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Copies of the Proceedings may be ordered on line for $50 each, plus shipping and handling. We accept Visa and Mastercard only. To place an order, click here. The Proceedings is also available below, as a series of PDF documents. To read them, you will need Adobe Acrobat or the Acrobat Reader installed on your computer. Acrobat Reader can be downloaded free of charge from Adobe's web site by clicking on the icon to the right. Table of Contents
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TBA
Al Gilman
Reverse-engineering the gene regulation network of E. coli
Uri AlonModeling molecular events in a small volume of living cytoplasm
Dennis BrayMechanisms of directional sensing in eukaryotic cells
Peter N. Devreotes
Monte Carlo simulation of realistic cellular microphysiology
Joel R. StilesSBW/SBML: a software platform and standard for systems biology
Hiroaki Kitano, Hamid Bolouri, Andrew Finney, Herbert Sauro, Michael Hucka, and John DoyleRepresenting and analyzing biological function with aMAZE, a database of molecular interactions and processes
Shoshana J. Wodak, Christian Lemer, Avi Naim, Yong Zhang, Gaurab Mukherjee, Didier Croes, Lorenz Wernisch, David Gilbert, and Jacques van HeldenMetabolic control analysis: a tool for understanding cellular behaviour, control and regulation
Jan-Hendrik S. HofmeyrAlternative designs for a genetic switch: analysis for switching times using the piecewise power-law representation within Biochemical Systems Theory
Michael A. Savageau
Extracting biological information from genome-wide gene expression studies
David Botstein
Quantitative proteome analysis: new technology and applications
Ruedi Aebersold, Hookeun Lee, David Han, Michael Wright, Huilin Zhou, Tim Griffin, Sam Purvine, and David GoodlettQuantitative gene expression profiling in the brain
David J. LockhartDynamic properties of cellular signaling networks
Tobias Meyer
Modeling cell cycle controls: an example of the "last step" of computational molecular biology
John J. Tyson and Bela NovakA systems engineering approach to the bacterial cell cycle: defining the genetic circuitry
Lucy ShapiroReceptor, ligand, and signaling pathway dynamics in the Epidermal Growth Factor system
Douglas A. LauffenburgerUnderstanding what we already know about the living cell: cellular bioinformatics, computational biochemistry, and the Silicon Cell
Hans V. Westerhoff, Boris N. Kholodenko, Christof Francke, Frank Bruggeman, Jan Lankelma, Hans (JJHM) van Beek, Barbara M. Bakker and Jacky L. Snoep
Network bioinformatics: from effect detection to comparative regulation
Adam P. Arkin
Protein interactions
David Eisenberg, Ioannis Xenarios, Joyce Duan, Lukasz Salwinski, Edward Marcotte, Matteo Pellegrini, Michael J. Thompson, and Todd YeatesExperimental evolution in yeast: a progress report
Jun-Yi Leu, Russell Dorer, Dawn Thompson, Sandra Arciniegas, and Andrew MurrayTowards a DNA sequence-based cis-regulatory network model for a major developmental specification process in the sea urchin embryo
Eric H. Davidson, R. Andrew Cameron, Jonathan P. Rast, Andrew Ransick, Paola Oliveri, Chiou-Hwa Yuh, Cristina Calestani, Veronica Hinman, Takuya Minokawa, Ochan Otim, C. Titus Brown, Carolina Livi, Pei Yun Lee, Peter Clarke, Elbert Branscomb, Leroy Hood, Lee Rowen, Hamid Bolouri, and Alistair RustGenomics, proteomics, and systems biology
Leroy Hood
A mathematical vision of TNF receptor interaction
Birgit Schoeberl, Ernst D. Gilles, Peter Scheurich, M. Fotin, G. Mueller, and H. WajantSpatial sensing of chemotactic gradients: a reaction-diffusion model
