研究者詳細

顔写真

ヤマダ　カズノリ
山田　和範
Kazunori Yamada
所属
未踏スケールデータアナリティクスセンター　ソーシャルインテグレーション研究部門
職名
教授
学位

  • 博士（生命科学）（東京大学）

  • 修士（薬学）（九州大学）

研究キーワード 3

  • 人工知能

  • 機械学習

  • 配列解析

研究分野 2

  • 情報通信 / 知能情報学 /

  • 情報通信 / 生命、健康、医療情報学 /

論文 40

  1. Simulating Metabolic Pathways to Enhance Interpretations of Metabolome Genome-wide Association Studies 査読有り

    Kodate S, Sato M, Hishinuma E, Kojima K, Motoike IN, ToMMo Study Group, Koshiba S, Yamamoto M, Yamada KD, Kinoshita K

    Scientific Reports　2025年

  2. Effect of Cumulative Exposure on the Efficacy of Paroxetine: a Population Pharmacokinetic-pharmacodynamic and Machine Learning Analyses 査読有り

    Shigetome K, Egarashi T, Tomita T, Higa N, Iwashita K, Morita K, Nishimura M, Kankeko T, Maeda H, Yamada KD, Kajiwara-Morita A, Oniki K, Yasui-Furukori N, Saruwatari J

    Pharmacometrics and Systems Pharmacology　2025年

  3. GPS: A Probabilistic Distributional Similarity with Gumbel Priors for Set-to-Set Matching 査読有り

    Lin F, Liu H, Zhang Z, Morales J, Zhang HK, Yamada KD, Kolachalama V, Saligrama V

    International Conference on Learning Representations　2025年

  4. Learning Random Numbers to Realize Appendable Memory System for Artificial Intelligence to Acquire New Knowledge after Deployment 査読有り

    Kubota A, Kodate S, Li Y, Lin F, Fukuda H, Baladram MS, Yamada KD

    Interdisciplinary Information Sciences　2025年

  5. Loss Distillation via Gradient Matching for Point Cloud Completion with Weighted Chamfer Distance 査読有り

    Lin F, Liu H, Zhou H, Hou S, Yamada KD, Fischer GS, Li Y, Zhang H, Zhang Z

    IEEE/RSJ International Conference on Intelligent Robots and Systems　2024年

  6. Question generation for English reading comprehension exercises using Transformers 査読有り

    Maas A, Yamada KD, Nagahama T, Kawada T, Horita T

    Letters on Informatics and Interdisciplinary Research　2024年

  7. InfoCD: A contrastive chamfer distance loss for point cloud completion 査読有り

    Lin F, Yue Y, Zhang Z, Hou S, Yamada KD, Kolachalama VB, Saligrama V

    Advances in Neural Information Processing Systems　2023年

  8. Hyperbolic chamfer distance for point cloud completion 査読有り

    Lin F, Yue Y, Hou S, Yu X, Xu Y, Yamada KD, Zhang Z

    International Conference on Computer Vision　2023年

  9. Serum fatty acid composition balance by fuzzy c-means method in individuals with or without metabolic dysfunction-associated fatty liver disease 査読有り

    Nagase Y, Satoh T, Shigetome K, Tokumaru N, Matsumoto E, Yamada KD, Imafuku T, Watanabe H, Maruyama T, Ogata Y, Yoshida M, Saruwatari J, Oniki K

