Jose C. Nacher

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 9

Top Topics

Protein Interaction

Gene Expression Profiles

Solvent Accessibility

Cancer Classification

Top Venues

J. Complex Networks

Int. J. Model. Simul. Sci. Comput.

Publications

Tomoshiro Ochiai, Jose C. Nacher
Determining cellular lineage directed networks in hematopoiesis using single-cell transcriptomic data and volatility-constrained correlation. Biosyst. 242 (2024)
Morihiro Hayashida, Hitoshi Koyano, Jose C. Nacher
Measuring the Similarity of Proteomes using Grammar-based Compression via Domain Combinations. BIOINFORMATICS (2020)
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) (2019)
Morihiro Hayashida, Jose C. Nacher, Hitoshi Koyano
Artificial Neural Network Approach to Prediction of Protein-RNA Residue-base Contacts. BIOINFORMATICS (2019)
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)
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) (2018)
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) (2018)
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) (2017)
Tomoshiro Ochiai, Jose C. Nacher
Predicting link directionality in gene regulation from gene expression profiles using volatility-constrained correlation. Biosyst. 145 (2016)
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) (2014)
Jose C. Nacher, Tatsuya Akutsu
Analysis on critical nodes in controlling complex networks using dominating sets. SITIS (2013)
Jose C. Nacher
Community structure of non-coding RNA interaction network. J. Integr. Bioinform. 10 (2) (2013)
Jose C. Nacher, Vladimir B. Ryabov
Nonlinear response of gene expression to chemical perturbations: A noise-detector model and its predictions. Biosyst. 107 (1) (2012)
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) (2012)
Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu
The role of internal duplication in the evolution of multi-domain proteins. Biosyst. 101 (2) (2010)
Jose C. Nacher, N. Araki
Structural characterization and modeling of ncRNA-protein interactions. Biosyst. 101 (1) (2010)
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) (2009)
Jose C. Nacher, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu
A Bipartite Graph Based Model of Protein Domain Networks. Complex (1) (2009)
Jose C. Nacher, Tomoshiro Ochiai
Transcription and noise in negative feedback loops. Biosyst. 91 (1) (2008)
Kazuhiro Takemoto, Jose C. Nacher, Tatsuya Akutsu
Correlation between structure and temperature in prokaryotic metabolic networks. BMC Bioinform. 8 (2007)
Jose C. Nacher, Jean-Marc Schwartz, Minoru Kanehisa, Tatsuya Akutsu
Identification of metabolic units induced by environmental signals. ISMB (Supplement of Bioinformatics) (2006)
Jose C. Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu
Clustering under the line graph transformation: application to reaction network. BMC Bioinform. 5 (2004)