J. Krishnan, Pablo A. Iglesias, and Lan MaRobustness vs. identifiability of regulatory modules?
Joerg Stelling and Ernst D. GillesModeling biological responses using gene expression profiling and linear dynamical systems
Claudia Rangel, David L. Wild, Francesco Falciani, Zoubin Ghahramani, and Alessia GaibaComparison of the small molecule metabolic pathways in Escherichia coli and Saccharomyces cerevisiae: non-orthologous displacements, gene fusions and protein interactions
Oliver Jardine and Sarah A. TeichmannDevelopmental simulations with Cellerator
Bruce E. Shapiro and Eric D. Mjolsness
[001] Data driven dynamics modeling of a signaling pathway
Jens Timmer, Ira Swameye, Thorsten Muller, Olivier Sandra, and Ursula Klingmuller[002] A Markov chain model of the MAPK signaling cascade
Maya R. Said, Douglas A. Lauffenburger, and Alan V. Oppenheim[003] A rationale for the 'design' of the MAP kinase pathway
Herbert M. Sauro[004] Kinetic simulations of the EGFR signaling network
Haluk Resat, David Dixon, and H. Steven Wiley[005] Context-dependent signaling in autocrine loops: modeling and experiments in the Epidermal Growth Factor Receptor system
Stanislav Y. Shvartsman, Paul Dent, Douglas A. Lauffenburger, and H. Steven Wiley[006] Control of protein phosphorylation by diffusion in cellular signaling pathways
Daniel E. Zak, Boris M. Slepchenko, and Boris N. Kholodenko[007] A detailed kinetic model of immunoreceptor signaling
James R. Faeder, William S. Hlavacek, Antonio Redondo, Carla Wofsy, Mikhail Blinov, and Byron Goldstein[008] Kinetic proofreading models for immunoreceptor signaling
William S. Hlavacek, Carla Wofsy, Byron Goldstein, Henry Metzger, and Antonio Redondo[009] Quantitative studies on the responses of signal transduction networks in terms of protein-protein interaction maps
Frank J. Bruggeman, Hans V. Westerhoff, and Boris N. Kholodenko[010] A mathematical vision of TNF receptor interaction
Birgit Schoeberl, Ernst-Dieter Gilles, Peter Scheurich, M. Fotin, G. Mueller, and H. Wajant[011] Analysis of a reaction-diffusion model of spatial sensing
J. Krishnan, Pablo A. Iglesias, and Lan Ma[012] Gene expression profiling in signaling-deficient B cells
Xiaocui Zhu, Owen N. Witte, David Fruman, Gregory Z. Ferl, Sam S. An, Amber C. Donahue, and Anne B. Satterthwaite[013] Progesterone and hydroxyflutamide: dose-response for activation of the androgen receptor in HepG2 cells
Rory B. Conolly and Kevin W. Gaido[014] Synergism in a mitotic signaling network
Jorrit J. Hornberg, Marloes R. Tijssen, and Jan Lankelma[015] Phosphoinositide cycles as biological triggers
Ron Skupsky and Ralph Nossal[016] Rho signaling: where is the feedback?
