| 2023.07.05 |
Synthesis and molecular structure of V-shaped liquid crystalline compounds: Spectroscopic, mesomorphic, DFT investigations, electrochemical and fluorescence studies.
Salwadi NFL, Ooi CC, Yeap GY, Suah FBM, Cherin S, Ito MM, Kikuchi K, Fukaya R, Kaneko K, Shimizu A. Journal of Molecular Structure. 2023; 1283: 135304. https://doi.org/10.1016/j.molstruc.2023.135304. |
| 2023.05.01 |
Maximizing External Action with Information Provision Over Multiple Rounds in Online Social Networks
Miyashita M, Shinomiya N, Kasamatsu D, Ishigaki G. IEICE Transactions on Information and Systems. 2023 May ( Accepted, To be published); E106-D(5): 847-855. |
| 2023.01.25 |
Simultaneous determination of heparan sulfate, chondroitin/dermatan sulfates, and hyaluronan glycosaminoglycan disaccharides by high-performance liquid chromatography using a reverse-phase column with adamantyl groups
Hanamatsu H, Makino S, Ohara M, Suda G, Yokota I, Nishihara S, Sakamoto N, Furukawa JI. J Chromatogr A. 2023 Jan 25; 1689: 463748. doi: 10.1016/j.chroma.2022.463748. PMID: 36586283. |
| 2023.01.18 |
A Method for Reducing the Instability of Negawatts Considering Changes in the Behavior of Consumers
Takai K, Tamura Y, Shinomiya N. Energies 16. 2023; 3: 1072. doi: 10.3390/en16031072. (IF:3.252,CiteScore:5.0) |
| 2023.01.13 |
Construction of mouse cochlin mutants with different GAG-binding specificities and their use for immunohistochemistry.
Murakami K, Tamura R, Ikehara S, Ota H, Ichimiya T, Matsumoto N, Matsubara H, Nishihara S, Ikehara Y, Yamamoto K. Biochem J. 2023 Jan 13;480(1):41-56. doi: 10.1042/BCJ20220339. PMID: 36511224; PMCID: PMC9987951. |
| 2023.01.05 |
Introducing Inductive Bias on Vision Transformers through Gram Matrix Similarity based Regularization.
Mormille LH, Broni-Bediako C, Atsumi M. Artifi cial Life and Robotics. 2023; 28(1):106-116. |
| 2022.12.27 |
Length-Based Curriculum Learning for Efficient Pre-training of Language Models.
Nagatsuka, K., Broni-Bediako, C. & Atsumi, M. New Generation Computing. 2023 (to appear); 41(1). |
| 2022.12.02 |
Worldwide Glycoscience Informatics Infrastructure: The GlySpace Alliance
Lisacek F, Tiemeyer M, Mazumder R, Aoki-Kinoshita KF. JACS Au. 2022 Dec 2; 3(1): 4-12. doi: 10.1021/jacsau.2c00477.
PMID: 36711080; PMCID: PMC9875223. |
| 2022.12 |
新型うつ傾向とネット依存・デジタル認知症傾向との関連の縦断分析
坂部創一，山崎秀夫. 環境情報科学学術研究論文集．36: 167-172． |
| 2022.12 |
Changes of signaling molecules in the axotomized rat facial nucleus.
Ishijima T, Nakajima K. J Chem Neuroanat. 2022 Dec; 126: 102179（ 12 pages）. doi: 10.1016/j.jchemneu.2022.102179. PMID: 36341893. |
| 2022.09.27 |
Morphological difference of Escherichia coli non-heme ferritin iron cores reconstituted in the presence and absence
of inorganic phosphate.
Kuwata T, Sato D, Yanagida Y, Aoki E, Fujiwara K, Yoshimura H, Ikeguchi M. J Biol Inorg Chem. 2022 Sep; 27(6): 583-594. doi: 10.1007/s00775-022-01952-5.PMID: 35986810. |
| 2022.09.27 |
Non-linear disulphide-centred S-shaped oligomers with inner and outer spacers connected by aromatic azo moieties.
