Inference of S-system models of genetic networks using a genetic local search. - Shuhei Kimura; Mariko Hatakeyama; Akihiko Konagaya (IEEE Congress on Evolutionary Computation, 2003)

Genome-Wide Functional Annotation Environment forin OBIGrid. - Akinobu Fukuzaki; Takeshi Nagashima; Kaori Ide; Fumikazu Konishi; Mariko Hatakeyama; Shigeyuki Yokoyama; Seiki Kuramitsu; Akihiko Konagaya (LSGRID, 2004)

OBIYagns: a grid-based biochemical simulator with a parameter estimator. - Shuhei Kimura; Takuji Kawasaki; Mariko Hatakeyama; Takashi Naka; Fumikazu Konishi; Akihiko Konagaya (Bioinform., 2004)

The Superstructure toward Open Bioinformatics Grid. - Akihiko Konagaya; Fumikazu Konishi; Mariko Hatakeyama; Kenji Satou (New Gener. Comput., 2004)

Inference of genetic networks using neural network models. - Shuhei Kimura; Katsuki Sonoda; Soichiro Yamane; Koki Matsumura; Mariko Hatakeyama (Congress on Evolutionary Computation, 2005)

Software-Aided Mass Spectrometry Analysis for Identification of Protein-Protein Interaction in Signal Transduction Pathways. - Aki Hasegawa; Kazumi Kuriyama-Matsumura; Xiaomei Yu; Mariko Hatakeyama; Akihiko Konagaya (ICDE Workshops, 2005)

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. - Shuhei Kimura; Kaori Ide; Aiko Kashihara; Makoto Kano; Mariko Hatakeyama; Ryoji Masui; Noriko Nakagawa; Shigeyuki Yokoyama; Seiki Kuramitsu; Akihiko Konagaya (Bioinform., 2005)

Function Approximation Approach to the Inference of Normalized Gaussian Network Models of Genetic Networks. - Shuhei Kimura; Katsuki Sonoda; Soichiro Yamane; Koki Matsumura; Mariko Hatakeyama (IJCNN, 2006)

Inference of Genetic Networks using a Reduced NGnet Model. - Shuhei Kimura; Katsuki Sonoda; Soichiro Yamane; Kotaro Yoshida; Koki Matsumura; Mariko Hatakeyama (IJCNN, 2007)

Function approximation approach to the inference of reduced NGnet models of genetic networks. - Shuhei Kimura; Katsuki Sonoda; Soichiro Yamane; Hideki Maeda; Koki Matsumura; Mariko Hatakeyama (BMC Bioinform., 2008)

Inference of genetic networks using linear programming machines: Application of a priori knowledge. - Shuhei Kimura; Yuichi Shiraishi; Mariko Hatakeyama (IJCNN, 2009)

Genetic network inference as a series of discrimination tasks. - Shuhei Kimura; Satoshi Nakayama; Mariko Hatakeyama (Bioinform., 2009)

Effective parameter estimation for S-system models using LPMs and evolutionary algorithms. - Shuhei Kimura; Yusuke Amano; Koki Matsumura; Mariko Okada-Hatakeyama (IEEE Congress on Evolutionary Computation, 2010)

Bootstrap Analysis of Genetic Networks inferred by the Method Using LPMs. - Shuhei Kimura; Koki Matsumura; Mariko Okada-Hatakeyama (ICCSA Workshops, 2010)

Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. - Yuichi Shiraishi; Shuhei Kimura; Mariko Okada (Bioinform., 2010)

Inference of Genetic Networks Using Lpms: Assessment of Confidence Values of Regulations. - Shuhei Kimura; Yuichi Shiraishi; Mariko Okada (J. Bioinform. Comput. Biol., 2010)

A rank-based statistical test for measuring synergistic effects between two gene sets. - Yuichi Shiraishi; Mariko Okada-Hatakeyama; Satoru Miyano (Bioinform., 2011)

