Publications

1) Peer-reviewed papers published on international journal

2023

M. Kanezawa, H. Shimokawahara, M. Tsuji, K. Suruga, A. Miyagi, M. Marunaka, T. Mukai, T. Kawaguchi, T.Y. Yang, I. Yamaguchi, M. Nagasaki, F. Matsuda, H. Matsubara. The Results of Genetic Analysis and Clinical Outcomes after Stent Deployment in Adult Patients with Isolated Peripheral Pulmonary Artery Stenosis, Eur Respir J. 2023.

M. Yamaki, H. Saito, T. Mimori, Y. Suzuki, M. Nagasaki, K. Suzuki, S. Satoh-Kuriwada, N. Shoji, K. Isono, T. Goto, H. Shirakawa, M. Komai. Analysis of Genetic Polymorphism of Bitter Taste Receptor TAS2R38 and TAS2R46, and Its Relationship with Eating and Drinking Habits in Japanese ToMMo Subjects, J Nutr Sci Vitaminol (Tokyo). 69(5):347-356, 2023.

F. Shimoda, T. Naito, Y. Kakuta, Y. Kawai, K. Tokunaga, NCBN Controls WGS Consortium, Y. Shimoyama, R. Moroi, H. Shiga, M. Nagasaki, Y. Kinouchi, A. Masamune. HLA-DQA1*05 and upstream variants of PPARGC1B are associated with infliximab persistence in Japanese Crohn’s disease patientsPharmacogenomics J. 23(6):141-148, 2023.

S.S. Khor, K. Ueno, N. Nishida, M. Kawashima, Y. Kawai, Y. Aiba, Y. Hitomi, M. Nagasaki, M. Nakamura, K Tokunaga. Novel HLA allele associations with susceptibility, staging, symptomatic state, autoimmune hepatitis and hepatocellular carcinoma events for primary biliary cholangitis in the Japanese population, Front Immunol. 14: 1151502, 2023.

Z. Liu, R. Liu, H. Gao, S. Jung, X. Gao, R. Sun, X. Liu, Y. Kim, H. S. Lee, Y. Kawai, M. Nagasaki, J. Umeno, K. Tokunaga, Y. Kinouchi, A. Masamune, W. Shi, C. Shen, Z. Guo, K. Yuan, FinnGen, C. International Inflammatory Bowel Disease Genetics, C. Chinese Inflammatory Bowel Disease Genetics, S. Zhu, D. Li, J. Liu, T. Ge, J. Cho, M. J. Daly, D. P. B. McGovern, B. D. Ye, K. Song, Y. Kakuta, M. Li, H. Huang. Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestriesNat Genet, 55(5): 796-806, 2023.

Y. Mori, K. Ueno, D. Chiba, K. Hashimoto, Y. Kawai, K. Baba, H. Tanaka, T. Aki, M. Ogasawara, N. Shibasaki, K. Tokunaga, T. Aizawa, M. Nagasaki. Genome-Wide Association Study and Transcriptome of Japanese Patients with Developmental Dysplasia of the Hip Demonstrates an Association with the Ferroptosis Signaling Pathway, Int. J. Mol. Sci, 24(5): 5019, 2023.

N. Nishida, J. Ohashi, G. Suda, T. Chiyoda, N. Tamaki, T. Tomiyama, S. Ogasawara, M.  Sugiyama, Y. Kawai, S.S. Khor, M. Nagasaki, A. Fujimoto, T. Tsuchiura, M. Ishikawa, K.  Matsuda, H. Yano, T. Yoshizumi, N. Izumi, K. Hasegawa, N. Sakamoto, M. Mizokami,  K.  Tokunaga. Prediction Model with HLA-A*33:03 Reveals Number of Days to Develop Liver Cancer from Blood Test, Int. J. Mol. Sci, 24(5): 4761, 2023.

Y. Sugawara, H. Kato, M. Nagasaki, Y. Yoshida, M. Fujisawa, N. Minegishi, M. Yamamoto,  M. Nangaku. CFH-CFHR1 hybrid genes in two cases of atypical hemolytic uremic syndrome, J Hum Genet, 68(6): 427-430, 2023.

M. Nagasaki, Y. Sekiya, A, Asakura, R. Teraoka, R. Otokozawa, H. Hashimoto, T. Kawaguchi, K. Fukazawa, Y. Inadomi, K. T. Murata, Y. Ohkawa, I. Yamaguchi, T. Mizuhara, K. Tokunaga, Y. Sekiya, T. Hanawa, R. Yamada, F. Matsuda. Design and implementation of hybrid cloud system for large-scale human genomic researchHum Genome Var, 10: 6,  2023.

2022

Z. Yu, K. Ueno, R. Funayama, M. Sakai, N. Nariai, K. Kojima, Y. Kikuchi, X. Li, C. Ono, J. Kanatani, J. Ono, K. Iwamoto, K. Hashimoto, K. Kinoshita, K. Nakayama, M. Nagasaki,  H. Tomita. Sex-Specific Differences in the Transcriptome of the Human Dorsolateral Prefrontal Cortex in Schizophrenia, Mol Neurobiol, 60(2): 1083-1098, 2022.

M. Fujiwara, H. Hashimoto, K. Doi, M. Kujiraoka, Y. Tanizawa, Y. Ishida, M. Sasaki, M. Nagasaki. Secure secondary utilization system of genomic data using quantum secure cloud. Sci Rep, 12, 18530, 2022.

