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1

Frontiers in glycomics: Bioinformatics and biomarkers in disease An NIH White Paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11–13, 2006)

Nicolle H. Packer, Claus-Wilhelm von der Lieth, Kiyoko F. Aoki-Kinoshita, Carlito B. Lebrilla, James C. Paulson, Rahul Raman, Pauline Rudd, Ram Sasisekharan, Naoyuki Taniguchi, William S. York

Journal:

Year:

2008

Language:

english

File:

PDF, 287 KB

english, 2008

2

UniCarbKB: Putting the pieces together for glycomics research

Matthew P. Campbell, Catherine A. Hayes, Weston B. Struwe, Marc R. Wilkins, Kiyoko F. Aoki-Kinoshita, David J. Harvey, Pauline M. Rudd, Daniel Kolarich, Frederique Lisacek, Niclas G. Karlsson, Nicolle

Journal:

Year:

2011

Language:

english

File:

PDF, 202 KB

english, 2011

3

A weightedq-gram method for glycan structure classification

Limin Li, Wai-Ki Ching, Takako Yamaguchi, Kiyoko F Aoki-Kinoshita

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 213 KB

english, 2010

4

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.

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 Hendr

Journal:

Journal of Biomedical Semantics

Year:

2010

Language:

english

File:

PDF, 530 KB

english, 2010

5

Using glycome databases for drug discovery

Aoki-Kinoshita, Kiyoko F

Journal:

Expert Opinion on Drug Discovery

Year:

2008

Language:

english

File:

PDF, 560 KB

english, 2008

6

Modeling genetic regulatory networks: a delay discrete dynamical model approach

Hao Jiang, Wai-Ki Ching, Kiyoko F. Aoki-Kinoshita, Dianjing Guo

Journal:

Journal of Systems Science and Complexity

Year:

2012

Language:

english

File:

PDF, 544 KB

english, 2012

7

Toolboxes for a standardised and systematic study of glycans

Campbell, Matthew P, Ranzinger, René, Lütteke, Thomas, Mariethoz, Julien, Hayes, Catherine A, Zhang, Jingyu, Akune, Yukie, Aoki-Kinoshita, Kiyoko F, Damerell, David, Carta, Giorgio, York, Will S, Hasl

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 760 KB

english, 2014

8

Introducing glycomics data into the Semantic Web

Aoki-Kinoshita, Kiyoko F, Bolleman, Jerven, Campbell, Matthew P, Kawano, Shin, Kim, Jin-Dong, Lütteke, Thomas, Matsubara, Masaaki, Okuda, Shujiro, Ranzinger, Rene, Sawaki, Hiromichi, Shikanai, Toshihi

Journal:

Journal of Biomedical Semantics

Year:

2013

Language:

english

File:

PDF, 1.22 MB

english, 2013

9

Frequent glycan structure mining of influenza virus data revealed a sulfated glycan motif that increased viral infection

Ichimiya, T., Nishihara, S., Takase-Yoden, S., Kida, H., Aoki-Kinoshita, K.

Journal:

Year:

2014

Language:

english

File:

PDF, 266 KB

english, 2014

10

UniCarbKB: building a knowledge platform for glycoproteomics

Campbell, M. P., Peterson, R., Mariethoz, J., Gasteiger, E., Akune, Y., Aoki-Kinoshita, K. F., Lisacek, F., Packer, N. H.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.15 MB

english, 2014

11

[IEEE 2010 Third International Joint Conference on Computational Science and Optimization - Huangshan, Anhui, China (2010.05.28-2010.05.31)] 2010 Third International Joint Conference on Computational Science and Optimization - Support Vector Machine Methods for the Prediction of Cancer Growth

Chen, Xi, Ching, Wai-Ki, Aoki-Kinoshita, Kiyoko F., Furuta, Koh

Year:

2010

Language:

english

File:

PDF, 161 KB

english, 2010

12

WURCS: The Web3 Unique Representation of Carbohydrate Structures

Tanaka, Kenichi, Aoki-Kinoshita, Kiyoko F., Kotera, Masaaki, Sawaki, Hiromichi, Tsuchiya, Shinichiro, Fujita, Noriaki, Shikanai, Toshihide, Kato, Masaki, Kawano, Shin, Yamada, Issaku, Narimatsu, Hisas

Journal:

Journal of Chemical Information and Modeling

Year:

2014

Language:

english

File:

PDF, 2.00 MB

english, 2014

13

Identification of Proteasome Components Required for Apical Localization of Chaoptin Using Functional Genomics

Yano, Hiroyuki, Yamamoto-Hino, Miki, Awano, Wakae, Aoki-Kinoshita, Kiyoko F., Tsuda-Sakurai, Kayoko, Okano, Hideyuki, Goto, Satoshi

Journal:

Journal of Neurogenetics

Year:

2012

Language:

english

File:

PDF, 641 KB

english, 2012

14

The RINGS Resource for Glycome Informatics Analysis and Data Mining on the Web

Akune, Yukie, Hosoda, Masae, Kaiya, Sakiko, Shinmachi, Daisuke, Aoki-Kinoshita, Kiyoko F.

