithmic Bioprocesses.

[4]  Vincent Danos,et al.  Scalable Simulation of Cellular Signaling Networks , 2007, APLAS.

[5]  Corrado Priami,et al.  The BlenX Language: A Tutorial , 2008, SFM.

[6]  Lorenzo Dematté,et al.  On Parallel Stochastic Simulation of Diffusive Systems , 2008, CMSB.

[7]  Luca Cardelli,et al.  BioAmbients: an abstraction for biological compartments , 2004, Theor. Comput. Sci..

[8]  Douglas A. Lauffenburger,et al.  International Research and Development in Systems Biology , 2005 .

[9]  Sylvia J. Spengler,et al.  Bioinformatics in the Information Age , 2000, Science.

[10]  Mudita Singhal,et al.  Simulation of Biochemical Networks using Copasi - A Complex Pathway Simulator , 2006, Proceedings of the 2006 Winter Simulation Conference.

[11]  Corrado Priami,et al.  Stochastic pi-Calculus , 1995, Comput. J..

[12]  Corrado Priami,et al.  Beta Binders for Biological Interactions , 2004, CMSB.

[13]  Thomas A. Henzinger,et al.  Compositional Methods for Probabilistic Systems , 2001, CONCUR.

[14]  M. Delorme,et al.  An Introduction to Cellular Automata , 1999 .

[15]  Peter H. Welch,et al.  Communicating Mobile Processes , 2004, 25 Years Communicating Sequential Processes.

[16]  Jeannette M. Wing.  An introduction to computer science for non-majors using principles of computation , 2007, SIGCSE.

[17]  D. Roos,et al.  Bioinformatics--Trying to Swim in a Sea of Data , 2001, Science.

[18]  Corrado Priami,et al.  Algorithmic systems biology , 2009, CACM.

[19]  Eberhard O Voit,et al.  Theoretical Biology and Medical Modelling Identification of Metabolic System Parameters Using Global Optimization Methods , 2022 .

[20]  Paolo Milazzo,et al.  The Calculus of Looping Sequences , 2008, SFM.

[21]  Mudita Singhal,et al.  COPASI - a COmplex PAthway SImulator , 2006, Bioinform..

[22]  Corrado Priami,et al.  Modelling the dynamics of biosystems , 2004, Briefings Bioinform..

[23]  D. Searls,et al.  Robots in invertebrate neuroscience , 2002, Nature.

[24]  Luca Cardelli,et al.  Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus , 2007, CMSB.

[25]  Arto Salomaa,et al.  Algorithmic Bioprocesses , 2009, Natural Computing Series.

[26]  Corrado Priami,et al.  Application of a stochastic name-passing calculus to representation and simulation of molecular processes , 2001, Inf. Process. Lett..

[27]  Stephen Gilmore,et al.  Process Algebra and Probabilistic Methods. Performance Modelling and Verification , 2001, Lecture Notes in Computer Science.

[28]  Cosimo Laneve,et al.  Formal molecular biology , 2004, Theor. Comput. Sci..

[29]  Corrado Priami,et al.  Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus , 2006, Bioinform..

[30]  Corrado Priami,et al.  From ODES to Language-Based, Executable Models of Biological Systems , 2009, Pacific Symposium on Biocomputing.

[31]  Robert Rosen,et al.  Essays on Life Itself , 1999 .

[32]  Hiroyuki Kuwahara,et al.  An efficient and exact stochastic simulation method to analyze rare events in biochemical systems. , 2008, The Journal of chemical physics.

[33]  F. Ciocchetta,et al.  An Automatic Translation of SBML into Beta-Binders , 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[34]  Marco Bernardo,et al.  LNCS -- Procs 8th Int. School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology , 2008 .

[35]  Paola Lecca,et al.  A new probabilistic generative model of parameter inference in biochemical networks , 2009, SAC '09.

[36]  T. Marshall,et al.  Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2b , 2006, Theoretical Biology and Medical Modelling.

[37]  H. Kitano.  Systems Biology: A Brief Overview , 2002, Science.

[38]  Corrado Priami,et al.  The Beta Workbench: a computational tool to study the dynamics of biological systems , 2008, Briefings Bioinform..

[39]  Darren J. Wilkinson,et al.  Bayesian inference for nonlinear multivariate diffusion models observed with error , 2008, Comput. Stat. Data Anal..

[40]  Alan Forrest,et al.  SPLINDID: a semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles , 2005, Bioinform..

[41]  Luca Cardelli,et al.  On the Computational Power of Biochemistry , 2008, AB.

[42]  Stephen Gilmore,et al.  Integrated Simulation and Model-Checking for the Analysis of Biochemical Systems , 2009, PASM@EPEW.

[43]  Eberhard O Voit,et al.  Theoretical Biology and Medical Modelling , 2022 .

[44]  Darren J. Wilkinson,et al.  Bayesian inference for a discretely observed stochastic kinetic model , 2008, Stat. Comput..

[45]  Sean Sedwards,et al.  Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes , 2007, Bioinform..

[46]  Peter J. Denning,et al.  Computing is a natural science , 2007, CACM.

[47]  J. Bergstra,et al.  Handbook of Process Algebra , 2001 .

[48]  David Harel,et al.  Statecharts in the making: a personal account , 2009, CACM.

[49]  S J Spengler,et al.  Techview: computers and biology. Bioinformatics in the information age. , 2000, Science.

[50]  E. Shapiro,et al.  Cellular abstractions: Cells as computation , 2002, Nature.

[51]  Carmen G. Moles,et al.  Parameter estimation in biochemical pathways: a comparison of global optimization methods. , 2003, Genome research.

[52]  Junbin Gao,et al.  Simulated maximum likelihood method for estimating kinetic rates in gene expression , 2007, Bioinform..

[53]  Paola Lecca,et al.  Modeling and Simulating Reaction-Diffusion Systems with State-Dependent Diffusion Coefficients , 2008 .