1. Yoshikazu Shizuri, Kensuke Nakamura, Shosuke Yamamura "Reaction of Alkenes with Unstable Cation Electrogenerated from Phenols", J. Chem. Soc. Chem. Commun., 530 (1985).
   
2. Yoshikazu Shizuri, Kensuke Nakamura, Shosuke Yamamura, Shigeru Ohba, Hiroshi Yamashita, Yoshihiko Saito "Total Synthesis of Isofutoquinol A, Futoquinol, Isodihydrofutoquinol A and B" Tetrahedron Lett., 27, 727, (1986).
   
3. Shigeru Ohba, Hiroshi Yamashita, Yoshihiko Saito, Yoshikazu Shizuri, Kensuke Nakamura Shosuke Yamamura "Structure of Isofutoquinol A", Acta cryst., c43, 172, (1987).
   
4. Yoshikazu Shizuri, Kensuke Nakamura, Hideyuki Shigemori, Kazuharu Suyama, Yoshishige Okuno, Shosuke Yamamura "Electroorganic Synthesis of Some Bioactive Substances", 'Recent Advance in Electroorganic Synthesis' Kodan-sha Ltd., Tokyo, Japan, 117 (1986).
   
5. Kensuke Nakamura, Yoshihiro Osamura, Suehiro Iwata "Second-Order Jahn-Teller Effect of Cyclobutadiene in Low-Lying States -- An MCSCF Study" Chem. Phys., 136, 67, (1989).
   
6. Kensuke Nakamura, Yoshihiro Osamura "Theoretical Study of the Stability of beta-hydroxy Carbonium ion as an Intermediate of Pinacol Rearrangement" Journal of the Chemical Society of Japan, Chemistry and Industrial Chemistry. 1390, (1989).
   
7. Kensuke Nakamura, Yoshihiro Osamura "An MO Study on the Possibility of Concerted Mechanism in the Pinacol Rearrangement" J. Phys. Org. Chem., 737, (1990).
   
8. Kensuke Nakamura, Yoshihiro Osamura "Theoretical Study on the Migratory Aptitude in the Pinacol Rearrangement" Tetrahedron Lett. 31, 251, (1990).
9. Kensuke Nakamura, Yoshihiro Osamura "Theoretical Study on the Reaction Mechanism and Migratory Aptitude of the Pinacol Rearrangement" J. Am. Chem. Soc., 115, 9112, (1993).
   
10. Kensuke Nakamura, K. N. Houk "Theoretical Study of the Mechanism and Stereo Selectivity of the Ring Opening of Formyloxirane" Heterocycles, 35, 631, (1993).
    
11. Kensuke Nakamura, K. N. Houk "Substituent Effects on Torquoselectivity. Computational investigations of the Thermal Ring Openings of Cyclobutenes Fused to Substituted Cyclohexenes" J. Org. Chem., 60, 686, (1995).
    
12. Kensuke Nakamura, K. N. Houk "Theoretical Studies of Dynamic Processes in Host-Guest Complexes" J. Am. Chem. Soc., 117, 1853, (1995).
    
13. K. N. Houk, Kensuke Nakamura, Chimin Sheu, Amy E. Keating "Gating as a Control Element in Constrictive Binding and Guest Realease by Hemicarcerands" Science 273, 627, (1996).
    
14. Toshiaki Okuno, Ken Ohmori, Shigeru Nishiyama, Shosuke Yamamura, Kensuke Nakamura, K. N. Houk, Kazuya Okamoto "Chemical Study on Hapalosin, a Cyclic Depsipeptide Possessing Multidrug Resistance Reversing Activities: Synthesis, Structure and Biological Activity" Tetrahedron, 52, 14723, (1997).
    
15. Kensuke Nakamura, Chimin Sheu, Amy E. Keating, K. N. Houk, R. G. Chapman, J. C. Sherman, W. L. Jorgensen "Self-Assembling Ternary Complex. Stabilities and Template Ratio in Carceplex Formation" J. Am. Chem. Soc., 119, 4321, (1997).
    
16. Masakatsu Takahashi, Hironori Konishi, Satoshi Iida, Kensuke Nakamura, Shosuke Yamamura, Shigeru Nishiyama "Phenolic Oxidation of o,o'-Dihalogenated Phenols" Tetrahedron, 55, 5295, (1999).
    
17. Juyoung Yoon, Kensuke Nakamura "Dissymmetric Hemicarcerands and Reaction inside Chiral Hemicarcerands" Bulletin of the Korean Chemnical Society, 20, 765, (1999).
    
