Information Processing in Cells and Tissues

Name: Information Processing in Cells and Tissues | 9th International Conference, IPCAT 2012, Cambridge, UK, March 31 -- April 2, 2012, Proceedings
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9th International Conference, IPCAT 2012, Cambridge, UK, March 31 -- April 2, 2012, Proceedings

Michael A. Lones Stephen L. Smith Sarah Teichmann Felix Naef Jonathan Oliver Martin Albrecht Trefzer(Herausgeber*in)

Springer (Verlag)

Erschienen am 22. März 2012

XII, 278 Seiten

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Inhalt

Title
Preface
Organization
Table of Contents
Genetic and Epigenetic Networks
Using Artificial Epigenetic Regulatory Networks to Control Complex Tasks within Chaotic Systems
Introduction
Gene Regulation and Epigenetics
Artificial Genetic Regulatory Networks
Artificial Epigenetic Regulatory Networks
Dynamical Systems
Standard Map
State Space Targeting
Experimentation
Evolution of the Networks
State Space Targeting Using Artificial Regulatory Networks
Results
Conclusions
References
A Gene Regulatory Network Simulation of Heterosis
Introduction
Biological Background
Random Boolean Networks
Network Construction
Generating Networks with Realistic Properties
Selection of Phenotypes Based on Network Responses to Several Environments
Network Evolution and Hybrid Vigor
Evolution Is Achieved by Mutation and Selection
Haploid and Diploid Networks Evolve towards Better Phenotypes
Simulating Hybrid Vigor
References
Comparing Discrete and Piecewise Affine Differential Equation Models of Gene Regulatory Networks
Introduction
Discrete Formalism
Piecewise Affine Differential Equations
Relating the Discrete and the PADE Formalism
Comparing the Dynamics
Discussion and Perspectives
References
Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data
References
Transcriptomics and Gene Regulation
CRISPR Transcript Processing: An Unusual Mechanism for Rapid Production of Desired Molecules
Background
Results
Conclusion
References
A Comprehensive Computational Model to Simulate Transcription Factor Binding in Prokaryotes
References
Signalling Pathways and Responses
Evolved Artificial Signalling Networks for the Control of a Conservative Complex Dynamical System
Introduction
Dynamical Systems
Chirikov's Standard Map
State Space Targeting
Artificial Signalling Networks
State Space Targeting with ASNs
Mappings
Methodology
Results
Conclusions
References
The Effect of Membrane Receptor Clustering on Spatio-temporal Cell Signalling Dynamics
Introduction
Models
Results
Transient Phase
Binding Events Analysis
Ligand Temporal Dynamics
Receptor Temporal Dynamics
Discussion
References
Systems Biology Analysis of Kinase Inhibitor Protein Target Profiles in Leukemia Treatments
References
Multispecific Interactions in Enzymatic Signalling Cascades
Introduction
Results
Product Inhibition
Inactive Enzyme Interference
Conclusions
References
Protein Structure and Metabolic Networks
Role of Physico-chemical Properties of Amino Acids in Protein's Structural Organization: A Network Perspective
Introduction
Methods
Results and Discussion
Transitions of Largest Clustersâ?? Sizes Depend on Length Scale and Physico-chemical Nature of Amino Acid Nodes
Assortative Mixing Behavior and Clustering Coefficients of Hydrophobic Residues in LRNs
Clique Occurrences and Perimeters Covered by Cliques
Conclusions
References
Tailored Strategies for the Analysis of Metabolomic Data
Introduction
Methods
Results
Conclusion
References
Patterning and Rhythm Generation
Evolving Locomotion for a Simulated 12-DOF Quadruped Robot
Introduction
Implementation
Results and Discussion
Conclusion and Future Work
References
Predictive Modelling of Stem Cell Differentiation and Apoptosis in C. elegans
Introduction
Model Construction
Results
References
Criticality of Spatiotemporal Dynamics in Contact Mediated Pattern Formation
Introduction
Methods
Regulatory Network Models
Information Complexity
Network, Dynamics and Pattern Encoding
Experimental Study
Results and Discussion
N-C-D Analysis of Pattern Sets
Relationship between Network Complexity and Pattern Complexity
Summary
References
Neural Modelling and Neural Networks
The Vasopressin System - Asynchronous Burst Firing as a Signal Encoding Mechanism
Introduction
Background: Homeostatic Role of Vasopressin
Network Structure and Regulation
The Modelling Approach
Spiking Model Equations
The Single Neuron Model and Communication Mechanisms
Building a Robust Signal Encoding and Response Network
Building and Testing a Vasopressin System
Supply and Demand
Conclusion
References
The Effective Calcium/Calmodulin Concentration Determines the Sensitivity of CaMKII to the Frequency of Calcium Oscillations
Introduction
CaMKII Activation Model
