Solving large scale puzzles with neural networks. - Masahiro Kajiura; Yutaka Akiyama; Yuichiro Anzai (TAI, 1989)

Parallelization of Space Plasma Particle Simulation. - Yutaka Akiyama; Kiyotaka Misoo; Yoshiharu Omura; Hiroshi Matsumoto; Minoru Saito; Tamotsu Noguchi; Kentaro Onizuka; Makoto Ando (ISHPC, 1997)

Parallel PDB Data Retriever "PDB Diving Booster". - Kentaro Onizuka; Tamotsu Noguchi; Minoru Saito; Yutaka Akiyama (ISHPC, 1997)

PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank). - Tamotsu Noguchi; Kentaro Onizuka; Yutaka Akiyama; Minoru Saito (ISMB, 1997)

Biological- and Chemical- Parallel Applications on a PC Cluster. - Yutaka Akiyama; Kentaro Onizuka; Tamotsu Noguchi; Makoto Ando (ISHPC, 1999)

ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides. - Makoto Ando; Yutaka Akiyama; Kentaro Onizuka; Tamotsu Noguchi (PDPTA, 1999)

Hierarchical Approach to Parallel Tree Search for Protein Conformational Analysis. - Makoto Ando; Yutaka Akiyama; Hideo Matsuda (PDPTA, 2000)

Quick selection of representative protein chain sets based on customizable requirements. - Tamotsu Noguchi; Kentaro Onizuka; Makoto Ando; Hideo Matsuda; Yutaka Akiyama (Bioinform., 2000)

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB). - Tamotsu Noguchi; Hideo Matsuda; Yutaka Akiyama (Nucleic Acids Res., 2001)

Using Data Compression for Multidimensional Distribution Analysis. - Kentaro Onizuka; Tamotsu Noguchi; Yutaka Akiyama; Hideo Matsuda (IEEE Intell. Syst., 2002)

Generation of 3D solid model from 3DX multi image micro CT (methods and application). - Ayuta Yamada; Hitoshi Tsunashima; Yoshinori Arai; Toru Ishizuka; Yutaka Akiyama (CARS, 2003)

Molecular Dynamics Simulation of Prion Protein by Large Scale Cluster Computing. - Masakazu Sekijima; Chie Motono; Satoshi Yamasaki; Kiyotoshi Kaneko; Yutaka Akiyama (ISHPC, 2003)

Distributed Genetic Algorithm for Inference of Biological Scale-Free Network Structure. - Daisuke Tominaga; Katsutoshi Takahashi; Yutaka Akiyama (ISHPC, 2003)

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. - Tamotsu Noguchi; Yutaka Akiyama (Nucleic Acids Res., 2003)

Optimizing substitution matrices by separating score distributions. - Yuichiro Hourai; Tatsuya Akutsu; Yutaka Akiyama (Bioinform., 2004)

FORTE: a profile-profile comparison tool for protein fold recognition. - Kentaro Tomii; Yutaka Akiyama (Bioinform., 2004)

High Performance 3D Convolution for Protein Docking on IBM Blue Gene. - Akira Nukada; Yuichiro Hourai; Akira Nishida; Yutaka Akiyama (ISPA, 2007)

Optimization and evaluation of parallel molecular dynamics simulation on blue gene/L. - Masakazu Sekijima; Junta Doi; Tamotsu Noguchi; Yutaka Akiyama; Shigenori Shimizu (Parallel and Distributed Computing and Networks, 2007)

Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation. - Masakazu Sekijima; Junta Doi; Shinya Honda; Tamotsu Noguchi; Shigenori Shimizu; Yutaka Akiyama (Inf. Media Technol., 2008)

High-throughput Automated Image Processing System for Cell Array Observations. - Daisuke Tominaga; Fukumi Iguchi; Katsuhisa Horimoto; Yutaka Akiyama (Inf. Media Technol., 2008)

Development of an Affinity Evaluation and Prediction System by Using the Shape complementarity Characteristic between proteins. - Koki Tsukamoto; Tatsuya Yoshikawa; Yuichiro Hourai; Kazuhiko Fukui; Yutaka Akiyama (J. Bioinform. Comput. Biol., 2008)

