The algorithmic analysis of hybrid systems
Theoretical Computer Science - Special issue on hybrid systems
Petri Nets and Grafcet: Tools for Modelling Discrete Event Systems
Petri Nets and Grafcet: Tools for Modelling Discrete Event Systems
Stochastic Petri Nets: An Introduction to the Theory
ACM SIGMETRICS Performance Evaluation Review - Special issue on Stochastic Petri Nets
LICS '96 Proceedings of the 11th Annual IEEE Symposium on Logic in Computer Science
Modeling of hybrid systems using continuous and hybrid Petri nets
PNPM '97 Proceedings of the 6th International Workshop on Petri Nets and Performance Models
Modeling interactome: scale-free or geometric?
Bioinformatics
Alignment of metabolic pathways
Bioinformatics
NeMoFinder: dissecting genome-wide protein-protein interactions with meso-scale network motifs
Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining
COPASI---a COmplex PAthway SImulator
Bioinformatics
Bioinformatics
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets
Computational Biology and Chemistry
An Introduction to Metabolic Networks and Their Structural Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Network motif discovery using subgraph enumeration and symmetry-breaking
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Introduction to generalized stochastic Petri nets
SFM'07 Proceedings of the 7th international conference on Formal methods for performance evaluation
Automated symbolic reachability analysis: with application to delta-notch signaling automata
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
NABEECO: biological network alignment with bee colony optimization algorithm
Proceedings of the 15th annual conference companion on Genetic and evolutionary computation
Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Neighborhood-Preserving mapping between trees
WADS'13 Proceedings of the 13th international conference on Algorithms and Data Structures
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Systems biology is a broad field that incorporates both computational and experimental approaches to provide a system level understanding of biological function. Initial forays into computational systems biology have focused on a variety of biological networks such as protein-protein interaction, signaling, transcription and metabolic networks. In this review we will provide an overview of available data relevant to systems biology, properties of biological networks, algorithms to compare and align networks and simulation and modeling techniques. Looking towards the future, we will discuss work on integrating additional functional information with biological networks, such as three dimensional structures and the complex environment of the cell. Combining and understanding this information requires development of novel algorithms and data integration techniques and solving these difficult computational problems will advance both computational and biological research.