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Algebraic Biology

This book constitutes the refereed proceedings of the Second International Conference on Algebraic Biology, AB 2007, held at the Castle of Hagenberg, Austria in July 2007 as part of the RISC Summer 2007, organized by the Research Institute for Symbolic Computation.

The 19 revised full papers presented together with 3 invited papers and 4 tutorials were carefully reviewed and selected from 40 submissions. The conference is the interdisciplinary forum for the presentation of research on all aspects of applications of symbolic computation (computer algebra, computational logic, and related methods) in biology as well as other problems in biology being approached with symbolic methods.

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Table of Contents

Algebraic Systems Biology: Theses and Hypotheses.- Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions.- Membrane Computing as a Framework for Bio-modeling (An Informal Glimpse).- Relating Attractors and Singular Steady States in the Logical Analysis of Bioregulatory Networks.- Translating Time-Course Gene Expression Profiles into Semi-algebraic Hybrid Automata Via Dimensionality Reduction.- On Proving the Absence of Oscillations in Models of Genetic Circuits.- Attenuation Regulation as a Term Rewriting System.- Glucose-Insulin Control of Type1 Diabetic Patients in H2/H??? Space Via Computer Algebra.- Exact Parameter Determination for Parkinson's Disease Diagnosis with PET Using an Algebraic Approach.- Efficient Haplotype Inference with Pseudo-boolean Optimization.- An Algebraic Algorithm for the Identification of Glass Networks with Periodic Orbits Along Cyclic Attractors.- Analyzing Pathways Using SAT-Based Approaches.- Algorithmic Algebraic Model Checking IV: Characterization of Metabolic Networks.- Cascaded Games.- On Differential Algebraic Decision Methods for the Estimation of Anaerobic Digestion Models.- Protein Structure Prediction Using Residual Dipolar Couplings.- A Stochastic Pi Calculus for Concurrent Objects.- Modeling Static Biological Compartments with Beta-binders.- Deducing Interactions in Partially Unspecified Biological Systems.- Reduction of Algebraic Parametric Systems by Rectification of Their Affine Expanded Lie Symmetries.- Prefix Reversals on Binary and Ternary Strings.- Toric Ideals of Phylogenetic Invariants for the General Group-Based Model on Claw Trees K 1,n .- Inference of Protein-Protein Interactions by Using Co-evolutionary Information.- A Short Survey of Automated Reasoning.- Inference of Complex Regulatory Network for the Cell Cycle System in Saccharomyces Cerevisiae.- Manifestation and Exploitation of Invariants in Bioinformatics.

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