Y. Hitomi, Y. Aiba, K. Ueno, N. Nishida, Y. Kawai, M. Kawashima, M. Tsuiji, C. Iwabuchi, S. Takada, N. Miyake, M. Nagasaki, K. Tokunaga, M. Nakamura. rs2013278 in the multiple immunological-trait susceptibility locus CD28 regulates the production of non-functional splicing isoforms, Hum Genomics, 16 (1): 46, 2022.

Y. Mori, M. Miyake, Y. Hosoda, A. Miki, A. Takahashi, Y. Muraoka, M. Miyata, T. Sato, H. Tamura, S. Ooto, R. Yamada, K. Yamashiro, M. Nakamura, A. Tajima, M. Nagasaki, S. Honda, A. Tsujikawa. Genome-wide survival analysis for macular neovascularization development in central serous chorioretinopathy revealed shared genetic susceptibility with polypoidal choroidal vasculopathy, 129 (9): 1034-1042, 2022.

Kakuta Y, Iwaki H, Umeno J, Kawai Y, Kawahara M, Takagawa T, Shimoyama Y, Naito T, Moroi R, Kuroha M, Shiga H, Watanabe K, Nakamura S, Nakase H, Sasaki M, Hanai H, Fuyuno Y, Hirano A, Matsumoto T, Kudo H, Minegishi N, Nakamura M, Hisamatsu T, Andoh A, Nagasaki M, Tokunaga K, Kinouchi Y, Masamune A. MENDEL Study Group. Crohn’s Disease and Early Exposure to Thiopurines are Independent Risk Factors for Mosaic Chromosomal Alterations in Patients with Inflammatory Bowel Diseases. J Crohns Colitis, 16(4): 643-655, 2022.

D. Konno, S. Sugino, TF. Shibata, K. Misawa, Y. Imamura-Kawasawa, J. Suzuki, K. Kido, M. Nagasaki, M. Yamauchi, Antiemetic effects of baclofen in a shrew model of postoperative nausea and vomiting: Whole-transcriptome analysis in the nucleus of the solitary tractCNS Neurosci Ther, 28(6): 922-931, 2022.

T. Mori, K. Ueno, K. Tokunaga, Y. Kawai, K. Matsuda, N. Nishida, K. Komine, S. Saito, M. Nagasaki, A single-nucleotide-polymorphism in the 5′-flanking region of msx1 gene as a predictive marker candidate for platinum-based therapy of esophageal carcinomaTherapeutic Advances in Medical Oncology, 14:17588359221080580, 2022.

Hitomi Y, Aiba Y, Ueno K, Nishida N, Kawai Y, Kawashima M, Yasunami M, Gervais O, Ito M, Cordell HJ, Mells GF, Nagasaki M, Tokunaga K, Tsuiji M, Nakamura M. rs9459874 and rs1012656 in CCR6/FGFR1OP confer susceptibility to primary biliary cholangitis. J Autoimmun, 126: 102775, 2022.

2021

H.J. Cordell, J.J. Fryett, K. Ueno, R. Darlay, Y. Aiba, Y. Hitomi, M. Kawashima, N. Nishida, S.S. Khor, O. Gervais, Y. Kawai, M. Nagasaki, K. Tokunaga, R. Tang, Y. Shi, Z. Li, B.D. Juran, E.J. Atkinson, A. Gerussi, M. Carbone, R. Asselta, A. Cheung, M. de Andrade, A. Baras, J. Horowitz, M.A.R. Ferreira, D. Sun, D.E. Jones, S. Flack, A. Spicer, V.L. Mulcahy, J. Byan, Y. Han, R.N. Sandford, K.N. Lazaridis, C.I. Amos, G.M. Hirschfield, M.F. Seldin, P. Invernizzi, K.A. Siminovitch, X. Ma, M. Nakamura, G.F. Mells, Canadian PBC Consortium, Chinese PBC Consortium, Italian PBC Study Group, Japan-PBC-GWAS Consortium, US PBC Consortium, and UK-PBC Consortium. An international genome-wide meta-analysis of primary biliary cholangitis: novel risk loci and candidate drugs. J Hepatol, 75(3): 572-581, 2021.

Yamauchi T, Ochi D, Matsukawa N, Saigusa D, Ishikuro M, Obara T, Tsunemoto Y, Kumatani S, Yamashita R, Tanabe O, Minegishi N, Koshiba S, Metoki H, Kuriyama S, Yaegashi N, Yamamoto M, Nagasaki M, Hiyama S, Sugawara J. Machine learning approaches to predict gestational age in normal and complicated pregnancies via urinary metabolomics analysis. Sci Rep, 11(1): 17777, 2021.

O. Gervais, K. Ueno, Y. Kawai, Y. Hitomi, Y. Aiba, M. Ueta, M. Nakamura, K. Tokunaga and M. Nagasaki. Regional heritability mapping identifies several novel loci (STAT4, ULK4, and KCNH5) for primary biliary cholangitis in the Japanese population. European Journal of Human Genetics, 29(8): 1282-1291, 2021.

