| 2009 | An Efficient Matching Algorithm for Encoded DNA Sequences and Binary Strings. Simone Faro, Thierry Lecroq |
| 2009 | Approximate Matching for Run-Length Encoded Strings Is 3sum-Hard. Kuan-Yu Chen, Ping-Hui Hsu, Kun-Mao Chao |
| 2009 | Average-Case Analysis of Perfect Sorting by Reversals. Mathilde Bouvel, Cédric Chauve, Marni Mishna, Dominique Rossin |
| 2009 | CPM's 20th Anniversary: A Statistical Retrospective. Elena Yavorska Harris, Thierry Lecroq, Gregory Kucherov, Stefano Lonardi |
| 2009 | Combinatorial Pattern Matching, 20th Annual Symposium, CPM 2009, Lille, France, June 22-24, 2009, Proceedings Gregory Kucherov, Esko Ukkonen |
| 2009 | Contracted Suffix Trees: A Simple and Dynamic Text Indexing Data Structure. Andrzej Ehrenfeucht, Ross M. McConnell, Sung-Whan Woo |
| 2009 | Deconstructing Intractability: A Case Study for Interval Constrained Coloring. Christian Komusiewicz, Rolf Niedermeier, Johannes Uhlmann |
| 2009 | Efficient Inference of Haplotypes from Genotypes on a Pedigree with Mutations and Missing Alleles (Extented Abstract). Wei-Bung Wang, Tao Jiang |
| 2009 | Fast RNA Structure Alignment for Crossing Input Structures. Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann |
| 2009 | Fast Searching in Packed Strings. Philip Bille |
| 2009 | Faster and Space-Optimal Edit Distance "1" Dictionary. Djamal Belazzougui |
| 2009 | Finding All Sorting Tandem Duplication Random Loss Operations. Matthias Bernt, Ming-Chiang Chen, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao, Martin Middendorf |
| 2009 | Generalized Substring Compression. Orgad Keller, Tsvi Kopelowitz, Shir Landau, Moshe Lewenstein |
| 2009 | Graph Mining: Patterns, Generators and Tools. Christos Faloutsos |
| 2009 | Haplotype Inference Constrained by Plausible Haplotype Data. Michael R. Fellows, Tzvika Hartman, Danny Hermelin, Gad M. Landau, Frances A. Rosamond, Liat Rozenberg |
| 2009 | LCS Approximation via Embedding into Local Non-repetitive Strings. Gad M. Landau, Avivit Levy, Ilan Newman |
| 2009 | Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time. Thu-Hien To, Michel Habib |
| 2009 | Linear Time Suffix Array Construction Using D-Critical Substrings. Ge Nong, Sen Zhang, Wai Hong Chan |
| 2009 | Maximum Motif Problem in Vertex-Colored Graphs. Riccardo Dondi, Guillaume Fertin, Stéphane Vialette |
| 2009 | Modeling and Algorithmic Challenges in Online Social Networks. Ravi Kumar |
| 2009 | Multiple Alignment of Biological Networks: A Flexible Approach. Yves-Pol Deniélou, Frédéric Boyer, Alain Viari, Marie-France Sagot |
| 2009 | New Complexity Bounds for Image Matching under Rotation and Scaling. Christian Hundt, Maciej Liskiewicz |
| 2009 | On the Value of Multiple Read/Write Streams for Data Compression. Travis Gagie |
| 2009 | Online Approximate Matching with Non-local Distances. Raphaël Clifford, Benjamin Sach |
| 2009 | Periodic String Comparison. Alexander Tiskin |
| 2009 | Permuted Longest-Common-Prefix Array. Juha Kärkkäinen, Giovanni Manzini, Simon J. Puglisi |
| 2009 | Quasi-distinct Parsing and Optimal Compression Methods. Amihood Amir, Yonatan Aumann, Avivit Levy, Yuri Roshko |
| 2009 | Reoptimization of the Shortest Common Superstring Problem. Davide Bilò, Hans-Joachim Böckenhauer, Dennis Komm, Richard Královic, Tobias Mömke, Sebastian Seibert, Anna Zych |
| 2009 | Sparse RNA Folding: Time and Space Efficient Algorithms. Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson |
| 2009 | Statistical Properties of Factor Oracles. Jérémie Bourdon, Irena Rusu |
| 2009 | Text Indexing, Suffix Sorting, and Data Compression: Common Problems and Techniques. Roberto Grossi |
| 2009 | The Structure of Level-k Phylogenetic Networks. Philippe Gambette, Vincent Berry, Christophe Paul |