Dr. Akira Kinjo
akira.kinjo@ubd.edu.bn
Associate Professor, Faculty of Science
EDUCATION
Ph.D in Genetics (SOKENDAI), M. Sc. in Chemistry (Kyoto University)
RESEARCH INTERESTS
Evolutionary developmental biology
Probabilistic models in biological sequence analysis
Monte Carlo and evolutionary simulations
FUTURE PROJECTS
Mathematical modeling in evolutionary developmental biology
Applications Invited
Time series analysis based on recurrent neural networks
Applications Invited
50
Scopus Publications
1398
Google Scholar Citations
21
Google Scholar h-index
32
Google Scholar i10-index
Scopus Publications
- BioHackathon 2015: Semantics of data for life sciences and reproducible research
Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan Bolton, Raoul J. P. Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin B. Cohen, Eric W. Deutsch, Jesualdo T. Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, and Toshihisa Takagi
F1000Research, ISSN: 20461402, eISSN: 1759796X, Published: 2020
F1000 Research Ltd - Cooperative “folding transition” in the sequence space facilitates function-driven evolution of protein families
Akira R. Kinjo
Journal of Theoretical Biology, ISSN: 00225193, eISSN: 10958541, Volume: 443, Pages: 18-27, Published: 14 April 2018
Elsevier BV - Mechanism of evolution by genetic assimilation: Equivalence and independence of genetic mutation and epigenetic modulation in phenotypic expression
Ken Nishikawa and Akira R. Kinjo
Biophysical Reviews, ISSN: 18672450, eISSN: 18672469, Pages: 667-676, Published: 1 April 2018
Springer Science and Business Media LLC - A new look at an old view of denaturant induced protein unfolding
Damien Hall, Akira R. Kinjo, and Yuji Goto
Analytical Biochemistry, ISSN: 00032697, eISSN: 10960309, Volume: 542, Pages: 40-57, Published: 1 February 2018
Elsevier BV - New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)
Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata, Naohiro Kobayashi, Toshimichi Fujiwara, Genji Kurisu, and Haruki Nakamura
Protein Science, ISSN: 09618368, eISSN: 1469896X, Pages: 95-102, Published: January 2018 - Neuro-symbolic representation learning on biological knowledge graphs
Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R Kinjo, Núria Queralt-Rosinach, and Robert Hoehndorf
Bioinformatics (Oxford, England), eISSN: 13674811, Pages: 2723-2730, Published: 1 September 2017
Oxford University Press (OUP) - Essential role of long non-coding RNAs in de novo chromatin modifications: the genomic address code hypothesis
Ken Nishikawa and Akira R. Kinjo
Biophysical Reviews, ISSN: 18672450, eISSN: 18672469, Pages: 73-77, Published: 1 April 2017
Springer Science and Business Media LLC - Protein Data Bank Japan (PDBj): Updated user interfaces, resource description framework, analysis tools for large structures
Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, and Haruki Nakamura
Nucleic Acids Research, ISSN: 03051048, eISSN: 13624962, Pages: D282-D288, Published: 1 January 2017
Oxford University Press (OUP) - VaProS: a database-integration approach for protein/genome information retrieval
Takashi Gojobori, Kazuho Ikeo, Yukie Katayama, Takeshi Kawabata, Akira R. Kinjo, Kengo Kinoshita, Yeondae Kwon, Ohsuke Migita, Hisashi Mizutani, Masafumi Muraoka, Koji Nagata, Satoshi Omori, Hideaki Sugawara, Daichi Yamada, and Kei Yura
Journal of Structural and Functional Genomics, ISSN: 1345711X, eISSN: 15700267, Pages: 69-81, Published: 1 December 2016
Springer Science and Business Media LLC - Molmil: A molecular viewer for the PDB and beyond
Gert-Jan Bekker, Haruki Nakamura, and Akira R. Kinjo
Journal of Cheminformatics, eISSN: 17582946, Published: 26 August 2016
Springer Science and Business Media LLC - Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins
Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, and Toshimichi Fujiwara
Journal of Biomedical Semantics, eISSN: 20411480, Published: 5 May 2016
Springer Science and Business Media LLC - Implementation of linked data in the life sciences at BioHackathon 2011
Kiyoko F Aoki-Kinoshita, Akira R Kinjo, Mizuki Morita, Yoshinobu Igarashi, Yi-an Chen, Yasumasa Shigemoto, Takatomo Fujisawa, Yukie Akune, Takeo Katoda, Anna Kokubu, Takaaki Mori, Mitsuteru Nakao, Shuichi Kawashima, Shinobu Okamoto, Toshiaki Katayama, and Soichi Ogishima
Journal of Biomedical Semantics, eISSN: 20411480, Published: January 07, 2015
Springer Science and Business Media LLC - Specific non-local interactions are not necessary for recovering native protein dynamics
Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, and Akira R. Kinjo
PLoS ONE, eISSN: 19326203, Published: 13 March 2014
Public Library of Science (PLoS) - Rigid-body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape-dependent manner