Asselta R, Paraboschi EM, Gerussi A, Cordell HJ, Mells GF, Sandford RN, Jones DE, Nakamura M, Ueno K, Hitomi Y, Kawashima M, Nishida N, Tokunaga K, Nagasaki M, Tanaka A, Tang R, Li Z, Shi Y, Liu X, Xiong M, Hirschfield G, Siminovitch KA, Canadian-US PBC Consortium, Italian PBC Genetics Study Group, UK-PBC Consortium, Japan PBC-GWAS Consortium, Carbone M, Cardamone G, Duga S, Gershwin ME, Seldin MF, Invernizzi P. X Chromosome Contribution to the Genetic Architecture of Primary Biliary Cholangitis. Gastroenterology, 160(7):2483-2495.e26, 2021.

C. Li, J. Qin, K. Kuroyanagi, L. Lu, M. Nagasaki, M. Satoru. High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net. Biosystems, 201: 104332, 2021.

Hitomi Y, Aiba Y, Kawai Y, Kojima K, Ueno K, Nishida N, Kawashima M, Gervais O, Khor SS, Nagasaki M, Tokunaga K, Nakamura M, Tsuiji M. rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis. Sci Rep, 11(1):4557, 2021.

Y. Kawai, Y. Hitomi, M. Ueta, S.S. Khor, K. Nakatani, C. Sotozono, S. Kinoshita, M. Nagasaki and K. Tokunaga. Mapping of susceptible variants for cold medicine-related Stevens-Johnson syndrome by whole-genome resequencing. NPJ Genom Med, 6(1): 9, 2021.

T. Tanjo, Y. Kawai, K. Tokunaga, O. Ogasawara and M. Nagasaki. Practical guide for managing large-scale human genome data in research. J Hum Genet, 66(1): 39-52, 2021.

2020

Y. Oka, M. Hamada, Y. Nakazawa, H. Muramatsu, Y. Okuno, K. Higasa, M. Shimada, H. Takeshima, K. Hanada, T. Hirano, T. Kawakita, H. Sakaguchi, T. Ichimura, S. Ozono, K. Yuge, Y. Watanabe, Y. Kotani, M. Yamane, Y. Kasugai, M. Tanaka, T. Suganami, S. Nakada, N. Mitsutake, Y. Hara, K. Kato, S. Mizuno, N. Miyake, Y. Kawai, K. Tokunaga, M. Nagasaki, S. Kito, K. Isoyama, M. Onodera, H. Kaneko, N. Matsumoto, F. Matsuda, K. Matsuo, Y. Takahashi, T. Mashimo, S. Kojima and T. Ogi. Digenic mutations in ALDH2 and ADH5 impair formaldehyde clearance and cause a multisystem disorder, AMeD syndrome. Sci Adv, 6(51): eabd7197, 2020.

X. Jia, T. Yamamura, R. Gbadegesin, M.T. McNulty, K. Song, C. Nagano, Y. Hitomi, D. Lee, Y. Aiba, S.S. Khor, K. Ueno, Y. Kawai, M. Nagasaki, E. Noiri, T. Horinouchi, H. Kaito, R. Hamada, T. Okamoto, K. Kamei, Y. Kaku, R. Fujimaru, R. Tanaka, Y. Shima, J. Research Consortium on Genetics of Childhood Idiopathic Nephrotic Syndrome in, J. Baek, H.G. Kang, I.S. Ha, K.H. Han, E.M. Yang, C. Korean Consortium of Hereditary Renal Diseases in, A. Abeyagunawardena, B. Lane, M. Chryst-Stangl, C. Esezobor, A. Solarin, C. Midwest Pediatric Nephrology, C. Dossier, G. Deschenes, Nephrovir, M. Vivarelli, H. Debiec, K. Ishikura, M. Matsuo, K. Nozu, P. Ronco, H.I. Cheong, M.G. Sampson, K. Tokunaga and K. Iijima. Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome. Kidney Int, 98(5): 1308-1322, 2020.

Yaoita N, Satoh K, Satoh T, Shimizu T, Saito S, Sugimura K, Tatebe S, Yamamoto S, Aoki T, Kikuchi N, Kurosawa R, Miyata S, Nagasaki M, Yasuda J, Shimokawa H. Identification of the Novel Variants in Patients With Chronic Thromboembolic Pulmonary Hypertension. J Am Heart Assoc, 9 (21): e015902, 2020.

H. Inada, M. Udono, K. Matsuda-Ito, K. Horisawa, Y. Ohkawa, S. Miura, T. Goya, J. Yamamoto, M. Nagasaki, K. Ueno, D. Saitou, M. Suyama, Y. Maehara, W. Kumamaru, Y. Ogawa, S. Sekiya and A. Suzuki. Direct reprogramming of human umbilical vein- and peripheral blood-derived endothelial cells into hepatic progenitor cells. Nat Commun, 11(1): 5292, 2020.

S. Sugino, D. Konno, Y. Kawai, M. Nagasaki, Y. Endo, T. Hayase, M. Yamazaki-Higuchi, Y. Kumeta, S. Tachibana, K. Saito, J. Suzuki, K. Kido, N. Kurosawa, A. Namiki and M. Yamauchi. Long non-coding RNA MIR4300HG polymorphisms are associated with postoperative nausea and vomiting: a genome-wide association study. Hum Genomics, 14(1): 31, 2020.

