• 小長谷明彦：AI活用による創薬の可能性，人と共生するAI革命, 第７章創薬する第１節, NTS出版 (2019). ISBN 978-4-86043-608-7 C3004
• 小長谷明彦：分子ロボティクスを用いた分子人工膵島細胞の実現を目指して, Precision Medicine, 2(5), pp.69-73 (2019).
• 小長谷明彦：分子ロボットが拓く未来の創薬, MDB技術予測レポート, 2050未来・世界を変える技術, 日本能率協会総合研究所 (2019).
• 小長谷明彦：　バイオ情報学-パーソナルゲノム解析から生体シミュレーションまで（電子情報通信レクチャーシリーズD-23），コロナ社(2009)　ISBN：978-4-339-01883-7

• Tan Tin Wee, Peter Arzberger, Akihiko Konagaya (Ed): Grid Computing in Life Sciences: Proceedings of the 2nd International Science Grid Workshop, Lsgrid 2005, World Scientific Publishing Co., Inc., (2006) ISBN: 978-981-4476-56-0

• Akihiko Konagaya, Kenji Satou (Ed): Grid Computing in Life Science: First International Life Science Grid Workshop, LSGRID 2004, LNBI 3370, Springer, (2005) ISBN 978-3-540-32251-1

• 小長谷明彦：遺伝子とコンピュータ　生命の設計図をひもとく，協立出版[2000]　ISBN:978-4-320-02952-1

【主な論文】

• Gregory Gutmann, Akihiko Konagaya: Predictive Simulation: Using Regression and Artificial Neural Networks to Negate Latency in Networked Interactive Virtual Reality, arXiv:1910.04703 [cs.HC] (2019).
  https://arxiv.org/abs/1910.04703
• Zhang Yuhui, Greg Gutmann, Konagaya Akihiko: Irregular Convolutional Auto-Encoder on Point Clouds, arXiv:1910.02686 [cs.LG] (2019).
  https://arxiv.org/abs/1910.02686
• Daisuke Inoue, Greg Gutmann, Takahiro Nitta, Takahiro Nitta, ARIF MD. RASHEDUL KABIR, Akihiko Konagaya, Kiyotaka Tokuraku, Kazuki Sada, Henry Hess, Akira Kakugo: Adaptation of Patterns of Motile Filaments under Dynamic Boundary Conditions, ACS Nano, (2019) online.
  https://doi.org/10.1021/acsnano.9b01450
• Atsuko Sato, Naoki Tanimura, Teruki Honma, Akihiko Konagaya: Significance of data selection in deep learning for reliable binding mode prediction of ligands in the active site of CYP3A4, Chemical and Pharmaceutical Bulletin,(2019) online.
  https://doi.org/10.1248/cpb.c19-00443
• Arif Pramudwlatmoko, Satoru Tsutoh, Gregory Gutmann, Yutaka Ueno, Akihiko Konagaya: A high‑performance haptic rendering system for virtual reality molecular modeling, Artificial Life and Robotics, (2019) online.
  https://doi.org/10.1007/s10015-019-00555-9
• Bharata Kalbuaji, Y-H. Taguchi, and Akihiko Konagaya: Discovery of a Robust Gene Regulatory Network with Complex Transcription Factor Network on Organ Cancer Cell-line RNA Sequence Data, CBI Journal,19, pp.32-55 (2019).
  DOI:10.1273/cbij.19.32
• Syeda Rubaiya Nasrin, Arif Md. Rashedul Kabir, Akihiko Konagaya, Tsukasa Ishihara, Kazuki Sada, Akira Kakugo: Stabilization of microtubules by cevipabulin, Biochemical and Biophysical Research Communications, Available online 26 June (2019).
  https://doi.org/10.1016/j.bbrc.2019.06.095
• Kento Matsuda, Arif Md. Rashedul Kabir, Naohide Akamatsu, Ai Saito, Shumpei Ishikawa, Tsuyoshi Matsuyama, Oliber Ditzer, Md. Sirajul Islam, Yuichi Ohya, Kazuki Sada, Akihiko Konagaya,  Akinori Kuzuya, Akira Kakugo: Artificial Smooth Muscle Model Composed of Hierarchically Ordered Microtubule Asters Mediated by DNA Origami Nanostructures, Nano Letters, Article ASAP  (2019) .
  DOI: 10.1021/acs.nanolett.9b01201
• Gregory Gutmann, Ryuzo Azuma, Akihiko Konagaya: A Virtual Reality Computational Platform Dedicated for the Emergence of Global Dynamics in a Massive Swarm of Objects, J. of he Imaging Society of Japan, 57(6), pp.647-653 (2018). PDF