    Nutrients　15　(4)　809-809　2023年

    出版者・発行元：

    DOI： 10.3390/nu15040809 　

    eISSN：2072-6643

  10. Identifying latent traits of questions for controllable machine generation 査読有り

    Maas A, Kawada T, Yamada K, Nagahama T, Horita T

    EdMedia + Innovate Learning　2022年

  11. Redox imaging of dextran sodium sulfate-induced colitis mice treated with nitric oxide synthase inhibitors 査読有り

    Yasukawa K, Yamada K, Tokuda H, Koyama S, Utsumi H

    Advances in Redox Research　6　100047-100047　2022年

    出版者・発行元：

    DOI： 10.1016/j.arres.2022.100047 　

    ISSN：2667-1379

  12. Relation is an option for processing context information 査読有り

    Yamada KD, Baladram MS, Lin F

    Frontiers in Artificial Intelligence　5　2022年

    出版者・発行元：

    DOI： 10.3389/frai.2022.924688 　

    eISSN：2624-8212

  13. Cosmos Propagation Network: Deep learning model for point cloud completion 査読有り

    Lin F, Xu Y, Zhang Z, Gao C, Yamada KD

    Neurocomputing　507　221-234　2022年

    出版者・発行元：

    DOI： 10.1016/j.neucom.2022.08.007 　

    ISSN：0925-2312

  14. Progress in research on implementing machine consciousness 査読有り

    Yamada KD, Baladram MS, Lin F

    Interdisciplinary Information Sciences　28　(1)　95-105　2022年

    出版者・発行元：

    DOI： 10.4036/iis.2022.r.02 　

    ISSN：1340-9050

    eISSN：1347-6157

  15. An effective convolutional neural network for visualized understanding transboundary air pollution based on Himawari-8 satellite images 査読有り

    Lin F, Gao C, Yamada KD

    IEEE Geoscience and Remote Sensing Letters　19　1-5　2022年

    DOI： 10.1109/LGRS.2021.3102939 　

  16. Developing a novel recurrent neural network architecture with fewer parameters and good learning performance 査読有り

    Yamada KD, Lin F, Nakamura T

    Interdisciplinary Information Sciences　27　(1)　25-40　2021年

    出版者・発行元：

    DOI： 10.4036/iis.2020.r.01 　

    ISSN：1340-9050

    eISSN：1347-6157

  17. Introduction to supervised machine learning for data science 査読有り

    Baladram MS, Koike A, Yamada KD

    Interdisciplinary Information Sciences　26　(1)　87-121　2020年

    出版者・発行元：

    DOI： 10.4036/iis.2020.a.03 　

    ISSN：1340-9050

    eISSN：1347-6157

  18. In vivo redox imaging of dextran sodium sulfate-induced colitis in mice using Overhauser-enhanced magnetic resonance imaging 国際誌 査読有り

    Yasukawa K, Hirago A, Yamada K, Tun X, Ohkuma K, Utsumi H

    Free Radical Biology and Medicine　136　1-11　2019年

    DOI： 10.1016/j.freeradbiomed.2019.03.025 　

  19. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization 査読有り

    Katoh K, Rozewicki J, Yamada KD

    Briefings in Bioinformatics　20　(4)　1160-1166　2019年

    DOI： 10.1093/bib/bbx108 　

    ISSN：1467-5463

    eISSN：1477-4054

  20. De novo profile generation based on sequence context specificity with the long short-term memory network 査読有り

    Yamada KD, Kinoshita K

    BMC Bioinformatics　2018年

    DOI： 10.1186/s12859-018-2284-1 　

  21. Parallelization of MAFFT for large-scale multiple sequence alignments 査読有り

    Nakamura T, Yamada KD, Tomii K, Katoh K

    Bioinformatics　34　(14)　2490-2492　2018年

    DOI： 10.1093/bioinformatics/bty121 　

    ISSN：1367-4803

    eISSN：1460-2059

  22. Derivative-free neural network for optimizing the scoring functions associated with dynamic programming of pairwise-profile alignment 査読有り

    Yamada KD

    Algorithms for molecular biology　2018年

    DOI： 10.1186/s13015-018-0123-6 　

  23. Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on crystal-packing propensity of amino acids 国際誌 査読有り

    Yamada KD, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, Tomii K

    Acta Crystallographica Section D　73　(Pt 9)　757-766　2017年

    DOI： 10.1107/S2059798317010932 　

  24. Identification of the sequence determinants of protein N-terminal acetylation through a decision tree approach 国際誌 査読有り