Yap PW, Osman F, Yeap GY, Nakamura Y, Kaneko K, Shimizu A, Ito MM. Liquid Crystals. 2023; 50(3): 379-392. https://doi.org/10.1080/02678292.2022.2127161. |
| 2022.09.14 |
Meeting report on the international symposium on microbial Glycoconjugates and the GlySpace alliance: from micro- to macroglycoscience (MiGGA symposium)
Hosoda M, Aoki K, Guerardel Y, Yamada I, Aoki-Kinoshita KF. Glycobiology. 2022 Nov 22; 32(12): 1066-1067. doi: 10.1093/
glycob/cwac062. PMID: 36103332. |
| 2022.08.25 |
糖鎖遺伝子発現情報からの糖鎖構造推定ツールGlycoMapleの開発
細田正恵，木下聖子，藤田盛久. Journal of Japanese Biochemical Society. 2022; 94（4）: 623-628. |
| 2022.08 |
Cortical nicotinic enhancement of tone-evoked heightened activities and subcortical nicotinic enlargement of activated areas in mouse auditory cortex.
Nakanishi M, Nemoto M, Kawai HD. Neuroscience Research. 2022 Aug; 181: 55-65. doi: 10.1016/j.neures.2022.04.001. PMID: 35381300. |
| 2022.07.28 |
Involvement of cochlin binding to sulfated heparan sulfate/heparin in the pathophysiology of autosomal dominant late-onset hearing loss (DFNA9)
Honda T, Kawasaki N, Yanagihara R, Tamura R, Murakami K, Ichimiya T, Matsumoto N, Nishihara S, Yamamoto K. PLoS One. 2022 Jul 28;17(7):e0268485. doi:10.1371/journal.pone.0268485. PMID: 35901072; PMCID: PMC9333281. |
| 2022.07.28 |
Regularizing self-attention on vision transformers with 2D spatial distance loss.
Mormille, L.H., Broni-Bediako, C. & Atsumi, M. Artificial Life and Robotics. 2022; 27(3):586-593. |
| 2022.07.02 |
Turkeys possess diverse Siaα2-3Gal glycans that facilitate their dual susceptibility to avian influenza viruses isolated from ducks and chickens.
Kobayashi D, Hiono T, Ichii O, Nishihara S, Takase-Yoden S, Yamamoto K, Kawashima H, Isoda N, Sakoda Y. Virus Res. 2022 Jul 2; 315: 198771. doi:10.1016/j.virusres.2022.198771. PMID: 35429616. |
| 2022.06.29 |
Events Occurring in the Axotomized Facial Nucleus.
Nakajima K, Ishijima T. Cells. 2022 Jun 29; 11(13): 2068(30 pages). doi: 10.3390/cells11132068. PMID: 35805151; PMCID: PMC9266054. |
| 2022.06.26 |
Fut9 Deficiency Causes Abnormal Neural Development in the Mouse Cerebral Cortex and Retina.
Abdullah A, Hayashi Y, Morimura N, Kumar A, Ikenaka K, Togayachi A, Narimatsu H, Hitoshi S. Neurochem Res. 2022 Sep; 47(9): 2793-2804. doi: 10.1007/s11064-022-03651-8. PMID: 35753011. |
| 2022.06.23 |
Glycoproteomics.
Bagdonaite I, Malaker SA, Polasky DA, Riley NM, Schjoldager K, Vakhrushev SY, Halim A, Aoki-
Kinoshita KF, Nesvizhskii AI, Bertozzi CR, Wandall HH, Parker BL, Thaysen-Andersen M, Scott NE. Nat Rev Methods Primers. 2022; 2: 1-29. PMID: 35696078. |
| 2022.06.14 |
Functions of Glycosylation and Related Web Resources for Its Prediction.
Aoki-Kinoshita KF. Methods in molecular biology （Clifton, N.J.）. 2022; 2499: 135-144. doi: 10.1007/978-1-0716-2317-6_6.
PMID: 35696078. |
| 2022.06.13 |
CarbArrayART: a new software tool for carbohydrate microarray data storage, processing, presentation, and reporting.
Akune Y, Arpinar S, Silva LM, Palma AS, Tajadura-Ortega, V, Aoki-Kinoshita KF, Ranzinger R, Liu Y, Feizi T. Glycobiology. 2022 Jun 13; 32(7): 552-555. doi: 10.1093/glycob/cwac018. PMID: 35352122; PMCID: PMC9191619. |
| 2022.05.23 |
Disaccharide-tag for highly sensitive identification of O-GlcNAc-modified proteins in mammalian cells
Abo H, Kume M, Pecori F, Miura T, Matsumoto N, Nishihara S, Yamamoto K. PLoS One. 2022 May 23;17(5):e0267804. doi: 10.1371/journal.pone.0267804. PMID: 35604954; PMCID: PMC9126400. |
| 2022.05.08 |
Computational Modeling of O-Linked Glycan Biosynthesis in CHO Cells.
