Publication

2024

Journal Paper

• Kaumbekova S, Sugita M, Sakaguchi N, Takahashi Y, Sadakane A, Umezawa M. Effect of Acetonitrile on the Conformation of Bovine Serum Albumin, ACS Omega, 9(48): 47680-47689, 2024. doi: 10.1021/acsomega.4c07274
• Li J, Yanagisawa K, Akiyama Y. CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation, Briefings in Bioinformatics, 25(5): bbae417, 2024. doi.org/10.1093/bib/bbae417
• Kobayashi M, Miyauchi A, Jimbo E.F, Oishi N, Aoki S, Watanabe M, Yoshikawa Y, Akiyama Y, Yamagata T, Osaka H. Synthetic aporphine alkaloids are potential therapeutics for Leigh syndrome, Scientific Reports, 14(1): 2045-2322, 2024. doi: 10.1038/s41598-024-62445-w
• Yanagisawa K, Fujie T, Takabatake K, Akiyama Y. QUBO Problem Formulation of Fragment-Based Protein–Ligand Flexible Docking, Entropy, 26(5):397, 2024. doi: 10.3390/e26050397

International Conference

• Boku T, Sugita M, Kobayashi R, Furuya S, Fujie T, Ohue M, Akiyama Y. Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization, In Proceedings of the 53rd International Conference on Parallel Processing (ICPP’24), Association for Computing Machinery, 1082-1091, 2024. doi: 10.1145/3673038.3673097

2023

Journal Paper

• Ryunosuke Yoshino, Nobuaki Yasuo, Yohsuke Hagiwara, Takashi Ishida, Daniel Ken Inaoka, Yasushi Amano, Yukihiro Tateishi, Kazuki Ohno, Ichiji Namatame, Tatsuya Niimi, Masaya Orita, Kiyoshi Kita, Yutaka Akiyama, and Masakazu Sekijima.Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro, and X-ray Crystallography, ACS Omega, 8(29): 25850-25860, 2023. doi: 10.1021/acsomega.3c01314
• Kudo G, Yanagisawa K, Yoshino R, Hirokawa T. AAp-MSMD: Amino Acid Preference Mapping on Protein–Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics, Journal of Chemical Information and Modeling, 63(24): 7768–7777, 2023. doi: 10.1021/acs.jcim.3c01677
• Li J, Yanagisawa K, Sugita M, Fujie T, Ohue M, Akiyama Y. CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides, Journal of Chemical Information and Modeling, 63(7): 2240–2250, 2023. doi: 10.1021/acs.jcim.2c01573
• Yuki Hosono, Satoshi Uchida, Moe Shinkai, Chad E. Townsend, Colin N. Kelly, Matthew R. Naylor, Hsiau-Wei Lee, Kayoko Kanamitsu, Mayumi Ishii, Ryosuke Ueki, Takumi Ueda, Koh Takeuchi, Masatake Sugita, Yutaka Akiyama, Scott R. Lokey, Jumpei Morimoto, Shinsuke Sando. Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides, Nature Communications, 14, 1416, 2023. doi: 10.1038/s41467-023-36978-z

2022

Journal Paper

• Sugita M, Fujie T, Yanagisawa K, Ohue M, Akiyama Y. Lipid composition is critical for accurate membrane permeability prediction of cyclic peptides by molecular dynamics simulations, Journal of Chemical Information and Modeling, 62(18): 4549-4560, 2022. doi: 10.1021/acs.jcim.2c00931
• Yanagisawa K, Kubota R, Yoshikawa Y, Ohue M, Akiyama Y. Effective protein-ligand docking strategy via fragment reuse and a proof-of-concept implementation, ACS Omega, 7(34): 30265-30274, 2022. doi: 10.1021/acsomega.2c03470
• Yanagisawa K, Yoshino R, Kudo G, Hirokawa T. Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes, International Journal of Molecular Sciences, 23(9): 4749, 2022. doi: 10.3390/ijms23094749
• Takabatake K, Yanagisawa K, Akiyama Y. Solving Generalized Polyomino Puzzles Using the Ising Model, Entropy, 24(3): 354, 2022. doi: 10.3390/e24030354