    Yamada KD, Omori S, Nish H, Miyagi M

    BMC Bioinformatics　18　(1)　289-289　2017年

    DOI： 10.1186/s12859-017-1699-4 　

  25. Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix 国際誌 査読有り

    Lim K, Yamada KD, Frith MC, Tomii K

    Journal of Structural and Functional Genomics　17　(4)　147-154　2016年

    DOI： 10.1007/s10969-016-9210-4 　

  26. Application of the MAFFT sequence alignment program to large data - reexamination of the usefulness of chained guide trees 査読有り

    Yamada KD, Tomii K, Katoh K

    Bioinformatics　32　(21)　3246-3251　2016年

    DOI： 10.1093/bioinformatics/btw412 　

    ISSN：1367-4803

    eISSN：1460-2059

  27. Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins 査読有り

    Yamada KD, Nishi H, Nakata J, Kinoshita K

    Biophysics and Physicobiology　13　157-163　2016年

    出版者・発行元： 一般社団法人 日本生物物理学会

    DOI： 10.2142/biophysico.13.0_157 　

    詳細を見る 詳細を閉じる

    <p>Functional sites on proteins play an important role in various molecular interactions and reactions between proteins and other molecules. Thus, mutations in functional sites can severely affect the overall phenotype. Progress of genome sequencing projects has yielded a wealth of information on single nucleotide variants (SNVs), especially those with less than 1% minor allele frequency (rare variants). To understand the functional influence of genetic variants at a protein level, we investigated the relationship between SNVs and protein functional sites in terms of minor allele frequency and the structural position of variants. As a result, we observed that SNVs were less abundant at ligand binding sites, which is consistent with a previous study on SNVs and protein interaction sites. Additionally, we found that non-rare variants tended to be located slightly apart from enzyme active sites. Examination of non-rare variants revealed that most of the mutations resulted in moderate changes of the physico-chemical properties of amino acids, suggesting the existence of functional constraints. In conclusion, this study shows that the mapping of genetic variants on protein structures could be a powerful approach to evaluate the functional impact of rare genetic variations.</p>

  28. Identification of hepta-histidine as a candidate drug for Huntington’s disease by in silico-in vitro-in vivo-integrated screens of chemical libraries 国際誌 査読有り

    Imamura T, Fujita K, Tagawa K, Ikura T, Chen X, Homma H, Tamura T, Mao Y, Taniguchi JB, Motoki K, Nakabayashi M, Ito N, Yamada K, Tomii K, Okano H, Kaye J, Finkbeiner S, Okazawa H

    Scientific Reports　6　33861-33861　2016年

    DOI： 10.1038/srep33861 　

  29. Intrinsically disordered region of influenza A NP regulates viral genome packaging via interactions with viral RNA and host PI(4,5)P2 国際誌 査読有り

    Kakisaka M, Yamada K, Yamaji-Hasegawa A, Kobayashi T, Aida Y

    Virology　496　116-126　2016年

    DOI： 10.1016/j.virol.2016.05.018 　

  30. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment 査読有り

    Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ

    Proteins　84　(S1)　323-348　2016年

    出版者・発行元：

    DOI： 10.1002/prot.25007 　

    ISSN：0887-3585

    eISSN：1097-0134

  31. Systematic exploration of an efficient amino acid substitution matrix: MIQS 査読有り

    Tomii K, Yamada K

    Methods in Molecular Biology　2016年

    DOI： 10.1007/978-1-4939-3572-7_11 　

  32. A new genotype of bovine leukemia virus in South America identified by NGS-based whole genome sequencing and molecular evolutionary genetic analysis 査読有り

    Polat M, Takeshima SN, Hosomichi K, Kim J, Miyasaka T, Yamada K, Arainga M, Murakami T, Matsumoto Y, de la Barra Diaz V, Panei CJ, González ET, Kanemaki M, Onuma M, Giovambattista G, Aida Y