Kouka T, Akase S, Sogabe I, Jin C, Karlsson NG, Aoki-Kinoshita, K.F. Molecules（ Basel, Switzerland）. 2022 Mar 8; 27（6）: 1766. doi: 10.3390/molecules27061766. PMID: 35335136; PMCID: PMC8950484. |
| 2022.04.22 |
GALAXY ver3: updated web application for glycosylation profiling based on 3D HPLC map
Yagi H, Amagasa E, Shiota M, Yamada I, Aoki-Kinoshita KF, Kato K. Glycobiology. 2022 Jul 13; 32（8）: 646-
650. doi: 10.1093/glycob/cwac025. PMID: 35452093. |
| 2022.01.05 |
Development of a novel monosaccharide substitution matrix for improved comparison of glycan structures.
Fujita, A, Aoki-Kinoshita, K.F. Carbohydrate research. 2022 Jan; 511: 108496. doi:10.1016/j.carres.2021.108496. PMID: 35030433. |
| 2021.12.02 |
DeepNGlyPred: A Deep Neural Network-Based Approach for Human N-Linked Glycosylation Site Prediction.
Pakhrin SC, Aoki-Kinoshita KF, Caragea D, Kc DB. Molecules. 2021 Dec 2;26(23):7314. doi: 10.3390/molecules26237314. PMID: 34885895; PMCID: PMC8658957. |
| 2021.11.25 |
SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures.
Tsuchiya S, Matsubara M, Aoki-Kinoshita KF, Yamada I. Molecules. 2021 Nov 25;26(23):7149. doi: 10.3390/molecules26237149. PMID: 34885724; PMCID: PMC8659005. |
| 2021.11.22 |
RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data.
Lee S, Ono T, Aoki-Kinoshita K. BMC Microbiol. 2021 Nov 22;21(1):325. doi: 10.1186/s12866-021-02384-y. PMID: 34809564; PMCID: PMC8607589. |
| 2021.10.18 |
Functional glyco-metagenomics elucidates the role of glycan-related genes in environments.
Takihara H, Miura N, Aoki-Kinoshita KF, Okuda S. BMC Bioinformatics. 2021 Oct 18;22(1):505. doi: 10.1186/s12859-021-04425-9. PMID: 34663219; PMCID: PMC8522060. |
| 2021.09.23 |
Dermatan-4-O-Sulfotransferase-1 Contributes to the Undifferentiated State of Mouse Embryonic Stem Cells
Ogura C, Nishihara S. Front Cell Dev Biol. 2021 Sep 23;9:733964. doi: 10.3389/fcell.2021.733964. PMID: 34631712; PMCID: PMC8495257. |
| 2021.09.09 |
GlycoBioinformatics
Aoki-Kinoshita KF, Lisacek F, Karlsson N, Kolarich D, Packer NH. Beilstein J Org Chem. 2021 Nov 9;17:2726-2728. doi: 10.3762/bjoc.17.184. PMID: 34858527; PMCID: PMC8593694. |
| 2021.07.13 |
Site-specific O-GlcNAcylation of Psme3 maintains mouse stem cell pluripotency by impairing P-body homeostasis.
Pecori F, Kondo N, Ogura C, Miura T, Kume M, Minamijima Y, Yamamoto K, Nishihara S. Cell Rep. 2021 Jul 13;36(2):109361. doi: 10.1016/j.celrep.2021.109361. PMID: 34260942. |
| 2021.06.25 |
Sulfated glycans containing NeuAcα2-3Gal facilitate the propagation of human H1N1 influenza A viruses in eggs.
Ichimiya T, Okamatsu M, Kinoshita T, Kobayashi D, Ichii O, Yamamoto N, Sakoda Y, Kida H, Kawashima H, Yamamoto K, Takase-Yoden S, Nishihara S. Virology. 2021 Jun 25;562:29-39. doi: 10.1016/j.virol.2021.06.008. Epub ahead of print. PMID: 34246113. |
| 2021.06.01 |
Glycome informatics: using systems biology to gain mechanistic insights into glycan biosynthesis.
Aoki-Kinoshita, K. Current opinion in chemical engineering 32 (2021): 100683.
https://doi.org/10.1016/j.coche.2021.100683 |
| 2021.04.19 |
Global mapping of glycosylation pathways in human-derived cells.
