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2020 – today
- 2024
[i1]Hiroaki Yamagiwa, Ryoma Hashimoto, Kiwamu Arakane, Ken Murakami
, Shou Soeda, Momose Oyama, Mariko Okada, Hidetoshi Shimodaira:
Predicting Drug-Gene Relations via Analogy Tasks with Word Embeddings. CoRR abs/2406.00984 (2024)- 2023
- [c19]Shuhei Kimura, Hirotaka Kitajima, Masato Tokuhisa, Mariko Okada:
Inference of Genetic Networks from Steady-State and Pseudo Time-Series of Single-Cell Gene Expression Data using Modified Random Forests. SSCI 2023: 1579-1586 - 2022
- [j15]Keita Iida, Jumpei Kondo, Johannes Nicolaus Wibisana, Masahiro Inoue, Mariko Okada:
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes. Bioinform. 38(18): 4330-4336 (2022)
2010 – 2019
- 2019
- [j14]Shuhei Kimura, Masato Tokuhisa, Mariko Okada:
Inference of genetic networks using random forests: Assigning different weights for gene expression data. J. Bioinform. Comput. Biol. 17(4): 1950015:1-1950015:21 (2019) - [c18]Shuhei Kimura, Masato Tokuhisa, Akiyuki Uemura, Mariko Okada:
Feature Selection based on Random Forests and its Application to a Modeling of Sewage Treatment Plant. TAAI 2019: 1-6 - 2018
- [c17]Shuhei Kimura, Masato Tokuhisa, Mariko Okada-Hatakeyama:
Inference of Genetic Networks Using Random Forests: Use of Different Weights for Time-Series and Static Gene Expression Data. BIBE 2018: 98-103 - 2017
- [j13]Trisevgeni Rapakoulia, Xin Gao, Yi Huang, Michiel J. L. de Hoon, Mariko Okada-Hatakeyama, Harukazu Suzuki, Erik Arner:
Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment. Bioinform. 33(23): 3696-3700 (2017) - [c16]Shuhei Kimura, Masato Tokuhisa, Mariko Okada-Hatakeyama:
Inference of genetic networks from time-series of gene expression levels using random forests. CIBCB 2017: 1-6 - 2016
- [c15]Shuhei Kimura, Masato Tokuhisa, Mariko Okada-Hatakeyama:
Simultaneous execution method of gene clustering and network inference. CIBCB 2016: 1-7 - [c14]Yuji Okamoto, Jun-ichi Imura, Mariko Okada-Hatakeyama:
Observer design of positive quadratic systems. ECC 2016: 843-848 - 2015
- [j12]Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama:
An Effective Method for the Inference of Reduced S-system Models of Genetic Networks. Inf. Media Technol. 10(1): 166-174 (2015) - [j11]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, Mariko Okada-Hatakeyama, Colin A. M. Semple:
Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response. PLoS Comput. Biol. 11(4) (2015) - [c13]Yuji Okamoto, Jun-ichi Imura, Mariko Okada-Hatakeyama:
Positive quadratic system representation of molecular interaction in a cell. ECC 2015: 1554-1559 - [c12]Shuhei Kimura, Mariko Okada-Hatakeyama:
Improvement of reliabilities of regulations using a hierarchical structure in a genetic network. IJCNN 2015: 1-7 - 2013
- [c11]Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama:
Development of an efficient parameter estimation method for the inference of Vohradský's neural network models of genetic networks. IJCNN 2013: 1-6 - 2012
- [c10]Shuhei Kimura, Koki Matsumura, Mariko Okada-Hatakeyama:
Inference of S-system models of genetic networks by solving linear programming problems and sets of linear algebraic equations. IJCNN 2012: 1-8 - 2011
- [j10]Yuichi Shiraishi, Mariko Okada-Hatakeyama, Satoru Miyano:
A rank-based statistical test for measuring synergistic effects between two gene sets. Bioinform. 27(17): 2399-2405 (2011) - [j9]Yoshimi Naruo, Takeshi Nagashima, Ryoko Ushikoshi-Nakayama, Yuko Saeki, Takashi Nakakuki, Takashi Naka, Hiroshi Tanaka, Shih-Feng Tsai, Mariko Okada-Hatakeyama:
