KAZUNORI D. YAMADA, R.Ph., Ph.D.

研究概要のページ

Research achievements

Affiliation

東北大学大学院・情報科学研究科・国際交流推進室/木下大林研究室・助教

Assistant professor, Graduate School of Information Sciences, Tohoku University

産業技術総合研究所・人工知能研究センター・インテリジェントバイオインフォマティクス研究チーム・協力研究員

Visiting researcher, Artificial Intelligence Research Center, AIST

Research interests

数理最適化，ニューラルネットワーク，配列類似性検索，マルチプルアライメント，ウイルス惹起性新規疾病

Mathematical optimization method, Neural network, Similarity search, Multiple alignment, Viral disease

Peer reviewed journal papers in English + preprint entries

  1. Yamada KD, Hyperparameter-free optimizer of gradient-descent method incorporating unit correction and moment estimation, bioRxiv, 348557, 2018
  2. Katoh K, Rozewicki J, Yamada KD, MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization, Briefings in Bioinformatics, accepted, 2017
  3. Yamada KD, Kinoshita K, De novo profile generation based on sequence context specificity with the long short-term memory network, BMC Bioinformatics, 19(1):272, 2018
  4. Nakamura T, Yamada KD, Tomii K, Katoh K, Parallelization of MAFFT for large-scale multiple sequence alignments, Bioinformatics, 34(14):2490-2492, 2018
  5. Yamada KD, Derivative-free neural network for optimizing the scoring functions associated with dynamic programming of pairwise-profile alignment, Algorithms for molecular biology, 13:5, 2018
  6. Yamada KD, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, Tomii K, Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on crystal-packing propensity of amino acids, Acta Crystallographica Section D, 73(9):757-766, 2017
  7. Yamada KD, Omori S, Nish H, Miyagi M, Identification of the sequence determinants of protein N-terminal acetylation through a decision tree approach, BMC Bioinformatics, 18(1):289, 2017
  8. Lim K, Yamada KD, Frith MC, Tomii K, Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix, Journal of Structural and Functional Genomics, 17(4):147-154, 2016
  9. Yamada KD, Tomii K, Katoh K, Application of the MAFFT sequence alignment program to large data - reexamination of the usefulness of chained guide trees, Bioinformatics, 32(21):3246-3251, 2016
  10. 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, Identification of hepta-histidine as a candidate drug for Huntington’s disease by in silico-in vitro-in vivo-integrated screens of chemical libraries, Scientific Reports, 6:33861, 2016
  11. 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, Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment, Proteins, 84(S1):323-348, 2016
  12. Kakisaka M, Yamada K, Yamaji-Hasegawa A, Kobayashi T, Aida Y, Intrinsically disordered region of influenza A NP regulates viral genome packaging via interactions with viral RNA and host PI(4,5)P2, Virology, 496:116-126, 2016
  13. Yamada KD, Nishi H, Nakata J, Kinoshita K, Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins, Biophysics and Physicobiology (BPPB), 13:157-163, 2016
  14. Tomii K, Yamada K, Systematic exploration of an efficient amino acid substitution matrix: MIQS, Methods in Molecular Biology, 1415:211-223, 2016
  15. 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, A new genotype of bovine leukemia virus in South America identified by NGS-based whole genome sequencing and molecular evolutionary genetic analysis, Retrovirology, 13(1):4, 2016
  16. Kakisaka M, Sasaki Y, Yamada K, Kondoh Y, Hikono H, Osada H, Tomii K, Saito T, Aida Y, A novel antiviral target structure involved in the RNA binding, dimerization, and nuclear export functions of the influenza A virus nucleoprotein, PLOS Pathogens, 11(7):e1005062, 2015
  17. Ito JI, Ikeda K, Yamada K, Mizuguchi K, Tomii K, PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs, Nucleic Acids Research (NAR), 43(D1):D392-D398, 2015
  18. Chutiwitoonchai N, Kakisaka M, Yamada K, Aida Y, 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, PLOS ONE, 9(8):e105081, 2014
  19. Yamada K, Tomii K, Revisiting amino acid substitution matrices for identifying distantly related proteins, Bioinformatics, 30(3):317-325, 2014
  20. Sasaki Y, Hagiwara K, Kakisaka M, Yamada K, Murakami T, Aida Y, Importin α3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function, PLOS ONE, 8(1):e55765, 2013
  21. Yamada K, Koyama H, Hagiwara K, Ueda A, Sasaki Y, Kanesashi SN, Ueno R, Nakamura HK, Kuwata K, Shimizu K, Suzuki M, Aida Y, Identification of a novel compound with antiviral activity against influenza A virus depending on PA subunit of viral RNA polymerase, Microbes and Infection, 14(9):740-747, 2012
  22. Hagiwara K, Kondoh Y, Ueda A, Yamada K, Goto H, Watanabe T, Nakata T, Osada H, Aida Y, Discovery of novel antiviral agents directed against the influenza A virus nucleoprotein using photo-cross-linked chemical arrays, Biochemical and Biophysical Research Communications (BBRC), 394:721-727, 2010