In silico Screening of protein-protein Interactions with All-to-All Rigid docking and Clustering: an Application to Pathway Analysis. - Yuri Matsuzaki; Yusuke Matsuzaki; Toshiyuki Sato; Yutaka Akiyama (J. Bioinform. Comput. Biol., 2009)

Design and Simulation of Hybrid de novo DNA Sequence Assembly for Large Eukaryotic Genomes. - Wisnu Ananta Kusuma; Yutaka Akiyama (PDPTA, 2010)

PDN impedance analysis of TSV-decoupling capacitor embedded Silicon interposer for 3D-integrated CMOS image sensor system. - Katsuya Kikuchi; Chihiro Ueda; Fumiaki Fujii; Yutaka Akiyama; Naoya Watanabe; Yasuhiro Kitamura; Toshio Gomyo; Toshikazu Okubo; Tetsuya Koyama; Tadashi Kamada; Masahiro Aoyagi; Kanji Otsuka (3DIC, 2011)

Fast DNA Sequence Clustering Based on Longest Common Subsequence. - Youhei Namiki; Takashi Ishida 002; Yutaka Akiyama (ICIC (3), 2012)

Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: An Application to Interaction Pathway Analysis. - Masahito Ohue; Yuri Matsuzaki; Takashi Ishida 002; Yutaka Akiyama (PRIB, 2012)

An Ultra-Fast Computing Pipeline for Metagenome Analysis with Next-Generation DNA Sequencers. - Shuji Suzuki; Takashi Ishida 002; Yutaka Akiyama (SC Companion, 2012)

Improvement of Protein-Protein Interaction Prediction by Integrating Template-Based and Template-Free Protein Docking. - Masahito Ohue; Yuri Matsuzaki; Takehiro Shimoda; Takashi Ishida 002; Yutaka Akiyama (BCB, 2013)

MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs. - Takehiro Shimoda; Takashi Ishida 002; Shuji Suzuki; Masahito Ohue; Yutaka Akiyama (BCB, 2013)

The MEGADOCK project: Ultra-high-speed protein-protein interaction prediction tools on supercomputing environments. - Takehiro Shimoda; Masahito Ohue; Yuri Matsuzaki; Takayuki Fujiwara; Nobuyuki Uchikoga; Takashi Ishida 002; Yutaka Akiyama (BCB, 2013)

Acceleration of sequence clustering using longest common subsequence filtering. - Youhei Namiki; Takashi Ishida 002; Yutaka Akiyama (BMC Bioinform., 2013)

MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments. - Yuri Matsuzaki; Nobuyuki Uchikoga; Masahito Ohue; Takehiro Shimoda; Toshiyuki Sato; Takashi Ishida 002; Yutaka Akiyama (Source Code Biol. Medicine, 2013)

Metagenomic Phylogenetic Classification Using Improved Naïve Bayes. - Yuki Komatsu; Takashi Ishida 002; Yutaka Akiyama (ICIC (3), 2014)

MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. - Masahito Ohue; Takehiro Shimoda; Shuji Suzuki; Yuri Matsuzaki; Takashi Ishida 002; Yutaka Akiyama (Bioinform., 2014)

CLAST: CUDA implemented large-scale alignment search tool. - Masahiro Yano; Hiroshi Mori; Yutaka Akiyama; Takuji Yamada; Ken Kurokawa (BMC Bioinform., 2014)

Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year. - Satoshi Matsuoka; Hitoshi Sato; Osamu Tatebe; Michihiro Koibuchi; Ikki Fujiwara; Shuji Suzuki; Masanori Kakuta; Takashi Ishida 002; Yutaka Akiyama; Toyotaro Suzumura; Koji Ueno; Hiroki Kanezashi; et al. (Supercomput. Front. Innov., 2014)

Faster sequence homology searches by clustering subsequences. - Shuji Suzuki; Masanori Kakuta; Takashi Ishida 002; Yutaka Akiyama (Bioinform., 2015)

Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures. - Takehiro Shimoda; Shuji Suzuki; Masahito Ohue; Takashi Ishida 002; Yutaka Akiyama (BMC Syst. Biol., 2015)

Efficient hyperparameter optimization by using Bayesian optimization for drug-target interaction prediction. - Tomohiro Ban; Masahito Ohue; Yutaka Akiyama (ICCABS, 2017)

Link Mining for Kernel-Based Compound-Protein Interaction Predictions Using a Chemogenomics Approach. - Masahito Ohue; Takuro Yamazaki; Tomohiro Ban; Yutaka Akiyama (ICIC (2), 2017)

