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Journal Articles
- 2024
[j16]Tomoshiro Ochiai, Jose C. Nacher:
Determining cellular lineage directed networks in hematopoiesis using single-cell transcriptomic data and volatility-constrained correlation. Biosyst. 242: 105248 (2024)- 2019
- [j15]Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu
, Jose C. Nacher:
Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles. J. Bioinform. Comput. Biol. 17(3): 1940007:1-1940007:11 (2019) - 2018
- [j14]Takuya Mori, Hayliang Ngouv, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher:
ncRNA-disease association prediction based on sequence information and tripartite network. BMC Syst. Biol. 12(1): 41-51 (2018) - [j13]Yu Bao, Morihiro Hayashida, Pengyu Liu, Masayuki Ishitsuka, Jose C. Nacher, Tatsuya Akutsu:
Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets. J. Comput. Biol. 25(10): 1071-1090 (2018) - 2017
- [j12]Jose C. Nacher, Tomoshiro Ochiai:
Analytical solution for the size of the minimum dominating set in complex networks. Int. J. Model. Simul. Sci. Comput. 8(1): 1750005:1-1750005:16 (2017) - 2016
- [j11]Tomoshiro Ochiai, Jose C. Nacher:
Predicting link directionality in gene regulation from gene expression profiles using volatility-constrained correlation. Biosyst. 145: 9-18 (2016) - 2014
- [j10]Jose C. Nacher, Tatsuya Akutsu:
Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets. J. Complex Networks 2(4): 394-412 (2014) - 2013
- [j9]Jose C. Nacher:
Community structure of non-coding RNA interaction network. J. Integr. Bioinform. 10(2) (2013) - 2012
- [j8]Jose C. Nacher, Vladimir B. Ryabov:
Nonlinear response of gene expression to chemical perturbations: A noise-detector model and its predictions. Biosyst. 107(1): 9-17 (2012) - [j7]Yang Zhao, Morihiro Hayashida, Jose C. Nacher, Hiroshi Nagamochi, Tatsuya Akutsu:
Protein complex prediction via improved verification methods using constrained domain-domain matching. Int. J. Bioinform. Res. Appl. 8(3/4): 210-227 (2012) - 2010
- [j6]Jose C. Nacher, N. Araki:
Structural characterization and modeling of ncRNA-protein interactions. Biosyst. 101(1): 10-19 (2010) - [j5]Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu:
The role of internal duplication in the evolution of multi-domain proteins. Biosyst. 101(2): 127-135 (2010) - 2009
- [j4]Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu:
Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs. Biosyst. 95(2): 155-159 (2009) - 2008
- [j3]Jose C. Nacher, Tomoshiro Ochiai:
Transcription and noise in negative feedback loops. Biosyst. 91(1): 76-82 (2008) - 2007
- [j2]Kazuhiro Takemoto, Jose C. Nacher, Tatsuya Akutsu:
Correlation between structure and temperature in prokaryotic metabolic networks. BMC Bioinform. 8 (2007) - 2004
- [j1]Jose C. Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu:
Clustering under the line graph transformation: application to reaction network. BMC Bioinform. 5: 207 (2004)
Conference and Workshop Papers
- 2020
- [c6]Morihiro Hayashida, Hitoshi Koyano, Jose C. Nacher:
Measuring the Similarity of Proteomes using Grammar-based Compression via Domain Combinations. BIOINFORMATICS 2020: 117-122 - 2019
- [c5]Morihiro Hayashida, Jose C. Nacher, Hitoshi Koyano:
Artificial Neural Network Approach to Prediction of Protein-RNA Residue-base Contacts. BIOINFORMATICS 2019: 163-167 - 2018
- [c4]Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher:
Convolutional Neural Network Approach to Lung Cancer Classification Integrating Protein Interaction Network and Gene Expression Profiles. BIBE 2018: 151-154 - 2013
- [c3]Jose C. Nacher, Tatsuya Akutsu:
Analysis on critical nodes in controlling complex networks using dominating sets. SITIS 2013: 649-654 - 2009
- [c2]Jose C. Nacher, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu:
A Bipartite Graph Based Model of Protein Domain Networks. Complex (1) 2009: 525-535 - 2006
- [c1]Jose C. Nacher, Jean-Marc Schwartz, Minoru Kanehisa, Tatsuya Akutsu:
Identification of metabolic units induced by environmental signals. ISMB (Supplement of Bioinformatics) 2006: 375-383
Parts in Books or Collections
- 2007
- [p1]Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu:
Topological aspects of protein networks. Emergent Intelligence of Networked Agents 2007: 147-158
Coauthor Index
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