2021

Journal Paper

• Li J, Yanagisawa K, Yoshikawa Y, Ohue M, Akiyama Y. Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning, Bioinformatics, 38(4): 1110-1117, 2022. doi: 10.1093/bioinformatics/btab726
• Takabatake K, Izawa K, Akikawa M, Yanagisawa K, Ohue M, Akiyama Y. Improved large-scale homology search by two-step seed search using multiple reduced amino acid alphabets, Genes, 12(9): 1455, 2021. doi: 10.3390/genes12091455
• Sugita M, Sugiyama S, Fujie T, Yoshikawa Y, Yanagisawa K, Ohue M, Akiyama Y. Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations, Journal of Chemical Information and Modeling, 61(7): 3681–3695, 2021. doi: 10.1021/acs.jcim.1c00380
• Yanagisawa K, Moriwaki Y, Terada T, Shimizu K. EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation, Journal of Chemical Information and Modeling, 61(6): 2744–2753, 2021. doi:10.1021/acs.jcim.1c00134
• Izawa K, Okamoto-Shibayama K, Kita D, Tomita S, Saito A, Ishida T, Ohue M, Akiyama Y, Ishihara K. Taxonomic and gene category analyses of subgingival plaques from a group of Japanese individuals with and without periodontitis, International Journal of Molecular Sciences, 22(10): 5298, 2021. doi:10.3390/ijms22105298
• Fujimoto K, Kimura Y, Allegretti JR, Yamamoto M, Zhang YZ, Katayama K, Tremmel G,Kawaguchi Y, Shimohigoshi M, Hayashi T, Uematsu M, Yamaguchi K, Furukawa Y, Akiyama Y,Yamaguchi R, Crowe SE, Ernst PB, Miyano S, Kiyono H, Imoto S, Uematsu S. Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation, Gastroenterology, 160(6): 2089-2102.e12, 2021. doi:10.1053/j.gastro.2021.02.013

International Conference

• Ohue M, Akiyama Y. MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions, In Proceedings of The 27th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’21), Advances in Parallel & Distributed Processing and Applications. (accepted)
• Ohue M, Watanabe H, Akiyama Y. MEGADOCK-Web-Mito: human mitochondrial protein-protein interaction prediction database, In Proceedings of The 27th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’21), Advances in Parallel & Distributed Processing and Applications. (accepted)
• Isawa K, Yanagisawa K, Ohue M, Akiyama Y. Antisense oligonucleotide activity analysis based on opening and binding energies to targets, In Proceedings of The 27th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’21), Advances in Parallel & Distributed Processing and Applications. (accepted)

2020

Journal Paper

• Ren A, Ishida T, Akiyama Y. Mathematical proof of the third order accuracy of the speedy double bootstrap method, Communications in Statistics - Theory and Methods, 49(16): 3950-3964, 2020. doi: 10.1080/03610926.2019.1594295
• Izawa K, Kubosaki A, Kobayashi N, Akiyama Y, Yamazaki A, Hashimoto K, Konuma R, Kamata Y, Hara-Kudo Y, Hasegawa K, Ikaga T, Watanabe M. Comprehensive Fungal Community Analysis of House Dust Using Next-Generation Sequencing, International Journal of Environmental Research and Public Health, 17(16): 5842, 2020. doi:10.3390/ijerph17165842
• Fujimoto K, Kimura Y, Shimohigoshi M, Satoh T, Sato S, Tremmel G, Uematsu M, Kawaguchi Y, Usui Y, Nakano Y, Hayashi T, Kashima K, Yuki Y, Yamaguchi K, Furukawa Y, Kakuta M, Akiyama Y, Yamaguchi R, Crowe SE, Ernst PB, Miyano S, Kiyono H, Imoto S, Uematsu S. Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts, Cell Host & Microbe, 2020, 28(3): 380-389, 2020. doi:10.1016/j.chom.2020.06.005
• Aoyama K, Kakuta M, Matsuzaki Y, Ishida T, Ohue M, Akiyama Y. Development of computational pipeline software for genome/exome analysis on the K computer, Supercomputing Frontiers and Innovations, 7(1): 37-54, 2020. doi: 10.14529/jsfi200102
• Matsuno S, Ohue M, Akiyama Y. Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces, Biophysics and Physicobiology, 17: 2-13, 2020. doi: 10.2142/biophysico.BSJ-2019050

