Publications

1) Peer-reviewed papers published on international journal

2017

– Ueta M, Sawai H, Shingaki R, Kawai Y, Sotozono C, Kojima K, Yoon KC, Kim MK, Seo KY, Joo CK, Nagasaki M, Kinoshita S and Tokunaga K. Genome-wide association study using the ethnicity-specific Japonica array: identification of new susceptibility loci for cold medicine-related Stevens–Johnson syndrome with severe ocular complications J Hum Genet Journal of Human Genetics, doi:10.1038/jhg.2016.160 2017/01/19 28100913 2017

– Matsuura K, Sawai H, Ikeo K, Ogawa S, Iio E, Isogawa M, Shimada N, Komori A, Toyoda H, Kumada T, Namisaki T, Yoshiji H, Sakamoto N, Nakagawa M, Asahina Y, Kurosaki M, Izumi N, Enomoto N, Kusakabe A, Kajiwara E, Itoh Y, Ide T, Tamori A, Matsubara M, Kawada N, Shirabe K, Tomita E, Honda M, Kaneko S, Nishina S, Suetsugu A, Hiasa Y, Watanabe H, Genda T, Sakaida I, Nishiguchi S, Takaguchi K, Tanaka E, Sugihara J, Shimada M, Kondo Y, Kawai Y, Kojima K, Nagasaki M, Tokunaga K, Tanaka Y Genome-wide Association Study Identifies TLL1 Variant Associated With Development of Hepatocellular Carcinoma After Eradication of Hepatitis C Virus Infection Gastroenterology Gastroenterology, doi:10.1053/j.gastro.2017.01.041 2017/02/03 28163062 2017

– Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang T, Farr KM, Fujita T, Hiwatashi Y, Hoshi Y, Imai T, Kasahara M, Librado P, Mao L, Mori H, Nishiyama T, Nozawa M, Pálfalvi G, Pollard ST, Rozas J, Sánchez-Gracia A, Sankoff D, Shibata TF, Shigenobu S, Sumikawa N, Uzawa T, Xie M, Zheng C, Pollock DD, Albert VA, Li S, and Hasebe M., The pitcher plant Cephalotus genome reveals genetic changes associated with carnivory, Nature Ecology & Evolution 1:0059, doi:10.1038/s41559-016-0059 (2017)

2016

– Kojima K, Kawai Y, Nariai N, Mimori T, Hasegawa T, Nagasaki M, Short tandem repeat number estimation from paired-end reads for multiple individuals by considering coalescent tree. BMC Genomics. 31;17 Suppl 5:494. doi: 10.1186/s12864-016-2821-0 2016/08 27586631 (Aug/2016)

– Takanori Hasegawa, Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori and Masao Nagasaki, AP-SKAT: highly-efficient genome-wide rare variant association test, BMC Genomics 2016 17:745 doi: 10.1186/s12864-016-3094-3 (21/Sep/2016)

– Yonghu Sun, Astrid Irwanto, Licht Toyo-oka, Myunghee Hong, Hong Liu, Anand Kumar Andiappan, Hyunchul Choi, Yuki Hitomi, Gongqi Yu, Yongxiang Yu, Fangfang Bao, Chuan Wang, Xian Fu, Zhenhua Yue, Honglei Wang, Huimin Zhang, Minae Kawashima, Kaname Kojima, Masao Nagasaki, Minoru Nakamura, Suk-Kyun Yang, Byong Duk Ye, Yosua Denise, Olaf Rotzschke, Kyuyoung Song, Katsushi Tokunaga, Furen Zhang & Jianjun Liu, Fine-mapping analysis revealed complex pleiotropic effect and tissue-specific regulatory mechanism of TNFSF15 in primary biliary cholangitis, Crohn’s disease and leprosy, Sci Rep. 2016 Jul, 6:31429

– Kazuko Ueno, Toshiro Iwagawa, Hiroshi Kuribayashi, Yukihiro Baba, Hiromitsu Nakauchi, Akira Murakami, Masao Nagasaki, Yutaka Suzuki & Sumiko Watanabe, Transition of differential histone H3 methylation in photoreceptors and other retinal cells during retinal differentiation, Scientific Reports 6, Article number: 29264 (2016) doi:10.1038/srep29264 (05/Jul/2016)

