Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks. - Naoki Nariai; SunYong Kim; Seiya Imoto; Satoru Miyano (Pacific Symposium on Biocomputing, 2004)

Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. - Naoki Nariai; Yoshinori Tamada; Seiya Imoto; Satoru Miyano (ECCB/JBI, 2005)

Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks. - Osamu Hirose; Naoki Nariai; Yoshinori Tamada; Hideo Bannai; Seiya Imoto; Satoru Miyano (ICCSA (3), 2005)

Combining Hierarchical Inference in Ontologies with Heterogeneous Data Sources Improves Gene Function Prediction. - Xiaoyu Jiang; Naoki Nariai; Martin Steffen; Simon Kasif; David Gold; Eric D. Kolaczyk (BIBM, 2008)

Integration of relational and hierarchical network information for protein function prediction. - Xiaoyu Jiang; Naoki Nariai; Martin Steffen; Simon Kasif; Eric D. Kolaczyk (BMC Bioinform., 2008)

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)

Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data. - William W. Greenwald; He Li; Erin N. Smith; Paola Benaglio; Naoki Nariai; Kelly A. Frazer (BMC Bioinform., 2017)

A crowdsourced set of curated structural variants for the human genome. - Lesley M. Chapman; Noah Spies; Patrick Pai; Chun Shen Lim; Andrew Carroll; Giuseppe Narzisi; Christopher M. Watson; Christos Proukakis; Wayne E. Clarke; Naoki Nariai; Eric T. Dawson; Garan Jones; et al. (PLoS Comput. Biol., 2020)