Information Processing in Cells and Tissues

1. Front Matter

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2. Genetic and Epigenetic Networks

   1. Using Artificial Epigenetic Regulatory Networks to Control Complex Tasks within Chaotic Systems

      • Alexander P. Turner, Michael A. Lones, Luis A. Fuente, Susan Stepney, Leo S. Caves, Andy M. Tyrrell

      Pages 1-11

   2. A Gene Regulatory Network Simulation of Heterosis

      • Peter Martin Ferdinand Emmrich, Hannah Elizabeth Roberts, Vera Pancaldi

      Pages 12-16

   3. Comparing Discrete and Piecewise Affine Differential Equation Models of Gene Regulatory Networks

      • Shahrad Jamshidi, Heike Siebert, Alexander Bockmayr

      Pages 17-24

   4. Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data

      • Fabien Corblin, Eric Fanchon, Laurent Trilling, Claudine Chaouiya, Denis Thieffry

      Pages 25-30

3. Transcriptomics and Gene Regulation

   1. CRISPR Transcript Processing: An Unusual Mechanism for Rapid Production of Desired Molecules

      • Marko Djordjevic, Konstantin Severinov, Magdalena Djordjevic

      Pages 31-34

   2. A Comprehensive Computational Model to Simulate Transcription Factor Binding in Prokaryotes

      • Nicolae Radu Zabet, Boris Adryan

      Pages 35-37

4. Signalling Pathways and Responses

   1. Evolved Artificial Signalling Networks for the Control of a Conservative Complex Dynamical System

      • Luis A. Fuente, Michael A. Lones, Alexander P. Turner, Susan Stepney, Leo S. Caves, Andy M. Tyrrell

      Pages 38-49

   2. The Effect of Membrane Receptor Clustering on Spatio-temporal Cell Signalling Dynamics

      • Bertrand R. Caré, Hédi A. Soula

      Pages 50-61

   3. Systems Biology Analysis of Kinase Inhibitor Protein Target Profiles in Leukemia Treatments

      • Jacques Colinge, Uwe Rix, Keiryn L. Bennett, Giulio Superti-Furga

      Pages 62-66

   4. Multispecific Interactions in Enzymatic Signalling Cascades

      • Daniel D. Seaton, J. Krishnan

      Pages 67-73

5. Protein Structure and Metabolic Networks

   1. Role of Physico-chemical Properties of Amino Acids in Protein’s Structural Organization: A Network Perspective

      • Dhriti Sengupta, Sudip Kundu

      Pages 74-81

   2. Tailored Strategies for the Analysis of Metabolomic Data

      • Kristen Feher, Kathrin Jürchott, Joachim Selbig

      Pages 82-89

6. Patterning and Rhythm Generation

   1. Evolving Locomotion for a Simulated 12-DOF Quadruped Robot

      • Gordon Klaus, Kyrre Glette, Mats Høvin

      Pages 90-98

   2. Predictive Modelling of Stem Cell Differentiation and Apoptosis in C. elegans

      • Antje Beyer, Ralf Eberhard, Nir Piterman, Michael O. Hengartner, Alex Hajnal, Jasmin Fisher

      Pages 99-104

   3. Criticality of Spatiotemporal Dynamics in Contact Mediated Pattern Formation

      • Nicholas S. Flann, Hamid Mohamadlou, Gregory J. Podgorski

      Pages 105-116

7. Neural Modelling and Neural Networks

   1. The Vasopressin System – Asynchronous Burst Firing as a Signal Encoding Mechanism

      • Duncan J. MacGregor, Tom F. Clayton, Gareth Leng

      Pages 117-130

   2. The Effective Calcium/Calmodulin Concentration Determines the Sensitivity of CaMKII to the Frequency of Calcium Oscillations

      • Thiago M. Pinto, Maria J. Schilstra, Volker Steuber

      Pages 131-135

   3. The Effect of Different Types of Synaptic Plasticity on the Performance of Associative Memory Networks with Excitatory and Inhibitory Sub-populations

      • Alex Metaxas, Reinoud Maex, Volker Steuber, Rod Adams, Neil Davey

      Pages 136-142

   4. Simulating Neurons in Reaction-Diffusion Chemistry

      • James Stovold, Simon O’Keefe

      Pages 143-149

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.

• bioinformatics
• biomedic modelling
• computational biology
• genetic networks
• neural networks
• pattern recognition
• systems biology

• Department of Electronics, University of York, York, UK

  Michael A. Lones, Stephen L. Smith, James A. Walker, Martin A. Trefzer

• MRC Laboratory of Molecular Biology, Cambridge, UK

  Sarah Teichmann

• The Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

  Felix Naef

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