Huang YF, Aoki K, Akase S, Ishihara M, Liu YS, Yang G, Kizuka Y, Mizumoto S, Tiemeyer M, Gao XD, Aoki-Kinoshita KF, Fujita M. Dev Cell. 2021 Apr 19;56(8):1195-1209.e7. doi: 10.1016/j.devcel.2021.02.023. Epub 2021 Mar 16. PMID: 33730547; PMCID: PMC8086148. |
| 2021.02.06 |
Dermatan sulphate promotes neuronal differentiation in mouse and human stem cells.
Ogura C, Hirano K, Mizumoto S, Yamada S, Nishihara S. J Biochem. 2021 Feb 6;169(1):55-64. doi: 10.1093/jb/mvaa087. PMID: 32730567. |
| 2021.01.14 |
A defined glycosylation regulatory network modulates total glycome dynamics during pluripotency state transition.
Pecori F, Yokota I, Hanamatsu H, Miura T, Ogura C, Ota H, Furukawa JI, Oki S, Yamamoto K, Yoshie O, Nishihara S. Sci Rep. 2021 Jan 14;11(1):1276. doi: 10.1038/s41598-020-79666-4. PMID: 33446700; PMCID: PMC7809059. |
| 2021.01.08 |
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data.
Watanabe Y, Aoki-Kinoshita KF, Ishihama Y, Okuda S. Nucleic Acids Res. 2021 Jan 8;49(D1):D1523-D1528. doi: 10.1093/nar/gkaa1012. PMID: 33174597; PMCID: PMC7778884. |
| 2021.01.08 |
The international glycan repository GlyTouCan version 3.0.
Fujita A, Aoki NP, Shinmachi D, Matsubara M, Tsuchiya S, Shiota M, Ono T, Yamada I, Aoki-Kinoshita KF. Nucleic Acids Res. 2021 Jan 8;49(D1):D1529-D1533. doi: 10.1093/nar/gkaa947. PMID: 33125071; PMCID: PMC7779025. |
| 2020.10.27 |
A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR).
Kellman BP, Zhang Y, Logomasini E, Meinhardt E, Godinez-Macias KP, Chiang AWT, Sorrentino JT, Liang C, Bao B, Zhou Y, Akase S, Sogabe I, Kouka T, Winzeler EA, Wilson IBH, Campbell MP, Neelamegham S, Krambeck FJ, Aoki-Kinoshita KF, Lewis NE. Beilstein J Org Chem. 2020 Oct 27;16:2645-2662. doi: 10.3762/bjoc.16.215. PMID: 33178355; PMCID: PMC7607430. |
| 2020.10.23 |
Mucin-type O-glycosylation controls pluripotency in mouse embryonic stem cells via Wnt receptor endocytosis.
Pecori F, Akimoto Y, Hanamatsu H, Furukawa JI, Shinohara Y, Ikehara Y, Nishihara S. J Cell Sci. 2020 Oct 23;133(20):jcs245845. doi: 10.1242/jcs.245845. PMID: 32973111 |
| 2020.07.17 |
The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences.
Yamada I, Shiota M, Shinmachi D, Ono T, Tsuchiya S, Hosoda M, Fujita A, Aoki N.P, Watanabe Y, Fujita N, Angata K, Kaji H, Narimatsu H, Okuda S, Aoki-Kinoshita K.F. Nat Methods. 2020 Jul;17(7):649-650. doi: 10.1038/s41592-020-0879-8. PMID: 32572234 |
| 2020.06.01 |
GlyGen data model and processing workflow.
Kahsay R, Vora J, Navelkar R, Mousavi R, Fochtman BC, Holmes X, Pattabiraman N, Ranzinger R, Mahadik R, Williamson T, Kulkarni S, Agarwal G, Martin M, Vasudev P, Garcia L, Edwards N, Zhang W, Natale DA, Ross K, Aoki-Kinoshita KF, Campbell MP, York WS, Mazumder R. Bioinformatics. 2020 Jun 1;36(12):3941-3943. doi: 10.1093/bioinformatics/btaa238. PMID: 32324859; PMCID: PMC7320628. |
| 2020.04.16 |
E190V substitution of H6 hemagglutinin is one of key factors for binding to sulfated sialylated glycan receptor and infection to chickens.
Kikutani Y, Okamatsu M, Nishihara S, Takase-Yoden S, Hiono, T, de Vries R, McBride R, Matsuno K, Kida H, Sakoda Y. Microbiol. Immunol. 2020 Apr;64(4):304-312. doi: 10.1111/1348-0421.12773. Epub 2020 Feb 5. PMID: 31943329. |
| 2020.02 |
Functional analysis of glycosylation using Drosophila melanogaster.
