Recursive regularization for inferring gene networks from time-course gene expression profiles. - Teppei Shimamura; Seiya Imoto; Rui Yamaguchi; André Fujita; Masao Nagasaki; Satoru Miyano (BMC Syst. Biol., 2009)

Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. - Shuichi Kawano; Teppei Shimamura; Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Ryo Yoshida; Cristin G. Print; Satoru Miyano (BIBM, 2010)

Network profiling analysis for generating modulator-dependent gene networks. - Teppei Shimamura; Seiya Imoto; Atsushi Niida; Masao Nagasaki; Rui Yamaguchi; Satoru Miyano (BIBM Workshops, 2010)

Discovery of Exogenous Variables in Data with More Variables Than Observations. - Yasuhiro Sogawa; Shohei Shimizu; Aapo Hyvärinen; Takashi Washio; Teppei Shimamura; Seiya Imoto (ICANN (1), 2010)

Model-free unsupervised gene set screening based on information enrichment in expression profiles. - Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; André Fujita; Teppei Shimamura; Satoru Miyano (Bioinform., 2010)

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. - Teppei Shimamura; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Satoru Miyano (Bioinform., 2010)

Estimating exogenous variables in data with more variables than observations. - Yasuhiro Sogawa; Shohei Shimizu; Teppei Shimamura; Aapo Hyvärinen; Takashi Washio; Seiya Imoto (Neural Networks, 2011)

Inferring Contagion in Regulatory Networks. - André Fujita; João Ricardo Sato; Marcos Angelo Almeida Demasi; Rui Yamaguchi; Teppei Shimamura; Carlos Eduardo Ferreira; Mari Cleide Sogayar; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Statistical model-based testing to evaluate the recurrence of genomic aberrations. - Atsushi Niida; Seiya Imoto; Teppei Shimamura; Satoru Miyano (Bioinform., 2012)

Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods. - Shuichi Kawano; Teppei Shimamura; Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Ryo Yoshida; Cristin G. Print; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

High performance computing of a fusion gene detection pipeline on the K computer. - Satoshi Ito; Yuichi Shiraishi; Teppei Shimamura; Kenichi Chiba; Satoru Miyano (BIBM, 2015)

Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. - Takanori Hasegawa; Tomoya Mori; Rui Yamaguchi; Teppei Shimamura; Satoru Miyano; Seiya Imoto; Tatsuya Akutsu (BMC Syst. Biol., 2015)

D3M: detection of differential distributions of methylation levels. - Yusuke Matsui; Masahiro Mizuta; Satoshi Ito; Satoru Miyano; Teppei Shimamura (Bioinform., 2016)

A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models. - Takanori Hasegawa; Atsushi Niida; Tomoya Mori; Teppei Shimamura; Rui Yamaguchi; Satoru Miyano; Tatsuya Akutsu; Seiya Imoto (Comput. Stat. Data Anal., 2016)

Tumor Subclonal Progression Model for Cancer Hallmark Acquisition. - Yusuke Matsui; Satoru Miyano; Teppei Shimamura (CIBB, 2017)

GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics. - Teppei Shimamura; Yusuke Matsui; Taisuke Kajino; Satoshi Ito; Takashi Takahashi; Satoru Miyano (CIBB, 2017)

phyC: Clustering cancer evolutionary trees. - Yusuke Matsui; Atsushi Niida; Ryutaro Uchi; Koshi Mimori; Satoru Miyano; Teppei Shimamura (PLoS Comput. Biol., 2017)

A latent allocation model for the analysis of microbial composition and disease. - Ko Abe; Masaaki Hirayama; Kinji Ohno; Teppei Shimamura (BMC Bioinform., 2018)

Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks. - Heewon Park; Teppei Shimamura; Seiya Imoto; Satoru Miyano (J. Comput. Biol., 2018)

A network of networks approach for modeling interconnected brain tissue-specific networks. - Hideko Kawakubo; Yusuke Matsui; Itaru Kushima; Norio Ozaki; Teppei Shimamura (Bioinform., 2019)

Model-based cell clustering and population tracking for time-series flow cytometry data. - Kodai Minoura; Ko Abe; Yuka Maeda; Hiroyoshi Nishikawa; Teppei Shimamura (BMC Bioinform., 2019)

ENIGMA: an enterotype-like unigram mixture model for microbial association analysis. - Ko Abe; Masaaki Hirayama; Kinji Ohno; Teppei Shimamura (BMC Genom., 2019)

Model-based clustering for flow and mass cytometry data with clinical information. - Ko Abe; Kodai Minoura; Yuka Maeda; Hiroyoshi Nishikawa; Teppei Shimamura (BMC Bioinform., 2020)

CYBERTRACK2.0: zero-inflated model-based cell clustering and population tracking method for longitudinal mass cytometry data. - Kodai Minoura; Ko Abe; Yuka Maeda; Hiroyoshi Nishikawa; Teppei Shimamura (Bioinform., 2021)

UNMF: a unified nonnegative matrix factorization for multi-dimensional omics data. - Ko Abe; Teppei Shimamura (Briefings Bioinform., 2023)