Mark T. Borisuk, Brian Ingalls, Anne J. Ridley, and Hamid Bolouri[017] Kinetic simulation study of cerebellar long-term depression
Shinya Kuroda, Nicolas Schweighofer, and Mitsuo Kawato
[018] Morphological control of InsP3-dependent calcium release in spiny dendrites
Boris Slepchenko, Kathleen B. Fernald, Ion I. Moraru, Charles C. Fink, and Leslie M. Loew[019] Effects of hidden calcium pools on cell electrical activity
Arthur Sherman, Leslie Satin, and Richard Bertram[020] Multi-parametric analysis of the apoptotic decision process in HT-29 cells
John Albeck, Suzanne Gaudet, Maya Said, Alan V. Oppenheim, Douglas A. Lauffenburger, and Peter K. Sorger[021] Creatine kinase in energy metabolic signaling in muscle
Olav Kongas and Johannes H. G. M. van Beek[022] Inheritance of chromosome positions throughout mitosis revealed by live cell imaging and computer simulations
Daniel Gerlich, Jan Ellenberg, Roland Eils, and Joel Beaudouin[023] Anatomy of a cell cycle checkpoint: the dynamics of MPF, Cdc25, and Chk1
Tau-Mu Yi and Pon-Nyong Yi[024] Construction of the Escherichia coli cell-cycle mechanism
Amy Gilbert, Charles Johnson, Quingwu Yang, and Paul A. Lindahl[025] Mathematical modeling of transcription regulation by protein assemblies at promoters: regulation of E2F dependent genes
Paul Brazhnik, Kurt Kohn, Pedro Mendes, and John Tyson[026] Method for simulating the kinetics of cell growth and division at the molecular level
Christopher Sewell, Charles Johnson, Jeffrey J. Morgan, and Paul A. Lindahl[027] Building a computer simulation of threonine synthesis in Escherichia coli
David A. Fell, Christophe Chassagnole, and Jean-Pierre Mazat[028] On the local regulation of aminoacyl-tRNA synthetases and amino acid biosynthetic enzymes in Escherichia coli
Emmeli Taberman, Mans Ehrenberg, and Johan Elf[029] The role of ribosome recycling, diffusion, and mRNA loop formation in translational regulation
Tom Chou[030] Why does natural selection maintain high G6PD activities?
Armindo Salvador and Michael A. Savageau[031] Red blood cell extreme pathways
Sharon Smith and Bernhard O. Palsson[032] In silico analysis of human erythrocyte using E-CELL system
Ayako Kinoshita, Yoichi Nakayama, and Masaru Tomita[033] A genome-scale in silico model of metabolic network in Saccharomyces cerevisiae
Iman Famili, Jochen Forster, Jens Nielsen, and Bernhard O. Palsson[034] The genome-scale metabolic extreme pathway structure in Haemophilus influenzae and Helicobacter pylori show differing degrees of network redundancy
Jason A. Papin, Nathan D. Price, Jeremy S. Edwards, and Berhard O. Palsson[035] Tumor treatment: the fight against a System
Jan Lankelma[036] Experimental analysis and modeling of Sigma E regulation in E. coli
Irina Grigorova, Sara E. Ades, and Carol A. Gross[037] Ion dynamics and the regulation of cellular development
Jose A. Feijo
[038] Modeling of the inherence of feedback regulation and stem cell behavior in granulopoiesis
Toshihiko Komatsuzaki and Yutaka Saikawa[039] MHV recombination in vitro and in silico
Karen A. Duca, Anselm Blumer, Mary A. Lokuta, and John O. Fleming[040] From physical models to gene action
Tanya K. Soboleva, Tony Pleasants, A. Jim Peterson, Birgitte T. T. M. van Rens, Tette van der Lende, and H. van der Steen[041] Modeling in time series: an integrated approach
Roumyana Kirova and Peter Tonellato[042] A Monte-Carlo simulation of cancer invasion using the extended Potts model
Stephen Turner and Jonathan A. Sherratt[043] Do morphogen gradients arise by diffusion?