International Conference

• Aoyama K, Watanabe H, Ohue M, Akiyama Y. Multiple HPC environments-aware container image configuration workflow for large-scale all-to-all protein-protein docking calculations, In Proceedings of the 6th Asian Conference on Supercomputing Frontiers (SCFA2020), Lecture Notes in Computer Science, 12082: 23-39, 2020. doi: 10.1007/978-3-030-48842-0_2
• Ohue M, Aoyama K, Akiyama Y. High-performance cloud computing for exhaustive protein-protein docking, In Proceedings of The 26th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’20), Advances in Parallel & Distributed Processing and Applications, 737-746, 2021. doi:10.1007/978-3-030-69984-0_5

2019

Journal Paper

• Chiba S, Ohue M, Gryniukova A, Borysko P, Zozulya S, Yasuo N, Yoshino R, Ikeda K, Shin WH, Kihara D, Iwadate M, Umeyama H, Ichikawa T, Teramoto R, Hsin KY, Gupta V, Kitano H, Sakamoto M, Higuchi A, Miura N, Yura K, Mochizuki M, Ramakrishnan C, Thangakani AM, Velmurugan D, Gromiha MM, Nakane I, Uchida N, Hakariya H, Tan M, Nakamura HK, Suzuki SD, Ito T, Kawatani M, Kudoh K, Takashina S, Yamamoto KZ, Moriwaki Y, Oda K, Kobayashi D, Okuno T, Minami S, Chikenji G, Prathipati P, Nagao C, Mohsen A, Ito M, Mizuguchi K, Honma T, Ishida T, Hirokawa T, Akiyama Y, Sekijima M. A prospective compound screening contest identified broader inhibitors for Sirtuin 1, Scientific Reports, 9: 19585, 2019. doi: 10.1038/s41598-019-55069-y
• Ohue M, Suzuki SD, Akiyama Y. Learning-to-rank technique based on ignoring meaningless ranking orders between compounds, Journal of Molecular Graphics and Modelling, 92:192-200, 2019. doi: 10.1016/j.jmgm.2019.07.009
• Yamamoto K, Yoshikawa Y, Ohue M, Inuki S, Ohno H, Oishi S. Synthesis of Triazolo- and Oxadiazolo-piperazines by Gold(I)-Catalyzed Domino Cyclization: Application to the Design of a MAP Kinase Inhibitor, Organic Letters, 21(2): 373-377, 2019. doi: 10.1021/acs.orglett.8b03500
• Ban T, Ohue M, Akiyama Y. NRLMFβ: Bata-distribution-rescored Neighborhood Regularized Logistic Matrix Factorization for Improving Performance of Drug–Target Interaction Prediction, Biochemistry and Biophysics Reports, 18: 100615, 2019. doi: 10.1016/j.bbrep.2019.01.008

International Conference

• Jiang K, Zhang D, Iino T, Kimura R, Nakajima T, Shimizu K, Ohue M, Akiyama Y. A playful tool for predicting protein-protein docking, In Proceedings of the 18th International Conference on Mobile and Ubiquitous Multimedia (MUM 2019), Article No. 40, 5 pages, 2019. doi:10.1145/3365610.3368409
• Ohue M, Yamasawa M, Izawa K, Akiyama Y. Parallelized pipeline for whole genome shotgun metagenomics with GHOSTZ-GPU and MEGAN, In Proceedings of the 19th annual IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE 2019), 152-156, 2019. doi: 10.1109/BIBE.2019.00035
• Ohue M, Ii R, Yanagisawa K, Akiyama Y. Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph, In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19), 122-128, Las Vegas, NV, USA, July 29, 2019.
• Aoyama K, Yamamoto Y, Ohue M, Akiyama Y. Performance evaluation of MEGADOCK protein-protein interaction prediction system implemented with distributed containers on a cloud computing environment, In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19), 175-181, Las Vegas, NV, USA, July 29, 2019.

