• Takabatake K, Yanagisawa K, Akiyama Y. Solving Generalized Polyomino Puzzles Using the Ising Model. Entropy, 24: 354, 2022.
  • 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): 1110-1 117, 2022.
  • Kosugi T, Ohue M. Quantitative estimate index for early-stage screening of  compounds  targeting  protein- protein interactions. International Journal of Molecular Sciences, 22(20): 10925, 2021.
  • 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.
  • 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.
  • 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.
  • 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), 9 pages, 2021.
  • 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), 12 pages, 2021.
  • 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), 14 pages, 2021.
  • Sugita S, Ohue M. Drug-target affinity prediction using applicability domain based  on  data  density.  In Proceedings of The 18th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2021), 6 pages, 2021.
  • Kosugi T, Ohue M. Quantitative estimate of protein-protein interaction targeting drug-likeness. In Proceedings of The 18th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2021), 8 pages, 2021.
  • Ohue M. Re-ranking of computational protein–peptide docking solutions with amino acid profiles of rigid-body docking results. In Proceedings of The 21st International Conference on Bioinformatics & Computational Biology (BIOCOMP’20), Advances in Computer Vision and Computational Biology, 749-758, 2021.  
  • 柳澤 渓甫.タンパク質立体構造情報を用いた薬剤バーチャルスクリーニング.JSBi Bioinformatics Review,2(1): 76–86,2021.
  • 大上 雅史. AlphaFoldのタンパク質立体構造予測の性能. 実験医学, 40(2): 427-430, 2022.
  • 大上 雅史. AlphaFold利用のすすめ. 実験医学, 40(2): 433-438, 2022.
  • Onishi T, Mihara M, Matsuda M, Sakamoto S, Kuwahata A, Sekino M, Kusakabe M, Handa H, Kitagawa Y. Application of magnetic nanoparticles for rapid detection and in situ diagnosis in clinical oncology. Cancers, 14(2): 364, 2022.
  • Shimizu N, Asatsuma-Okumura T, Yamamoto J, Yamaguchi Y, Handa H, Ito T. PLZF and its fusion proteins are pomalidomide-dependent CRBN neosubstrates. Communications Biology, 4(1): 1277, 2021.
  • Okuda M, Suwa T, Suzuki H, Yamaguchi Y, Nishimura Y. Three human RNA polymerases interact with TFIIH via a common RPB6 subunit. Nucleic Acids Research, 50(1): 1–16, 2022.
  • Tsukahara T, Sahara Y, Ribeiro N, Tsukahara R, Gotoh M, Sakamoto S, Handa H, Murakami-Murofushi K. Adenine nucleotide translocase 2, a putative target protein for 2-carba cyclic phosphatidic acid in microglial cells. Cellular Signalling, 82: 109951, 2021.
  • Ito T, Yamaguchi Y, Handa H. Exploiting ubiquitin ligase cereblon as a target for small-molecule compounds in medicine and chemical biology. Cell Chemical Biology, 28(7): 987–999, 2021.
  • Okamura H, Trinh GH, Dong, Z, Masaki Y, Seio K, Nagatsugi F. Selective and stable base pairing by alkynylated nucleosides featuring a spatially-separated recognition interface. Nucleic Acids Res., 2022 https://doi.org/10.1093/nar/gkac140
  • Masaki Y, Maruyama A, Yoshida K, Tomori T, Kishimura T, Seio K. Oligodeoxynucleotides Modified with 2'-O-(Cysteinylaminobutyl)carbamoylethylribothymidine Residues for Native Chemical Ligation with Peptide at Internal Positions. Bioconjug Chem. 33(2): 272-278, 2022.
  • 清尾 康志.核酸と免疫-核酸を認識する自然免疫のメカニズム.化学と教育, 69(11): 464-467, 2021
  • 正木慶昭,清尾康志.アンチセンス核酸におけるRNaseH依存型オフターゲット効果.実験医学(増刊) 39(17) 151-156, 2021



  • Sugita M, Kuwano I, Higashi T, Motoyama K, Arima H, Hirata F. Computational screening of a functional cyclodextrin derivative for suppressing a side-effect of Doxorubicin, J. Phys. Chem. B 2021, 125, 9, 2308–2316
  • 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.
  • Sugita M, Onishi I, Irisa M, Yoshida N, Hirata F. Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory, Molecules, 26: 271, 2021.
  • Ito S, Senoo A, Nagatoishi S, Ohue M, Yamamoto M, Tsumoto K, Wakui N. Structural basis for binding mechanism of human serum albumin complexed with cyclic peptide dalbavancin. Journal of Medicinal Chemistry, 63(22): 14045–14053, 2020.
