Parallel algorithm for efficient calculation of second derivatives of conformational energy function in internal coordinates. - Shugo Nakamura; Mitsunori Ikeguchi; Kentaro Shimizu (J. Comput. Chem., 1998)

Prediction of protein structure classes and secondary structures by means of hidden Markov models. - Hiroshi Yoshikawa; Mitsunori Ikeguchi; Shugo Nakamura; Kentaro Shimizu; Junta Doi (Syst. Comput. Jpn., 1999)

Automatic Improvement of Scheduling Policies in Parsley Parallel Programming Environment. - Masakazu Sekijima; Shinya Takasaki; Shugo Nakamura; Kentaro Shimizu (IASTED PDCS, 2002)

New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates. - Shugo Nakamura; Daisuke Kyono; Mitsunori Ikeguchi; Kentaro Shimizu (J. Comput. Chem., 2002)

Design and Implementation of a Parallel Programming Environment Based on Distributed Shared Arrays. - Wataru Kaneko; Akira Nomoto; Yasuo Watanabe; Shugo Nakamura; Kentaro Shimizu (ISHPC, 2003)

Programming Environment Based on Distributed Shared Arrays for High-Performance Scientific Computing. - Akira Nomoto; Wataru Kaneko; Tohru Terada; Shugo Nakamura; Kentaro Shimizu (SAINT Workshops, 2004)

Distributed Shared Arrays: Portable Shared-Memory Programming Interface for Multiple Computer Systems. - Akira Nomoto; Yasuo Watanabe; Wataru Kaneko; Shugo Nakamura; Kentaro Shimizu (Clust. Comput., 2004)

Insight of the Signal Motif of GPI-(like)-anchored Proteins by using SVM. - Cao Wei; Kazuya Sumikoshi; Tohru Terada; Shugo Nakamura; Kentaro Shimizu (BIOCOMP, 2006)

Prediction of Protein-Protein Interaction Sites Using Only Sequence Information and Using Both Sequence and Structural Information. - Masanori Kakuta; Shugo Nakamura; Kentaro Shimizu (Inf. Media Technol., 2008)

Computational Protocol for Screening GPI-anchored Proteins. - Cao Wei; Kazuya Sumikoshi; Tohru Terada; Shugo Nakamura; Katsuhiko Kitamoto; Kentaro Shimizu (BICoB, 2009)

Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines. - Seizi Someya; Masanori Kakuta; Mizuki Morita; Kazuya Sumikoshi; Cao Wei; Ge Zhenyi; Osamu Hirose; Shugo Nakamura; Tohru Terada; Kentaro Shimizu (Adv. Bioinformatics, 2010)

Industry Track: An Image Classification and Browsing System for Farm Inspection. - Masaki Ishihara; Shugo Nakamura; Takayuki Baba; Masahiko Sugimura; Susumu Endo; Yusuke Uehara; Daiki Masumoto (ISM, 2011)

Prospects for Tertiary Structure Prediction of RNA Based on Secondary Structure Information. - Satoshi Yamasaki; Shugo Nakamura; Kazuhiko Fukui (J. Chem. Inf. Model., 2012)

Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine. - Masayuki Yarimizu; Cao Wei; Yusuke Komiyama; Kokoro Ueki; Shugo Nakamura; Kazuya Sumikoshi; Tohru Terada; Kentaro Shimizu (Adv. Bioinformatics, 2015)

Development of a sugar-binding residue prediction system from protein sequences using support vector machine. - Masaki Banno; Yusuke Komiyama; Cao Wei; Yuya Oku; Kokoro Ueki; Kazuya Sumikoshi; Shugo Nakamura; Tohru Terada; Kentaro Shimizu (Comput. Biol. Chem., 2017)

An ODE-based neural network with Bayesian optimization. - Hirotada Honda; Takashi Sano 002; Shugo Nakamura; Mitsuaki Ueno; Hiroki Hanazawa; Nguyen Manh Duc Tuan (JSIAM Lett., 2023)

From Coupled Oscillators to Graph Neural Networks: Reducing Over-smoothing via a Kuramoto Model-based Approach. - Tuan Nguyen; Hirotada Honda; Takashi Sano 002; Vinh Nguyen; Shugo Nakamura; Tan Minh Nguyen (AISTATS, 2024)

Understanding Neural ODE prediction decision using SHAP. - Phuong Dinh; Deddy Jobson; Takashi Sano 002; Hirotada Honda; Shugo Nakamura (NLDL, 2024)

Investigation of Frame Differences as Motion Cues for Video Object Segmentation. - Sota Kawamura; Hirotada Honda; Shugo Nakamura; Takashi Sano 002 (CoRR, 2025)