R. Nakamura, K. Misawa, G. Tohnai, M. Nakatochi, S. Furuhashi, N. Atsuta, N. Hayashi, D. Yokoi, H. Watanabe, H. Watanabe, M. Katsuno, Y. Izumi, K. Kanai, N. Hattori, M. Morita, A. Taniguchi, O. Kano, M. Oda, K. Shibuya, S. Kuwabara, N. Suzuki, M. Aoki, Y. Ohta, T. Yamashita, K. Abe, R. Hashimoto, I. Aiba, K. Okamoto, K. Mizoguchi, K. Hasegawa, Y. Okada, T. Ishihara, O. Onodera, K. Nakashima, R. Kaji, Y. Kamatani, S. Ikegawa, Y. Momozawa, M. Kubo, N. Ishida, N. Minegishi, M. Nagasaki and G. Sobue. A multi-ethnic meta-analysis identifies novel genes, including ACSL5, associated with amyotrophic lateral sclerosis. Communications Biology, 3(1): 526, 2020.

K. Horisawa, M. Udono, K. Ueno, Y. Ohkawa, M. Nagasaki, S. Sekiya and A. Suzuki. The Dynamics of Transcriptional Activation by Hepatic Reprogramming Factors. Mol Cell, 79(4): 660-676.e8, 2020.

D. Okamoto, Y. Kawai, Y. Kakuta, T. Naito, T. Torisu, A. Hirano, J. Umeno, Y. Fuyuno, D. Li, T. Nakano, Y. Izumiyama, R. Ichikawa, K. Hiramoto, R. Moroi, M. Kuroha, Y. Kanazawa, H. Shiga, K. Tokunaga, M. Nakamura, M. Esaki, T. Matsumoto, D.P.B. McGovern, M. Nagasaki, Y. Kinouchi and A. Masamune. Genetic Analysis of Ulcerative Colitis in Japanese Individuals Using Population-specific SNP Array. Inflamm Bowel Dis, 26(8): 1177-1187, 2020.

O. Gervais, K. Ueno, Y. Kawai, Y. Hitomi, K. Misawa, S. Teraguchi, Y.Y. Wang, K. Tokunaga and M. Nagasaki. Genomic Heritabilities and Correlations of 17 Traits Related to Obesity and Associated Conditions in the Japanese Population. G3 (Bethesda), 10(7): 2221-2228, 2020.

Y. Kakuta, R. Ichikawa, Y. Fuyuno, A. Hirano, J. Umeno, T. Torisu, K. Watanabe, A. Asakura, T. Nakano, Y. Izumiyama, D. Okamoto, T. Naito, R. Moroi, M. Kuroha, Y. Kanazawa, T. Kimura, H. Shiga, T. Naito, M. Esaki, Y. Kawai, K. Tokunaga, M. Nakamura, T. Matsumoto, M. Nagasaki, Y. Kinouchi, M. Unno and A. Masamune. An Integrated Genomic and Transcriptomic Analysis Reveals Candidates of Susceptibility Genes for Crohn’s Disease in Japanese Populations. Sci Rep, 10(1): 10236, 2020.

T. Kaneyasu, S. Mori, H. Yamauchi, S. Ohsumi, S. Ohno, D. Aoki, S. Baba, J. Kawano, Y. Miki, N. Matsumoto, M. Nagasaki, R. Yoshida, S. Akashi-Tanaka, T. Iwase, D. Kitagawa, K. Masuda, A. Hirasawa, M. Arai, J. Takei, Y. Ide, O. Gotoh, N. Yaguchi, M. Nishi, K. Kaneko, Y. Matsuyama, M. Okawa, M. Suzuki, A. Nezu, S. Yokoyama, S. Amino, M. Inuzuka, T. Noda and S. Nakamura. Prevalence of disease-causing genes in Japanese patients with BRCA1/2-wildtype hereditary breast and ovarian cancer syndrome. NPJ Breast Cancer, 6: 25, 2020.

K. Yoshida, K. Yokota, Y. Kutsuwada, K. Nakayama, K. Watanabe, A. Matsumoto, H. Miyashita, S.s. Khor, K. Tokunaga, Y. Kawai, M. Nagasaki and S. Iwamoto. Genome‐Wide Association Study of Lean Nonalcoholic Fatty Liver Disease Suggests Human Leukocyte Antigen as a Novel Candidate Locus. Hepatology Communications, 4(8): 1124-1135, 2020.

K. Misawa, T. Hasegawa, E. Mishima, P. Jutabha, M. Ouchi, K. Kojima, Y. Kawai, M. Matsuo, N. Anzai, and M. Nagasaki. Contribution of Rare Variants of the SLC22A12 Gene to the Missing Heritability of Serum Urate Levels. Genetics, 214(4): 1079-1090, 2020.

K. Ueno, Y. Aiba, Y. Hitomi, S. Shimoda, H. Nakamura, O. Gervais, Y. Kawai, M. Kawashima, N. Nishida, S. S. Kohn, K. Kojima, S. Katsushima, A. Naganuma, K. Sugi, T. Komatsu, T. Mannami, K. Matsushita, K. Yoshizawa, F. Makita, T. Nikami, H. Nishimura, H. Kouno, H. Kouno, H. Ohta, T. Komura, S. Tsuruta, K. Yamauchi, T. Kobata, A. Kitasato, T. Kuroki, S. Abiru, S. Nagaoka, A. Komori, H. Yatsuhashi, K. Migita, H. Ohira, A. Tanaka, H. Takikawa, M. Nagasaki, K. Tokunaga, M. Nakamura, and PBC-GWAS Consoritium in Japan, Integrated GWAS and mRNA Microarray Analysis Identified IFNG and CD40L as the Central Upstream Regulators in Primary Biliary Cholangitis. American Association for the Study of Liver Diseases, 4(5): 724-738, 2020.

