Editorial, special issue on bioinformatics

Abstract

Bioinformatics has been an active research area bordering biology and computer science since about a decade ago. Combinatorial optimization methods have proven to be productive in various branches of bioinformatics, e.g., genomic distance computation, DNA sequence analysis and RNA fold prediction, etc. I am honored to have the chance to edit this special issue on bioinformatics aiming at attracting more bioinformatics research using combinatorial optimization methods. There are six papers in this special issue, four of which are selected from ISAAC 2005 (the 16th International Symposium on Algorithms and Computation). The first paper is “Improved Algorithms for Largest Cardinality 2-Interval Pattern Problem,” by Erdong Chen, Linji Yang and Hao Yuan. The authors followed the 2interval model for the RNA secondary structure proposed by Vialette. They improved the running times of three polynomially solvable cases; namely, proceding & nesting, crossing, and a special case on nesting & crossing when the input intervals are disjoint. The second paper is “A 2-Approximation for the Preceding-and-Crossing Structured 2-Interval Pattern Problem,” by Minghui Jiang. Like the first paper, this one is also based on a similar model. The author presented a simple approximation solution for the general preceding & crossing case (which is known to be NP-complete). The previous approximation factor of 6 is reduced to 2. The third paper “Efficient Algorithms for Finding a Longest Common Increasing Subsequence,” by Wun-Tat Chan, Yong Zhang, Stanley P.Y. Fung, Deshi Ye and Hong Zhu, focuses on computing the longest sequence among all increasing sequences that are subsequences of the m given sequences. The running times of the previous algorithms were greatly improved. For example, when m = 2 the previous time bound is O(n2) while the new bound is almost linear for practical datasets. In the fourth paper “An Efficient Polynomial Space and Polynomial Delay Algorithm for Enumeration of Maximal Motifs in a Sequence,” Hiroki Arimura and Takeaki