Publications のバックアップ(No.1)

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TopPage | Profile | Research? | Publications | 日本語

Journal Papers †

• Tomohiro Ban, Masahito Ohue, Yutaka Akiyama: "Multiple Grid Arrangement Improves Ligand Docking with Unknown Binding Sites: Application to the Inverse Docking Problem", Computational Biology and Chemistry. (in press)
  [ PubMed | Journal Website ]

• Shogo D. Suzuki, Masahito Ohue, Yutaka Akiyama: "PKRank: A novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM", Artificial Life and Robotics. (in press)
  [ PubMed | Journal Website ]

• Naoki Wakui, Ryunosuke Yoshino, Nobuaki Yasuo, Masahito Ohue, Masakazu Sekijima: Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: a molecular dynamics simulation approach, Journal of Molecular Graphics and Modelling, 79: 166-174, 2018. doi: 10.1016/j.jmgm.2017.11.011
  [ PubMed | Journal Website ]

• Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue*, Yutaka Akiyama*: MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions, BMC Bioinformatics (APBC2018). (accepted)
  [ PubMed | Journal Website | slide ]

• Keisuke Yanagisawa, Shunta Komine, Rikuto Kubota, Masahito Ohue, Yutaka Akiyama: Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm, Computational Biology and Chemistry (APBC2018). (accepted)
  [ PubMed | Journal Website | slide ]

• Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama: "Spresso: An ultrafast compound pre-screening method based on compound decomposition", Bioinformatics, 33(23): 3836-3843, 2017.
  [ PubMed | Journal Website ]

• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Yutaka Akiyama: "Rigid-docking approaches to explore protein-protein interaction space", Advances in Biochemical Engineering/Biotechnology (Network Biology), 160: 33-55, 2017.
  [ PubMed | Journal Website ]

• Shuji Suzuki, Takashi Ishida, Masahito Ohue, Masanori Kakuta, Yutaka Akiyama: "GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data", Methods in Molecular Biology, the volume on Protein Function Prediction, 1611: 15-25, 2017.
  [ PubMed | Journal Website ]

• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Yutaka Akiyama: "Specificity of broad protein interaction surfaces for proteins with multiple binding partners", Biophysics and Physicobiology, 13: 105-115, 2016.
  [ PubMed | Journal Website ]

• Takehiro Shimoda, Shuji Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama: "Protein-Protein Docking on Hardware Accelerators: Comparison of GPU and MIC Architectures", BMC Systems Biology (In Proc. of APBC2015), 9(Suppl 1): S6, 2015.
  [ PubMed | Journal Website ]

• Masahito Ohue†, Takehiro Shimoda†, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers", Bioinformatics, 30(22): 3281-3283, 2014.
  [ PubMed | Journal Website ]

• Masahito Ohue†, Yuri Matsuzaki†, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data", Protein and Peptide Letters, 21(8): 766-778, 2014.
  [ PubMed | Journal Website ]

• Yuri Matsuzaki†, Masahito Ohue†, Nobuyuki Uchikoga, Yutaka Akiyama: "Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis", Protein and Peptide Letters, 21(8): 790-798, 2014.
  [ PubMed | Journal Website ]

• Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama: "Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods", BMC Proceedings, 7(Suppl 7): S6, 2013.
  [ PubMed | Journal Website ]

• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida, Yutaka Akiyama: "MEGADOCK 3.0: A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments", Source Code for Biology and Medicine, 8(1):18, 2013.
  [ PubMed | BioMedCentral ]

• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama: "Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints", PLoS ONE, 8(7): e69365, 2013.
  [ PubMed | PLoS ]