Peer reviewed journal papers in Japanese

  1. 山田和範, 富井健太郎, 遠縁タンパク質検索に適した新規アミノ酸置換行列, 生物物理, 55(3):133-136, 2015

Conference papers

    Nothing so far.

Awards & Honors

  1. Research Award, Yamada KD, Kinoshita K, Development of de novo generator of amino acid sequence profile using LSTM framework, IIBMP2017, 2017
  2. Excellent Poster Award, Yamada K, Tomii K, Development of a novel amino acid substitution matrix for remote homology detection, IIBMP2013, 2013
  3. Poster Award, Yamada K, Tomii K, Developing a novel amino acid substitution matrix suitable for detecting distantly related proteins, BiWO2013, 2013

Research product

De novo profile generator based on recurrent neural network method, LSTM.
N-terminal acetylation predictor based on decision tree classification.
PSSM-PSSM pairwise aligner with neural network enhanced scoring function of dynamic programming.

Classes

  • Data science training camp I, Tohoku University, 2017 Spring
  • Data science training camp II / Big data challenge, Tohoku University, 2017 Spring
  • Big-data skill-up training, Tohoku University, 2017 Autumn
  • Data science training camp I, Tohoku University, 2017 Autumn
  • Data science training camp II / Big data challenge, Tohoku University, 2017 Autumn
  • Data science training camp II / Big data challenge, Tohoku University, 2016 Spring
  • Big-data skill-up training, Tohoku University, 2016 Autumn
  • Data science training camp I, Tohoku University, 2016 Autumn
  • Big-data skill-up training, Tohoku University, 2015 Autumn
  • Data science training camp I, Tohoku University, 2015 Autumn

Professional memberships

  • 日本バイオインフォマティクス学会
  • 日本蛋白質科学会
  • 日本生物物理学会
  • 数学連携セミナー

Grants

  • 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，科研費・若手研究 (2018 - 2020)，研究課題番号：18K18143，(代表 1,820,000円)
  • 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，科研費・基盤研究C (2016 - 2020)，研究課題番号：16K07464，(分担 4,940,000円)

Favorite website

所属研究室のサイト
以前の所属研究室のサイト
開発に携わっているソフトウェア関連のデータ等を集めたサイト
開発したアミノ酸置換行列を用いた配列検索サーバー
産総研発タンパク質立体構造予測サーバー
開発に携わっているマルチプルアライナー
データ科学の研究に関することをまとめたサイト
バイオインフォマティクスの研究に関することをまとめたサイト
SCOPの相同・非相同の分類についてまとめた研究成果
フリーで使えるMOEのようなソフトウェア

Contact

E-mail: kyamada [AT] ecei.tohoku.ac.jp