| 2023 | ITiCSE | BeLLE: Multinational Research Collaboration on Bebras & ViLLE. | Heidi Kaarto, Heikki Hyyr, Marika Parviainen |
| 2018 | CPM | Computing longest common square subsequences. | Takafumi Inoue, Shunsuke Inenaga, Heikki Hyyr, Hideo Bannai, Masayuki Takeda |
| 2017 | SPIRE | Mining Bit-Parallel LCS-length Algorithms. | Heikki Hyyr |
| 2016 | SOFSEM | Compacting a Dynamic Edit Distance Table by RLE Compression. | Heikki Hyyr, Shunsuke Inenaga |
| 2010 | SOFSEM | Dynamic Edit Distance Table under a General Weighted Cost Function. | Heikki Hyyr, Kazuyuki Narisawa, Shunsuke Inenaga |
| 2008 | IWOCA | Notes on generating completely condensed d-neighborhoods. | Heikki Hyyr |
| 2008 | SPIRE | An Efficient Linear Space Algorithm for Consecutive Suffix Alignment under Edit Distance (Short Preliminary Paper). | Heikki Hyyr |
| 2005 | SOFSEM | Fast Bit-Vector Algorithms for Approximate String Matching Under Indel Distance. | Heikki Hyyr, Yoan J. Pinzn, Ayumi Shinohara |
| 2005 | SPIRE | Restricted Transposition Invariant Approximate String Matching Under Edit Distance. | Heikki Hyyr |
| 2004 | DIS | Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance. | Shunsuke Inenaga, Hideo Bannai, Heikki Hyyr, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano |
| 2004 | SPIRE | An Improvement and an Extension on the Hybrid Index for Approximate String Matching. | Heikki Hyyr |
| 2004 | WABI | Finding Optimal Pairs of Patterns. | Hideo Bannai, Heikki Hyyr, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano |
| 2003 | SPIRE | Bit-Parallel Approximate String Matching Algorithms with Transposition. | Heikki Hyyr |
| 2003 | SPIRE | A Practical Index for Genome Searching. | Heikki Hyyr, Gonzalo Navarro |
| 2002 | CPM | Faster Bit-Parallel Approximate String Matching. | Heikki Hyyr, Gonzalo Navarro |
| 2001 | SPIRE | On Using Two-Phase Filtering in Indexed Approximate String Matching with Application to Searching Unique Oligonucleotides. | Heikki Hyyr |