Arthur D. Lander, Qing Nie, and Frederic Y. M. Wan[045] A simulation model of ischemia in the rat brain
Jerker Westin, Lars Hillered, Torgny Groth, Mark Dougherty, and Bo Johansson[046] A cerebral framework for integrating biologically plausible mechanisms in large connectionist models
Nicolas Rougier and Frederic Alexandre[047] Neural plasticity with different time constants
Gabriele Scheler[048] Formal modeling, simulation and analysis of developmental processes in Caenorhabditis elegans
Naaman Kam, Irun R. Cohen, David Harel, Amir Pnueli, E. Jane Albert Hubbard, and Michael J. Stern[049] A simulation of the accumulation of mitochondrial DNA mutations with age
David C. Samuels, Joanna L. Elson, and Patrick F. Chinnery
[050] Flux in metabolic pathways from one 13C NMR spectrum
Johannes H. G. M. van Beek, Harald G. J. van Mil, and David J. C. Alders[051] Comprehensive analysis of intracellular metabolites by capillary electrophoresis mass spectrometry
Tomoyoshi Soga, Takaaki Nishioka, Masaru Tomita, Yuki Ueno, and Hisako Naraoka[052] Highly parallel single cell monitoring of receptor-triggered membrane translocation of a calcium sensing protein module
Mary N. Teruel and Tobias Meyer[053] Guidance of avian neural crest cells by ephrin-B ligands
Andrew Ewald and Scott E. Fraser[054] GFP tracking and quantification in transgenic developing somatic embryos of soybean (Glycine max (L) Merrill)
Marco T. Buenrostro-Nava, Peter P. Ling, and John J. Finer[055] Correction curve normalization for microarray data
Tadashi Kadowaki
[056] Regulatory networks revealed by transcriptional profiling in the yeast
Wei Wang, J. Michael Cherry, David Botstein, and Hao Li[057] Genomic expression programs of human cell lines in response to physiological stress
John I. Murray, Michael Whitfield, David Botstein, and Patrick O. Brown[058] Metabolic reconstruction of mouse transcriptome using the RIKEN set of 18,816 mouse cDNA arrays
Hidemasa Bono, Hideo Matsuda, Takeya Kasukawa, Itoshi Nikaido, Yoshihide Hayashizaki, and Yasushi Okazaki[059] Gene clustering algorithm GS4M5D
Wim de Boer and Jan Lankelma[060] Dependence of the magnitude of stochastic fluctuations in prokaryotic gene expression on the transcription and translation initiation rates
Andrzej M. Kierzek[061] A quantitative method for reverse engineering gene networks from microarray experiments using regulatory strengths
Alberto de la Fuente, Paul Brazhnik, and Pedro Mendes[062] Modeling a Hox gene network
Jason Kastner, Scott Fraser, and Jerry Solomon[063] Simulation studies for the identification of genetic networks from cDNA array and regulatory activity data
Daniel E. Zak, Francis J. Doyle III, Gregory E. Gonye, and James S. Schwaber[064] Searching for limited connectivity in genetic network models
E. P. van Someren, L. F. A. Wessels, M. J. T. Reinders, and Eric Backer[065] Methods for inference of genetic regulatory networks
Annette Evangelisti, William S. Hlavacek, John Ambrosiano, Michael Wall, David Sharp, J. Mark Ettinger, and Dan Hill[066] Testing hypothesis on genetic network structures
Dirk Repsilber and Hans Liljenstrom[067] A network genomic analysis of microbial genomes
Christian V. Forst[068] Inferring functional relationships using genome-wide dependency networks
Johan Rung, Patrick Kemmeren, Thomas Schlitt, Alvis Brazma, and Jaak Vilo[069] A network analysis of expression time series
Gregory T. Dewey and Ashish Bhan[070] The DBRF method for inferring a gene network from large-scale steady-state gene expression data
Koji M. Kyoda, Shuichi Onami, and Hiroaki Kitano[071] Modeling and determination of the regulation of gene expression: the binary switch model
David Venet, Carine Maenhaut, and Hugues Bersini
