On Approximate String Matching of Unique Oligonucleotides (97 KB)
Co-work with Martti Juhola and Mauno Vihinen.
Included in the proceedings of the 10th World Congress on Health and Medical Informatics (Medinfo 2001), IOS Press.
On Applying String Matching in Searching Unique Oligonucleotides (53 KB)
Included in the proceedings of the 2001 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS 2001), CS Press.
On Using Two-Phase Filtering in Indexed Approximate String Matching with Application to Searching unique Oligonucleotides (99 KB)
Published in the proceedings of the 8th International Symposium on String Processing and information Retrieval (SPIRE 2001), IEEE Press.
Extending and Explaining the Bit-Parallel Approximate String Matching Algorithm of Myers (146 KB)
Technical report A2001-10 of the Department of Computer and Information Sciences, University of Tampere.
Errata
Faster Bit-Parallel Approximate String Matching (293 KB)
Co-work with Gonzalo Navarro.
Published in the proceedings of the 13th International Symposium on Combinatorial Pattern Matching (CPM 2002), Lecture Notes in Computer Science, Springer-Verlag.
A Bit-Vector Algorithm for Computing Levenshtein and Damerau Edit Distances (133 KB)
Included in the proceedings of the Prague Stringology Conference 2002 (PSC 2002).
Errata
Bit-Parallel Approximate String Matching Algorithms with Transposition (134 KB)
Published in the proceedings of the 10th International Symposium on String Processing and information Retrieval (SPIRE 2003), Lecture Notes in Computer Science, Springer-Verlag.
Errata
A Practical Index for Genome Searching (119 KB)
Co-work with Gonzalo Navarro.
Published in the proceedings of the 10th International Symposium on String Processing and information Retrieval (SPIRE 2003), Lecture Notes in Computer Science, Springer-Verlag.
Errata
Practical Methods for Approximate String Matching (579 KB)
PhD Thesis (public defense was on December 5th, 2003).
Increased Bit-Parallelism for Approximate String Matching (161 KB)
Co-work with Kimmo Fredriksson and Gonzalo Navarro.
Published in the proceedings of the 3rd International Workshop on Experimental and Efficient Algorithms (WEA 2004), Lecture Notes in Computer Science, Springer-Verlag.
Finding Optimal Pairs of Patterns (168 KB)
Co-work with Hideo Bannai, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai and Satoru Miyano.
Published in the proceedings of the 4th Workshop on Algorithms in Bioinformatics (WABI 2004), Lecture Notes in Computer Science (Bioinformatics), Springer-Verlag. A poster based on the paper was also displayed in the 12th International Conference on Intelligent Systems for Molecular Biology / the 3rd European Conference on Computational Biology (ISMB/ECCB 2004).
Bit-Parallel LCS-length Computation Revisited (156 KB)
Included in the proceedings of the 15th Australasian Workshop on Combinatorial Algorithms (AWOCA 2004).
A Note on Bit-Parallel Alignment Computation (105 KB)
Included in the proceedings of the Prague Stringology Conference '04 (PSC 2004).
An Improvement and an Extension on the Hybrid Index for Approximate String Matching (71 KB)
A two-page abstract is published in the proceedings of the 11th International Symposium on String Processing and Information retrieval (SPIRE 2004), Lecture Notes in Computer Science, Springer-Verlag.
Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance (199 KB)
Co-work with Shunsuke Inenaga, Hideo Bannai, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai and Satoru Miyano.
Published in the proceedings of the 7th International Conference on Discovery Science (DS 2004), Lecture Notes in Computer Science , Springer-Verlag.
On Bit-Parallel Processing of Multibyte Text (156 KB)
Co-work with Jun Takaba, Ayumi Shinohara and Masayuki Takeda.
Published in the proceedings of the 1st Asia Information Retrieval Symposium (AIRS 2004), Lecture Notes in Computer Science 3411, Springer-Verlag.
Fast Bit-Vector Algorithms for Approximate String Matching under Indel-Distance (108 KB)
Co-work with Yoan Pinzon and Ayumi Shinohara.
Published in the proceedings of the 32st Annual Conference on Current Trends in Theory and Practice of Informatics (SOFSEM 2005), Lecture Notes in Computer Science 3381, Springer-Verlag.
On Boyer-Moore Preprocessing (192 KB)
Technical report D2004-1 of the Department of Computer Sciences, University of Tampere.
New Bit-Parallel Algorithm for Approximate String Matching under Indel Distance (193 KB)
Co-work with Yoan Pinzon and Ayumi Shinohara.
Published in the proceedings of the 4th International Workshop on Experimental and Efficient Algorithms (WEA 2005), Lecture Notes in Computer Science 3503, Springer-Verlag.
Bit-Parallel Computation of Local Similarity Score Matrices with Unitary Weights (173 KB)
Co-work with Gonzalo Navarro.
Included in the proceedings of the Prague Stringology Conference '05 (PSC 2005).
Restricted Transposition Invariant Approximate String Matching Under Edit Distance (148 KB)
Published in the proceedings of the 12th International Symposium on String Processing and Information retrieval (SPIRE 2005), Lecture Notes in Computer Science 3772, Springer-Verlag.
Tighter Packed Bit-Parallel NFA for Approximate String Matching (102 KB)
A 2-page abstract based on this short paper will appear in the proceedings of the 11th International Conference on Implementation and Application of Automata (CIAA 2006), Lecture Notes in Computer Science 4094, Springer-Verlag.
Offline publications:
A Bit-Vector Algorithm for Computing Levenshtein and Damerau Edit Distances
A slightly modified version of the paper in PSC 2002 conference.
Published in Nordic Journal of Computing 10:1 (2003).
Errata
On Exact String Matching of Unique Oligonucleotides
Co-work with Martti Juhola and Mauno Vihinen.
Published in Computers in Biology and Medicine 35:2 (2005).
Bit-parallel Witnesses and their Applications to Approximate String Matching
Co-work with Gonzalo Navarro. This is an extension of our
paper that was in CPM 2002 conference.
Published in Algorithmica 41:3 (2005).
Bit-Parallel Approximate String Matching Algorithms with Transposition
This is a slight extension of a paper that appeared in SPIRE 2003 conference.
Published in Journal of Discrete Algorithms 3:2-4 (2005).
Errata
An O(N^2) Algorithm for Discovering Optimal Boolean Pattern Pairs
Co-work with Hideo Bannai, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai and Satoru Miyano.
This is an extension of a paper that appeared in WABI 2004 conference.
Published in IEEE Transactions on Computational Biology and Bioinformatics 1:4 (2004).
Genome-wide selection of unique and valid oligonucleotides
Co-work with Martti Juhola and Mauno Vihinen.
Published in Nucleic Acids Research (methods online) 33:13 (2005).
Increased Bit-Parallelism for Approximate and Multiple String Matching
Co-work with Kimmo Fredriksson and Gonzalo Navarro. This is an extension of our
paper that was in WEA 2004 conference.
Published in The ACM Journal of Experimental Algorithmics 10 (2005)
Bit-Parallel Computation of Local Similarity Score Matrices with Unitary Weights
Co-work with Gonzalo Navarro. This is an extension of our paper from PSC 2005 conference.
Published in International Journal of Foundations of Computer Science 17:6 (2006).
Improving the Bit-Parallel NFA of Baeza-Yates and Navarro for Approximate String Matching
To be published in Information Processing Letters.
An efficient linear space algorithm for consecutive suffix alignment under edit distance.
Published in the proceedings of the 15th International Symposium on String Processing and Information retrieval (SPIRE 2008), Lecture Notes in Computer Science 5280, Springer-Verlag.