Nishihara S. Glycoconj J. 2020 Feb;37(1):1-14. doi: 10.1007/s10719-019-09892-0. Epub 2019 Nov 26. PMID: 31773367. |
| 2020.01.28 |
GlyGen: Computational and Informatics Resources for Glycoscience.
York WS, Mazumder R, Ranzinger R, Edwards N, Kahsay R, Aoki-Kinoshita KF, Campbell MP, Cummings RD, Feizi T, Martin M, Natale DA, Packer NH, Woods RJ, Agarwal G, Arpinar S, Bhat S, Blake J, Castro LJG, Fochtman B, Gildersleeve J, Goldman R, Holmes X, Jain V, Kulkarni S, Mahadik R, Mehta A, Mousavi R, Nakarakommula S, Navelkar R, Pattabiraman N, Pierce MJ, Ross K, Vasudev P, Vora J, Williamson T, Zhang W. Glycobiology. 2020 Jan 28;30(2):72-73. doi: 10.1093/glycob/cwz080. PMID: 31616925; PMCID: PMC7335483. |
| 2020.01.28 |
The GlySpace Alliance: toward a collaborative global glycoinformatics community.
Aoki-Kinoshita KF, Lisacek F, Mazumder R, York WS, Packer NH. Glycobiology. 2020 Jan 28;30(2):70-71. doi: 10.1093/glycob/cwz078. PMID:31573039; PMCID: PMC6992953. |
| 2019.10.20 |
Highly sulfated hyaluronic acid maintains human induced pluripotent stem cells under feeder-free and bFGF-free conditions.
Miura T, Yuasa N, Ota H, Habu M, Kawano M, Nakayama F, Nishihara S. Biochem Biophys Res Commun. 2019 Oct 20;518(3):506-512. doi: 10.1016/j.bbrc.2019.08.082. Epub 2019 Aug 19. PMID: 31439376 |
| 2019.08.20 |
Updates to the Symbol Nomenclature for Glycans guidelines.
Neelamegham S, Aoki-Kinoshita K, Bolton E, Frank M, Lisacek F, Lütteke T, O'Boyle N, Packer NH, Stanley P, Toukach P, Varki A, Woods RJ; SNFG Discussion Group. Glycobiology. 2019 Aug 20;29(9):620-624. doi: 10.1093/glycob/cwz045. PMID: 31184695; PMCID: PMC7335484. |
| 2019.08.15 |
LM-GlycomeAtlas Ver. 1.0: A Novel Visualization Tool for Lectin Microarray-Based Glycomic Profiles of Mouse Tissue Sections.
Nagai-Okatani C, Aoki-Kinoshita KF, Kakuda S, Nagai M, Hagiwara K, Kiyohara K, Fujita N, Suzuki Y, Sato T, Angata K, Kuno A. Molecules. 2019 Aug 15;24(16):2962. doi: 10.3390/molecules24162962. PMID: 31443278; PMCID: PMC6719194. |
| 2019.07.22 |
Towards a standardized bioinformatics infrastructure for N- and O-glycomics.
Rojas-Macias MA, Mariethoz J, Andersson P, Jin C, Venkatakrishnan V, Aoki NP, Shinmachi D, Ashwood C, Madunic K, Zhang T, Miller RL, Horlacher O, Struwe WB, Watanabe Y, Okuda S, Levander F, Kolarich D, Rudd PM, Wuhrer M, Kettner C, Packer NH, Aoki-Kinoshita KF, Lisacek F, Karlsson NG. Nat Commun. 2019 Jul 22;10(1):3275. doi: 10.1038/s41467-019-11131-x. PMID: 31332201; PMCID: PMC6796180. |
| 2019.07.15 |
Cell Profiling Based on Sugar-Chain-Cell Binding Interaction and Its Application to Typing and Quality Verification of Cells.
Shinchi H, Nakamura T, Ota H, Nishihara S, Wakao M, Suda Y. Chembiochem. 2019 Jul 15;20(14):1810-1816. doi: 10.1002/cbic.201900028. Epub 2019 May 21. PMID: 30816597. |
| 2019.07.15 |
presentation of a paper
GlycanFormatConverter: a conversion tool for translating the complexities of glycans.
Tsuchiya S, Yamada I, Aoki-Kinoshita KF. Bioinformatics. 2019 Jul 15;35(14):2434-2440. doi: 10.1093/bioinformatics/bty990. PMID: 30535258; PMCID: PMC6612873. |