Journal:

Omics A Journal of Integrative Biology

Year:

2010

Language:

english

File:

PDF, 536 KB

english, 2010

15

Knowledge discovery for pancreatic cancer using inductive logic programming

Aoki-Kinoshita, Kiyoko F., Ching, Wai-Ki, Maeshiro, Kensei, Shimada, Kazuaki, Hiraoka, Nobuyoshi, Qiu, Yushan, Furuta, Koh

Journal:

IET Systems Biology

Year:

2014

Language:

english

File:

PDF, 159 KB

english, 2014

16

GlycoRDF: an ontology to standardize glycomics data in RDF

Ranzinger, R., Aoki-Kinoshita, K. F., Campbell, M. P., Kawano, S., Lutteke, T., Okuda, S., Shinmachi, D., Shikanai, T., Sawaki, H., Toukach, P., Matsubara, M., Yamada, I., Narimatsu, H.

Journal:

Year:

2015

Language:

english

File:

PDF, 279 KB

english, 2015

17

Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules

Zhu, S., Udaka, K., Sidney, J., Sette, A., Aoki-Kinoshita, K. F., Mamitsuka, H.

Journal:

Year:

2006

Language:

english

File:

PDF, 151 KB

english, 2006

18

The GlycomeAtlas tool for visualizing and querying glycome data

Konishi, Y., Aoki-Kinoshita, K. F.

Journal:

Year:

2012

Language:

english

File:

PDF, 123 KB

english, 2012

19

Using Databases and Web Resources for Glycomics Research

Aoki-Kinoshita, K. F.

Journal:

Molecular & Cellular Proteomics

Year:

2013

Language:

english

File:

PDF, 87 KB

english, 2013

20

On using physico-chemical properties of amino acids in string kernels for protein classification via support vector machines

Li, Limin, Aoki-Kinoshita, Kiyoko F., Ching, Wai-Ki, Jiang, Hao

Journal:

Journal of Systems Science and Complexity

Year:

2015

Language:

english

File:

PDF, 237 KB

english, 2015

21

The Lectin Frontier Database (LfDB), and Data Generation Based on Frontal Affinity Chromatography

Hirabayashi, Jun, Tateno, Hiroaki, Shikanai, Toshihide, Aoki-Kinoshita, Kiyoko, Narimatsu, Hisashi

Journal:

Year:

2015

Language:

english

File:

PDF, 1.63 MB

english, 2015

22

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

Katayama, Toshiaki, Wilkinson, Mark D, Aoki-Kinoshita, Kiyoko F, Kawashima, Shuichi, Yamamoto, Yasunori, Yamaguchi, Atsuko, Okamoto, Shinobu, Kawano, Shin, Kim, Jin-Dong, Wang, Yue, Wu, Hongyan, Kano,

Journal:

Journal of Biomedical Semantics

Year:

2014

Language:

english

File:

PDF, 564 KB

english, 2014

23

Implementation of linked data in the life sciences at BioHackathon 2011

Aoki-Kinoshita, Kiyoko F, Kinjo, Akira R, Morita, Mizuki, Igarashi, Yoshinobu, Chen, Yi-an, Shigemoto, Yasumasa, Fujisawa, Takatomo, Akune, Yukie, Katoda, Takeo, Kokubu, Anna, Mori, Takaaki, Nakao, Mi

Journal:

Journal of Biomedical Semantics

Year:

2015

Language:

english

File:

PDF, 2.34 MB

english, 2015

24

An Introduction to Bioinformatics for Glycomics Research

Aoki-Kinoshita, Kiyoko F., Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 210 KB

english, 2008

25

The Fifth ACGG-DB Meeting Report: Towards an International Glycan Structure Repository

Aoki-Kinoshita, K. F., Sawaki, H., An, H. J., Campbell, M., Cao, Q., Cummings, R., Hsu, D. K., Kato, M., Kawasaki, T., Khoo, K.-H., Kim, J., Kolarich, D., Li, X., Liu, M., Matsubara, M., Okuda, S., Pa