• Sarel J. Fleishman, Timothy A. Whitehead, Eva-Maria Strauch, Jacob E. Corn, Sanbo Qin, Huan-Xiang Zhou, Julie C. Mitchell, Omar N. A. Demerdash, Mayuko Takeda-Shitaka, Genki Terashi, Iain H. Moal, Xiaofan Li, Paul A. Bates, Martin Zacharias, Hahnbeom Park, Jun-su Ko, Hasup Lee, Chaok Seok, Thomas Bourquard, Julie Bernauer, Anne Poupon, Jerome Aze, Seren Soner, Sefik Kerem Oval., Pemra Ozbek, Nir Ben Tal, Turkan Haliloglu, Howook Hwang, Thom Vreven, Brian G. Pierce, Zhiping Weng, Laura Perez-Cano, Carles Pons, Juan Fernandez-Recio, Fan Jiang, Feng Yang, Xinqi Gong, Libin Cao, Xianjin Xu, Bin Liu, Panwen Wang, Chunhua Li, Cunxin Wang, Charles H. Robert, Mainak Guharoy, Shiyong Liu, Yangyu Huang, Lin Li, Dachuan Guo, Ying Chen, Yi Xiao, Nir London, Zohar Itzhaki, Ora Schueler-Furman, Yuval Inbar, Vladimir Patapov, Mati Cohen, Gideon Schreiber, Yuko Tsuchiya, Eiji Kanamori, Daron M. Standley, Haruki Nakamura, Kengo Kinoshita, Camden M. Driggers, Robert G. Hall, Jessica L. Morgan, Victor L. Hsu, Jian Zhan, Yuedong Yang, Yaoqi Zhou, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Weiyi Zhang, Carlos J. Camacho, Krishna P. Kilambi, Aroop Sircar, Jeffrey J. Gray, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, Raed Khashan, Stephen Bush, Denis Fouches, Alexander Tropsha, Juan Esquivel-Rodriguez, Daisuke Kihara, P. Benjamin Stranges, Ron Jacak, Brian Kuhlman, Sheng-You Huang, Xiaoqin Zou, Shoshana J. Wodak, Joel Janin and David Baker: "Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology", Journal of Molecular Biology, 414(2), 289-302, Nov 25 2011.
  [ PubMed | ScienceDirect ]

• Masahito Ohue, Yuri Matsuzaki, Yutaka Akiyama: "Docking-calculation-based Method for Predicting Protein-RNA Interactions", Genome Informatics, 25(1), 25-39, Aug 3 2011.
  [ PubMed | J-stage ]

• Masahito Ohue, Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama: "MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data and its application to systems biology study", IPSJ Transactions on Mathematical Modeling and Its Applications, 3(3), 91-106, 2010. (in Japanese)
  [ IPSJ Digital Library ]

　(†: These authors have equally contributed.)

International Conferences (Full Paper, Oral Presentation) †

• Tomohiro Ban, Masahito Ohue, Yutaka Akiyama: "Efficient Hyperparameter Optimization by Using Bayesian Optimization for Drug-Target Interaction Prediction", In Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2017), Orlando, FL, USA, October 19-21, 2017. (accepted)
  [ Paper | Slide ]

• Masahito Ohue, Takuro Yamazaki, Tomohiro Ban, Yutaka Akiyama: "Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach", In Proceedings of the Thirteenth International Conference On Intelligent Computing (ICIC2017) (Lecture Notes in Computer Science), 10362, 549-558, Liverpool,UK August 7-10, 2017.
  [ Paper | arXiv | Slide ]

• Shogo D. Suzuki, Masahito Ohue, Yutaka Akiyama: "Learning-to-rank based compound virtual screening by using pairwise kernel with multiple heterogeneous experimental data", In Proceedings of 22nd International Symposium on Artificial Life and Robotics (AROB 22nd 2017), 114-119, 2017.
  [ Paper | Slide ]

• Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama: "ESPRESSO: An ultrafast compound pre-screening method based on compound decomposition", In Proceedings of The 27th International Conference on Genome Informatics (GIW 2016), 2016.
  [ Paper | Slide ]

• Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama: "MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs", In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013), 2nd International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio2013), 884-890, 2013.
  [ ACM Digital Library ]

• Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama: "Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods", Proceedings of Great Lakes Bioinformatics Conference 2013 (GLBIO2013). 100-109, 2013.
  [ Paper | Slide ]

• Masahito Ohue, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis", In Proceedings of The 7th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB2012), Lecture Notes in Bioinformatics 7632, 178-187, Springer Heidelberg, 2012.
  [ SpringerLink | Slide ]

International Conferences (Short Paper, Oral Presentation) †

• Masahito Ohue, Yuri Matsuzaki, Yutaka Akiyama: "Development of a Protein-RNA Interaction Prediction Method Based on a Docking Calculation", The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010), T02/P077, Dec 2010.