S. Kuriyama, H. Metoki, M. Kikuya, T. Obara, M. Ishikuro, C. Yamanaka, M. Nagai, H. Matsubara, T. Kobayashi, J. Sugawara, G. Tamiya, A. Hozawa, N. Nakaya, N. Tsuchiya, T. Nakamura, A. Narita, M. Kogure, T. Hirata, I. Tsuji, F. Nagami, N. Fuse, T. Arai, Y. Kawaguchi, S. Higuchi, M. Sakaida, Y. Suzuki, N. Osumi, K. Nakayama, K. Ito, S. Egawa, K. Chida, E. Kodama, H. Kiyomoto, T. Ishii, A. Tsuboi, H. Tomita, Y. Taki, H. Kawame, K. Suzuki, N. Ishii, S. Ogishima, S. Mizuno, T. Takai-Igarashi, N. Minegishi, J. Yasuda, K. Igarashi, R. Shimizu, M. Nagasaki, O. Tanabe, S. Koshiba, H. Hashizume, H. Motohashi, T. Tominaga, S. Ito, K. Tanno, K. Sakata, A. Shimizu, J. Hitomi, M. Sasaki, K. Kinoshita, H. Tanaka, T. Kobayashi, S. Kure, N. Yaegashi, and M. Yamamoto. Cohort Profile: Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study (TMM BirThree Cohort Study): Rationale, Progress and Perspective. Int J Epidemiol, 49(1): 18-19m, 2020.

Y.W. Kim, Y.J. Kim, H.S. Cheong, Y. Shiga, K. Hashimoto, Y.J. Song, S.H. Kim, H.J. Choi, K.M. Nishiguchi, Y. Kawai, M. Nagasaki, T. Nakazawa, K.H. Park, D.M. Kim and J.W. Jeoung. Exploring the Novel Susceptibility Gene Variants for Primary Open-Angle Glaucoma in East Asian Cohorts: The GLAU-GENDISK Study. Sci Rep, 10(1): 221, 2020.

A. Hozawa, K. Tanno, N. Nakaya, T. Nakamura, N. Tsuchiya, T. Hirata, A. Narita, M. Kogure, K. Nochioka, R. Sasaki, N. Takanashi, K. Otsuka, K. Sakata, S. Kuriyama, M. Kikuya, O. Tanabe, J. Sugawara, K. Suzuki, Y. Suzuki, E.N. Kodama, N. Fuse, H. Kiyomoto, H. Tomita, A. Uruno, Y. Hamanaka, H. Metoki, M. Ishikuro, T. Obara, T. Kobayashi, K. Kitatani, T. Takai-Igarashi, S. Ogishima, M. Satoh, H. Ohmomo, A. Tsuboi, S. Egawa, T. Ishii, K. Ito, S. Ito, Y. Taki, N. Minegishi, N. Ishii, M. Nagasaki, K. Igarashi, S. Koshiba, R. Shimizu, G. Tamiya, K. Nakayama, H. Motohashi, J. Yasuda, A. Shimizu, T. Hachiya, Y. Shiwa, T. Tominaga, H. Tanaka, K. Oyama, R. Tanaka, H. Kawame, A. Fukushima, Y. Ishigaki, T. Tokutomi, N. Osumi, T. Kobayashi, F. Nagami, H. Hashizume, T. Arai, Y. Kawaguchi, S. Higuchi, M. Sakaida, R. Endo, S. Nishizuka, I. Tsuji, J. Hitomi, M. Nakamura, K. Ogasawara, N. Yaegashi, K. Kinoshita, S. Kure, A. Sakai, S. Kobayashi, K. Sobue, M. Sasaki, and M. Yamamoto. Study profile of The Tohoku Medical Megabank Community-Based Cohort Study. J Epidemiol, 31(1): 65-76, 2020.

2019

K. Ishizawa, M. Yamanaka, Y. Saiki, E. Miyauchi, S. Fukushige, T. Akaishi, A. Asao, T. Mimori, R. Saito, Y. Tojo, R. Yamashita, M. Abe, A. Sakurada, N.A. Pham, M. Li, Y. Okada, T. Ishii, N. Ishii, S. Kobayashi, M. Nagasaki, M. Ichinose, M.S. Tsao, and A. Horii. CD45(+)CD326(+) Cells are Predictive of Poor Prognosis in Non-Small Cell Lung Cancer Patients. Clin Cancer Res, 25(22): 6756-6763, 2019.

K. Shido, K. Kojima, K. Yamasaki, A. Hozawa, G. Tamiya, S. Ogishima, N. Minegishi, Y. Kawai, K. Tanno, Y. Suzuki, M. Nagasaki, and S. Aiba. Susceptibility Loci for Tanning Ability in the Japanese Population Identified by a Genome-Wide Association Study from the Tohoku Medical Megabank Project Cohort Study. J Invest Dermatol, 139(7): 1605-1608.e1613, 2019.

Y. Amano, Y. Akazawa, J. Yasuda, K. Yoshino, K. Kojima, N. Kobayashi, S. Matsuzaki, M. Nagasaki, Y. Kawai, N. Minegishi, N. Ishida, N. Motoki, A. Hachiya, Y. Nakazawa, M. Yamamoto, K. Koike and T. Takeshita. A low-frequency IL4R locus variant in Japanese patients with intravenous immunoglobulin therapy-unresponsive Kawasaki disease. Pediatr Rheumatol Online J, 17(1): 34, 2019.