2018

Journal Paper

• Tajimi T, Wakui N, Yanagisawa K, Yoshikawa Y, Ohue M, Akiyama Y. Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques, BMC Bioinformatics, 19(Suppl 19): 527, 2018. doi: 10.1186/s12859-018-2529-z
• Kami D, Kitani T, Nakamura A, Wakui N, Mizutani R, Ohue M, Kametani F, Akimitsu N, Gojo S. The DEAD-box RNA-binding protein DDX6 regulates parental RNA decay for cellular reprogramming to pluripotency, PLoS ONE, 13(10): e0203708, 2018. doi: 10.1371/journal.pone.0203708
• Wakayama N, Toshimoto K, Maeda K, Hotta S, Ishida T, Akiyama Y, Sugiyama Y. In Silico Prediction of Major Clearance Pathways of Drugs among 9 Routes with Two-Step Support Vector Machines, Pharmaceutical Research, 35: 197, 2018. doi: 10.1007/s11095-018-2479-1
• Mochizuki M, Suzuki SD, Yanagisawa K, Ohue M, Akiyama Y. QEX: Target-specific druglikeness filter enhances ligand-based virtual screening, Molecular Diversity, 1-8, 2018. doi: 10.1007/s11030-018-9842-3
• Yanagisawa K, Komine S, Kubota R, Ohue M, Akiyama Y. Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm, Computational Biology and Chemistry, 74: 399-406, 2018. doi: 10.1016/j.compbiolchem.2018.03.013 (In Proc. APBC2018)
• Hayashi T, Matsuzaki Y, Yanagisawa K, Ohue M, Akiyama Y. MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions, BMC Bioinformatics, 19(Suppl 4): 62, 2018. doi: 10.1186/s12859-018-2073-x (In Proc. APBC2018)
• Suzuki SD, Ohue M, Akiyama Y. PKRank: A novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM, Artificial Life and Robotics. 23(2): 205-212, 2018. doi: 10.1007/s10015-017-0416-8
• Ramakrishnan C, Thangakani AM, Velmurugan D, Krishnan DA, Sekijima M, Akiyama Y, Gromiha MM. Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques, Journal of Biomolecular Structure and Dynamics, 36(6): 1566-1576, 2018. doi: 10.1080/07391102.2017.1329098
• Ban T, Ohue M, Akiyama Y. Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem, Computational Biology and Chemistry, 73: 139-146, 2018. doi: 10.1016/j.compbiolchem.2018.02.008
• Wakui N, Yoshino R, Yasuo N, Ohue M, Sekijima M. 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

2017

Journal Paper

• Kakuta M, Suzuki S, Izawa K, Ishida T, Akiyama Y. A massively parallel sequence similarity search for metagenomic sequencing data, International Journal of Molecular Sciences, 18(10): 2124, 2017. doi: 10.3390/ijms18102124
• Chiba S, Ishida T, Ikeda K, Mochizuki M, Teramoto R, Taguchi Y-h, Iwadate M, Umeyama H, Ramakrishnan C, Thangakani AM, Velmurugan D, Gromiha MM, Okuno T, Kato K, Minami S, Chikenji G, Suzuki SD, Yanagisawa K, Shin WH, Kihara D, Yamamoto KZ, Moriwaki Y, Yasuo N, Yoshino R, Zozulya S, Borysko P, Stavniichuk R, Honma T, Hirokawa T, Akiyama Y, Sekijima M. An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes, Scientific Reports 7, Article number: 12038, 2017. doi: 10.1038/s41598-017-10275-4
• Yoshino R, Yasuo N, Hagiwara Y, Ishida T, Inaoka DK, Amano Y, Tateishi Y, Ohno K, Namatame I, Niimi T, Orita M, Kita K, Akiyama Y, Sekijima M. In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease, Scientific Reports 7, Article number: 6666, 2017. doi: 10.1038/s41598-017-06411-9
• Yanagisawa K, Komine S, Suzuki SD, Ohue M, Ishida T, Akiyama Y. Spresso: An ultrafast compound pre-screening method based on compound decomposition, Bioinformatics, 33(23): 3836-3843, 2017. doi: 10.1093/bioinformatics/btx178
• Suzuki S, Ishida T, Ohue M, Kakuta M, Akiyama Y. 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. doi: 10.1007/978-1-4939-7015-5_2
• Matsuzaki Y, Uchikoga N, Ohue M, Akiyama Y. Rigid-docking approaches to explore protein-protein interaction space, Advances in Biochemical Engineering/Biotechnology (the volume on Network Biology), 160: 33-55, 2017. doi: 10.1007/10_2016_41