– Junya Yamagishi, Yukuto Sato, Natsuko Shinozaki, Bin Ye, Akito Tsuboi, Masao Nagasaki and Riu Yamashita, Comparison of boiling and robotics automation method in DNA extraction for metagenomic sequencing of human oral microbes, PLoS One 11: e0154389 (2016) doi:10.1371/journal.pone.0154389 (22/Apr/2016)

– Nagasaki M, Kawai Y, Kojima K, Mimori T, Yamaugchi-Kabata Y., Construction of 1070 Whole-genome Japanese Reference Panel and Bioinformatics, Journal of Japanese Biochemical Society, 88(1): 15-24 (2016) doi:10.14952/SEIKAGAKU.2016.880015 (25/Feb/2016)

– Xiaoqing Pan, Naoki Nariai, Noriko Fukuhara, Sakae Saito, Yukuto Sato, Fumiki Katsuoka, Kaname Kojima, Yoko Kuroki, Inaho Danjoh, Rumiko Saito, Shin Hasegawa, Yoko Okitsu, Aiko Kondo, Yasushi Onishi, Fuji Nahami, Hideyasu Kiyomoto, Atsushi Hozawa, Nobuo Fuse, Masao Nagasaki, Ritsko Shimizu, Jun Yasuda, Hideo Harigae and Masayuki Yamamoto, Monitoring of minimal residual disease in early T-cell precursor acute lymphoblastic leukaemia by next-generation sequencing, British Journal of Hematology, dos: 10.1111/bjh.13948 (29/Jan/2016)

– Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yosuke Kawai and Masao Nagasaki, A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes, BMC Genomics 17(Suppl 1):2 (2016)

2015

– Yumi Yamaguchi-Kabata, Naoki Nariai, Yosuke Kawai, Yukuto Sato, Kaname Kojima, Minoru Tateno, Fumiki Katsuoka, Jun Yasuda, Masayuki Yamamoto, and Masao Nagasaki, iJGVD: an integrative Japanese genome variation database based on whole-genome sequencing, Human Genome Variation 2, Article number: 15050 doi:10.1038/hgv.2015.50 (26/Nov/2015)

– Masao Nagasaki, Jun Yasuda, Fumiki Katsuoka, Naoki Nariai, Kaname Kojima, Yosuke Kawai, Yumi Yamaguchi-Kabata, Junji Yokozawa, Inaho Danjoh, Sakae Saito, Yukuto Sato, Takahiro Mimori, Kaoru Tsuda, Rumiko Saito, Xiaoqing Pan, Satoshi Nishikawa, Shin Ito, Yoko Kuroki, Osamu Tanabe, Nobuo Fuse, Shinichi Kuriyama, Hideyasu Kiyomoto, Atsushi Hozawa, Naoko Minegishi, James Douglas Engel, Kengo Kinoshita, Shigeo Kure, Nobuo Yaegashi, ToMMo Japanese Reference Panel Project & Masayuki Yamamoto, Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals, Nature Communications, Volume:6, Article number: 8018 DOI:doi:10.1038/ncomms9018 (21/Aug/2015)

– Takahiro Mori, Makiko Sumii, Fumiyoshi Fujishima, Kazuko Ueno, Mitsuru Emi, Masao Nagasaki, Chikashi Ishioka and Natsuko Chiba, Somatic alteration and depleted nuclear expression of BAP1 in human esophageal squamous cell carcinoma, Cancer Science, 106(9), doi:10.1111/cas.12722(10/Aug/2015)

– Yosuke Kawai, Takahiro Mimori, Kaname Kojima, Naoki Nariai, Inaho Danjoh, Rumiko Saito, Jun Yasuda, Masayuki Yamamoto, and Masao Nagasaki, Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals, Journal of Human Genetics 2015; 60: 581–587. (2015)

