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ORCIDKiyoko F. Aoki-Kinoshita
Publications
- 2022
[c10]Eiji Shinkawa, Koichi Nagatsuka, Yuki Murata, Tamiko Ono, Masae Hosoda, Kiyoko F. Aoki-Kinoshita
, Masayasu Atsumi:
Prediction and Analysis of Drug-Glycoprotein Interactions with Mutual Attention Neural Networks. SCIS/ISIS 2022: 1-5- 2021
- [j34]Hayato Takihara, Nobuaki Miura, Kiyoko F. Aoki-Kinoshita, Shujiro Okuda:
Functional glyco-metagenomics elucidates the role of glycan-related genes in environments. BMC Bioinform. 22(1): 505 (2021) - [j33]Yu Watanabe, Kiyoko F. Aoki-Kinoshita, Yasushi Ishihama, Shujiro Okuda:
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. Nucleic Acids Res. 49(Database-Issue): D1523-D1528 (2021) - [j32]Akihiro Fujita, Nobuyuki P. Aoki, Daisuke Shinmachi, Masaaki Matsubara, Shinichiro Tsuchiya, Masaaki Shiota, Tamiko Ono, Issaku Yamada, Kiyoko F. Aoki-Kinoshita:
The international glycan repository GlyTouCan version 3.0. Nucleic Acids Res. 49(Database-Issue): D1529-D1533 (2021) - 2020
- [j31]Robel Y. Kahsay, Jeet Vora, Rahi Navelkar, Reza Mousavi, Brian C. Fochtman, Xavier Holmes, Nagarajan Pattabiraman, René Ranzinger, Rupali Mahadik, Tatiana Williamson, Sujeet Kulkarni, Gaurav Agarwal, Maria Jesus Martin, Preethi Vasudev, Leyla J. García, Nathan Edwards, Wenjin Zhang, Darren A. Natale, Karen Ross, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, William S. York, Raja Mazumder:
GlyGen data model and processing workflow. Bioinform. 36(12): 3941-3943 (2020) - 2019
- [j30]Shinichiro Tsuchiya, Issaku Yamada, Kiyoko F. Aoki-Kinoshita:
GlycanFormatConverter: a conversion tool for translating the complexities of glycans. Bioinform. 35(14): 2434-2440 (2019) - [i1]Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi:
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research 8: 1677 (2019) - 2017
- [j29]Masae Hosoda, Yukie Akune, Kiyoko F. Aoki-Kinoshita:
Development and application of an algorithm to compute weighted multiple glycan alignments. Bioinform. 33(9): 1317-1323 (2017) - [j28]Masaaki Matsubara, Kiyoko F. Aoki-Kinoshita, Nobuyuki P. Aoki, Issaku Yamada, Hisashi Narimatsu:
WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures. J. Chem. Inf. Model. 57(4): 632-637 (2017) - 2016
- [j27]Christopher B. Barnett, Kiyoko F. Aoki-Kinoshita, Kevin J. Naidoo:
The Glycome Analytics Platform: an integrative framework for glycobioinformatics. Bioinform. 32(19): 3005-3011 (2016) - [j26]Wenpin Hou, Yushan Qiu, Nobuyuki Hashimoto, Wai-Ki Ching, Kiyoko F. Aoki-Kinoshita:
A systematic framework to derive N-glycan biosynthesis process and the automated construction of glycosylation networks. BMC Bioinform. 17(S-7): 240 (2016) - [j25]Kiyoko F. Aoki-Kinoshita, Sanjay Agravat, Nobuyuki P. Aoki, Sena Arpinar, Richard D. Cummings, Akihiro Fujita, Noriaki Fujita, Gerald M. Hart, Stuart M. Haslam, Toshisuke Kawasaki, Masaaki Matsubara, Kelley W. Moreman, Shujiro Okuda, Michael Pierce, René Ranzinger, Toshihide Shikanai, Daisuke Shinmachi, Elena Solovieva, Yoshinori Suzuki, Shinichiro Tsuchiya, Issaku Yamada, William S. York, Joseph Zaia, Hisashi Narimatsu:
GlyTouCan 1.0 - The international glycan structure repository. Nucleic Acids Res. 44(Database-Issue): 1237-1242 (2016) - 2015