Journal:

Year:

2013

Language:

english

File:

PDF, 361 KB

english, 2013

26

Identification of Genes Required for Neural-Specific Glycosylation Using Functional Genomics

Yamamoto-Hino, Miki, Kanie, Yoshimi, Awano, Wakae, Aoki-Kinoshita, Kiyoko F., Yano, Hiroyuki, Nishihara, Shoko, Okano, Hideyuki, Ueda, Ryu, Kanie, Osamu, Goto, Satoshi, Perrimon, Norbert

Journal:

Year:

2010

Language:

english

File:

PDF, 1.34 MB

english, 2010

27

MIRAGE: The minimum information required for a glycomics experiment

York, W. S., Agravat, S., Aoki-Kinoshita, K. F., McBride, R., Campbell, M. P., Costello, C. E., Dell, A., Feizi, T., Haslam, S. M., Karlsson, N., Khoo, K.-H., Kolarich, D., Liu, Y., Novotny, M., Packe

Journal:

Year:

2014

Language:

english

File:

PDF, 218 KB

english, 2014

28

[ACM Press the 12th ACM SIGKDD international conference - Philadelphia, PA, USA (2006.08.20-2006.08.23)] Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining - KDD '06 - A new efficient probabilistic model for mining labeled ordered trees

Hashimoto, Kosuke, Aoki-Kinoshita, Kiyoko F., Ueda, Nobuhisa, Kanehisa, Minoru, Mamitsuka, Hiroshi

Year:

2006

Language:

english

File:

PDF, 924 KB

english, 2006

29

A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology

Hashimoto, Kosuke, Aoki-Kinoshita, Kiyoko Flora, Ueda, Nobuhisa, Kanehisa, Minoru, Mamitsuka, Hiroshi

Journal:

ACM Transactions on Knowledge Discovery from Data

Year:

2008

Language:

english

File:

PDF, 1.01 MB

english, 2008

30

A probabilistic model for mining labeled ordered trees: capturing patterns in carbohydrate sugar chains

N. Ueda, K. Aoki-kinoshita, A. Yamaguchi, T. Akutsu, H. Mamitsuka

Year:

2005

Language:

english

File:

PDF, 1.44 MB

english, 2005

31

GlyTouCan 1.0 – The international glycan structure repository

Aoki-Kinoshita, Kiyoko, Agravat, Sanjay, Aoki, Nobuyuki P., Arpinar, Sena, Cummings, Richard D., Fujita, Akihiro, Fujita, Noriaki, Hart, Gerald M., Haslam, Stuart M., Kawasaki, Toshisuke, Matsubara, M

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.47 MB

english, 2015

32

ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains

Aoki-Kinoshita, K. F., Ueda, N., Mamitsuka, H., Kanehisa, M.

Journal:

Year:

2006

Language:

english

File:

PDF, 498 KB

english, 2006

33

The Glycome Analytics Platform an integrative framework for glycobioinformatics

Barnett, Christopher B., Aoki-Kinoshita, Kiyoko F., Naidoo, Kevin J.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.15 MB

english, 2016

34

Phenotype-based clustering of glycosylation-related genes by RNAi-mediated gene silencing

Yamamoto-Hino, Miki, Yoshida, Hideki, Ichimiya, Tomomi, Sakamura, Sho, Maeda, Megumi, Kimura, Yoshinobu, Sasaki, Norihiko, Aoki-Kinoshita, Kiyoko F., Kinoshita-Toyoda, Akiko, Toyoda, Hidenao, Ueda, Ry

Journal:

Year:

2015

Language:

english

File:

PDF, 1.15 MB

english, 2015

35

Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database

Akune, Yukie, Lin, Chi-Hung, Abrahams, Jodie L., Zhang, Jingyu, Packer, Nicolle H., Aoki-Kinoshita, Kiyoko F., Campbell, Matthew P.

Journal:

Carbohydrate Research

Year:

2016

Language:

english

File:

PDF, 756 KB

english, 2016

36

The minimum information required for a glycomics experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets

Struwe, Weston B, Agravat, Sanjay, Aoki-Kinoshita, Kiyoko F, Campbell, Matthew P, Costello, Catherine E, Dell, Anne, Ten Feizi,, Haslam, Stuart M, Karlsson, Niclas G, Khoo, Kay-Hooi, Kolarich, Daniel

Journal:

Year:

2016

Language:

english

File:

PDF, 208 KB

english, 2016

37

Latest developments in Semantic Web technologies applied to the Glycosciences

Aoki-Kinoshita, Kiyoko F., Aoki, Nobuyuki P., Fujita, Akihiro, Fujita, Noriaki, Kawasaki, Toshisuke, Matsubara, Masaaki, Okuda, Shujiro, Shikanai, Toshihide, Shinmachi, Daisuke, Solovieva, Elena, Suzu

Journal:

Perspectives in Science

Year:

2016

Language:

english

File:

PDF, 528 KB

english, 2016

38

A systematic framework to deriveN-glycan biosynthesis process and the automated construction of glycosylation networks

Hou, Wenpin, Qiu, Yushan, Hashimoto, Nobuyuki, Ching, Wai-Ki, Aoki-Kinoshita, Kiyoko F.