– Yukuto Sato, Junya Yamagishi, Riu Yamashita, Natsuko Shinozaki, Bin Ye, Takuji Yamada, Masayuki Yamamoto, Masao Nagasaki and Akito Tsuboi, Inter-individual differences in the oral bacteriome are greater than intra-day fluctuations in individuals, PLOS ONE,  10(6): e0131607 (2015)

– Takahiro Mimori, Naoki Nariai, Kaname Kojima, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata and Masao Nagasaki, Estimating copy numbers of alleles from population-scale high-throughput sequencing data, BMC Bioinformatics, 16(Suppl 1):S4 (2015)

– Naoki Nariai, Kaname Kojima, Sakae Saito, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Jun Yasuda, Masao Nagasaki, HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data, BMC Genomics, 16(Suppl 2):S7 (2015)

2014

– Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata and Masao Nagasaki, TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads, BMC Genomics, 15(Suppl 10):S5 (2014)

– Takanori Hasega, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano and Seiya Imoto, Inference of Gene Regulatory Networks Incorporating Multi-Source Biological Knowledge via a State Space Model with L1 Regularization, PLoS ONE, 9(8): e105942 (2014) doi: 0.1371/journal.pone.0105942 (27/Aug/2014)

– Yukuto Sato, Kaname Kojima, Naoki Nariai, Yumi Yamaguchi-Kabata, Yosuke Kawai, Mamoru Takahashi, Takahiro Mimori, Masao Nagasaki.
SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing, BMC Genomics, 15:664 (2014), doi:10.1186/1471-2164-15-664 (4/Aug/2014)

– Motoike IN, Matsumoto M, Danjoh I, Katsuoka F, Kojima K, Nariai N, Sato Y, Yamaguchi-Kabata Y, Ito S, Kudo H, Nishijima I, Nishikawa S, Pan X, Saito R, Saito S, Saito T, Shirota M, Tsuda K, Yokozawa J, Igarashi K, Minegishi N, Tanabe O, Fuse N, Nagasaki M, Kinoshita K, Yasuda J, Yamamoto M,
Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population,
BMC Genomics, 15:673, (2014) doi:10.1186/1471-2164-15-673 (1/Aug/2014)

– Kaname Kojima, Naoki Nariai, Takahiro Mimori, Yumi Yamaguchi-Kabata, Yukuto Sato, Yosuke Kawai and Masao Nagasaki,
HapMonster: a Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-informative Reads,
Lecture Notes in Bioinformatics, 8542, 107-118 (2014) (3/Jul/2014)

– Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Tetsuo Shibuya and Masao Nagasaki, SVEM: a Structural Variant Estimation Method using Multi-Mapped Reads on Breakpoints, Lecture Notes in Bioinformatics, 8542, 208-219. (2014) (2/Jul/2014)

– Takanori Hasega, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto and Satoru Miyano, An efficient method of exploring simulation models by assimilating literature and biological observational data, Biosystems, 121, 54-66 (2014), doi: 10.1016/j.biosystems.2014.06.001. (5/Jul/2014)

– Chen Li, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya and Satoru Miyano, CSML2SBML: A novel tool fro converting quantitative biological pathway models from CSML to SBML, Biosystems, 121:22-28 (2014) doi: 10.1016/j.biosystems.2014.05.004. (27/May/2014)

– Tohru Fujiwara, Noriko Fukuhara, Ryo Funayama, Naoki Nariai, Mayumi Kamata, Takeshi Nagashima, Kaname Kojima, Yasushi Onishi, Yoji Sasahara, Kenichi Ishizawa, Masao Nagasaki, Keiko Nakayama and Hideo Harigae, Identification of acquired mutations by whole-genome sequencing in GATA-2 deficiency evolving into myelodysplasia and acute leukemia, Annals of Hematology, 93(9),1515-1522 (2014) doi: 10.1007/s00277-014-2090-4 (30/Apr/2014)

 

2013

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

– Kaname Kojima, Naoki Nariai, Takahiro Mimori, Mamoru Takahashi, Yumi Yamaguchi-Kabata, Yukuto Sato, and Masao Nagasaki,
A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads,
Bioinformatics. doi:10.1093/bioinformatics/btt503 (2013)