- [j24]René Ranzinger, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, Shin Kawano, Thomas Lütteke, Shujiro Okuda, Daisuke Shinmachi, Toshihide Shikanai, Hiromichi Sawaki, Philip V. Toukach, Masaaki Matsubara, Issaku Yamada, Hisashi Narimatsu:
GlycoRDF: an ontology to standardize glycomics data in RDF. Bioinform. 31(6): 919-925 (2015) - [j23]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, Soichi Ogishima:
Implementation of linked data in the life sciences at BioHackathon 2011. J. Biomed. Semant. 6: 3 (2015) - [j22]Limin Li, Kiyoko F. Aoki-Kinoshita, Wai-Ki Ching, Hao Jiang:
On using physico-chemical properties of amino acids in string kernels for protein classification via support vector machines. J. Syst. Sci. Complex. 28(2): 504-516 (2015) - 2014
- [j20]Toshiaki Katayama, Mark D. Wilkinson, Kiyoko F. Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi-an Chen, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Alexandru Constantin:
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J. Biomed. Semant. 5: 5 (2014) - [j19]Matthew P. Campbell, René Ranzinger, Thomas Lütteke, Julien Mariethoz, Catherine A. Hayes, Jingyu Zhang, Yukie Akune, Kiyoko F. Aoki-Kinoshita, David Damerell, Giorgio Carta, William S. York, Stuart M. Haslam, Hisashi Narimatsu, Pauline M. Rudd, Niclas G. Karlsson, Nicolle H. Packer, Frédérique Lisacek:
Toolboxes for a standardised and systematic study of glycans. BMC Bioinform. 15(S-1): S9 (2014) - [j18]Kenichi Tanaka, Kiyoko F. Aoki-Kinoshita, Masaaki Kotera, Hiromichi Sawaki, Shinichiro Tsuchiya, Noriaki Fujita, Toshihide Shikanai, Masaki Kato, Shin Kawano, Issaku Yamada, Hisashi Narimatsu:
WURCS: The Web3 Unique Representation of Carbohydrate Structures. J. Chem. Inf. Model. 54(6): 1558-1566 (2014) - [j17]Matthew P. Campbell, Robyn Peterson, Julien Mariethoz, Elisabeth Gasteiger, Yukie Akune, Kiyoko F. Aoki-Kinoshita, Frédérique Lisacek, Nicolle H. Packer:
UniCarbKB: building a knowledge platform for glycoproteomics. Nucleic Acids Res. 42(Database-Issue): 215-221 (2014) - 2013
- [j16]Kiyoko F. Aoki-Kinoshita, Jerven T. Bolleman, Matthew P. Campbell, Shin Kawano, Jin-Dong Kim, Thomas Lütteke, Masaaki Matsubara, Shujiro Okuda, René Ranzinger, Hiromichi Sawaki, Toshihide Shikanai, Daisuke Shinmachi, Yoshinori Suzuki, Philip V. Toukach, Issaku Yamada, Nicolle H. Packer, Hisashi Narimatsu:
Introducing glycomics data into the Semantic Web. J. Biomed. Semant. 4: 39 (2013) - 2012
- [j14]Hao Jiang, Wai-Ki Ching, Kiyoko F. Aoki-Kinoshita, Dianjing Guo:
Modeling genetic regulatory networks: a delay discrete dynamical model approach. J. Syst. Sci. Complex. 25(6): 1052-1067 (2012) - [c9]Masae Hosoda, Yukie Akune, Kiyoko F. Aoki-Kinoshita:
Multiple Tree Alignment with Weights Applied to Carbohydrates to Extract Binding Recognition Patterns. PRIB 2012: 49-58 - 2011
- [j13]Toshiaki Katayama, Mark D. Wilkinson, Rutger A. 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 Jean Pierre Bonnal, José María Fernández, Takatomo Fujisawa, Paul M. K. Gordon, Naohisa Goto, Syed Haider, Todd W. Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Gregory Von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, E. 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 H. Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi:
