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)

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)

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)

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