Epidermal growth factor receptor mutation in combination with expression of MIG6 alters gefitinib sensitivity. - Yoshimi Naruo; Takeshi Nagashima; Ryoko Ushikoshi-Nakayama; Yuko Saeki; Takashi Nakakuki; Takashi Naka; Hiroshi Tanaka; Shih-Feng Tsai; Mariko Okada-Hatakeyama (BMC Syst. Biol., 2011)

Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway. - Saswati Dana; Takashi Nakakuki; Mariko Hatakeyama; Shuhei Kimura; Soumyendu Raha (Comput. Methods Programs Biomed., 2011)

Inference of S-system models of genetic networks by solving linear programming problems and sets of linear algebraic equations. - Shuhei Kimura; Koki Matsumura; Mariko Okada-Hatakeyama (IJCNN, 2012)

Development of an efficient parameter estimation method for the inference of Vohradský's neural network models of genetic networks. - Shuhei Kimura; Masanao Sato; Mariko Okada-Hatakeyama (IJCNN, 2013)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

Positive quadratic system representation of molecular interaction in a cell. - Yuji Okamoto; Jun-ichi Imura; Mariko Okada-Hatakeyama (ECC, 2015)

Improvement of reliabilities of regulations using a hierarchical structure in a genetic network. - Shuhei Kimura; Mariko Okada-Hatakeyama (IJCNN, 2015)

An Effective Method for the Inference of Reduced S-system Models of Genetic Networks. - Shuhei Kimura; Masanao Sato; Mariko Okada-Hatakeyama (Inf. Media Technol., 2015)

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response. - Stuart Aitken; Shigeyuki Magi; Ahmad M. N. Alhendi; Masayoshi Itoh; Hideya Kawaji; Timo Lassmann; Carsten O. Daub; Erik Arner; Piero Carninci; Alistair R. R. Forrest; Yoshihide Hayashizaki; Levon M. Khachigian; et al. (PLoS Comput. Biol., 2015)

Simultaneous execution method of gene clustering and network inference. - Shuhei Kimura; Masato Tokuhisa; Mariko Okada-Hatakeyama (CIBCB, 2016)

Observer design of positive quadratic systems. - Yuji Okamoto; Jun-ichi Imura; Mariko Okada-Hatakeyama (ECC, 2016)

Inference of genetic networks from time-series of gene expression levels using random forests. - Shuhei Kimura; Masato Tokuhisa; Mariko Okada-Hatakeyama (CIBCB, 2017)

Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment. - Trisevgeni Rapakoulia; Xin Gao 001; Yi Huang; Michiel J. L. de Hoon; Mariko Okada-Hatakeyama; Harukazu Suzuki; Erik Arner (Bioinform., 2017)

Inference of Genetic Networks Using Random Forests: Use of Different Weights for Time-Series and Static Gene Expression Data. - Shuhei Kimura; Masato Tokuhisa; Mariko Okada-Hatakeyama (BIBE, 2018)

Feature Selection based on Random Forests and its Application to a Modeling of Sewage Treatment Plant. - Shuhei Kimura; Masato Tokuhisa; Akiyuki Uemura; Mariko Okada (TAAI, 2019)

Inference of genetic networks using random forests: Assigning different weights for gene expression data. - Shuhei Kimura; Masato Tokuhisa; Mariko Okada (J. Bioinform. Comput. Biol., 2019)

ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes. - Keita Iida; Jumpei Kondo; Johannes Nicolaus Wibisana; Masahiro Inoue; Mariko Okada (Bioinform., 2022)

Inference of Genetic Networks from Steady-State and Pseudo Time-Series of Single-Cell Gene Expression Data using Modified Random Forests. - Shuhei Kimura; Hirotaka Kitajima; Masato Tokuhisa; Mariko Okada (SSCI, 2023)

Predicting Drug-Gene Relations via Analogy Tasks with Word Embeddings. - Hiroaki Yamagiwa; Ryoma Hashimoto; Kiwamu Arakane; Ken Murakami; Shou Soeda; Momose Oyama; Mariko Okada; Hidetoshi Shimodaira (CoRR, 2024)