Y.Y. Wang, T. Mimori, S.S. Khor, O. Gervais, Y. Kawai, Y. Hitomi, K. Tokunaga, and M. Nagasaki. HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel. Hum Genome Var, 6: 29, 2019.

S. Tadaka, F. Katsuoka, M. Ueki, K. Kojima, S. Makino, S. Saito, A. Otsuki, C. Gocho, M. Sakurai-Yageta, I. Danjoh, I.N. Motoike, Y. Yamaguchi-Kabata, M. Shirota, S. Koshiba, M. Nagasaki, N. Minegishi, A. Hozawa, S. Kuriyama, A. Shimizu, J. Yasuda, N. Fuse, G. Tamiya, M. Yamamoto, and K. Kinoshita. 3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome. Hum Genome Var, 6: 28, 2019.

T. Nishiyama, M. Nakatochi, A. Goto, M. Iwasaki, T. Hachiya, Y. Sutoh, A. Shimizu, C. Wang, H. Tanaka, M. Watanabe, A. Hosono, Y. Tamai, T. Yamada, T. Yamaji, N. Sawada, K. Fukumoto, K. Otsuka, K. Tanno, H. Tomita, K. Kojima, M. Nagasaki, A. Hozawa, A. Hishida, T. Sasakabe, Y. Nishida, M. Hara, H. Ito, I. Oze, Y. Nakamura, H. Mikami, R. Ibusuki, T. Takezaki, T. Koyama, N. Kuriyama, K. Endoh, K. Kuriki, T.C. Turin, T. Naoyuki, S. Katsuura-Kamano, H. Uemura, R. Okada, S. Kawai, M. Naito, Y. Momozawa, M. Kubo, M. Sasaki, M. Yamamoto, S. Tsugane, K. Wakai, and S. Suzuki. Genome-wide association meta-analysis and Mendelian randomization analysis confirm the influence of ALDH2 on sleep duration in the Japanese population. Sleep, 42(6): zsz046, 2019.

M. Nagasaki, Y. Kuroki, T.F. Shibata, F. Katsuoka, T. Mimori, Y. Kawai, N. Minegishi, A. Hozawa, S. Kuriyama, Y. Suzuki, H. Kawame, F. Nagami, T. Takai-Igarashi, S. Ogishima, K. Kojima, K. Misawa, O. Tanabe, N. Fuse, H. Tanaka, N. Yaegashi, K. Kinoshita, S. Kure, J. Yasuda, and M. Yamamoto. Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing. Hum Genome Var, 6: 27, 2019.

T. Mizuguchi, T. Suzuki, C. Abe, A. Umemura, K. Tokunaga, Y. Kawai, M. Nakamura, M. Nagasaki, K. Kinoshita, Y. Okamura, S. Miyatake, N. Miyake, and N. Matsumoto. A 12-kb structural variation in progressive myoclonic epilepsy was newly identified by long-read whole-genome sequencing. J Hum Genet, 64(5): 359-368, 2019.

Y. Kakuta, Y. Kawai, T. Naito, A. Hirano, J. Umeno, Y. Fuyuno, Z. Liu, D. Li, T. Nakano, Y. Izumiyama, R. Ichikawa, D. Okamoto, H. Nagai, S. Matsumoto, K. Yamamoto, N. Yokoyama, H. Chiba, Y. Shimoyama, M. Onodera, R. Moroi, M. Kuroha, Y. Kanazawa, T. Kimura, H. Shiga, K. Endo, K. Negoro, J. Yasuda, M. Esaki, K. Tokunaga, M. Nakamura, T. Matsumoto, D.P.B. McGovern, M. Nagasaki, Y. Kinouchi, T. Shimosegawa, and A. Masamune. A Genome-wide Association Study Identifying RAP1A as a Novel Susceptibility Gene for Crohn’s Disease in Japanese Individuals. J Crohns Colitis, 13(5): 648-658, 2019.

T. Mimori, J. Yasuda, Y. Kuroki, T.F. Shibata, F. Katsuoka, S. Saito, N. Nariai, A. Ono, N. Nakai-Inagaki, K. Misawa, K. Tateno, Y. Kawai, N. Fuse, A. Hozawa, S. Kuriyama, J. Sugawara, N. Minegishi, K. Suzuki, K. Kinoshita, M. Nagasaki, and M. Yamamoto. Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing. Pharmacogenomics J, 19(2): 136-146, 2019.

Y. Yamaguchi-Kabata, J. Yasuda, A. Uruno, K. Shimokawa, S. Koshiba, Y. Suzuki, N. Fuse, H. Kawame, S. Tadaka, M. Nagasaki, K. Kojima, F. Katsuoka, K. Kumada, O. Tanabe, G. Tamiya, N. Yaegashi, K. Kinoshita, M. Yamamoto, and S. Kure. Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals. Hum Genet, 138(4): 389-409, 2019.