  DOI:10.11370/isj.57.647
• Go Yoshizawa, Rinie van Est, Daisuke Yoshinaga, Mikihito Tanaka, Ryuma Shineha, Akihiko Konagaya: Responsible innovation in molecular robotics in Japan, Chem-Bio Informatics Journal, 18, pp.164-172 (2018).
  DOI:10.1273/cbij.18.164
• Ryuzo Azuma, Sae Kishi, Greg Gutmann, Akihiko Konagaya: “All-atom molecular dynamics of film supported flat-shaped DNA origami in water“, Chem-Bio Informatics Journal, 18, pp.96-118 (2018).
  DOI:10.1273/cbij.18.96
• Kenta Yoshida, Kazuya Maeda, Akihiko Konagaya, Hiroyuki Kusuhara: “Accurate Estimation of In Vivo Inhibition Constants of Inhibitors and Fraction Metabolized of Substrates with Physiologically Based Pharmacokinetic Drug–Drug Interaction Models Incorporating Parent Drugs and Metabolites of Substrates with Cluster Newton Method“, DRUG METABOLISM AND DISPOSITION, 46, pp.1805-1816 (2018)
  DOI:10.1124/dmd.118.081828
• 加藤拓也，稲本万里子，小長谷明彦：深層学習法による源氏絵の流派推定，
  人工知能学会全国大会（第32回），2D1-05，鹿児島 6月6日 (2018).
• 津野駿幸，稲本万里子，小長谷明彦：仮想空間上の灯明光源効果を用いた時代屏風の再現，人工知能学会全国大会（第32回），2K2-02，鹿児島  6月6日 (2018).
• 小長谷 明彦: 特集「AI 創薬の可能性について」の企画にあたって(その２), 日本化学会情報化学部会誌, Vol. 35 (2017) No. 3,10月号 p. 198-.
  DOI:10.11546/cicsj.35.198
• Shun Asami, Daisuke Kiga, Akihiko Konagaya: Constraint-based Perturvation Analysis with Cluster Newton Method : A Case Study of Personalized Parameter Estimations with Irinotecan Whole-Body Physiologically Based Pharmacokinetic Model, BMC Systems Biology, Vol.11 (Suppl 7): 129 (2017). 
  DOI: 10.1186/s12918-017-0513-2
• 小長谷 明彦: 特集「AI 創薬の可能性について」の企画にあたって, 日本化学会情報化学部会誌, Vol. 35 (2017) No. 2 July p. 156-157.
  DOI:10.11546/cicsj.35.156
• 渡邊健太, 小長谷明彦: セマンティックウェブを活用した医薬文書理解支援システムの構築, 日本化学会情報化学部会誌, Vol. 35 (2017) No. 2 July p. 180-185.
  DOI:10.11546/cicsj.35.180
• Atsuko Sato, Hitomi Yuki, Chiduru Watanabe, Jun-ichi Saito, Akihiko Konagaya, Teruki Honma: Prediction of the site of CYP3A4 metabolism of tolterodine by molecular dynamics simulation from multiple initial structures of the CYP3A4-tolterodine complex, Chem-Bio Informatics Journal, 17, 38-52 (2017).
  DOI: 10.1273/cbij.17.38
• Greg Gutmann Daisuke Inoue, Akira Kakugo, Akihiko Konagaya: Parallel Interaction Detection Algorithms for a Particle-based Live Controlled Real-time Microtubule Gliding Simulation System Accelerated by GPGPU, Inter. J. of New Generation Computing (NGC), First Online 03 March  (2017).SharedIt
  DOI: 10.1007/s00354-017-0011-5
• Daisuke Inoue, Takahiro Nitta, Rashedul Kabir, Kazuki Sada, Jian Ping Gong, Akihiko Konagaya, Akira Kakugo: Sensing surface mechanical deformation using active probes driven by motor proteins, Nature Communications, 7:12557, Oct. 3 (2016).
  DOI: 10.1038/ncomms12557
• Greg Gutmann Daisuke Inoue, Akira Kakugo, Akihiko Konagaya: Real-Time 3D Microtubule Gliding Simulation Accelarated by GPU Computing, Inter. J. of Automation and Computing (IJAC), 19 Feb. 2 (2016), pp. 1-9.
  DOI: 10.1007/s11633-015-0947-1
• Greg Gutmann Daisuke Inoue, Akira Kakugo, Akihiko Konagaya: Using a Master and Slave approach for GPGPU Computing to Achieve Optimal Scaling in a 3D Real-Time Simulation, in Proc. the IEEE Ann. Int. Conf. on Nano/Micro Engineerd and Molecular Systems (NEMS), Matsushima, Japan, 17-20 April, (2016), A3L-E-4