[072] Producing a molecular parts list for systems biology
Heidi J. Sofia and Jorge F. Reyes-Spindola[073] Integrated clustering and motif detection for genome-wide expression and sequence data
Dan Hill, William Hlavacek, J. Ambrosiano, M. E. Wall, D. H. Sharp, T. Cleland, S. M. Mniszewski, and A. Evangelisti[074] FamilyRelations: comparative sequence analysis of genomic data
C. Titus Brown, Tristan D. Buysscher, and Eric H. Davidson[075] Automatic detection of putative cis-regulatory motifs
Mark Robinson, Hamid Bolouri, and Eric H. Davidson[076] Comparison of the small molecule metabolic pathways in Escherichia coli and Saccharomyces cerevisiae
Oliver Jardine and Sara A. Teichmann[077] Rat genome database disease centric rat gene initiative
Simon Twigger, Jian Lu, Mary Shimoyama, Roumyana Kirova, Dean Pasko, Chin-fu Chen, Rajni Nigam, Hanping Long, Jaili Chen, Jed Mathis, Jessica Ginster, and Peter Tonellato[078] New insights in clinical impact of molecular genetic data by knowledge-driven data mining
Daniel Berrar, Martin Granzow, Werner Dubitzky, Roland Eils, Stephan Stilgenbauer, Klaus Wilgenbus, Hartmut Dohner, and Peter Lichter[079] Integration of a cancer research knowledge base with a cross-hierarchy modeling platform
Roger Day and William Shirey[080] Sequence-oriented modelling of gene expression
Sabine Arnold, Martin Siemann, and Matthias Reuss
[081] Biosystems engineering: applying methods from systems theory to biological systems
Andreas Kremling, T. Sauter, E. Bullinger, M. Ederer, F. Allgower, and E. D. Gilles[082] The mereological structure of chemical reactions: implications for biochemical simulation
William Andersen and Ursula Kummer[083] Large fluctuations in coupled metabolic reactions
Johan Elf and Mans Ehrenberg[084] Dynamic flux balance analysis for metabolic modeling
Radhakrishnan Mahadevan, Jeremy S. Edwards, and Francis J. Doyle III[085] Analysis of steady-state protein homeostatic regulatory mechanisms in perturbed environments
Christopher Sewell, Jeffrey J. Morgan, and Paul A. Lindahl[086] Analysis and design of gene switches composed of positive feedback loops
Tetsuya Kobayashi, Luonan Chen, and Kazuyuki Aihara[087] Reliable computation by circuits of unreliable biochemical gates
Maria A. Neimark and Erik Winfree[088] Robustness analysis of a self-oscillating molecular network in Dictyostelium discoideum
Lan Ma and Pablo A. Iglesias[089] Conservation of robustness: proof of Bode's sensitivity integral formula for nonlinear systems and its implications for biology
John Doyle, Herbert Sauro, and Tau-Mu Yi[090] Thermodynamics of biochemical reaction systems at three levels
Robert A. Alberty[091] Phosphorylation of muscle glycogen synthase maintains metabolic homeostasis
Robert G. Shulman, Douglas L. Rothman, James Schafer, and David Fell
[092] Applying URC fuzzy logic to model complex biological systems in the language of biologists
Bahrad A. Sokhansanj, Garry H. Rodrigue, and J. Patrick Fitch[093] Standardized language dedicated to biological function
Pierre Maziere, Claude Granier, Franck Molina, Bernard Pau, Charles Auffray, and Magali Roux-Rouquie[094] Use of formal diagramming techniques to build a systems understanding of complex biological processes
Pamela K. Fink, L. Tandy Herren, and Paula J. Enrietto[095] Diagrammatic notation and computational structure of gene networks
Ron Maimon and Sam Browning[096] Modeling biological systems in hybrid concurrent constraint programming
Alexander Bockmayr and Arnaud Courtois[097] Towards the automated generation of inflammation pathway hypotheses from experimental data and prior knowledge
Rick Stanton, Deborah van Alphen, Martin Hagen, Tim McPhail, and Chris Saris[098] Generating hypotheses in Self-Organizing Maps