Spresso: an ultrafast compound pre-screening method based on compound decomposition. - Keisuke Yanagisawa; Shunta Komine; Shogo D. Suzuki; Masahito Ohue; Takashi Ishida 002; Yutaka Akiyama (Bioinform., 2017)

PKRank: a novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM. - Shogo D. Suzuki; Masahito Ohue; Yutaka Akiyama (Artif. Life Robotics, 2018)

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. - Takanori Hayashi; Yuri Matsuzaki; Keisuke Yanagisawa; Masahito Ohue; Yutaka Akiyama (BMC Bioinform., 2018)

Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques. - Takashi Tajimi; Naoki Wakui; Keisuke Yanagisawa; Yasushi Yoshikawa; Masahito Ohue; Yutaka Akiyama (BMC Bioinform., 2018)

Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem. - Tomohiro Ban; Masahito Ohue; Yutaka Akiyama (Comput. Biol. Chem., 2018)

Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm. - Keisuke Yanagisawa; Shunta Komine; Rikuto Kubota; Masahito Ohue; Yutaka Akiyama (Comput. Biol. Chem., 2018)

Parallelized Pipeline for Whole Genome Shotgun Metagenomics with GHOSTZ-GPU and MEGAN. - Masahito Ohue; Marina Yamasawa; Kazuki Izawa; Yutaka Akiyama (BIBE, 2019)

A playful tool for predicting protein-protein docking. - Keren Jiang; Di Zhang; Tsubasa Iino; Risa Kimura; Tatsuo Nakajima; Kana Shimizu; Masahito Ohue; Yutaka Akiyama (MUM, 2019)

Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph. - Masahito Ohue; Ryota Ii; Keisuke Yanagisawa; Yutaka Akiyama (CoRR, 2019)

Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein-Protein Docking Calculations. - Kento Aoyama; Hiroki Watanabe; Masahito Ohue; Yutaka Akiyama (SCFA, 2020)

High-performance cloud computing for exhaustive protein-protein docking. - Masahito Ohue; Kento Aoyama; Yutaka Akiyama (CoRR, 2020)

Development of Computational Pipeline Software for Genome/Exome Analysis on the K Computer. - Kento Aoyama; Masanori Kakuta; Yuri Matsuzaki; Takashi Ishida 002; Masahito Ohue; Yutaka Akiyama (Supercomput. Front. Innov., 2020)

MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions. - Masahito Ohue; Yutaka Akiyama (CoRR, 2021)

Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations. - Masatake Sugita; Satoshi Sugiyama; Takuya Fujie; Yasushi Yoshikawa; Keisuke Yanagisawa; Masahito Ohue; Yutaka Akiyama (J. Chem. Inf. Model., 2021)

Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning. - Jianan Li; Keisuke Yanagisawa; Yasushi Yoshikawa; Masahito Ohue; Yutaka Akiyama (Bioinform., 2022)

Solving Generalized Polyomino Puzzles Using the Ising Model. - Kazuki Takabatake; Keisuke Yanagisawa; Yutaka Akiyama (Entropy, 2022)

Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. - Masatake Sugita; Takuya Fujie; Keisuke Yanagisawa; Masahito Ohue; Yutaka Akiyama (J. Chem. Inf. Model., 2022)

CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. - Jianan Li; Keisuke Yanagisawa; Masatake Sugita; Takuya Fujie; Masahito Ohue; Yutaka Akiyama (J. Chem. Inf. Model., 2023)

Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization. - Taisuke Boku; Masatake Sugita; Ryohei Kobayashi 001; Shinnosuke Furuya; Takuya Fujie; Masahito Ohue; Yutaka Akiyama (ICPP, 2024)

CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation. - Jianan Li; Keisuke Yanagisawa; Yutaka Akiyama (Briefings Bioinform., 2024)

QUBO Problem Formulation of Fragment-Based Protein-Ligand Flexible Docking. - Keisuke Yanagisawa; Takuya Fujie; Kazuki Takabatake; Yutaka Akiyama (Entropy, 2024)

PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations. - Kairi Furui; Takafumi Shimizu; Yutaka Akiyama; S. Roy Kimura; Yoh Terada; Masahito Ohue (J. Chem. Inf. Model., 2025)