18. Nobuaki Kashihara, Sakino To-e, Kensuke Nakamura, Kazuo Umezawa, Shosuke Yamamura, Shigeru Nishiyama "Synthesis and Biological Activities of Hapalosin Derivatives with Modification at the C12 Position" Bioorganic & Medicinal Chemistry Letters, 10, 101, (2000).
    
19. Kensuke Nakamura and K. N. Houk "Theoretical Studies of the Wilcox Molecular Torsion Balance. Is the Edge-to Face Aromatic Interaction Important?" Organic Letters, 1, 2049, (1999).
    
20. Sang-Hyeup Lee, Juyoung Yoon, Kensuke Nakamura, Yoon-Sik Lee "Efficient Synthesis and Ring-Opening Reactions of trans- and cis-oxazoline-5-carboxylates" Organic Letters, 2,1243, (2000).
    
21. Kensuke Nakamura, Nobuo Tomioka, Akiko Itai, "Preparation of 3D-Coordinate from Chemical Structural Formula" JCPE Journal, 12, 177, (2000).
    
22. Hee Ok Jang, Kensuke Nakamura, Soung-Soo Yi, Jong Seung Kim, Jung Ran Go, Juyoung Yoon "Immobilization of Azacrown Ligand onto a Fluorophore" Journal of Inclusion Phenomena and Macrocyclic Chemistry, 40, 313, (2001).
    
23. Matthew J. Walker, Bruce N. Hietbrink, Bert E. Thomas IV, Kensuke Nakamura, E. Adam Kallel, K. N. Houk "Torquoselectivity Induced by Lone Pair Conjugation in the Electrocyclic Reaction of 1-Aza-Polyene" Journal of Organic Chemistry, 66, 6669, (2001).
    
24. Sang-Hyeup Lee, Xin Qi, Juyoung Yoon, Kensuke Nakamura and Yoon-Sik Lee "Preparation of beta-amino-alpha-mercapto acids and amides: stereocontrolled synthesis of 2'-sulfur analogues of the taxol C-13 side chain, both syn and anti S-acetyl-N-benzoyl- 3-phenylisocysteine" Tetrahedron, 58, 2777, (2002).
    
25. Kimiko Hashimoto, Takatoshi Matsumoto, Kensuke Nakamura, Shu-ichi Ohwada, Tatsuro Ohuchi, Manabu Horikawa, Katsuhiro Konno, Haruhisa Shirahama "Molecular Orbital Calculation for the Model Compounds of Kainoid Amino Acids, Agonist of Excitatory Amino Acid Receptors. Does the Kainoid C4-Substituent Directly Interact with the Receptors?" Bioorganic & Medicinal Chemistry, 10, 1373, (2002).
    
26. Hideaki Oikawa, Kensuke Nakamura, Hiroaki Toshima, Tomonobu Toyomasu, and Takeshi Sassa "Proposed Mechanism for the Reaction Catalyzed by a Diterpene Cyclase, Aphidicolan-16beta-ol Synthase: Experimental Results on Biomimetic Cyclization and Examination of the Cyclization Pathway by ab initio Calculations" J. Am. Chem. Soc., 124, 9145, (2002).
    
27. Sook Kyung Kim, Mi Yeon Bang, Sang-Hyeon Lee, Kensuke Nakamura, Seon-Woog Cho, and Juyoung Yoon "New Fluorescent Chemosensors for Cationic Guests: 1,8-Bis(azacrown) anthracenes" Journal of Inclusion Phenomena and Macrocyclic Chemistry, 43, 71, (2002).
    
28. Mitsuru Oka, Kunihisa Baba, Kensuke Nakamura, Lulu Dong, Hitoshi Hamajima, Ryouichi Unno and Yukiharu Matsumoto "Synthesis of 1-Azabicyclic Systems by Double Cyclization" Journal of Heterocyclic Chemistry, 40, 177, (2003).
    
29. Kensuke Nakamura, Takeshi Kawabata, Kei Yura, and Nobuhiro Go "Novel types of two-domain multi-copper oxidases: Possible missing link in the evolution" FEBS Lett., 553, pp. 239-244, (2003).
    
30. Aekyung Kang, Sook Kyung Kim, Kensuke Nakamura, Ju Hyun Park, Yeo Joon Yoon, Kap-Duk Lee, and Juyoung Yoon "A New Cavitand Ionophore bearing Two Rigid Crown Ether Groups" Tetrahedron Lett., 46, pp. 245-248,(2004).
    