International Conference

• Ban T, Ohue M, Akiyama Y. 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), 1-6, 2017. doi: 10.1109/ICCABS.2017.8114299
• Ohue M, Yamazaki T, Ban T, Akiyama Y. Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach, Intelligent Computing Theories and Application (In Proceedings of ICIC2017, Lecture Notes in Computer Science), 10362, 549-558, 2017. doi: 10.1007/978-3-319-63312-1_48
• Suzuki SD, Ohue M, Akiyama Y. Learning-to-rank based compound virtual screening by using pairwise kernel with multiple heterogeneous experimental data, In Proceedings of The 22nd International Symposium on Artificial Life and Robotics (AROB 2017), 114-119, 2017.

2016

Journal Paper

• Kasahara K, Ma B, Goto K, DasGupta B, Higo J, Fukuda I, Mashimo T, Akiyama Y, Nakamura H. myPresto/omegagene: a GPU-accelerated Molecular Dynamics Simulator Tailored for Enhanced Conformational Sampling Methods with a Non-Ewald Electrostatic Scheme, Biophysics and Physicobiology, 13: 209-216, 2016. doi: 10.2142/biophysico.13.0_209
• Ose A, Toshimoto K, Ikeda K, Maeda K, Yoshida S, Yamashita F, Hashida M, Ishida T, Akiyama Y, Sugiyama Y. Development of a Support Vector Machine-Based System to Predict Whether a Compound Is a Substrate of a Given Drug Transporter Using Its Chemical Structure, Journal of Pharmaceutical Sciences, 105(77): 2222-2230, 2016. doi: 10.1016/j.xphs.2016.04.023
• Suzuki S, Kakuta M, Ishida T, Akiyama Y. GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering, PLoS ONE, 11(8): e0157338, 2016. doi: 10.1371/journal.pone.0157338
• Uchikoga N, Matsuzaki Y, Ohue M, Akiyama Y. Specificity of broad protein interaction surfaces for proteins with multiple binding partners, Biophysics and Physicobiology, 13: 105-115, 2016. doi: 10.2142/biophysico.13.0_105

International Conference

• Yanagisawa K, Komine S, Suzuki SD, Ohue M, Ishida T, Akiyama Y. ESPRESSO: An ultrafast compound pre-screening method based on compound decomposition, In Proceedings of The 27th International Conference on Genome Informatics (GIW 2016), 7 pages, 2016.

2015

Journal Paper

• Chiba S, Ikeda K, Ishida T, Gromiha MM, Taguchi Y-h, Iwadate M, Umeyama H, Hsin KY, Kitano H, Yamamoto K, Sugaya N, Kato K, Okuno T, Chikenji G, Mochizuki M, Yasuo N, Yoshino R, Yanagisawa K, Ban T, Teramoto R, Ramakrishnan C, Thangakani AM, Velmurugan D, Prathipati P, Ito J, Tsuchiya Y, Mizuguchi K, Honma T, Hirokawa T, Akiyama Y, Sekijima M. Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target, Scientific Reports, 5: 17209, 2015. doi: 10.1038/srep17209
• Yanagisawa K, Ishida T, Akiyama Y. Drug Clearance Pathway Prediction Based on Semi-supervised Learning, IPSJ Transactions on Bioinformatics (TBIO), 8: 21-27, 2015. doi: 10.2197/ipsjtbio.8.21
• Suzuki S, Kakuta M, Ishida T, Akiyama Y. Faster sequence homology searches by clustering subsequences, Bioinformatics, 31(8): 1183-1190, 2015. doi: 10.1093/bioinformatics/btu780
• Shimoda T, Suzuki S, Ohue M, Ishida T, Akiyama Y. Protein-Protein Docking on Hardware Accelerators: Comparison of GPU and MIC Architectures, BMC Systems Biology, 9(Suppl 1): S6, 2015. doi: 10.1186/1752-0509-9-S1-S6