Epidermal growth factor receptor mutation in combination with expression of MIG6 alters gefitinib sensitivity. BMC Syst. Biol. 5: 29 (2011) - [j8]Saswati Dana, Takashi Nakakuki, Mariko Hatakeyama, Shuhei Kimura, Soumyendu Raha:
Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway. Comput. Methods Programs Biomed. 101(1): 1-22 (2011) - 2010
- [j7]Yuichi Shiraishi, Shuhei Kimura, Mariko Okada:
Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. Bioinform. 26(8): 1073-1081 (2010) - [j6]Shuhei Kimura, Yuichi Shiraishi, Mariko Okada:
Inference of Genetic Networks Using Lpms: Assessment of Confidence Values of Regulations. J. Bioinform. Comput. Biol. 8(4): 661-677 (2010) - [c9]Shuhei Kimura, Yusuke Amano, Koki Matsumura, Mariko Okada-Hatakeyama:
Effective parameter estimation for S-system models using LPMs and evolutionary algorithms. IEEE Congress on Evolutionary Computation 2010: 1-8 - [c8]Shuhei Kimura, Koki Matsumura, Mariko Okada-Hatakeyama:
Bootstrap Analysis of Genetic Networks inferred by the Method Using LPMs. ICCSA Workshops 2010: 296-299
2000 – 2009
- 2009
- [j5]Shuhei Kimura, Satoshi Nakayama, Mariko Hatakeyama:
Genetic network inference as a series of discrimination tasks. Bioinform. 25(7): 918-925 (2009) - [c7]Shuhei Kimura, Yuichi Shiraishi, Mariko Hatakeyama:
Inference of genetic networks using linear programming machines: Application of a priori knowledge. IJCNN 2009: 1617-1624 - 2008
- [j4]Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Hideki Maeda, Koki Matsumura, Mariko Hatakeyama:
Function approximation approach to the inference of reduced NGnet models of genetic networks. BMC Bioinform. 9 (2008) - 2007
- [c6]Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Kotaro Yoshida, Koki Matsumura, Mariko Hatakeyama:
Inference of Genetic Networks using a Reduced NGnet Model. IJCNN 2007: 932-937 - 2006
- [c5]Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, Mariko Hatakeyama:
Function Approximation Approach to the Inference of Normalized Gaussian Network Models of Genetic Networks. IJCNN 2006: 2218-2225 - 2005
- [j3]Shuhei Kimura, Kaori Ide, Aiko Kashihara, Makoto Kano, Mariko Hatakeyama, Ryoji Masui, Noriko Nakagawa, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya:
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinform. 21(7): 1154-1163 (2005) - [c4]Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, Mariko Hatakeyama:
Inference of genetic networks using neural network models. Congress on Evolutionary Computation 2005: 1738-1745 - [c3]Aki Hasegawa, Kazumi Kuriyama-Matsumura, Xiaomei Yu, Mariko Hatakeyama, Akihiko Konagaya:
Software-Aided Mass Spectrometry Analysis for Identification of Protein-Protein Interaction in Signal Transduction Pathways. ICDE Workshops 2005: 1157 - 2004
- [j2]Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya:
OBIYagns: a grid-based biochemical simulator with a parameter estimator. Bioinform. 20(10): 1646-1648 (2004) - [j1]Akihiko Konagaya, Fumikazu Konishi, Mariko Hatakeyama, Kenji Satou:
The Superstructure toward Open Bioinformatics Grid. New Gener. Comput. 22(2): 167-176 (2004) - [c2]Akinobu Fukuzaki, Takeshi Nagashima, Kaori Ide, Fumikazu Konishi, Mariko Hatakeyama, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya:
Genome-Wide Functional Annotation Environment forin OBIGrid. LSGRID 2004: 82-91 - 2003
- [c1]Shuhei Kimura, Mariko Hatakeyama, Akihiko Konagaya:
Inference of S-system models of genetic networks using a genetic local search. IEEE Congress on Evolutionary Computation 2003: 631-638
Coauthor Index
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