Bernd Bruckner and Henning Hofmeister[100] Network analysis of Escherichia coli metabolic models
Navtej S. Juty, Sergei Dronov, Igor Goryanin, Charlie Hodgman, and Hugh D. Spence[101] Diet planning for E. coli
Steve Eker, Peter Karp, Patrick Lincoln, and Pedro Romero[102] Computer-aided analysis of large metabolic and signaling networks
Klaus Mauch, Knut Behrendt, and Matthias Reuss[103] Systems biology mining of APO lipoprotein metabolic pathways
Matej Oresic, Aram Adourian, Sabina Bijlsma, Clary Clish, Eugene Davidov, Elly Faber, Louis Havekes, Sonja Jespersen, Nicole Morel, Eric Neumann, Phil Snell, Gerwin Spijksma, Albert Tas, Jan van der Greef, Elwin Verheij, Jack Vogels, and Florian Wulfert
[104] Designing object-based cell simulation system: E-CELL 3
Kouichi Takahashi, Yohei Yamada, Masayuki Okayama, and Masaru Tomita[105] Design and development of software environment for whole cell simulation
Yusuke Saito, Takeshi Sakurada, Kouichi Takahashi, and Masaru Tomita[106] The Virtual Cell modeling environment
James C. Schaff, Ion I. Moraru, Leslie M. Loew, John Wagner, Boris M. Slepchenko, Daniel Lucio, and Frank R. Morgan[107] Jarnac: An SBW compliant systems biology simulation tool
Herbert M. Sauro[108] Developmental Simulations with Cellerator
Bruce E. Shapiro and Eric D. Mjolsness[109] Metabolizer: A Java simulation environment for whole-cell models
Markus Schwehm, Stefan Hees, Esther Rheinbay, and Michael Schroder[110] Parallel simulation engines for whole-cell models
Markus Schwehm, Nils Gehlenborg, Hendrik Post, Amelie Stein, and Kirstin Weber[111] STODE-automatic stochastic simulation of systems described by differential equations
Carel van Gend and Ursula Kummer[112] Logical modeling of developmental genetic regulatory networks with NetBuilder
Maria J. Schilstra and Hamid Bolouri[113] FluxAnalyzer: studying structure and fluxes in metabolic networks
Steffen Klamt and Ernst-Dieter Gilles[114] ProcessDB: a cellular process database supporting large-scale iterative kinetic modeling in cell biology
Ann K. Chasson and Robert D. Phair[115] Database of models for ligand-receptor binding in electronic exchange formats
Michael Blinov, William Hlavacek, James R. Faeder, Byron Goldstein, Alan S. Perelson, Richard G. Posner, Antonio Redondo, and Carla Wofsy[116] Applications of XML in the Virtual Cell
Daniel Lucio, Jim Schaff, and John Wagner[117] NeuroML: a lingua franca for computational modeling in neuroscience
Fred Howell, Nigel Goddard, R.Cannon, Michael Hucka, K. Shankar, P. Rogister, M.-O. Gewaltig, D. Beeman, H. Cornelis, and E. De Schutter[118] An application framework for predictive modeling of biological processes
Carolyn Cho, Kam-Chuen Jim, Zhuang Zuo, Ramprasad Ramakrishna, Dean Bottino, G. Scott Lett, and Adam Muzikant[119] Elementary modes of metabolism, and software for their determination and analysis
Mark G. Poolman, David A. Fell, and David Lightfoot[120] The Systems Biology Markup Language (SBML): a standard for the exchange of biochemical network models
Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri, John Doyle, and Hiroaki Kitano
[121] Coordination of dynein motor enzymes for generation for 3-dimensional flagellar bending waves
Charles J. Brokaw[122] Mode of action of antimicrobial peptide cecropin B on Escherichia coli
Shiu-Chiu Chan, Chia-Ching Chang, and Hueih Min Chen[123] The evolution of metabolic networks: growth under constraints
Amit Puniyani and Rajan M. Lukose[124] A genetic algorithm model of mutation and evolvability
Stevan J. Anastasoff, Jennifer A. Nelson, and Tan Bao[125] Rule of population density of halophiles in the deep-sea
Hideki Kobayashi, Hideto Takami, and Koki Horikoshi[126] Do gene waves exist in excitable biosystems?