    Retrovirology　13　2016年

    DOI： 10.1186/s12977-016-0239-z 　

    eISSN：1742-4690

  33. 遠縁タンパク質検索に適した新規アミノ酸置換行列 査読有り

    Yamada K, Tomii K

    生物物理　55　(3)　133-136　2015年

    出版者・発行元： The Biophysical Society of Japan General Incorporated Association

    DOI： 10.2142/biophys.55.133 　

    ISSN：0582-4052

    eISSN：1347-4219

    詳細を見る 詳細を閉じる

    Amino acid similarity search methods are fundamental tools for inferring protein structure and function. Optimization of amino acid substitution matrices is indispensable to improve search performance. We explored matrices that are ideal for detecting distantly related proteins in the PCA subspace that represents a set of typical existing matrices, and derived a novel sensitive matrix: MIQS. Test results show that the MIQS detection performance is superior to those of existing matrices and other sequence comparison methods. This refinement of the amino acid substitution matrix might influence many fields of sequence analysis. MIQS is available at http://csas.cbrc.jp/Ssearch/.

  34. A novel antiviral target structure involved in the RNA binding, dimerization, and nuclear export functions of the influenza A virus nucleoprotein 国際誌 査読有り

    Kakisaka M, Sasaki Y, Yamada K, Kondoh Y, Hikono H, Osada H, Tomii K, Saito T, Aida Y

    PLOS Pathogens　11　(7)　e1005062　2015年

    DOI： 10.1371/journal.ppat.1005062 　

  35. PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs 査読有り

    Ito JI, Ikeda K, Yamada K, Mizuguchi K, Tomii K

    Nucleic Acids Research (NAR)　2015年

    DOI： 10.1093/nar/gku1144 　

  36. Comparative analysis of seven viral nuclear export signals (NESs) reveals the crucial role of nuclear export mediated by the third NES consensus sequence of nucleoprotein (NP) in influenza A virus replication 国際誌 査読有り

    Chutiwitoonchai N, Kakisaka M, Yamada K, Aida Y

    PLOS ONE　9　(8)　e105081　2014年

    DOI： 10.1371/journal.pone.0105081 　

  37. Revisiting amino acid substitution matrices for identifying distantly related proteins 査読有り

    Yamada K, Tomii K

    Bioinformatics　2014年

    DOI： 10.1093/bioinformatics/btt694 　

  38. Importin α3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function 国際誌 査読有り

    Sasaki Y, Hagiwara K, Kakisaka M, Yamada K, Murakami T, Aida Y

    PLOS ONE　8　(1)　e55765　2013年

    DOI： 10.1371/journal.pone.0055765 　

  39. Identification of a novel compound with antiviral activity against influenza A virus depending on PA subunit of viral RNA polymerase 国際誌 査読有り

    Yamada K, Koyama H, Hagiwara K, Ueda A, Sasaki Y, Kanesashi SN, Ueno R, Nakamura HK, Kuwata K, Shimizu K, Suzuki M, Aida Y

    Microbes and Infection　14　(9)　740-7　2012年

    DOI： 10.1016/j.micinf.2012.02.012 　

  40. Discovery of novel antiviral agents directed against the influenza A virus nucleoprotein using photo-cross-linked chemical arrays 国際誌 査読有り

    Hagiwara K, Kondoh Y, Ueda A, Yamada K, Goto H, Watanabe T, Nakata T, Osada H, Aida Y

    Biochemical and Biophysical Research Communications　394　(3)　721-7　2010年

    DOI： 10.1016/j.bbrc.2010.03.058 　

︎全件表示 ︎最初の5件までを表示

共同研究・競争的資金等の研究課題 2

  1. 人工知能で目指すアミノ酸配列類似性検索法の高速化および高感度化研究 競争的資金

    山田和範

    2018年4月 ～ 2020年3月

  2. MAFFT多重アラインメントプログラムの大量配列データへの対応と機能拡張 競争的資金

    加藤和貴

    2016年4月 ～ 2020年3月