Bhaskar Dasgupta, Haruki Nakamura, and Akira R. Kinjo
Proteins: Structure, Function and Bioinformatics, ISSN: 08873585, eISSN: 10970134, Pages: 77-89, Published: January 2014 - Exhaustive comparison and classification of ligand-binding surfaces in proteins
Yoichi Murakami, Kengo Kinoshita, Akira R. Kinjo, and Haruki Nakamura
Protein Science, ISSN: 09618368, eISSN: 1469896X, Pages: 1379-1391, Published: October 2013 - The 3rd DBCLS BioHackathon: Improving life science data integration with Semantic Web technologies
Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul JP Bonnal, Brad Chapman, Peter JA Cock, Tore Eriksson, Paul MK Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R Kinjo, Fumikazu Konishi, Kyung-Hoon Kwon, Alberto Labarga, Anna-Lena Lamprecht, Yu Lin, Pierre Lindenbaum, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Pjotr Prins, Taro L Saito, Matthias Samwald, Venkata P Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger A Vos, David Withers, Chisato Yamasaki, Christian M Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, and Toshihisa Takagi
Journal of Biomedical Semantics, eISSN: 20411480, Published: February 11, 2013
Springer Science and Business Media LLC - Counterbalance of ligand-and self-coupled motions characterizes multispecificity of Ubiquitin
Bhaskar Dasgupta, Haruki Nakamura, and Akira R Kinjo
Protein Science, ISSN: 09618368, eISSN: 1469896X, Pages: 168-178, Published: February 2013 - Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures
Methods in Molecular Biology, ISSN: 10643745, Volume: 932, Pages: 295-315, Published: 2013 - GIRAF: A method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution
Akira R. Kinjo and Haruki Nakamura
Biophysics (Japan), eISSN: 13492942, Pages: 79-94, Published: 2012
Biophysical Society of Japan - Composite structural motifs of binding sites for delineating biological functions of proteins
Akira R. Kinjo and Haruki Nakamura
PLoS ONE, eISSN: 19326203, Published: 8 February 2012
Public Library of Science (PLoS) - Protein Data Bank Japan (PDBj): Maintaining a structural data archive and resource description framework format
A. R. Kinjo, H. Suzuki, R. Yamashita, Y. Ikegawa, T. Kudou, R. Igarashi, Y. Kengaku, H. Cho, D. M. Standley, A. Nakagawa, and H. Nakamura
Nucleic Acids Research, ISSN: 03051048, eISSN: 13624962, Published: January 2012
Oxford University Press (OUP) - Functional characterization of protein domains common to animal viruses and mouse
Akira R Kinjo, Yutaro Kumagai, Huy Dinh, Osamu Takeuchi, and Daron M Standley
10th Int. Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Computational Biology - Proceedings from Asia Pacific Bioinformatics Network (APBioNet), Issue: SUPPL. 3, Published: 2011
Springer Science and Business Media LLC - Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners
Bhaskar Dasgupta, Haruki Nakamura, and Akira R. Kinjo
Journal of Molecular Biology, ISSN: 00222836, eISSN: 10898638, Volume: 411, Pages: 713-727, Published: 19 August 2011
Elsevier BV - The 2nd DBCLS BioHackathon: Interoperable bioinformatics Web services for integrated applications
Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano, Jan Aerts, Kiyoko F Aoki-Kinoshita, Kazuharu Arakawa, Bruno Aranda, Raoul JP Bonnal, José M Fernández, Takatomo Fujisawa, Paul MK Gordon, Naohisa Goto, Syed Haider, Todd Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Greg von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, Luke McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, and Toshihisa Takagi
Journal of Biomedical Semantics, eISSN: 20411480, Published: August 02, 2011
Springer Science and Business Media LLC - Bridging the gap between single-template and fragment based protein structure modeling using Spanner
Mieszko Lis
Immunome Research, eISSN: 17457580, Published: 2011
OMICS Publishing Group
RECENT PUBLICATIONS
1. Kinjo AR. Cooperative “folding transition†in the sequence space facilitates function-driven evolution of protein families. Journal of Theoretical Biology 443:18-27 (2018)
2. Nishikawa K, Kinjo AR. Mechanism of evolution by genetic assimilation: Equivalence and independence of genetic mutation and epigenetic modulation in phenotypic expression. Biophysical Reviews 10:667–676 (2018)
3. Hall D, Kinjo AR, Goto Y. A new look at an old view of denaturant induced protein unfolding. Analytical Biochemistry 542:40-57 (2018) [DOI:10.1016/j.ab.2017.11.011]
4. Kinjo AR, Bekker G-J, Wako H, Endo S, Tsuchiya Y, Sato H, Nishi H, Kinoshita K, Suzuki H, Kawabata T, Yokochi M, Iwata T, Kobayashi N, Fujiwara T, Kurisu G, Nakamura H. New tools and functions in Data-out activities at Protein Data Bank Japan (PDBj). Protein Science (2017)
5. Kinjo AR. Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment. Biophysics and Physicobiology 14:99-110 (2017)