  • Launay G, Ohue M, Santero JP, Matsuzaki M, Hilpert C, Uchikoga N, Hayashi T, Martin J. Evaluation of CONSRANK-like scoring functions for rescoring ensembles of protein-protein docking poses. Frontiers in Molecular Biosciences, 7:559005, 2020.
  • 大上雅史. 構造情報に基づくタンパク質間相互作用の計算予測. ファインケミカル, 2020年10月号, 49(10): 25-31, シーエムシー出版, 2020.大上雅史.
  • 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. Metagenome data on intestinal phage-bacteria associations aids the development of phage therapy against pathobionts, Cell Host & Microbe, 28(3):380-389, 2020.
  • 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.
  • 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. (in press) (arXiv, 2006.08905 [cs.DC], 2020.)
  • 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.
  • Kurayama F, Bahadur NM, Furusawa T, Suzuki N. Facile preparation of aminosilane-alginate hybrid beads for enzyme immobilization: Kinetics and equilibrium studies, International Journal of Biological Macromolecules, 150: 1203-1212, 2020.
  • Yamamoto J, Suwa T, Murase Y, Tateno S, Mizutome H, Asatsuma-Okumura T, Shimizu N., Kishi T, Momose S, Kizaki M, Ito T, Yamaguchi Y, Handa H. ARID2 is a pomalidomide-dependent CRL4CRBN substrate in multiple myeloma cells. Nature Chemical Biology, 16, 1208-1217, 2020.
  • Cho J, Hiramoto M, Masaike Y, Sakamoto S, Imai Y, Imai Y, Handa H, Imai T. UGGT1 retains proinsulin in the endoplasmic reticulum in an arginine dependent manner. Biochem. Biophys. Res. Commun., 527, 668-675, 2020
  • Kishimura T, Tomori T, Masaki Y, Seio K. Synthesis of 2'-O-alkylcarbamoylethyl-modified oligonucleotides with enhanced nuclease resistance that form isostable duplexes with complementary RNA. Bioorganic & Medicinal Chemistry Letters, 35: 127779, 2021.
  • Hara Y, Mizobe Y, Inoue YU, Hashimoto Y, Motohashi N, Masaki Y, Seio K, Takeda S, Nagata T, Wood MJA, Inoue T, Aoki Y. Novel EGFP reporter cell and mouse models for sensitive imaging and quantification of exon skipping. Scientific Reports. 2020 Jun 22;10(1):10110.


  • 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.
  • 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.
  • 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 H, Suzuki SD, Ito T, Kawatani M, Kudoh K, Takashina S, Yamamoto K, 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.
  • 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.
  • Ban T, Ohue M, Akiyama Y. NRLMFβ: Beta-distribution-rescored Neighborhood Regularized Logistic Matrix Factorization for Improving the Performance of Drug–Target Interaction Prediction, Biochemistry and Biophysics Reports, 18, 100615, 2019.
  • 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.
  • 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.
  • 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.
  • 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.
  • Kurayama F, Bahadur NM, Sato M, Furusawa T, Suzuki N. One‐step preparation of organic‐inorganic hybrid capsules based on simultaneous gelation and silicification, Engineering Reports, 1, e12061, 2019.
  • Tateno S, Iida M, Fujii S, Suwa T, Katayama M, Tokuyama H, Yamamoto J, Ito T, Sakamoto S, Handa H, Yamaguchi Y. Genome-wide screening reveals a role for subcellular localization of CRBN in the anti-myeloma activity of pomalidomide, Scientific Reports, 10, 4012, 2020.
  • Takahashi H, Ranjan A, Chen S, Suzuki H, Shibata M, Hirose T, Hirose H, Sasaki K, Abe R, Chen K, He Y, Zhang Y, Takigawa I, Tsukiyama T, Watanabe M, Fujii S, Iida M, Yamamoto J, Yamaguchi Y, Suzuki Y, Matsumoto M, Nakayama K, Washburn M, Saraf A, Florens L, Sato S, Tomomori-Sato C, Conaway R, Conaway J, Hatakeyama S. The role of Mediator and Little Elongation Complex in transcription termination, Nature Communications, 11, 1063, 2020.
  • Sekino M, Kuwahata A, Fujita S, Matsuda S, Kaneko M, Chikaki S, Sakamoto S, Saito I, Handa H, Kusakabe M. Development of an optimized dome-shaped magnet for rapid magnetic immunostaining, AIP ADVANCES, 10, 025317, 2020.
  • Sekino M, Kuwahata A, Yoshibe A, Imai K, Kaneko M, Chikaki S, Saito I, Tsuruma A, Sakamoto S, Handa H, Matsuda A, Kusakabe M. Development of an automatic magnetic immunostaining system for rapid diagnosis of cancer metastasis. AIP ADVANCES, 10, 015106, 2020.
