| 2009 | Modeling and Algorithmic Challenges in Online Social Networks. | Ravi Kumar |
| 2009 | Deconstructing Intractability: A Case Study for Interval Constrained Coloring. | Christian Komusiewicz, Rolf Niedermeier, Johannes Uhlmann |
| 2009 | Generalized Substring Compression. | Orgad Keller, Tsvi Kopelowitz, Shir Landau, Moshe Lewenstein |
| 2009 | Permuted Longest-Common-Prefix Array. | Juha Krkkinen, Giovanni Manzini, Simon J. Puglisi |
| 2009 | New Complexity Bounds for Image Matching under Rotation and Scaling. | Christian Hundt, Maciej Liskiewicz |
| 2009 | CPM's 20th Anniversary: A Statistical Retrospective. | Elena Yavorska Harris, Thierry Lecroq, Gregory Kucherov, Stefano Lonardi |
| 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 |
| 2009 | On the Value of Multiple Read/Write Streams for Data Compression. | Travis Gagie |
| 2009 | Haplotype Inference Constrained by Plausible Haplotype Data. | Michael R. Fellows, Tzvika Hartman, Danny Hermelin, Gad M. Landau, Frances A. Rosamond, Liat Rozenberg |
| 2009 | An Efficient Matching Algorithm for Encoded DNA Sequences and Binary Strings. | Simone Faro, Thierry Lecroq |
| 2009 | Graph Mining: Patterns, Generators and Tools. | Christos Faloutsos |
| 2009 | Contracted Suffix Trees: A Simple and Dynamic Text Indexing Data Structure. | Andrzej Ehrenfeucht, Ross M. McConnell, Sung-Whan Woo |
| 2009 | Maximum Motif Problem in Vertex-Colored Graphs. | Riccardo Dondi, Guillaume Fertin, Stphane Vialette |
| 2009 | Multiple Alignment of Biological Networks: A Flexible Approach. | Yves-Pol Denilou, Frdric Boyer, Alain Viari, Marie-France Sagot |
| 2009 | Online Approximate Matching with Non-local Distances. | Raphal Clifford, Benjamin Sach |
| 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, Cdric Chauve, Marni Mishna, Dominique Rossin |
| 2009 | Statistical Properties of Factor Oracles. | Jrmie Bourdon, Irena Rusu |
| 2009 | Reoptimization of the Shortest Common Superstring Problem. | Davide Bil, Hans-Joachim Bckenhauer, Dennis Komm, Richard Krlovic, Tobias Mmke, Sebastian Seibert, Anna Zych |
| 2009 | Fast Searching in Packed Strings. | Philip Bille |
| 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 | Faster and Space-Optimal Edit Distance "1" Dictionary. | Djamal Belazzougui |
| 2009 | Sparse RNA Folding: Time and Space Efficient Algorithms. | Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson |
| 2009 | Fast RNA Structure Alignment for Crossing Input Structures. | Rolf Backofen, Gad M. Landau, Mathias Mhl, Dekel Tsur, Oren Weimann |