Clustering under the line graph transformation: application to reaction network. - Jose C. Nacher; Nobuhisa Ueda; Takuji Yamada; Minoru Kanehisa; Tatsuya Akutsu (BMC Bioinform., 2004)

Identification of metabolic units induced by environmental signals. - Jose C. Nacher; Jean-Marc Schwartz; Minoru Kanehisa; Tatsuya Akutsu (ISMB (Supplement of Bioinformatics), 2006)

Correlation between structure and temperature in prokaryotic metabolic networks. - Kazuhiro Takemoto; Jose C. Nacher; Tatsuya Akutsu (BMC Bioinform., 2007)

Topological aspects of protein networks. - Jose C. Nacher; Morihiro Hayashida; Tatsuya Akutsu (Emergent Intelligence of Networked Agents, 2007)

Transcription and noise in negative feedback loops. - Jose C. Nacher; Tomoshiro Ochiai (Biosyst., 2008)

A Bipartite Graph Based Model of Protein Domain Networks. - Jose C. Nacher; Tomoshiro Ochiai; Morihiro Hayashida; Tatsuya Akutsu (Complex (1), 2009)

Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs. - Jose C. Nacher; Morihiro Hayashida; Tatsuya Akutsu (Biosyst., 2009)

Structural characterization and modeling of ncRNA-protein interactions. - Jose C. Nacher; N. Araki (Biosyst., 2010)

The role of internal duplication in the evolution of multi-domain proteins. - Jose C. Nacher; Morihiro Hayashida; Tatsuya Akutsu (Biosyst., 2010)

Nonlinear response of gene expression to chemical perturbations: A noise-detector model and its predictions. - Jose C. Nacher; Vladimir B. Ryabov (Biosyst., 2012)

Protein complex prediction via improved verification methods using constrained domain-domain matching. - Yang Zhao 018; Morihiro Hayashida; Jose C. Nacher; Hiroshi Nagamochi; Tatsuya Akutsu (Int. J. Bioinform. Res. Appl., 2012)

Analysis on critical nodes in controlling complex networks using dominating sets. - Jose C. Nacher; Tatsuya Akutsu (SITIS, 2013)

Community structure of non-coding RNA interaction network. - Jose C. Nacher (J. Integr. Bioinform., 2013)

Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets. - Jose C. Nacher; Tatsuya Akutsu (J. Complex Networks, 2014)

Predicting link directionality in gene regulation from gene expression profiles using volatility-constrained correlation. - Tomoshiro Ochiai; Jose C. Nacher (Biosyst., 2016)

Analytical solution for the size of the minimum dominating set in complex networks. - Jose C. Nacher; Tomoshiro Ochiai (Int. J. Model. Simul. Sci. Comput., 2017)

ncRNA-disease association prediction based on sequence information and tripartite network. - Takuya Mori; Hayliang Ngouv; Morihiro Hayashida; Tatsuya Akutsu; Jose C. Nacher (BMC Syst. Biol., 2018)

Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets. - Yu Bao; Morihiro Hayashida; Pengyu Liu 002; Masayuki Ishitsuka; Jose C. Nacher; Tatsuya Akutsu (J. Comput. Biol., 2018)

Artificial Neural Network Approach to Prediction of Protein-RNA Residue-base Contacts. - Morihiro Hayashida; Jose C. Nacher; Hitoshi Koyano (BIOINFORMATICS, 2019)

Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles. - Teppei Matsubara; Tomoshiro Ochiai; Morihiro Hayashida; Tatsuya Akutsu; Jose C. Nacher (J. Bioinform. Comput. Biol., 2019)

Measuring the Similarity of Proteomes using Grammar-based Compression via Domain Combinations. - Morihiro Hayashida; Hitoshi Koyano; Jose C. Nacher (BIOINFORMATICS, 2020)

Determining cellular lineage directed networks in hematopoiesis using single-cell transcriptomic data and volatility-constrained correlation. - Tomoshiro Ochiai; Jose C. Nacher (Biosyst., 2024)