• Bulibuli Mahemuti, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya: Investigation of the Microtubule Dynamics with Probabilistic Data Association Filter, in Proc. the IEEE Ann. Int. Conf. on Nano/Micro Engineerd and Molecular Systems (NEMS), Matsushima, Japan, 17-20 April, (2016), A3L-E-5

• Daisuke Inoue, Bulbul Mahemoti, Arif Md. Rashedul Kabir, Tamann Ishrat Farhana, Kiyotaka Tokuraku, Kazuki Sada, Akihiko Konagaya, Akira Kakugo: Depletion force induced collective motion of microtubules driven by knesin, Nanoscale,  (2015) online

• Yuexing Han, Akito Hara, Akinori Kuzuya, Rousuke Watanabe, Yuichi Ohya, Akihiko Konagaya: Automatic Recognition of DNA Pliers in Atomic Force Microscopy Images, New Generation Computing, 33(3), 253-270 (2015) doi: 10.1007/s00354-015-0305-4

• Philippe Gaudreau, Ken Hayami, Y. Aoki, Hassan Safouhi, Akihiko Konagaya:
  Improvements to the cluster Newton method for underdetermined inverse problems.J. Computational Applied Mathematics283:122-141(2015) DOI:10.1137/120885462

• Yutaka Ueno, Shuntaro Ito, Akihiko Konagaya: Implementing a modeling software for animated protein-complex interactions using a physics simulation library.J. Bioinformatics and Computational Biology12(6)(2014) DOI: 10.1142/S0219720014420037

• Greg Gutmann, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya: Real-Time 3D Microtubule Gliding Simulation, Life System Modeling and Simulation, Communications in Compuer and Information Science, vol. 461, pp.13-22 (2014) DOI:10.1007/978-3-662-45283-7_2

• Masami Hagiya, Akihiko Konagaya, Satoshi Kobayashi, Satoshi Murata: Molecular Robots with Sensors and Intelligence, Accounts of Chemical Research, 47(6), 1681-1690 (2014)  DOI: 10.1021/ar400318d

• 青木康憲、速水謙、小長谷明彦: 劣決定逆問題に対するCluster Newton法とその薬物動態モデルへの応用, 応用数理,2014年24巻4号 pp.7-15 (ベストオーサー賞受賞）PDF

• Yoshida K, Maeda K, Kusuhara H, Konagaya A: Estimation of feasible solution space using Cluster Newton Method: application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models, BMC Systems Biology 2013, 7 (Suppl 3): S3 (2013) doi:10.1186/1752-0509-7-S3-S3

• Murata S, Konagaya A, Kobayashi S, Saito H, Hagiya M: Molecular Robotics: A New Paradigm for Artifacts,New Generation Computing, Ohmsha, Ltd. and Springer, vol.31, no.1, pp.27-45 (2013) 10.1007/s00354-012-0121-z