J. Sugawara, D. Ochi, R. Yamashita, T. Yamauchi, D. Saigusa, M. Wagata, T. Obara, M. Ishikuro, Y. Tsunemoto, Y. Harada, T. Shibata, T. Mimori, J. Kawashima, F. Katsuoka, T. Igarashi-Takai, S. Ogishima, H. Metoki, H. Hashizume, N. Fuse, N. Minegishi, S. Koshiba, O. Tanabe, S. Kuriyama, K. Kinoshita, S. Kure, N. Yaegashi, M. Yamamoto, S. Hiyama, and M. Nagasaki. Maternity Log study: a longitudinal lifelog monitoring and multiomics analysis for the early prediction of complicated pregnancy. BMJ Open, 9(2): e025939, 2019.

J. Yasuda, K. Kinoshita, F. Katsuoka, I. Danjoh, M. Sakurai-Yageta, I.N. Motoike, Y. Kuroki, S. Saito, K. Kojima, M. Shirota, D. Saigusa, A. Otsuki, J. Kawashima, Y. Yamaguchi-Kabata, S. Tadaka, Y. Aoki, T. Mimori, K. Kumada, J. Inoue, S. Makino, M. Kuriki, N. Fuse, S. Koshiba, O. Tanabe, M. Nagasaki, G. Tamiya, R. Shimizu, T. Takai-Igarashi, S. Ogishima, A. Hozawa, S. Kuriyama, J. Sugawara, A. Tsuboi, H. Kiyomoto, T. Ishii, H. Tomita, N. Minegishi, Y. Suzuki, K. Suzuki, H. Kawame, H. Tanaka, Y. Taki, N. Yaegashi, S. Kure, F. Nagami, K. Kosaki, Y. Sutoh, T. Hachiya, A. Shimizu, M. Sasaki, and M. Yamamoto. Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare. J Biochem, 165(2): 139-158, 2019.

Y. Hitomi, K. Ueno, Y. Kawai, N. Nishida, K. Kojima, M. Kawashima, Y. Aiba, H. Nakamura, H. Kouno, H. Kouno, H. Ohta, K. Sugi, T. Nikami, T. Yamashita, S. Katsushima, T. Komeda, K. Ario, A. Naganuma, M. Shimada, N. Hirashima, K. Yoshizawa, F. Makita, K. Furuta, M. Kikuchi, N. Naeshiro, H. Takahashi, Y. Mano, H. Yamashita, K. Matsushita, S. Tsunematsu, I. Yabuuchi, H. Nishimura, Y. Shimada, K. Yamauchi, T. Komatsu, R. Sugimoto, H. Sakai, E. Mita, M. Koda, Y. Nakamura, H. Kamitsukasa, T. Sato, M. Nakamuta, N. Masaki, H. Takikawa, A. Tanaka, H. Ohira, M. Zeniya, M. Abe, S. Kaneko, M. Honda, K. Arai, T. Arinaga-Hino, E. Hashimoto, M. Taniai, T. Umemura, S. Joshita, K. Nakao, T. Ichikawa, H. Shibata, A. Takaki, S. Yamagiwa, M. Seike, S. Sakisaka, Y. Takeyama, M. Harada, M. Senju, O. Yokosuka, T. Kanda, Y. Ueno, H. Ebinuma, T. Himoto, K. Murata, S. Shimoda, S. Nagaoka, S. Abiru, A. Komori, K. Migita, M. Ito, H. Yatsuhashi, Y. Maehara, S. Uemoto, N. Kokudo, M. Nagasaki, K. Tokunaga, and M. Nakamura. POGLUT1, the putative effector gene driven by rs2293370 in primary biliary cholangitis susceptibility locus chromosome 3q13.33. Sci Rep, 9(1): 102, 2019.

Y. Kakuta, Y. Izumiyama, D. Okamoto, T. Nakano, R. Ichikawa, T. Naito, R. Moroi, M. Kuroha, Y. Kanazawa, T. Kimura, H. Shiga, H. Kudo, N. Minegishi, Y. Kawai, K. Tokunaga, M. Nagasaki, Y. Kinouchi, Y. Suzuki, and A. Masasmune. High-resolution melt analysis enables simple genotyping of complicated polymorphisms of codon 18 rendering the NUDT15 diplotype. J Gastroenterol, 55(1): 67-77, 2019.

Y. Hitomi, K. Nakatani, K. Kojima, N. Nishida, Y. Kawai, M. Kawashima, Y. Aiba, M. Nagasaki, M. Nakamura, and K. Tokunaga. NFKB1 and MANBA Confer Disease Susceptibility to Primary Biliary Cholangitis via Independent Putative Primary Functional Variants. Cell Mol Gastroenterol Hepatol, 7(3): 515-532, 2019.

2018

M. Kumondai, A. Ito, E. Hishinuma, A. Kikuchi, T. Saito, M. Takahashi, C. Tsukada, S. Saito, J. Yasuda, M. Nagasaki, N. Minegishi, M. Yamamoto, A. Kaneko, I. Teramoto, M. Kimura, N. Hirasawa, and M. Hiratsuka. Development and application of a rapid and sensitive genotyping method for pharmacogene variants using the single-stranded tag hybridization chromatographic printed-array strip (STH-PAS). Drug Metab Pharmacokinet, 33(6): 258-263, 2018.

Hasegawa, K. Kojima, Y. Kawai and M. Nagasaki. Time-Series Filtering for Replicated Observations via a Kernel Approximate Bayesian Computation. IEEE Transactions on Signal Processing, 66(23): 6148-6161, 2018.