31. Tadaaki Ohgiya, Kensuke Nakamura, and Shigeru Nishiyama "Total Synthesis of (+)-Tanikolide, Using Regioselective Elimination of a Vicinal Dibromoalkane" Bulletin of the Chemical Society of Japan. 78, pp. 1549-1554, (2005).
    
32. Kensuke Nakamura and Nobuhiro Go "Function and molecular evolution of multicopper blue proteins" Cellular and Molecular Life Science. 62, pp. 2050-2066, (2005)
    
33. Miho Yamada Mizutani, Yoshihiro Takamatsu, Tazuko Ichinose, Kensuke Nakamura, Akiko Itai "Effective handling of induced-fit motion in flexible docking" Proteins. 63, pp. 878-891, (2006)
    
34. Miho Yamada Mizutani, Kensuke Nakamura, Tazuko Ichinose, and Akiko Itai "Starting Point to Molecular Design: Efficient Automated 3D Model Builder Key3D", Chem. Pharm.Bull. 54(12), pp.1680-1685 (2006)
    
35. Gong Xiujun, Kensuke Nakamura, H Yu, Kei Yura, Nobuhiro Go "BAAQ:An Inrastructure for Application Integration and Knowledge Discovery in Bioinformatics", IEEE Transactions on Information Technology in Biomedicine", 11(4), pp. 428-434 (2007)
    
36. Junichi Shiina, Masataka Oikawa, Kensuke Nakamura, Rika Obata, Shigeru Nishiyama "Synthesis of pingusane-type sesquiterpenoids, acutifolone A and pinguisenol along with bisacutifolones through the Diels-Alder dimerization reaction", European Journal of Organic Chemistry 2007, pp.5190-5197 (2007)
    
37. Takashi Oishi, Ken-ichi Tanaka, Takuya Hashimoto, Yoko Shinbo, Kanokwan Jumtee, Takeshi Bamba, Eiichiro Fukusaki, Hideyuki Suzuki, Daisuke Shibata, Hiroki Takahashi, Hiroko Asahi, Ken Kurokawa, Yukiko Nakamura, Aki Hirai, Kensuke Nakamura, Md. Altaf-Ul-Amin, Shigehiko Kanaya "An approach to peak detection in GC-MS chromatograms and application of KNApSAcK database in prediction of candidate metabolites" Plant Biotechnology. 26, pp. 167-174, (2009)
    
38. Kyoko Murayama, Takamasa Tanabe, Yuichi Ishikawa, Kensuke Nakamura, Shigeru Nishiyama "A synthetic study on gymnastatins F and Q: the tandem Michael and aldol reaction approach" Tetrahedron Letters. 50, 3191-3194, (2009)
    
39. Kenichi Tanaka, Kensuke Nakamura, Tamio Saito, Hiroyuki Osada, Aki Hirai, Hiroki Takahashi, Shigehiko Kanaya, Md. Altaf-Ul-Amin "Metabolic pathway prediction based on inclusive relation between cyclic substructures" Plant Biotechnology. 26, 459-468, (2009)
    
40. Kensaku Nishikata, Masayoshi Wada, Hiroki Takahashi, Kensuke Nakamura Shigehiko Kanaya, Md Altaf-Ul-Amin "Predicting conformation of protein complexes by determining statisitically significant domain-domain interactions" Plant Biotechnology. 26, 495-501, (2009)
    
41. Kensuke Nakamura, Aki Hirai, Md. Altaf-Ul-Amin, Hiroki Takahashi "MetalMine: a database of functional metal-binding sites in proteins" Plant Biotechnology. 26, 517-521, (2009)
    
42. Kensuke Nakamura, Taku Oshima, Takuya Morimoto, Shun Ikeda, Hirofumu Yoshikawa, Yuh Shiwa, Shu Ishikawa, Margaret C. Linak, Aki Hirai, Hiroki Takahashi, Md. Altaf-Ul Amin, Naotake Ogasawara, Shigehiko Kanaya "Sequence-specific error profile of Illumina sequencers" Nucleic Acids Research Open access:gkr344 (2011)
    

Nara Institute of Science and Technology
Graduate School of Information Science
8916-5 Takayama, Ikoma-shi
Nara, 630-0101 JAPAN

Tel: +81-743-72-5257 / Fax : +81-743-72-5258
E-mail : kensuke-nm at is.naist.jp