| 2005 | Weighted Directed Word Graph. | Meng Zhang, Liang Hu, Qiang Li, Jiubin Ju |
| 2005 | A Linear Tree Edit Distance Algorithm for Similar Ordered Trees. | Hlne Touzet |
| 2005 | Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements. | Jijun Tang, Bernard M. E. Moret |
| 2005 | An Efficient Algorithm for Generating Super Condensed Neighborhoods. | Lus M. S. Russo, Arlindo L. Oliveira |
| 2005 | Incremental Inference of Relational Motifs with a Degenerate Alphabet. | Nadia Pisanti, Henry Soldano, Mathilde Carpentier |
| 2005 | The Median Problem for the Reversal Distance in Circular Bacterial Genomes. | Enno Ohlebusch, Mohamed Ibrahim Abouelhoda, Kathrin Hockel, Jan Stallkamp |
| 2005 | Hardness of Optimal Spaced Seed Design. | Franois Nicolas, Eric Rivals |
| 2005 | Linear-Time Construction of Compressed Suffix Arrays Using o(n log n)-Bit Working Space for Large Alphabets. | Joong Chae Na |
| 2005 | On the Longest Common Rigid Subsequence Problem. | Bin Ma, Kaizhong Zhang |
| 2005 | An Extension of the Burrows Wheeler Transform and Applications to Sequence Comparison and Data Compression. | Sabrina Mantaci, Antonio Restivo, Giovanna Rosone, Marinella Sciortino |
| 2005 | Exact and Approximation Algorithms for DNA Tag Set Design. | Ion I. Mandoiu, Dragos Trinca |
| 2005 | Succinct Suffix Arrays Based on Run-Length Encoding. | Veli Mkinen, Gonzalo Navarro |
| 2005 | Text Indexing with Errors. | Moritz G. Maa, Johannes Nowak |
| 2005 | A Fast Algorithm for Approximate String Matching on Gene Sequences. | Zheng Liu, Xin Chen, James Borneman, Tao Jiang |
| 2005 | Using PQ Trees for Comparative Genomics. | Gad M. Landau, Laxmi Parida, Oren Weimann |
| 2005 | A New Compressed Suffix Tree Supporting Fast Search and Its Construction Algorithm Using Optimal Working Space. | Dong Kyue Kim, Heejin Park |
| 2005 | On the Complexity of Sparse Exon Assembly. | Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson |
| 2005 | Reducing the Size of NFAs by Using Equivalences and Preorders. | Lucian Ilie, Roberto Solis-Oba, Sheng Yu |
| 2005 | An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery. | Paul Horton, Wataru Fujibuchi |
| 2005 | Two Dimensional Parameterized Matching. | Carmit Hazay, Moshe Lewenstein, Dekel Tsur |
| 2005 | Prefix-Free Regular-Expression Matching. | Yo-Sub Han, Yajun Wang, Derick Wood |
| 2005 | Speeding up Parsing of Biological Context-Free Grammars. | Daniel Fredouille, Christopher H. Bryant |
| 2005 | A Simple Fast Hybrid Pattern-Matching Algorithm. | Frantisek Franek, Christopher G. Jennings, William F. Smyth |
| 2005 | Parametric Analysis for Ungapped Markov Models of Evolution. | David Fernndez-Baca, Balaji Venkatachalam |
| 2005 | A New Periodicity Lemma. | Kangmin Fan, William F. Smyth, R. Jaime Simpson |