A weight estimation method using LDA for multi-band speech recognition. - Koji Iwano; Kaname Kojima; Sadaoki Furui (INTERSPEECH, 2006)

An efficient grid layout algorithm for biological networks utilizing various biological attributes. - Kaname Kojima; Masao Nagasaki; Euna Jeong; Mitsuru Kato; Satoru Miyano (BMC Bioinform., 2007)

Fast grid layout algorithm for biological networks with sweep calculation. - Kaname Kojima; Masao Nagasaki; Satoru Miyano (Bioinform., 2008)

BFL: a node and edge betweenness based fast layout algorithm for large scale networks. - Tatsunori B. Hashimoto; Masao Nagasaki; Kaname Kojima; Satoru Miyano (BMC Bioinform., 2009)

Identifying Hidden Confounders in Gene Networks by Bayesian Networks. - Tomoya Higashigaki; Kaname Kojima; Rui Yamaguchi; Masato Inoue; Seiya Imoto; Satoru Miyano (BIBE, 2010)

Searching Optimal Bayesian Network Structure on Constraint Search Space: Super-Structure Approach. - Seiya Imoto; Kaname Kojima; Eric Perrier; Yoshinori Tamada; Satoru Miyano (JSAI-isAI Workshops, 2010)

A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets. - André Fujita; Kaname Kojima; Alexandre Galvão Patriota; João Ricardo Sato; Patricia Severino; Satoru Miyano (Bioinform., 2010)

An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. - Kaname Kojima; Masao Nagasaki; Satoru Miyano (BMC Bioinform., 2010)

Cell Illustrator 4.0: A Computational Platform for Systems Biology. - Masao Nagasaki; Ayumu Saito; Euna Jeong; Chen Li 007; Kaname Kojima; Emi Ikeda; Satoru Miyano (Silico Biol., 2010)

Identification of Granger Causality between Gene Sets. - André Fujita; João Ricardo Sato; Kaname Kojima; Luciana Rodrigues Gomes; Masao Nagasaki; Mari Cleide Sogayar; Satoru Miyano (J. Bioinform. Comput. Biol., 2010)

Optimal Search on Clustered Structural Constraint for Learning Bayesian Network Structure. - Kaname Kojima; Eric Perrier; Seiya Imoto; Satoru Miyano (J. Mach. Learn. Res., 2010)

Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. - Kaname Kojima; Seiya Imoto; Rui Yamaguchi; André Fujita; Mai Yamauchi; Noriko Gotoh; Satoru Miyano (BMC Genom., 2012)

Functional clustering of time series gene expression data by Granger causality. - André Fujita; Patricia Severino; Kaname Kojima; João Ricardo Sato; Alexandre Galvão Patriota; Satoru Miyano (BMC Syst. Biol., 2012)

A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads. - Kaname Kojima; Naoki Nariai; Takahiro Mimori; Mamoru Takahashi; Yumi Yamaguchi-Kabata; Yukuto Sato; Masao Nagasaki (Bioinform., 2013)

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference. - Naoki Nariai; Osamu Hirose; Kaname Kojima; Masao Nagasaki (Bioinform., 2013)

iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. - Takahiro Mimori; Naoki Nariai; Kaname Kojima; Mamoru Takahashi; Akira Ono; Yukuto Sato; Yumi Yamaguchi-Kabata; Masao Nagasaki (BMC Syst. Biol., 2013)

HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads. - Kaname Kojima; Naoki Nariai; Takahiro Mimori; Yumi Yamaguchi-Kabata; Yukuto Sato; Yosuke Kawai; Masao Nagasaki (AlCoB, 2014)

SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints. - Tomohiko Ohtsuki; Naoki Nariai; Kaname Kojima; Takahiro Mimori; Yukuto Sato; Yosuke Kawai; Yumi Yamaguchi-Kabata; Tetsuo Shibuya; Masao Nagasaki (AlCoB, 2014)

Estimating copy numbers of alleles from population-scale high-throughput sequencing data. - Takahiro Mimori; Naoki Nariai; Kaname Kojima; Yukuto Sato; Yosuke Kawai; Yumi Yamaguchi-Kabata; Masao Nagasaki (BMC Bioinform., 2015)

HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data. - Naoki Nariai; Kaname Kojima; Sakae Saito; Takahiro Mimori; Yukuto Sato; Yosuke Kawai; Yumi Yamaguchi-Kabata; Jun Yasuda; Masao Nagasaki (BMC Genom., 2015)

A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes. - Naoki Nariai; Kaname Kojima; Takahiro Mimori; Yosuke Kawai; Masao Nagasaki (BMC Genom., 2016)

Time-Series Filtering for Replicated Observations via a Kernel Approximate Bayesian Computation. - Takanori Hasegawa; Kaname Kojima; Yosuke Kawai; Masao Nagasaki (IEEE Trans. Signal Process., 2018)

A genotype imputation method for de-identified haplotype reference information by using recurrent neural network. - Kaname Kojima; Shu Tadaka; Fumiki Katsuoka; Gen Tamiya; Masayuki Yamamoto; Kengo Kinoshita (PLoS Comput. Biol., 2020)