– Siti Razila Abdul Razak, Kazuko Ueno, Naoya Takayama, Naoki Nariai, Masao Nagasaki, Rika Saito, Hideto Koso, Chen-Yi Lai, Miyako Murakami, Koichiro Tsuji, Tatsuo Michiue, Hiromitsu Nakauchi, Makoto Otsu and Sumiko Watanabe
Profiling of MicroRNA in Human and Mouse ES and iPS Cells Reveals Overlapping but Distinct MicroRNA Expression Patterns,
PLoS ONE. 8(9): e73532. doi:10.1371/journal.pone.0073532 (2013)

– Naoki Nariai, Osamu Hirose, Kaname Kojima and Masao Nagasaki,
TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference,
Bioinformatics. 29 (18):2292-2299 (2013)

– Takafumi Hiramoto, Yasuhiro Ebihara, Yoko Mizoguchi, Kazuhiro Nakamura, Kiyoshi Yamaguchi, Kazuko Ueno, Naoki Nariai, Shinji Mochizuki, Shohei Yamamoto, Masao Nagasaki, Yoichi Furukawa, Kenzaburo Tani, Hiromitsu Nakauchi, Masao Kobayashi and Kohichiro Tsuji,
Wnt3a stimulates maturation of impaired neutrophils developed from severe congenital neutropenia patient-derived pluripotent stem cells,
Proc Natl Acad Sci U S A. doi:10.1073/pnas.1217039110 (2013)

2012

-Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki and Satoru Miyano, ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs, BMC Bioinformatics, 13:279   (2012)

– Masao Nagasaki*, André Fujita, Yayoi Sekiya, Ayumu Saito, Emi Ikeda, Chen Li and Satoru Miyano, XiP: a computational environment to create, extend, and share workflows, Bioinformatics, 28:21 (2012)

– Koso H, Takeda H, Yew CC, Ward JM, Nariai N, Ueno K, Nagasaki M, Watanabe S, Rust AG, Adams DJ, Copeland NG, Jenkins NA, Transposon mutagenesis identifies genes that transform neural stem cells into glioma-initiating cells, Proc Natl Acad Sci U S A, doi:10.1073/pnas.1217039110 (2012)

– Yamamoto M, Yamaguchi R, Munakata K, Takashima K, Nishiyama M, Hioki K, Ohnishi Y, Nagasaki M, Imoto S, Miyano S, Ishige A, Watanabe K, A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development, BMC Genomics. 13:335, (2012)

– Yamauchi M, Yamaguchi R, Nakata A, Kohno T, Nagasaki M, Shimamura T, Imoto S, Saito A, Ueno K, Hatanaka Y, Yoshida R, Higuchi T, Nomura M, Beer DG, Yokota J, Miyano S, Gotoh N, Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma, PLoS One. 7:9, (2012)

– Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, Aoki M, Hosono N, Kubo M, Miya F, Arai Y, Takahashi H, Shirakihara T, Nagasaki M, Shibuya T, Nakano K, Watanabe-Makino K, Tanaka H, Nakamura H, Kusuda J, Ojima H, Shimada K, Okusaka T, Ueno M, Shigekawa Y, Kawakami Y, Arihiro K, Ohdan H, Gotoh K, Ishikawa O, Ariizumi S, Yamamoto M, Yamada T, Chayama K, Kosuge T, Yamaue H, Kamatani N, Miyano S, Nakagama H, Nakamura Y, Tsunoda T, Shibata T, Nakagawa H, Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators, Nat Genet. 27;44(7), (2012)

– Kawano S, Shimamura T, Niida A, Imoto S, Yamaguchi R, Nagsaki M, Yoshida R, Print C, Miyano S, Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods, Transactions on Computational Biology and Bioinformatics, 9(4): 966-972 (2012)

– Fujimori S, Hirai N, Masuoka K, Oshikubo T, Yamashita T, Washio T, Saito A, Nagasaki M, Miyano S, Miyamoto-Sato E, IRView: a database and viewer for protein interacting regions, Bioinformatics, 28:10 (2012)