  • Asatsuma-Okumura T, Ando H, De Simone M, Yamamoto J, Sato T, Shimizu N, Asakawa K, Yamaguchi Y, Ito T, Guerrini L, Handa H. p63 is a cereblon substrate involved in thalidomide teratogenicity, Nature Chemical Biology, 15: 1077-1084, 2019.
  • Ando H, Sato T, Ito T, Yamamoto J, Sakamoto S, Nitta N, Asatsuma-Okumura T, Shimizu N, Mizushima R, Aoki I, Imai T, Yamaguchi Y, Berk AJ, Handa H. Cereblon control of zebrafish brain size by regulation of neural stem cell proliferation, iScience, 15: 95-108, 2019.
  • Onishi T, Matsuda S, Nakamura Y, Kuramoto J, Tsuruma A, Sakamoto S, Suzuki S, Fuchimoto D, Onishi A, Chikaki S, Kaneko M, Kuwahata A, Sekino M, Yasuno H, Hanyu N, Kurita T, Takei H, Sakatani T, Taruno K, Nakamura S, Hayashida T, Jinno H, Kusakabe M, Handa H, Kameyama K, Kitagawa Y. Magnetically-promoted rapid immunofluorescence staining for frozen tissue sections, The Journal of Histochemistry and Cytochemistry, 67: 575-587, 2019.
  • Takeshita L, Yamada Y, Masaki Y, Seio K. Synthesis of Deoxypseudouridine 5'-Triphosphate Bearing the Photoremovable Protecting Group at the N1 Position Capable of Enzymatic Incorporation to DNA. Journal of Organic Chemistry, 85(4): 1861-1870, 2020.
  • Masaki Y, Yamamoto K, Yoshida K, Maruyama A, Tomori T, Iriyama Y, Nakajima H, Kanaki T, Seio K. Modification of oligonucleotides with weak basic residues via the 2'-O-carbamoylethyl linker for improving nuclease resistance without loss of duplex stability and antisense activity. Organic & Biomolecular Chemistry, 17(19): 4835-4842, 2019.



  • 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 Mitogen Activated Protein (MAP) Kinase Inhibitor, Organic Letters, 21(2): 373-377, 2018.
  • 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, 527, 2018
  • 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.
  • 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.
  • Mochizuki M, Suzuki SD, Yanagisawa K, Ohue M, Akiyama Y. QEX: Target-specific druglikeness filter enhances ligand-based virtual screening, Molecular Diversity, 23: 11–18, 2019.
  • 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.
  • 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.
  • 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.
  • Suzuki H, Okamoto-Katsuyama M, Suwa T, Maeda R, Tamura T, Yamaguchi Y. TLP-mediated global transcriptional repression after double-strand DNA breaks slows down DNA repair and induces apoptosis, Scientific Reports,9, 4868, 2019.
  • Kabe Y, Sakamoto S, Hatakeyama M, Yamaguchi Y, Suematsu M, Itonaga M, Handa H. Application of high-performance magnetic nanobeads to biological sensing devices, Analytical and Bioanalytical Chemistry, 411: 1825–1837, 2019.
  • Kabe Y, Suematsu M, Sakamoto S, Hirai M, Koike I, Hishiki T, Matsuda A, Hasegawa Y, Tsujita K, Ono M, Minegishi N, Hozawa A, Murakami Y, Kubo M, Itonaga M, Handa H. Development of a highly-sensitive device for counting the number of disease-specific exosomes in human sera, Clincal Chemistry, 64(10): 1463-1473, 2018.
  • Kimura A, Kitajima M, Nishida K, Serada S, Fujimoto M, Naka T, Fujii-Kuriyama Y, Sakamato S, Ito T, Handa H, Tanaka T, Yoshimura A, Suzuki H. NQO1 inhibits the TLR-dependent production of selective cytokines by promoting IκB-ζ degradation, Journal of Experimental Medicine, 215 (8): 2197–2209, 2018.
  • Kanamori T, Masaki Y, Oda Y, Ohzeki H, Ohkubo A, Sekine M, Seio K. DNA triplex-based fluorescence turn-on sensors for adenosine using a fluorescent molecular rotor 5-(3-methylbenzofuran-2-yl) deoxyuridine, Organic & Biomolecular Chemistry, 17(8): 2077-2080, 2019.
  • Masaki Y, Inde T, Maruyama A, Seio K. Tolerance of N2-heteroaryl modifications on guanine bases in a DNA G-quadruplex. Organic & Biomolecular Chemistry, 17(4): 859-866, 2019.