• Masahito Ohue, Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama: "In silico prediction of PPI network with structure-based all-to-all docking", InCoB2010 - the 9th International Conference on Bioinformatics (poster selected for short talk), #143, Sep 2010.

Invited Talk †

• Masahito Ohue, "MEGADOCK: An all-to-all protein-protein interaction prediction system based on tertiary structures information", IIT Madras-Tokyo Tech Joint Workshop on Bioinformatics and Large Scale Data Analysis, Indian Institute of Technology Madras, Jul 15-16 2011.

Posters on International Conferences †

• Masahito Ohue, Yuki Yamamoto, Takanori Hayashi, Yuri Matsuzaki, Yutaka Akiyama. "Cloud Computing for All-to-All Protein-Protein Docking on Azure HPC'', 2218-Pos, Ernest N. Morial Convention Center, New Orleans, LA, USA, 2/14 2017.

• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Yutaka Akiyama. "Interaction Surfaces of Proteins Involved in Bacterial-Chemotaxis with Rigid-Body Docking Decoys", Biophysical Society 61st Annual Meeting, 1426-Pos, Ernest N. Morial Convention Center, New Orleans, LA, USA, 2/13 2017.

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama. "MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers", Biophysical Society 60th Annual Meeting, Los Angeles CA USA, Mar 1, 2016.

• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Yutaka Akiyama. "Analysis of Physico-Chemical Properties of Protein Docking Decoys Generated by Rigid-Body Docking", Biophysical Society 60th Annual Meeting, Los Angeles CA USA, Mar 1, 2016.

• Masahito Ohue, Yutaka Akiyama: "A rescoring method of protein-peptide docking prediction with amino acid profiles of rigid-body search results", The Fourteenth Asia Pacific Bioinformatics Conference (APBC2016), P188, San Francisco Bay Area CA USA, Jan 11-13 2016.

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Takashi Ishida, Yutaka Akiyama: "A comparative study of GPU and MIC accelerations in fast Fourier transform-based protein-protein docking", 3nd IIT Madras – Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics, P26, Chennai India, Nov 2015.

• Tomohiro Ban, Masahito Ohue, Yutaka Akiyama: "Improving protein-ligand docking and inverse docking prediction by deepening conformation search on multiple grids", 3nd IIT Madras – Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics, P27, Chennai India, Nov 2015.

• Keisuke Yanagisawa, Shunta Komine, Masahito Ohue, Takashi Ishida, Yutaka Akiyama: "Fast pre-filtering for virtual screening based on compound fragmentation", 3nd IIT Madras – Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics, P34, Chennai India,　Nov 2015.

• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama. "Analysis of amino acid properties in interaction surfaces of decoys generated by re-docking", Biophysical Society 59th Annual Meeting, 2379-Pos, Baltimore MD USA, Feb. 2015.

• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Yutaka Akiyama: "Prediction of human-virus protein-protein interactions by exhaustive rigid docking", Biophysical Society 59th Annual Meeting, L3397-Pos, Baltimore MD USA, Feb. 2015.

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "MEGADOCK 4.0: an ultra–high-performance protein-protein docking software for heterogeneous supercomputers", APBC 2015, Jan. 2015.

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "MEGADOCK 4.0: an ultra–high-performance protein-protein docking software for heterogeneous supercomputers", GIW/ISCB-Asia 2014, P081, Dec. 2014.

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments", The Asia hub for e-drug discovery symposium 2014 (AHeDD' 2014), P1, Nov. 2014. [Best Poster Award]

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments", Biophysical Society Thematic Meeting Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Sep. 2014.

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments", Biophysical Society Thematic Meeting Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Sep. 2014.

• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama. "Re-docking scheme to explore docking search space by using interaction profiles", Biophysical Society 58th Annual Meeting, Feb. 2014.

• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takashi Ishida, Yutaka Akiyama: "Prediction of protein-protein interactions based on tertiary structures and transcription information", Biophysical Society 58th Annual Meeting, Feb. 2014.

• Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama: "Improvement of protein-protein interaction prediction by integrating template-based and template-free protein docking", ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013), Sep 2013. (Poster)

• Takehiro Shimoda, Masahito Ohue, Yuri Matsuzaki, Takayuki Fujiwara, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "The MEGADOCK project: Ultra-high-performance protein-protein interaction prediction tools on supercomputing environments", ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013), Sep 2013. (Poster)

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Kohei Yamamoto, Takayuki Fujiwara, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida, Yutaka Akiyama: "Protein-protein interaction prediction based on rigid-body docking with ultra-high-performance computing technique: applications to affinity prediction on CAPRI round 21 and interactome analyses", CAPRI 2013 5th Evaluation Meeting, pp.62, Apr 2013. (Poster)

• Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "Protein-protein interaction network prediction by using rigid-body docking tool MEGADOCK", Biophysical Society 57th Annual Meeting, Feb 2013. (Poster)

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "MEGADOCK: a High-speed Protein-protein Interaction Prediction System by All-to-all Physical Docking", ISCB-Asia/SCCG 2012, Poster 33 Dec 2012. (Poster)

• Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways", ISCB-Asia/SCCG 2012, Poster 35, Dec 2012. (Poster)

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking", 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012), Poster W23, Jul 2012.

• Yuri Matsuzaki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama: "Application of Exhaustive Protein-Protein Interaction Prediction System by Using Protein Docking to Signal Transduction Pathways", 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012), Poster L01, Jul 2012.

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "MEGADOCK: A Rapid Screening System of Protein-Protein Interactions by Exhaustive Docking", 3DSIG: The 8th structural bioinformatics and computational biophysics meeting, Poster ID 29, Jul 2012.

• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Yutaka Akiyama: "Application of Exhaustive Protein-Protein Interaction Prediction System by Using Protein Docking to Signal Transduction Pathways", 3DSIG: The 8th structural bioinformatics and computational biophysics meeting, Poster ID 70, Jul 2012.

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "Protein Complex Structure Prediction with Normal Mode Ensemble and Physical Docking", Bioinformatics week in Odaiba 2011 (BiWO2011), Jan 2012.

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "Bound state structure estimation of protein-protein complex using rigid-body protein-protein docking method", The 10th Asia-Pacific Bioinformatics Conference (APBC2012), Jan 2012.

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "Binding Conformation Prediction of a Protein Complex Using Physical Docking", GCOE Compview Final Symposium (Preliminary event of ISAAC 2011), Dec 2011.

• Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "MEGADOCK: a Fast Protein-protein Interaction Prediction System by Exhaustive Docking", 12th International Conference on Systems Biology (ICSB 2011), Sep 2011.

• Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama. MEGADOCK: A fast protein-protein interaction prediction system by exhaustive docking, The 9th International Workshop on Advanced Genomics, Jul 2011.

• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takashi Ishida, Yutaka Akiyama, "Exhaustive protein-protein interaction prediction with MEGADOCK and its application to signaling pathway estimation", Asia Hub for e-Drug Discovery (AHeDD) Symoposium 2010, Dec 2010.

• Yuri Matsuzaki, Masahito Ohue, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama: "A computational screening system of protein-protein interactions: connecting protein structural information to biological pathway estimation", 11th International Conference on Systems Biology (ICSB 2010), Oct 2010.

• Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama: "A Computational Screening System of Protein-protein Interactions: Connecting Structural Information to Pathway Estimation", The 2nd Bio Super Computing Symposium(BSCS2), Poster no.51, Mar 2010.

• Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Toshiyuki Sato, Yutaka Akiyama: "MEGADOCK: An all-to-all protein-protein interaction prediction system - Improving the accuracy using boosting and binding energy reranking", The 2nd Bio Super Computing Symposium(BSCS2), Poster no.55, Mar 2010.

• Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Yutaka Akiyama: "Improvement of all-to-all protein-protein interaction prediction system MEGADOCK", The 20th International Conference on Genome Informatics(GIW2009), Poster No. 033, Dec 2009.

• Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Yutaka Akiyama: "Improvement of all-to-all protein-protein interaction prediction system MEGADOCK", CBI-KSBSB JOINT CONFERENCE (Bioinfo2009), P10-101, Nov 2009.

• Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama: "A Computational Screening System of Protein-protein Interactions Using Tertiary Structure Data: an Application to Signaling Pathway Analysis, CBI-KSBSB JOINT CONFERENCE(Bioinfo2009), P11-114, Nov 2009.

• Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama: "In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis", The 10th International Conference on Systems Biology (ICSB 2009), Sep 2009.

• Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama: "A computational screening system of protein-protein interactions using tertiary structure data: with application to pathway analysis", Joint Computational Science Workshop 2009, Jul 2009.

Technical Reports †

• Masahito Ohue, Takehiro Shimoda, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "Protein-Protein Docking System on Large-Scale GPU Clusters", IPSJ-SIG Technical Report, 2014-BIO-38(32): 1-4, Jun 2014.

• Masahito Ohue, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "An Application of Protein-Protein Interaction Prediction to Human Apoptotsis Signal Transduction Pathway Analysis by Using MEGADOCK", IPSJ-SIG Technical Report, 2012-BIO-32(13): 1-8, Dec 2012.

• Kohei Yamamoto, Masahito Ohue, Takashi Ishida, Yutaka Akiyama: "Improvement of the Accuracy for Protein-Protein Interaction Network Prediction Based on Tertiary Structural Information", IPSJ-SIG Technical Report, 2012-BIO-32(14): 1-8, Dec 2012.

• Masahito Ohue, Takashi Ishida, Yutaka Akiyama: "Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model", IPSJ-SIG Technical Report, 2011-BIO-29(21): 1-3, Jun 2012.

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama: "Docking-calculation-based All-to-all Protein-RNA Interaction Prediction", IPSJ-SIG Technical Report, 2011-BIO-25(30): 1-8, Jun 2011.

• Kohei Yamamoto, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "A visualization method and accuracy improvement for protein-protein interaction predictions", IPSJ-SIG Technical Report, 2011-BIO-25(31): 1-8, Jun 2011.

• Masahito Ohue, Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama: "MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data and its application to systems biology study", IPSJ-SIG Technical Report, 2010-MPS-78(3): 1-9, May 2010.

• Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Toshiyuki Sato, Yutaka Akiyama: "Improvement of accuracy of the protein-protein docking calculation by a re-ranking method and its application to all-to-all protein-protein interaction predictions", IPSJ-SIG Technical Report, 2010-BIO-20(3): 1-8, Mar 2010.

• Yusuke Matsuzaki, Masahito Ohue, Yuri Matsuzaki, Toshiyuki Sato, Masakazu Sekijima, Yutaka Akiyama: "Improvement of rigid-body prediction for unbound docking based on protein feature", IPSJ-SIG Technical Report, 2010-BIO-20(4): 1-8, Mar 2010.

• Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Yutaka Akiyama: "Improvement of the classification performance in all-to-all protein-protein interaction prediction system", IPSJ-SIG Technical Report, 2009-BIO-18(3): 1-8，Sep 2009.

• Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Toshiyuki Sato, Yutaka Akiyama: "Improvement of all-to-all protein-protein interaction prediction system by introducing physicochemical interaction", IPSJ-SIG Technical Report, 2009-BIO-17(11): 1-8，May 2009.

Award †

• Tejima Memorial Research Award (2015)
• AHeDD'2014 Best Poster Award (2014)
• JSPS Ikushi Prize (2014)
  • Awardees List (http://www.jsps.go.jp/english/e-ikushi-prize/awards_fy2013_01.html)
• The 73rd National Convention of IPSJ Student Award (2011)
• The 78th IPSJ SIGMPS Presentation Award (2010)
• 2009 IPSJ SIGBIO Best Student Presentation Award (2010)
• DEIM2010 Excellent Student Presentation Award (2010)
• IEICE Hokuriku Excellent Student Presentation Award (2006)

Thesis †

• Ph.D. thesis: Protein-Protein Interaction Network Prediction Based on Tertiary Structure Data, Tokyo Institute of Technology, Graduate School of Information Science and Engineering, Department of Computer Science (Ph.D. in Eng.)
• master thesis: 立体構造情報に基づく網羅的タンパク質間相互作用予測に関する研究, Tokyo Institute of Technology, Graduate School of Information Science and Engineering, Department of Computer Science (M.Eng.)
• bachelor thesis: 物理化学的相互作用の導入によるタンパク質間相互作用予測の高精度化, Tokyo Institute of Technology, Dept. of Conputer Science.
• associate degree thesis: 遺伝子発現データ解析のための新しい属性選択手法の提案, Ishikawa National College of Technology, Dept. of Electronics and Information Engineering.

     

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