2014

Journal Paper

• Yano M, Mori H, Akiyama Y, Yamada T, Kurokawa K. CLAST: CUDA implemented large-scale alignment search tool, BMC Bioinformatics, 15: 406, 2014. doi: 10.1186/s12859-014-0406-y
• Ohue M, Shimoda T, Suzuki S, Matsuzaki Y, Ishida T, Akiyama Y. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers, Bioinformatics, 30(22): 3281-3283, 2014. doi: 10.1093/bioinformatics/btu532
• Ohue M, Matsuzaki Y, Uchikoga N, Ishida T, Akiyama Y. MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data, Protein and Peptide Letters, 21(8): 766-778, 2014. doi: 10.2174/09298665113209990050
• Suzuki S, Kakuta M, Ishida T, Akiyama Y. GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array, PLoS ONE, 9(8): e103833, 2014. doi: 10.1371/journal.pone.0103833
• Matsuoka S, Sato H, Tatebe O, Koibuchi M, Fujiwara I, Suzuki S, Kakuta M, Ishida T, Akiyama Y, Suzumura T, Ueno K, Kanezashi H, Miyoshi T. Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year, Supercomputing Frontiers and Innovations, 1(2): 89-107, 2014. doi: 10.14529/jsfi140206
• Toshimoto K, Wakayama N, Kusama M, Maeda K, Sugiyama Y, Akiyama Y. In silico prediction of major drug clearance pathways by support vector machines with feature-selected descriptors, Drug Metabolism and Disposition 42(11):1811-1819, 2014. doi: 10.1124/dmd.114.057893
• You H, Kim GE, Na CH, Lee S, Lee CJ, Cho KH, Akiyama Y, Ishida T, No KT. An empirical model for gas phase acidity and basicity estimation, SAR and QSAR in Environmental Research, 25(2): 91-115, 2014. doi: 10.1080/1062936X.2013.864997
• Matsuzaki Y, Ohue M, Uchikoga N, Akiyama Y. Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis, Protein and Peptide Letters, 21(8), 790-798, Jun 2014. doi: 10.2174/09298665113209990066

International Conference

• Komatsu Y, Ishida T, Akiyama Y. Metagenomic Phylogenetic Classification Using Improved Naïve Bayes, Intelligent Computing in Bioinformatics (In Proceedings of ICIC2014, Lecture Notes in Computer Science), 8590: 262-270, 2014. doi: 10.1007/978-3-319-09330-7_32
• Ban T, Ishida T, Akiyama Y. Improved conformational search for protein-ligand docking based on optimal arrangement of multiple small search grids, In Proceedings of the 20th International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'14), 6 pages, 2014.

2013

Journal Paper

• Ohue M, Matsuzaki Y, Shimoda T, Ishida T, Akiyama Y. Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods, BMC Proceedings, 7(Suppl 7):S6, 2013. doi: 10.1186/1753-6561-7-S7-S6
• Hagiwara Y, Ohno K, Orita M, Koga R, Endo T, Akiyama Y, Sekijima M. Accelerating Quantum Chemistry Calculations with Graphical Processing Units - Toward in High-Density (HD) Silico Drug Discovery, Current Computer Aided-Drug Design, 9(3), 396-401, 2013. doi: 10.2174/15734099113099990031
• Matsuzaki Y, Uchikoga N, Ohue M, Shimoda T, Sato T, Ishida Y, Akiyama Y. 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. doi: 10.1186/1751-0473-8-18
• Uchikoga N, Matsuzaki Y, Ohue M, Hirokawa T, Akiyama Y. Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints, PLoS ONE, 8(7), e69365, 2013. doi: 10.1371/journal.pone.0069365
• Namiki Y, Ishida T, Akiyama Y. Acceleration of sequence clustering using longest common subsequence filtering, BMC Bioinformatics, 14(Suppl 8): S7, 2013. doi: 10.1186/1471-2105-14-S8-S7
• Ren A, Ishida T, Akiyama Y. Assessing statistical reliability of phylogenetic trees via a speedy double bootstrap method, Molecular Phylogenetics and Evolution, 67(2): 429-435, 2013. doi: 10.1016/j.ympev.2013.02.011
• Oates ME, Romero P, Ishida T, Ghalwash M, Mizianty MJ, Xue B, Dosztányi Z, Uversky VN, Obradovic Z, Kurgan L, Dunker AK, Gough J. D2P2: database of disordered protein predictions, Nucleic Acids Research, 41(D1): D508-D516, 2013. doi: 10.1093/nar/gks1226

