| 2012 | A Linear Kernel for the Complementary Maximal Strip Recovery Problem. Haitao Jiang, Binhai Zhu |
| 2012 | An Efficient Linear Pseudo-minimization Algorithm for Aho-Corasick Automata. Omar AitMous, Frédérique Bassino, Cyril Nicaud |
| 2012 | Approximation Algorithms and Hardness Results for Shortest Path Based Graph Orientations. Dima Blokh, Danny Segev, Roded Sharan |
| 2012 | Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Helsinki, Finland, July 3-5, 2012. Proceedings Juha Kärkkäinen, Jens Stoye |
| 2012 | Compressed String Dictionary Look-Up with Edit Distance One. Djamal Belazzougui, Rossano Venturini |
| 2012 | Computing the Burrows-Wheeler Transform of a String and Its Reverse. Enno Ohlebusch, Timo Beller, Mohamed Ibrahim Abouelhoda |
| 2012 | Computing the Rooted Triplet Distance between Galled Trees by Counting Triangles. Jesper Jansson, Andrzej Lingas |
| 2012 | Constant-Time Word-Size String Matching. Dany Breslauer, Leszek Gasieniec, Roberto Grossi |
| 2012 | Cross-Document Pattern Matching. Gregory Kucherov, Yakov Nekrich, Tatiana Starikovskaya |
| 2012 | Document Listing for Queries with Excluded Pattern. Wing-Kai Hon, Rahul Shah, Sharma V. Thankachan, Jeffrey Scott Vitter |
| 2012 | Efficient Algorithm for Circular Burrows-Wheeler Transform. Wing-Kai Hon, Tsung-Han Ku, Chen-Hua Lu, Rahul Shah, Sharma V. Thankachan |
| 2012 | Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees. Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu |
| 2012 | Efficient Two-Dimensional Pattern Matching with Scaling and Rotation and Higher-Order Interpolation. Christian Hundt, Florian Wendland |
| 2012 | FEMTO: Fast Search of Large Sequence Collections. Michael P. Ferguson |
| 2012 | Faster and Simpler Minimal Conflicting Set Identification - (Extended Abstract). Aïda Ouangraoua, Mathieu Raffinot |
| 2012 | Finding Longest Common Segments in Protein Structures in Nearly Linear Time. Yen Kaow Ng, Hirotaka Ono, Ling Ge, Shuai Cheng Li |
| 2012 | Fixed-Parameter Algorithms for Finding Agreement Supertrees. David Fernández-Baca, Sylvain Guillemot, Brad Shutters, Sudheer Vakati |
| 2012 | Gene Regulation, Protein Networks and Disease: A Computational Perspective. Ron Shamir |
| 2012 | Hardness of Longest Common Subsequence for Sequences with Bounded Run-Lengths. Guillaume Blin, Laurent Bulteau, Minghui Jiang, Pedro J. Tejada, Stéphane Vialette |
| 2012 | Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. Saad Sheikh, Rolf Backofen, Yann Ponty |
| 2012 | Least Random Suffix/Prefix Matches in Output-Sensitive Time. Niko Välimäki |
| 2012 | Local Exact Pattern Matching for Non-fixed RNA Structures. Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Schmiedl, Sebastian Will |
| 2012 | Minimum Leaf Removal for Reconciliation: Complexity and Algorithms. Riccardo Dondi, Nadia El-Mabrouk |
| 2012 | Near Linear Time Construction of an Approximate Index for All Maximum Consecutive Sub-sums of a Sequence. Ferdinando Cicalese, Eduardo Sany Laber, Oren Weimann, Raphael Yuster |
| 2012 | On Approximating String Selection Problems with Outliers. Christina Boucher, Gad M. Landau, Avivit Levy, David Pritchard, Oren Weimann |
| 2012 | On the Closest String via Rank Distance. Liviu Petrisor Dinu, Alexandru Popa |
| 2012 | Partitioning into Colorful Components by Minimum Edge Deletions. Sharon Bruckner, Falk Hüffner, Christian Komusiewicz, Rolf Niedermeier, Sven Thiel, Johannes Uhlmann |
| 2012 | Pattern Matching in Multiple Streams. Raphaël Clifford, Markus Jalsenius, Ely Porat, Benjamin Sach |
| 2012 | Simple and Efficient LZW-Compressed Multiple Pattern Matching. Pawel Gawrychowski |
| 2012 | Speeding Up q-Gram Mining on Grammar-Based Compressed Texts. Keisuke Goto, Hideo Bannai, Shunsuke Inenaga, Masayuki Takeda |
| 2012 | The Complexity of String Partitioning. Anne Condon, Ján Manuch, Chris Thachuk |
| 2012 | The Maximum Number of Squares in a Tree. Maxime Crochemore, Costas S. Iliopoulos, Tomasz Kociumaka, Marcin Kubica, Jakub Radoszewski, Wojciech Rytter, Wojciech Tyczynski, Tomasz Walen |
| 2012 | The Parameterized Complexity of the Shared Center Problem. Zhi-Zhong Chen, Lusheng Wang, Wenji Ma |
| 2012 | Time-Space Trade-Offs for Longest Common Extensions. Philip Bille, Inge Li Gørtz, Benjamin Sach, Hjalte Wedel Vildhøj |
| 2012 | Towards an Optimal Space-and-Query-Time Index for Top-k Document Retrieval. Wing-Kai Hon, Rahul Shah, Sharma V. Thankachan |
| 2012 | Wavelet Trees for All. Gonzalo Navarro |