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J. Biomed. Semant. 2: 4 (2011) - 2010
- [j12]Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord H. Barboza, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi:
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. 1: 8 (2010) - [j11]Limin Li, Wai-Ki Ching, Takako Yamaguchi, Kiyoko F. Aoki-Kinoshita:
A weighted q-gram method for glycan structure classification. BMC Bioinform. 11(S-1): 33 (2010) - 2008
- [j9]Kosuke Hashimoto, Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka:
A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology. ACM Trans. Knowl. Discov. Data 2(1): 6:1-6:30 (2008) - 2006
- [j8]Shanfeng Zhu, Keiko Udaka, John Sidney, Alessandro Sette, Kiyoko F. Aoki-Kinoshita, Hiroshi Mamitsuka:
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinform. 22(13): 1648-1655 (2006) - [j7]Minoru Kanehisa, Susumu Goto, Masahiro Hattori, Kiyoko F. Aoki-Kinoshita, Masumi Itoh, Shuichi Kawashima, Toshiaki Katayama, Michihiro Araki, Mika Hirakawa:
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34(Database-Issue): 354-357 (2006) - [c7]Kiyoko F. Aoki-Kinoshita, Minoru Kanehisa, Ming-Yang Kao, Xiang-Yang Li, Weizhao Wang:
A 6-Approximation Algorithm for Computing Smallest Common AoN-Supertree with Application to the Reconstruction of Glycan Trees. ISAAC 2006: 100-110 - [c6]Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Hiroshi Mamitsuka, Minoru Kanehisa:
ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. ISMB (Supplement of Bioinformatics) 2006: 25-34 - [c5]Kosuke Hashimoto, Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka:
A new efficient probabilistic model for mining labeled ordered trees. KDD 2006: 177-186 - 2005
- [j6]Kiyoko F. Aoki, Hiroshi Mamitsuka, Tatsuya Akutsu, Minoru Kanehisa:
A score matrix to reveal the hidden links in glycans. Bioinform. 21(8): 1457-1463 (2005) - [j5]Nobuhisa Ueda, Kiyoko F. Aoki-Kinoshita, Atsuko Yamaguchi, Tatsuya Akutsu, Hiroshi Mamitsuka:
A Probabilistic Model for Mining Labeled Ordered Trees: Capturing Patterns in Carbohydrate Sugar Chains. IEEE Trans. Knowl. Data Eng. 17(8): 1051-1064 (2005) - [c4]Raymond Wan, Hiroshi Mamitsuka, Kiyoko F. Aoki:
Cleaning microarray expression data using Markov random fields based on profile similarity. SAC 2005: 206-207 - 2004
- [j4]Atsuko Yamaguchi, Kiyoko F. Aoki, Hiroshi Mamitsuka:
Finding the maximum common subgraph of a partial k-tree and a graph with a polynomially bounded number of spanning trees. Inf. Process. Lett. 92(2): 57-63 (2004) - [j3]Kiyoko F. Aoki, Atsuko Yamaguchi, Nobuhisa Ueda, Tatsuya Akutsu, Hiroshi Mamitsuka, Susumu Goto, Minoru Kanehisa:
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res. 32(Web-Server-Issue): 267-272 (2004) - [j2]Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Tatsuya Akutsu, Minoru Kanehisa, Hiroshi Mamitsuka:
Managing and Analyzing Carbohydrate Data. SIGMOD Rec. 33(2): 33-38 (2004) - [c3]Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka:
Application of a new probabilistic model for recognizing complex patterns in glycans. ISMB/ECCB (Supplement of Bioinformatics) 2004: 6-14 - [c2]Nobuhisa Ueda, Kiyoko F. Aoki, Hiroshi Mamitsuka:
A General Probabilistic Framework for Mining Labeled Ordered Trees. SDM 2004: 357-368
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