International Conference

• Shimoda T, Ishida Y, Suzuki S, Ohue M, Akiyama Y. MEGADOCK-GPU: An accelerated protein-protein docking calculation on GPUs, In Proceedings of the 4th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB2013) (ParBio workshop 2013), 2013. doi: 10.1145/2506583.2506693
• Obata Y, Ishida T, Natsume T, Akiyama Y. Acceleration of tandem mass spectrometry analysis software CoCoozo using multi-core CPUs and graphics processing units, In Proceedings of the 19th International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'13), 6 pages, 2013.
• Ren A, Ishida T, Akiyama Y. SDBP: An easy-to-use R program package for assessing reliability of estimated phylogenetic trees based on the speedy double bootstrap method, In Proceedings of the 19th International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'13), 6 pages, 2013.

2012

Journal Paper

• Suzuki S, Ishida T, Kurokawa K, Akiyama Y. GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics, PLoS ONE, 7(5), e36060, 2012. doi: 10.1371/journal.pone.0036060

International Conference

• Ohue M, Matsuzaki Y, Ishida Y, Akiyama Y. Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis, Pattern Recognition in Bioinformatics (In Proceedings of PRIB2012, Lecture Notes in Computer Science), 7632: 178-187, 2012. doi: 10.1007/978-3-642-34123-6_16
• Namiki Y, Ishida T, Akiyama Y. Fast DNA Sequence Clustering Based on Longest Common Subsequence, Emerging Intelligent Computing Technology and Applications (In Proceedings of ICIC2012, Communications in Computer and Information Science), 304: 453-460, 2012. doi: 10.1007/978-3-642-31837-5_66

2011

Journal Paper

• Kusuma WA, Ishida T, Akiyama Y. A Combined Approach for de novo DNA Sequence Assembly of Very Short Reads, IPSJ Transactions on Bioinformatics (TBIO), 4: 21-33, 2011. doi: 10.2197/ipsjtbio.4.21
• Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology, Journal of Molecular Biology, 414(2): 289-302, 2011. doi: 10.1016/j.jmb.2011.09.031

International Conference

• Kusuma WA, Akiyama Y. Metagenome Fragment Binning Based on Characterization Vectors, ICBBT 2011, 2011.

2010

Journal Paper

• Kusuma M, Toshimoto K, Maeda K, Hirai Y, Imai S, Chiba K, Akiyama Y, Sugiyama Y. In Silico Classification of Major Clearance Pathways of Drugs with Their Physiochemical Parameters, Drug Metabolism and Disposition, 38(8): 1362-1370, 2010. doi: 10.1124/dmd.110.032789
• Uchikoga N, Hirokawa T. Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes, BMC Bioinformatics, 11:236, 2010. doi: 10.1186/1471-2105-11-236

International Conference

• Kusuma WA, Akiyama Y. Design and simulation of hybrid de novo DNA sequence assembly for large eukaryotic genome, In Proceedings of the 16th Int’l Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'10), 6 pages, 2010.

2009

Journal Paper

• Matsuzaki Y, Matsuzaki Y, Sato T, Akiyama Y. In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis, Journal of Bioinformatics and Computational Biology, 7(6): 991-1012, 2009. doi: 10.1142/S0219720009004461

2008

Journal Paper

• Tsukamoto K, Yoshikawa T, Hourai Y, Fukui K, Akiyama Y. Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins, Journal of Bioinformatics and Computational Biology, 6(6): 1133-56, 2008. doi: 10.1142/S0219720008003904
• Tominaga D, Iguchi F, Horimoto K, Akiyama Y. High-throughput Automated Image Processing System for Cell Array Observations, Information and Media Technologies, 3(1): 71-78, 2008. doi: 10.2197/ipsjdc.3.728
• Sekijima M, Doi J, Honda S, Noguchi T, Shimizu S, Akiyama Y. Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation, Information and Media Technologies, 3(1): 201-210, 2008. doi: 10.11185/imt.3.201