  • Masaki Y, Yamamoto K, Inde T, Yoshida K, Maruyama A, Nagata T, Tanihata J, Takeda S, Sekine M, Seio K. Synthesis of 2'-O-(N-methylcarbamoylethyl) 5-methyl-2-thiouridine and its application to splice-switching oligonucleotides. Bioorganic & Medicinal Chemistry Letters, 29(2): 160-163, 2019.
  • Ando K, Saneyoshi H, Seio K, Sekine M. A theoretical study on the elimination reaction of acrylonitrile from 2′-O-cyanoethylated nucleosides by Bu4NF, Tetrahedron, 75(1): 1-9, 2019.
  • Masaki Y, Iriyama Y, Nakajima H, Kuroda Y, Kanaki T, Furukawa S, Sekine M, Seio K. Application of 2'-O-(2-N-Methylcarbamoylethyl) Nucleotides in RNase H-Dependent Antisense Oligonucleotides, Nucleic Acid Therapeutics, 28(5), 2018.
  • Inde T, Nishizawa S, Hattori Y, Kanamori T, Yuasa H, Seio K, Sekine M, Ohkubo A. Synthesis of and triplex formation in oligonucleotides containing 2'-deoxy-6-thioxanthosine, Bioorganic & Medicinal Chemistry, 26(13): 3785-3790, 2018.
  • Tomori T, Nagaoka K, Takeshita L, Shiozawa T, Miyatake Y, Masaki Y, Sekine M, Seio K. Deoxynucleoside Triphosphate Containing Pyridazin-3-one Aglycon as a Thymidine Triphosphate Substitute for Primer Extension and Chain Elongation by Klenow fragments, The Journal of Organic Chemistry. 83(15): 8353-8363, 2018.
  • Seio K, Kanamori T, Masaki Y. Solvent- and environment-dependent fluorescence of modified nucleobases, Tetrahedron Letters, 59(21): 1977-1985, 2018.
  • 坂本 聡、半田 宏 抗体標識蛍光磁性ビーズを用いた迅速磁気免疫染色法の開発, まぐね(Magnetics Japan)、日本応用磁気学会、13(4): 167-173, 2018.
  • 田中俊行、畠山 士、安野 寛、羽生尚広、坂本 聡、半田 宏 蛍光磁性ビーズを利用した高速高感度免疫測定システムの開発メディカル・サイエンス・ダイジェスト(Medical Science Digest), 44(8): 201-204, 2018.
  • 清尾 康志, 金森 功吏, 正木 慶昭 核酸塩基にヘテロアリール基や蛍光色素を導入した分子ローター型蛍光核酸の開発 有機合成化学協会誌, 76 巻 8 号: 792-801, 2018.



  • 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. 
  • 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: 205212, 2018
  • 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. 
  • 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), 6 pages, 2017. 
  • 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. 
  • 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, 12038, 2017. 
  • Ohue M, Yamazaki T, Ban T, Akiyama Y. 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, 2017.
  • 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, 6666, 2017. 
  • 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.
  • 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.
  • 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.
  • Kaneko M, Chikaki S, Matsuda S, Kuwahata A, Namita M, Saito I, Sakamoto S, Kusakabe M, Sekino M. Development of magnet configurations for magnetic immunostaining, AIP ADVANCES, 8: 056732, 2018.
  • Mori T, Ito T, Liu S, Ando H, Sakamoto S, Yamaguchi Y, Tokunaga E, Shibata N, Handa H, Hakoshima T. Structural basis of thalidomide enantiomer binding to cereblon, Scientific Reports, 8(1):1294, 2018.
  • Boccitto M, Lee N, Sakamoto S, Spruce L, Handa H, Clardy J, Seeholzer S, Kalb R. The Neuroprotective Marine Compound Psammaplysene A Binds the RNA Binding Protein HNRNPK. Marine Drugs, 15(8): 246, 2017.
  • Inde T, Masaki Y, Maruyama A, Ito Y, Makio N, Miyatake Y, Tomori T, Sekine M, Seio K. Synthesis of oligonucleotides containing 2-N-heteroarylguanine residues and their effect on duplex/triplex stability, Organic & Biomolecular Chemistry, 15(39): 8371-8383, 2017.
  • Ohno K, Sugiyama D, Takeshita L, Kanamori T, Masaki Y, Sekine M, Seio K. Synthesis of photocaged 6-O-(2-nitrobenzyl)guanosine and 4-O-(2-nitrobenzyl) uridine triphosphates for photocontrol of the RNA transcription reaction, Bioorganic and Medicinal Chemistry, 25(21): 6007-6015, 2017.
  • Seio K, Tokugawa M, Kaneko K, Shiozawa T, Masaki, Y. A Systematic Study of the Synthesis of 2ʹ-Deoxynucleosides by Mitsunobu Reaction, Synlett, 28(15): 2014-2017, 2017.