The refereed proceedings of the 9th Annual International Computing and Combinatorics Conference, COCOON 2003, held in Big Sky, MT, USA in July 2003.The 52 revised full papers presented together with 3 invited contributions were carefully reviewed and selected from 114 submissions. The papers are organized in topical sections on computational geometry, computational biology, computability and complexity theory, graph theory and graph algorithms, automata and Petri net theory, distributed computing, Web-based computing, scheduling, graph drawing, and fixed-parameter complexity theory.

Invited Lecture.- LIAR!.- Experiments for Algorithm Engineering.- Empirical Exploration of Perfect Phylogeny Haplotyping and Haplotypers.- Computational Geometry I.- Cylindrical Hierarchy for Deforming Necklaces.- Geometric Algorithms for Agglomerative Hierarchical Clustering.- Traveling Salesman Problem of Segments.- Subexponential-Time Algorithms for Maximum Independent Set and Related Problems on Box Graphs.- Computational Biology I.- A Space Efficient Algorithm for Sequence Alignment with Inversions.- On the Similarity of Sets of Permutations and Its Applications to Genome Comparison.- On All-Substrings Alignment Problems.- Computational/Complexity Theory I.- The Specker-Blatter Theorem Revisited.- On the Divergence Bounded Computable Real Numbers.- Sparse Parity-Check Matrices over Finite Fields.- Graph Theory/Algorithms I.- On the Full and Bottleneck Full Steiner Tree Problems.- The Structure and Number of Global Roundings of a Graph.- On Even Triangulations of 2-Connected Embedded Graphs.- Automata/Petri Net Theory.- Petri Nets with Simple Circuits.- Automatic Verification of Multi-queue Discrete Timed Automata.- Graph Theory/Algorithms II.- List Total Colorings of Series-Parallel Graphs.- Finding Hidden Independent Sets in Interval Graphs.- Matroid Representation of Clique Complexes.- Complexity Theory II.- On Proving Circuit Lower Bounds against the Polynomial-Time Hierarchy: Positive and Negative Results.- The Complexity of Boolean Matrix Root Computation.- A Fast Bit-Parallel Algorithm for Matching Extended Regular Expressions.- Distributed Computing.- Group Mutual Exclusion Algorithms Based on Ticket Orders.- Distributed Algorithm for Better Approximation of the Maximum Matching.- Efficient Mappings for Parity-Declustered Data Layouts.- Web-Based Computing.-Approximate Rank Aggregation.- Perturbation of the Hyper-Linked Environment.- Fast Construction of Generalized Suffix Trees over a Very Large Alphabet.- Complexity Theory III.- Complexity Theoretic Aspects of Some Cryptographic Functions.- Quantum Sampling for Balanced Allocations.- Graph Theory/Algorithms III.- Fault-Hamiltonicity of Product Graph of Path and Cycle.- How to Obtain the Complete List of Caterpillars.- Randomized Approximation of the Stable Marriage Problem.- Computational Geometry II.- Tetris is Hard, Even to Approximate.- Approximate MST for UDG Locally.- Efficient Construction of Low Weight Bounded Degree Planar Spanner.- Graph Theory/Algorithms IV.- Isoperimetric Inequalities and the Width Parameters of Graphs.- Graph Coloring and the Immersion Order.- Optimal MST Maintenance for Transient Deletion of Every Node in Planar Graphs.- Scheduling.- Scheduling Broadcasts with Deadlines.- Improved Competitive Algorithms for Online Scheduling with Partial Job Values.- Majority Equilibrium for Public Facility Allocation.- Computational Geometry III.- On Constrained Minimum Pseudotriangulations.- Pairwise Data Clustering and Applications.- Covering a Set of Points with a Minimum Number of Turns.- Graph Drawing.- Area-Efficient Order-Preserving Planar Straight-Line Drawings of Ordered Trees.- Bounds for Convex Crossing Numbers.- On Spectral Graph Drawing.- Computational Biology II.- On a Conjecture on Wiener Indices in Combinatorial Chemistry.- Double Digest Revisited: Complexity and Approximability in the Presence of Noisy Data.- Fast and Space-Efficient Location of Heavy or Dense Segments in Run-Length Encoded Sequences.- Genomic Distances under Deletions and Insertions.- Fixed-Parameter Complexity Theory.- Minimal Unsatisfiable Formulas with Bounded Clause-Variable Difference are Fixed-Parameter Tractable.