2011

– Shin Suzuki, Tomohiro Yasuda, Yuichi Shiraishi, Satoru Miyano, Masao Nagasaki, ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information, BMC Bioinformatics 12(Suppl 14):S7 (2011)
– Yoshida K, Sanada M, Shiraishi Y, Nowak D, Nagata Y, Yamamoto R, Sato Y, Sato-Otsubo A, Kon A, Nagasaki M, Chalkidis G, Suzuki Y, Shiosaka M, Kawahata R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Ishiyama K, Mori H, Nolte F, Hofmann WK, Miyawaki S, Sugano S, Haferlach C, Koeffler HP, Shih LY, Haferlach T, Chiba S, Nakauchi H, Miyano S, Ogawa S. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 11:478(7367):64-69 (2011)
– Yamauchi M, Yoshino I, Yamaguchi R, Shimamura T, Nagasaki M, Imoto S, Niida A, Koizumi F, Kohno T, Yokota J, Miyano S, Gotoh N, N-cadherin expression is a potential survival mechanism of gefitinib-resistant lung cancer cells. Am J Cancer Res 1(7):823-833 (2011)
– Jeong E, Nagasaki M, Ikeda E, Sekiya Y, Saito A, Miyano S. Bioinformatics. CSO validator: improving manual curation workflow for biological pathways. 1:27(17):2471-2472 (2011)
– Hasegawa T, Yamaguchi R, Nagasaki M, Imoto S, Miyano S. Comprehensive pharmacogenomic pathway screening by data assimilation. Lecture Notes in Bioinformatics. 6674: 160-171 (2011)
– Shimamura T, Imoto S, Shimada Y, Hosono Y, Niida A, Nagasaki M,Yamaguchi R, Takahashi T, Miyano S. A Novel Network Profiling Analysis Reveals System Changes in Epithelial-Mesenchymal Transition. PLoS ONE 6(6): e20804. doi:10.1371/journal.pone.0020804 (2011)
– Nagasaki M, Saito A, Fujita A, Tremmel G, Ueno K, Ikeda E, Jeong E, Miyano S. Systems biology model repository for macrophage pathway simulation. Bioinformatics. 27(11),1591-1593 (2011)
– Li C, Nagasaki M, Hock Koh C, Miyano S. Online model checking approach based parameter estimation to a neuronal fate decision simulation model in C. elegans with hybrid functional Petri net with extension, Mol. Biosyst., DOI:10.1039/C0MB00253D (2011)
– Tamada Y, Yamaguchi R, Imoto S, Hirose O, Yoshida R, Nagasaki M, Miyano S, SiGN-SSM: open source parallel software for estimating gene networks with state space models. Bioinformatics. 2011 15;27(8):1172-3. (2011)
– Hock Koh C, Nagasaki M, Saito A, Li C, Wong L, Miyano S, MIRACH: Efficient Model Checker for Quantitative Biological Pathway Models, Bioinformatics (2011)
– Jeong E, Nagasaki M, Ueno K, Miyano S. Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinformatics, Feb 15;12 Suppl 1:S8 (2011)
– Chalkidis G, Nagasaki M, Miyano S. High performance hybrid functional Petri net simulations of biological pathway models on CUDA. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(6):1545-1556 (2011)
– Matsuno H, Nagasaki M, Miyano S. Hybrid Petri net based modeling for biological pathway simulation. Natural Computing. 10, 1099-1120 (2011)
– Tamada Y, Imoto S, Araki H, Nagasaki M, Print C, Charnock-Jones DS, Miyano S. Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(3), 683-697 (2011)