Results
References
The Effect of Different Types of Synaptic Plasticity on the Performance of Associative Memory Networks with Excitatory and Inhibitory Sub-populations
Introduction
Materials and Methods
Network Models
Plasticity
Learning
Measures of Memory Performance
Simulator
Results
Varying Plasticity
Effect of Fixed Weight Size on Performance
Discussion
References
Simulating Neurons in Reaction-Diffusion Chemistry
References
Biomedical Modelling and Signal Processing
Extending an Established Simulation: Exploration of the Possible Effects Using a Case Study in Experimental Autoimmune Encephalomyelitis
The Proposed Methodology
The Proposed Case Study
Experimental Autoimmune Encephalomyelitis
Induction of Disease
Spontaneous Recovery from Disease
The CD200-CD200R Immune-Regulatory Pathway
Implementation of the Simulation
Evaluation of the Initial Model of the CD200 Pathway
Discussion and Conclusions
References
Human Uterine Excitation Patterns Leading to Labour: Synchronization or Propagation?
Introduction
Uterine Smooth Muscle Cell Electrophysiology and Models
Emergence of Tissue Electrophysiology
Connexins, Coupling and Conduction Velocity
Time Series Recordings
Uterine Tissue Geometry and Architecture
Integrated Model
Discussion and Conclusions
References
Evolving Computational Dynamical Systems to Recognise Abnormal Human Motor Function
Introduction
Materials and Methods
Data Sets
Classifier Architectures
Evolutionary Algorithm
Results
Conclusions
References
Heat-Maps and Visualization for Heterogeneous Biomedical Data Based on Information Distance Geometry
References
Information Processing and Representation
Bio-inspired Information Processing Applied to Engineering Systems
Introduction
Biological Investigation and Artificial Implementation
Heart Electronic System
Cellular Regulatory Networks Chemical System
Discussion
Application Areas
Medicine (Cancer)
Materials Science and Engineering (Active Materials)
Environment (Articial Photosynthesis)
Conclusion
References
Understanding the Regulation of Predatory and Anti-prey Behaviours for an Artificial Organism
Introduction
Predatory and Anti-prey Behaviours
Single Celled Organisms
Early Multi-cellular Organisms
Regulation between the Two Opposing Behaviours
Artificial Biochemical Network
How Are the Behaviours Encoded within the Networks?
The Evolved ABN
Assigning the w and b Values
Conclusion
References
Closing the Gap between Life and Physics
Introduction
Linking Life and Physics
Solid State Physics
Conclusion
References
Algebraic Analysis of the Computation in the Belousov-Zhabotinksy Reaction
Introduction
Discretisation
Krohn-Rhodes Theory
Analysis of BZ Reaction
Discussion and Conclusion
References
Algorithmic Approaches in Computational Biology
Improving Transcription Factor Binding Site Predictions by Using Randomised Negative Examples
Introduction
Background
Description of Data
Genomic Data
Randomised Negative Example Datasets
Methods
Pre-processing (Preparing Training and Test Sets)
The Classifier and Its Performance Measures
Cross-Validation
Post-processing (Filtering Short Predictions)
Results and Discussion
Yeast Dataset
Mouse Dataset
Visualisation of the Predictions
Conclusion
References
Finding the Minimal Gene Regulatory Function in the Presence of Undefined Transitional States Using a Genetic Algorithm
Introduction
Boolean Function Simplification Using the Quine-McCluskey Algorithm
Gene Feedback Detection
Boolean Function Minimization with Multi-objective Genetic Algorithms
Application of the Genetic Algorithm to a Melanoma Dataset
Conclusions and Future Work
References
Extracting Tailored Protein Complexes from Protein-Protein Interaction Networks
Introduction
Methods
Personalized Protein Ranking by Spreading Activation in PPI Networks
Personalized Ranking as Pattern Restoration
Personalized PageRank (PPR) Algorithm
Continuous-Attractor Dynamics (CAD) Algorithm
Comparison Experiment
Yeast Protein-Protein Interaction Network
Parameter Values
Results
Personalized Protein Ranking by Either the PPR or CAD Algorithm
Comparing the Performance of Personalized Protein Ranking between the PPR Algorithm and the CAD Algorithm
Comparing the Robustness against Changes in the Seed Pattern
Personalized Protein Ranking by Spreading Activation Tolerates Errors in PPI Networks
Personalized Protein Ranking for a Specific Example
Discussion
References
A Parallel Algorithm for Multiple Biological Sequence Alignment
Introduction
Biological Sequences
Sequence Alignment
Related Work
Method
Applying the Longest Common Subsequence Algorithm
Parallel Iterative Algorithm
Implementation
Simulation and Results
Conclusions and Future Work
References
Author Index

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