Paul R. Shorten, Tanya K. Soboleva, and Tony A.B. Pleasants[127] Protein network visualization with JDIP
Lukasz Salwinski, Ioannis Xenarios, and David Eisenberg
Four-dimensional organization of cellular signal transduction cascades
Nick Markevich, Anatoly B. Kiyatikin, Daniel E. Zak, John G. Pastorino, Jan B. Hoek, and Boris N. KholodenkoSpatial sensing of chemotactic gradients: a reaction-diffusion model
J. Krishnan, Pablo A. Iglesias, and Lan MaA mathematical vision of TNF receptor interaction
B. Schoeberl, E. D. Gilles, P. Scheurich, M. Fotin, G. Mueller, and H. WajantKinetic simulation study of cerebellar long-term depression
Shinya Kuroda, Nicolas Schweighofer, and Mitsuo Kawato
Building a computer simulation of threonine synthesis in Escherichia coli
David A. Fell, Christophe Chassagnole, and Jean‚Pierre MazatRobustness vs. identifiability of regulatory modules?
Joerg Stelling and Ernst D. GillesFlux in metabolic pathways from one 13C NMR spectrum
Johannes H. G. M. van Beek, Herald G. J. van Mil, and David J. C. AldersCreatine kinase in energy metabolic signaling in muscle
Olav Kongas and Johannes H. G. M. van BeekModeling of the inherence of feedback regulation and stem cell behavior in granulopoiesis
Toshihiko Komatsuzaki and Yutaka Saikawa
A quantitative method for reverse engineering gene networks from microarray experiments using regulatory strengths
Albert de la Fuente, Paul Brazhnik, and Pedro MendesSearching for limited connectivity in genetic network models
E. P. van Someren, L. F. A. Wessels, M. J. T. Reinders, and E. BackerSimulation studies for the identification of genetic networks from cDNA array and regulatory activity data
Daniel E. Zak, Francis J. Doyle III, Gregory E. Gonye, and James S. SchwaberModeling and determination of the regulation of gene expression: the binary switch model
David Venet, Carine Maenhaut, and Hugues BersiniModeling biological responses using gene expression profiling and linear dynamical systems
Claudia Rangel, David L. Wild, Francesco Falciani, Zoubin Ghahramani, and Alessia GaibaComparison of the small molecule metabolic pathways in Escherichia coli and Saccharomyces cerevisiae: non-orthologous displacements, gene fusions and protein interactions
Oliver Jardine and Sarah A. TeichmannIntegration of a cancer research knowledgebase with a cross-hierarchy modeling platform
Roger Day and William ShireyNew insights in clinical impact of molecular genetic data by knowledge-driven data mining
Daniel Berrar, Martin Granzow, Werner Dubitzky, Peter Lichter, Roland Eils, Stephan Stilgenbauer, Klaus Wilgenbus, and Hartmut Dohner
Biosystems engineering: applying methods from systems theory to biological systems
A.Kremling, T. Sauter, E. Bullinger, M. Ederer, F. Allgower, and E. D. GillesMetabolic control analysis in a nutshell
Jan -Hendrik S. HofmeyrModeling biological reactivity: statecharts vs. Boolean logic
Naaman Kam, David Harel, and Irun R. CohenDiagrammatic notation and computational structure of gene networks
Ron Maimon and Sam BrowningElementary models of metabolism, and software for their determination and analysis
Mark G. Poolman, David A. Fell, and David LightfootSTODE-automatic stochastic simulation of systems described by differential equations
Carel van Gend and Ursula KummerParallel stochastic simulation of whole-cell models
Markus SchwehmDevelopmental simulations with Cellerator
Bruce E. Shapiro and Eric D. MjolsnessThe ERATO Systems Biology Workbench: architectural evolution
Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri, John Doyle, and Hiroaki Kitano