2010

– Do JH, Nagasaki M, Miyano S. The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. Biosystems. 100, 178-184 (2010)
– Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe G, Boroevich KA, Nagasaki M, Yamaguchi R, Shibuya T, Kubo M, Miyano S, Nakamura Y, Tsunoda T. Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nature Genetics. 42, 931-936 (2010)
– Fujita A, Nagasaki M, Imoto S, Saito A, Ikeda E, Shimamura T, Yamaguchi R, Hayashizaki Y, Miyano S. Comparison of gene expression profiles produced by CAGE, Illumina microarray and Real Time RT-PCR. Genome Informatics. 24, 56-68 (2010)
– Kaufmann K, Nagasaki M, Jauregui R. Modelling the molecular interactions in the flower developmental network of Arabidopsis thaliana. In Silico Biology. 10, 8 (2010)
– Kawano S, Shimamura T, Niida A, Imoto S, Yamaguchi R, Nagasaki M, Yoshida R, Print C, Miyano S. Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. Proc. IEEE 10th International Symposium on Bioinformatics & Bioengineering. (Peer-reviewed original paper, acceptance rate 17.2%), 253-258 (2010)
– Koh CH#, Nagasaki M#, Saito A, Wong L, Miyano S. DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics. 26 (14),1794-1796 (2010) (#Joint first authors)
– Kojima K, Imoto S, Nagasaki M, Miyano, S. Gene regulatory network clustering for graph layout based on microarray gene expression data. Genome Informatics. 24, 84-95 (2010)
– Kojima K, Nagasaki M#, Miyano S. An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinformatics. 11,335 (2010) (#Corresponding author)
– Li C*, Nagasaki M*#, Saito A, Miyano S. Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. BMC Systems Biology. 4,39 (2010) (*Equally contributed; #Corresponding author)
– Nagasaki M#, Saito A, Jeong E, Li C, Kojima K, Ikeda E, Miyano S. Cell Illustrator 4.0: A computational platform for systems biology. In Silico Biology. 10, 0002 (2010) (#Corresponding author)
– Niida A, Imoto S, Yamaguchi R, Nagasaki M, Miyano S. Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues. PLoS ONE. 5(6),e10910 (2010)
– Niida A, Imoto S, Yamaguchi R, Nagasaki M, Fujita A, Shimamura T, Miyano S. Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinformatics, 26(24): 3090-3097, (2010)
– Shimamura T, Imoto S, Yamaguchi R, Nagasaki M, Miyano S. Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics. 26 (8),1064-1072 (2010)
– Shimamura T, Imoto S, Nagasaki M, Yamauchi M, Yamaguchi R, Fujita A, Tamada Y, Gotoh N, Miyano S. Collocation-based sparse estimation for constructing dynamic gene networks. Genome Informatics. 24, 164-178 (2010)

2009

– Tasaki S, Nagasaki M, Kozuka-Hata H, Semba K, Gotoh N, Hattori S, Inoue J, Yamamoto T, Miyano S, Sugano S, Oyama M. Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling. PLoS ONE. 5(11), e13926 (2010)
– Araki H, Tamada Y, Imoto S, Dunmore B, Sanders D, Humphrey S, Nagasaki M, Doi A, Nakanishi Y, Yasuda K, Tomiyasu Y, Tashiro K, Print C, Charnock-Jones DS, Kuhara S, Miyano S. Analysis of PPARalpha-dependent and PPARalpha-independent transcript regulation following fenofibrate treatment of human endothelial cells. Angiogenesis. 12 (3), 221-229 (2009)
– Hashimoto TB*, Nagasaki M*#, Kojima K, Miyano S. BFL: a node and edge betweenness based fast layout algorithm for large scale networks. BMC Bioinformatics. 10,19 (2009) (*Equally contributed; #Corresponding author)
– Kojima K, Yamaguchi R, Imoto S, Yamauchi M, Nagasaki M, Yoshida R, Shimamura T, Ueno K, Higuchi T, Gotoh N, Miyano S. A state space representation of VAR models with sparse learning for dynamic gene networks. Genome Informatics. 22,56-68 (2009)
– Li C*, Nagasaki M*#, Ueno K, Miyano S. Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Systems Biology. 3,42 (2009) (*Equally contributed; #Corresponding author)
– Nakamura K, Yoshida R, Nagasaki M, Miyano S, Higuchi T. Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing. Pacific Symposium on Biocomputing. 14,227-238 (2009)
– Shimamura T, Imoto S, Yamaguchi R, Fujita A, Nagasaki M, Miyano S. Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Systems Biology. 3,41 (2009)
– Tamada Y, Araki H, Imoto S, Nagasaki M, Doi A, Nakanishi Y, Tomiyasu Y, Yasuda K, Dunmore B, Sanders D, Humphreys S, Print C, Charnock-Jones DS, Tashiro K, Kuhara S, Miyano S. Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks. Pacific Symposium on Biocomputing. 14,251-263 (2009)
– Watanabe-Fukuda Y, Yamamoto M, Miura N, Fukutake M, Ishige A, Yamaguchi R, Nagasaki M, Saito A, Imoto S, Miyano S, Takeda J, Watanabe K. Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine. J. Gastroenterology. 44 (5),380-389 (2009)
– Yamamoto, T., Bannai, H., Nagasaki, M. Miyano, S. Better decomposition heuristics for the maximum-weight connected graph problem using betweenness centrality. Lecture Notes in Artificial Intelligence. 5808, 465–472 (2009)
– Yoshikawa N*, Nagasaki M*, Sano M, Tokudome S, Ueno K, Shimizu N, Imoto S, Miyano S, Suematsu M, Fukuda K, Morimoto C, Tanaka H. Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism. Am J Physiol Endocrinol Metab. 296(6),E1363-E1373 (2009) (*Equally contributed)