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.44 MB

english, 2016

39

A Practical Guide to Using Glycomics Databases || Carbohydrate Structure Database (CSDB): Examples of Usage

Aoki-Kinoshita, Kiyoko F.

Year:

2017

Language:

english

File:

PDF, 2.64 MB

english, 2017

40

A Practical Guide to Using Glycomics Databases || The CAZy Database/the Carbohydrate-Active Enzyme (CAZy) Database: Principles and Usage Guidelines

Aoki-Kinoshita, Kiyoko F.

Year:

2017

Language:

english

File:

PDF, 678 KB

english, 2017

41

A Practical Guide to Using Glycomics Databases || Development of Carbohydrate Nomenclature and Representation

Aoki-Kinoshita, Kiyoko F.

Year:

2017

Language:

english

File:

PDF, 812 KB

english, 2017

42

A Practical Guide to Using Glycomics Databases ||

Aoki-Kinoshita, Kiyoko F.

Year:

2017

Language:

english

File:

PDF, 15.73 MB

english, 2017

43

A Practical Guide to Using Glycomics Databases || Glyco3D: A Suite of Interlinked Databases of 3D Structures of Complex Carbohydrates, Lectins, Antibodies, and Glycosyltransferases

Aoki-Kinoshita, Kiyoko F.

Year:

2017

Language:

english

File:

PDF, 1.18 MB

english, 2017

44

A Practical Guide to Using Glycomics Databases || GlycoProtDB: A Database of Glycoproteins Mapped with Actual Glycosylation Sites Identified by Mass Spectrometry

Aoki-Kinoshita, Kiyoko F.

Year:

2017

Language:

english

File:

PDF, 686 KB

english, 2017

45

A Practical Guide to Using Glycomics Databases || KEGG GLYCAN

Aoki-Kinoshita, Kiyoko F.

Year:

2017

Language:

english

File:

PDF, 645 KB

english, 2017

46

The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data

Liu, Yan, McBride, Ryan, Stoll, Mark, Palma, Angelina S, Silva, Lisete, Agravat, Sanjay, Aoki-Kinoshita, Kiyoko F, Campbell, Matthew P, Costello, Catherine E, Dell, Anne, Haslam, Stuart M, Karlsson, N

Journal:

Year:

2016

Language:

english

File:

PDF, 160 KB

english, 2016

47

Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans

Tsuchiya, Shinichiro, Aoki, Nobuyuki P., Shinmachi, Daisuke, Matsubara, Masaaki, Yamada, Issaku, Aoki-Kinoshita, Kiyoko F., Narimatsu, Hisashi

Journal:

Carbohydrate Research

Year:

2017

Language:

english

File:

PDF, 2.63 MB

english, 2017

48

Development and Application of an Algorithm to Compute Weighted Multiple Glycan Alignments

Hosoda, Masae, Akune, Yukie, Aoki-Kinoshita, Kiyoko F.

Journal:

Year:

2017

Language:

english

File:

PDF, 387 KB

english, 2017

49

WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures

Matsubara, Masaaki, Aoki-Kinoshita, Kiyoko F., Aoki, Nobuyuki P., Yamada, Issaku, Narimatsu, Hisashi

Journal:

Journal of Chemical Information and Modeling

Year:

2017

Language:

english

File:

PDF, 984 KB

english, 2017

50

[Institution of Engineering and Technology 12th International Symposium on Operations Research and its Applications in Engineering, Technology and Management (ISORA 2015) - Luoyang, China (21-24 Aug. 2015)] 12th International Symposium on Operations Research and its Applications in Engineering, Technology and Management (ISORA 2015) - A multiple linear regression model for structure of n-linked oligosaccharides

Wai-Ki Ching,, Aoki-Kinoshita, K.F., Wenpin Hou,, Xiaoqing Cheng,

Year:

2015

Language:

english

File:

PDF, 179 KB

english, 2015