Information Processing in Cells and Tissues
9th International Conference, IPCAT 2012, Cambridge, UK, March 31 -- April 2, 2012, Proceedings
Published on 22. March 2012
XII, 278 pages
978-3-642-28792-3 (ISBN)
Description
This book constitutes the refereed proceedings of the 9th International Conference on Information in Cells and Tissues, IPCAT 2012, held in Cambridge, UK, in March/April 2012.
The 13 revised full papers presented together with 26 extended abstracts were carefully reviewed and selected from numerous submissions. The papers cover a wide range of topics in disciplines related to genetic and epigenetic networks, transcriptomics and gene regulation, signalling pathways and responses, protein structure and metabolic networks, patterning and rhythm generation, neural modelling and neural networks, biomedical modelling and signal processing, information processing and representation, and algorithmic approaches in computational biology.
The 13 revised full papers presented together with 26 extended abstracts were carefully reviewed and selected from numerous submissions. The papers cover a wide range of topics in disciplines related to genetic and epigenetic networks, transcriptomics and gene regulation, signalling pathways and responses, protein structure and metabolic networks, patterning and rhythm generation, neural modelling and neural networks, biomedical modelling and signal processing, information processing and representation, and algorithmic approaches in computational biology.
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Michael A. Lones | Stephen L. Smith | Sarah Teichmann
Information Processing in Cells and Tissues
9th International Conference, IPCAT 2012, Cambridge, UK, March 31 -- April 2, 2012, Proceedings
Book
04/2012
Springer
€53.49
Shipment within 7-9 days
Content
- 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
