| 2007 | AINA | Kinetic Analysis of Ligand-Receptor Complex Formation with the Aid of Computer Simulation. | Hiroshi Kobayashi, Ryuzo Azuma, Akihiko Konagaya |
| 2007 | CCGRID | RABC: A Conceptual Design of Pervasive Infrastructure for Browser Computing based on Ajax technologies. | Fumikazu Konishi, Manabu Ishii, Shingo Ohki, Ryo Umetsu, Akihiko Konagaya |
| 2007 | FPL | An FPGA Implementation of Multiple Sequence Alignment Based on Carrillo-Lipman Method. | Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya |
| 2007 | FPL | High speed tablation system using an FPGA designed for distribution tables of frequent DNA subsequences. | Yoshiki Yamaguchi, Tsutomu Maruyama, Fumikazu Konishi, Akihiko Konagaya |
| 2006 | CCGRID | OBIGrid: Towards the 'Ba' for Sharing Resources, Services and Knowledge for Bioinformatics. | Akihiko Konagaya |
| 2006 | EuroPar | Improving the Research Environment of High Performance Computing for Non-cluster Experts Based on Knoppix Instant Computing Technology. | Fumikazu Konishi, Manabu Ishii, Shingo Ohki, Yusuke Hamano, Shuichi Fukuda, Akihiko Konagaya |
| 2006 | EuroPar | Multidimensional Dynamic Programming for Homology Search on Distributed Systems. | Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya |
| 2006 | EuroPar | Topic 17: High-Performance Bioinformatics. | Craig A. Stewart, Michael Schroeder, Concettina Guerra, Akihiko Konagaya |
| 2005 | FPL | Multidimensional Dynamic Programming for Homology Search. | Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya |
| 2005 | ICDE | Software-Aided Mass Spectrometry Analysis for Identification of Protein-Protein Interaction in Signal Transduction Pathways. | Aki Hasegawa, Kazumi Kuriyama-Matsumura, Xiaomei Yu, Mariko Hatakeyama, Akihiko Konagaya |
| 2004 | FPL | Three-Dimensional Dynamic Programming for Homology Search. | Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya |
| 2004 | ISMB | TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks. | Naohiko Heida, Yoshikazu Hasegawa, Yoshiki Mochizuki, Katsura Hirosawa, Akihiko Konagaya, Tetsuro Toyoda |
| 2004 | LREC | PBIE: A Data Preparation Toolkit Toward Developing a Parsing-Based Information Extraction System. | Junko Hosaka, Igor Kurochkin, Akihiko Konagaya |
| 2003 | CEC | Inference of S-system models of genetic networks using a genetic local search. | Shuhei Kimura, Mariko Hatakeyama, Akihiko Konagaya |
| 2003 | EACL | Effect of utilizing terminology on extraction of protein-protein interaction information from biomedical literature. | Junko Hosaka, Judice L. Y. Koh, Akihiko Konagaya |
| 2003 | SMC | High dimensional function optimization using a new genetic local search suitable for parallel computers. | Shuhei Kimura, Akihiko Konagaya |
| 2003 | SC | Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations. | Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Noriyuki Futatsugi, Atsushi Suenaga, Naoki Takada, Akihiko Konagaya |
| 2002 | FPL | High Speed Homology Search Using Run-Time Reconfiguration. | Yoshiki Yamaguchi, Yosuke Miyajima, Tsutomu Maruyama, Akihiko Konagaya |
| 2002 | PSB | High Speed Homology Search with FPGAs. | Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya |
| 2002 | SRDS | OBIGrid: Towards a New Distributed Platform for Bioinformatics. | Akihiko Konagaya |
| 1994 | ISMB | Stochastic Motif Extraction Using Hidden Markov Model. | Yukiko Fujiwara, Minoru Asogawa, Akihiko Konagaya |
| 1993 | ISMB | Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities. | Hidetoshi Tanaka, Masato Ishikawa, Kiyoshi Asai, Akihiko Konagaya |
| 1992 | ALT | A Stochastic Approach to Genetic Information Processing. | Akihiko Konagaya |
| 1992 | PPSN | An Asynchronous Fine-Grained Parallel Genetic Algorithm. | Tsutomu Maruyama, Akihiko Konagaya, Koichi Konishi |
| 1991 | ICML | Learning Stochastic Motifs from Genetic Sequences. | Kenji Yamanishi, Akihiko Konagaya |
| 1985 | ISCA | Design of a High-speed Prolog Machine (HPM). | Ryosei Nakazaki, Akihiko Konagaya, Shinichi Habata, Hideo Shimazu, Mamoru Umemura, Masahiro Yamamoto, Minoru Yokota, Takashi Chikayama |