2008

– Hatanaka Y, Nagasaki M, Yamaguchi R, Obayashi T, Numata K, Fujita A, Shimamura T, Tamada Y, Imoto S, Kinoshita K, Nakai K, Miyano S. A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human. Genome Informatics. 20,212-221 (2008)
– Jeong E, Nagasaki M, Miyano S. Rule-based reasoning for system dynamics in cell systems. Genome Informatics. 20,25-36 (2008)
– Kojima K, Nagasaki M#, Miyano S. Fast grid layout algorithm for biological networks with sweep calculation. Bioinformatics. 24 (12),1433-1441 (2008) (#Corresponding author)
– Nagasaki M, Saito A, Li C, Jeong E, Miyano S. Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Systems Biology. 2,53 (2008)
– Numata K, Yoshida R, Nagasaki M, Saito S, Imoto S, Miyano S. ExonMiner: Web service for analysis of GeneChip exon array data. BMC Bioinformatics. 9,494 (2008)
– Yamaguchi R, Imoto S, Yamauchi M, Nagasaki M, Yoshida R, Shimamura T, Hatanaka Y, Ueno K, Higuchi T, Gotoh N, Miyano S. Predicting differences in gene regulatory systems by state space models. Genome Informatics. 21,101-113 (2008)
– Yoshida R, Nagasaki M, Yamaguchi R, Imoto S, Miyano S, Higuchi T. Bayesian learning of biological pathways on genomic data assimilation. Bioinformatics. 24 (22),2592-2601 (2008)

2007

– Jeong E*, Nagasaki M*#, Saito A, Miyano S. Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways. In Silico Biology. 7(6),623-638 (2007) (*Equally contributed; #Corresponding author)
– Jeong E, Nagasaki M, Miyano S. Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway. Genome Informatics. 18,225-236 (2007)
– Kojima K*, Nagasaki M*#, Jeong E, Kato M, Miyano S. An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics. 8,76 (2007) (*Equally contributed; #Corresponding author)
– Saito A*, Nagasaki M*, Oyama M*, Kozuka-Hata H, Sugano S, Yamamoto T, Miyano S, AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. BMC Bioinformatics. 8,15 (2007) (*Equally contributed)
– Yamaguchi R, Yamamoto M, Imoto S, Nagasaki M, Yoshida R, Tsuiji K, Ishige A, Asou H, Watanabe K, Miyano S. Identification of activated transcription factors from microarray gene expression data of Kampo-medicine treated mice. Genome Informatics. 18,119-129 (2007)
– Yoshida R, Numata K, Imoto S, Nagasaki M, Doi A, Ueno K, Miyano S. Computational discovery of aberrant splice variations with genome-wide exon expression profiles. Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering. 715-722 (2007)

