| 2024 | ICPP | Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization. | Taisuke Boku, Masatake Sugita, Ryohei Kobayashi, Shinnosuke Furuya, Takuya Fujie, Masahito Ohue, Yutaka Akiyama |
| 2019 | BIBE | Parallelized Pipeline for Whole Genome Shotgun Metagenomics with GHOSTZ-GPU and MEGAN. | Masahito Ohue, Marina Yamasawa, Kazuki Izawa, Yutaka Akiyama |
| 2019 | MUM | A playful tool for predicting protein-protein docking. | Keren Jiang, Di Zhang, Tsubasa Iino, Risa Kimura, Tatsuo Nakajima, Kana Shimizu, Masahito Ohue, Yutaka Akiyama |
| 2012 | SC | An Ultra-Fast Computing Pipeline for Metagenome Analysis with Next-Generation DNA Sequencers. | Shuji Suzuki, Takashi Ishida, Yutaka Akiyama |
| 2010 | PDPTA | Design and Simulation of Hybrid de novo DNA Sequence Assembly for Large Eukaryotic Genomes. | Wisnu Ananta Kusuma, Yutaka Akiyama |
| 2007 | ISPA | High Performance 3D Convolution for Protein Docking on IBM Blue Gene. | Akira Nukada, Yuichiro Hourai, Akira Nishida, Yutaka Akiyama |
| 2000 | PDPTA | Hierarchical Approach to Parallel Tree Search for Protein Conformational Analysis. | Makoto Ando, Yutaka Akiyama, Hideo Matsuda |
| 1999 | PDPTA | ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides. | Makoto Ando, Yutaka Akiyama, Kentaro Onizuka, Tamotsu Noguchi |
| 1997 | ISMB | PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank). | Tamotsu Noguchi, Kentaro Onizuka, Yutaka Akiyama, Minoru Saito |
| 1989 | ICTAI | Solving large scale puzzles with neural networks. | Masahiro Kajiura, Yutaka Akiyama, Yuichiro Anzai |