2006

– Doi A, Nagasaki M, Matsuno H, Miyano S. Simulation-based validation of the p53 transcriptional activity with hybrid functional Petri net. In Silico Biology. 6(1-2),1-13 (2006)
– Doi A, Nagasaki M, Ueno K, Matsuno H, Miyano S. A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity. Genome Informatics. 17 (1),112-23 (2006)
– Nagasaki M, Yamaguchi R, Yoshida R, Imoto S, Doi A, Tamada Y, Matsuno H, Miyano S, Higuchi T. Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Informatics. 17(1),46-61 (2006)
– Saito A, Nagasaki M, Doi A, Ueno K, Miyano S. Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loop by hybrid function Petri net with extension. Genome Informatics. 17 (1),100-111 (2006)
– Tasaki S*, Nagasaki M*, Oyama M, Hata H, Ueno K, Yoshida R, Higuchi T, Sugano S, Miyano S. Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Informatics. 17 (2),226-238 (2006) (*Equally contributed)
– Yoshida R, Numata K, Imoto S, Nagasaki M, Doi A, Ueno K, Miyano S. A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST arrays. Genome Informatics. 17(1),88-99 (2006)

-2004

– Kato M*, Nagasaki M*, Doi A , Miyano S. Automatic drawing of biological networks using cross cost and subcomponent data. Genome Informatics. 16 (2),22-31 (2005) (*Equally contributed)
– Doi A, Fujita S, Matsuno H, Nagasaki M, Miyano S. Constructing biological pathway models with hybrid functional Petri nets. In Silico Biology. 4(3),271-291 (2004)
– Nagasaki M, Doi A, Matsuno H, Miyano S. A versatile Petri net based architecture for modeling and simulation of complex biological processes. Genome Informatics. 15 (1),180-197 (2004)
– Nagasaki M, Doi A, Matsuno H, Miyano S. Integrating biopathway databases for large-scale modeling and simulation. Proc. Second Asia-Pacific Bioinformatics Conference. 43-52 (2004)
– Doi A, Nagasaki M, Fujita S, Matsuno H, Miyano S. Genomic Object Net: II. Modeling biopathways by hybrid functional Petri net with extension. Applied Bioinformatics. 2,185-188 (2003)
– Matsuno H, Fujita S, Doi A, Nagasaki M, Miyano S. Towards biopathway modeling and simulation. Lecture Notes in Computer Science. 2679,3-22 (2003)
– Nagasaki M, Doi A, Matsuno H, Miyano S. Recreating biopathway databases towards simulation. Lecture Notes in Computer Science, 2602,191-192 (2003)
– Nagasaki M, Doi A, Matsuno H, Miyano S. Genomic Object Net: I. A platform for modeling and simulating biopathways. Applied Bioinformatics. 2,181-184 (2003)
– Matsuno H, Doi A, Nagasaki M, Miyano S. Hybrid Petri net representation of gene regulatory network. Pacific Symposium on Biocomputing. 5,341-352 (2000)
– Nagasaki M, Onami S, Miyano S, Kitano H. Bio-calculus: its concept and molecular interaction. Genome Informatics. 10,133-143 (1999)

2) Review that was published in the international Journal

1. Miyano S, Yamaguchi R, Tamada Y, Nagasaki M, Imoto S. Gene networks viewed through two models. Lecture Notes in Computer Science. 5462, 54-66 (2009)

3) books

1. Saito A, Nagasaki M, Miyano S. Hybrid functional Petri net with extension for dynamic pathway modeling. In “Modeling in Systems Biology – The Petri Net Approach” (Koch I, Reisig W, Schreiber F (Eds.)), Springer, 101-120 (2010)
2. Nagasaki M, Saito A, Doi A, Matsuno H, Miyano S. “Foundations of Systems Biology – Using Cell Illustrator and Pathway Databases”, Springer (2009)
3. Nagasaki M, Doi A, Matsuno H, Miyano S. Computational modeling of biological processes with Petri net based architecture. In “Bioinformatics Technologies” (Chen YP (Ed)). Springer Press. 179-243 (2005)