T. Naito, N. Yokoyama, Y. Kakuta, K. Ueno, Y. Kawai, M. Onodera, R. Moroi, M. Kuroha, Y. Kanazawa, T. Kimura, H. Shiga, K. Endo, M. Nagasaki, A. Masamune, Y. Kinouchi, and T. Shimosegawa. Clinical and genetic risk factors for decreased bone mineral density in Japanese patients with inflammatory bowel disease. J Gastroenterol Hepatol, 33(11): 1873-1881, 2018.

K.Z. Latt, K. Honda, M. Thiri, Y. Hitomi, Y. Omae, H. Sawai, Y. Kawai, S. Teraguchi, K. Ueno, M. Nagasaki, A. Mabuchi, H. Kaga, A. Komatsuda, K. Tokunaga, and E. Noiri. Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy. Sci Rep, 8(1): 15576, 2018.

Watanabe, T. Saito, E.M.G. Rico, E. Hishinuma, M. Kumondai, M. Maekawa, A. Oda, D. Saigusa, S. Saito, J. Yasuda, M. Nagasaki, N. Minegishi, M. Yamamoto, H. Yamaguchi, N. Mano, N. Hirasawa and M. Hiratsuka. Functional characterization of 40 CYP2B6 allelic variants by assessing efavirenz 8-hydroxylation. Biochem Pharmacol, 156: 420-430, 2018.

Y. Kakuta, Y. Kawai, D. Okamoto, T. Takagawa, K. Ikeya, H. Sakuraba, A. Nishida, S. Nakagawa, M. Miura, T. Toyonaga, K. Onodera, M. Shinozaki, Y. Ishiguro, S. Mizuno, M. Takahara, S. Yanai, R. Hokari, T. Nakagawa, H. Araki, S. Motoya, T. Naito, R. Moroi, H. Shiga, K. Endo, T. Kobayashi, M. Naganuma, S. Hiraoka, T. Matsumoto, S. Nakamura, H. Nakase, T. Hisamatsu, M. Sasaki, H. Hanai, A. Andoh, M. Nagasaki, Y. Kinouchi, T. Shimosegawa, A. Masamune, and Y. Suzuki. NUDT15 codon 139 is the best pharmacogenetic marker for predicting thiopurine-induced severe adverse events in Japanese patients with inflammatory bowel disease: a multicenter study. J Gastroenterol, 53(9): 1065-1078, 2018.

X. Jia, T. Horinouchi, Y. Hitomi, A. Shono, S.S. Khor, Y. Omae, K. Kojima, Y. Kawai, M. Nagasaki, Y. Kaku, T. Okamoto, Y. Ohwada, K. Ohta, Y. Okuda, R. Fujimaru, K. Hatae, N. Kumagai, E. Sawanobori, H. Nakazato, Y. Ohtsuka, K. Nakanishi, Y. Shima, R. Tanaka, A. Ashida, K. Kamei, K. Ishikura, K. Nozu, K. Tokunaga, and K. Iijima. Strong Association of the HLA-DR/DQ Locus with Childhood Steroid-Sensitive Nephrotic Syndrome in the Japanese Population. J Am Soc Nephrol, 29(8): 2189-2199, 2018.

E. Hishinuma, Y. Narita, S. Saito, M. Maekawa, F. Akai, Y. Nakanishi, J. Yasuda, M. Nagasaki, M. Yamamoto, H. Yamaguchi, N. Mano, N. Hirasawa, and M. Hiratsuka. Functional Characterization of 21 Allelic Variants of Dihydropyrimidine Dehydrogenase Identified in 1070 Japanese Individuals. Drug Metab Dispos, 46(8): 1083-1090, 2018.

J. Yasuda, F. Katsuoka, I. Danjoh, Y. Kawai, K. Kojima, M. Nagasaki, S. Saito, Y. Yamaguchi-Kabata, S. Tadaka, I.N. Motoike, K. Kumada, M. Sakurai-Yageta, O. Tanabe, N. Fuse, G. Tamiya, K. Higasa, F. Matsuda, N. Yasuda, M. Iwasaki, M. Sasaki, A. Shimizu, K. Kinoshita, and M. Yamamoto. Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project. BMC Genomics, 19(1): 551, 2018.

S. Koshiba, I. Motoike, D. Saigusa, J. Inoue, M. Shirota, Y. Katoh, F. Katsuoka, I. Danjoh, A. Hozawa, S. Kuriyama, N. Minegishi, M. Nagasaki, T. Takai-Igarashi, S. Ogishima, N. Fuse, S. Kure, G. Tamiya, O. Tanabe, J. Yasuda, K. Kinoshita, and M. Yamamoto. Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project. Genes Cells, 23(6): 406-417, 2018.

K. Ueno, T. Iwagawa, G. Ochiai, H. Koso, H. Nakauchi, M. Nagasaki, Y. Suzuki, and S. Watanabe. Author Correction: Analysis of Muller glia specific genes and their histone modification using Hes1-promoter driven EGFP expressing mouse. Sci Rep, 8(1): 8946, 2018.

N. Nishida, Y. Aiba, Y. Hitomi, M. Kawashima, K. Kojima, Y. Kawai, K. Ueno, H. Nakamura, N. Yamashiki, T. Tanaka, S. Tamura, A. Mori, S. Yagi, Y. Soejima, T. Yoshizumi, M. Takatsuki, A. Tanaka, K. Harada, S. Shimoda, A. Komori, S. Eguchi, Y. Maehara, S. Uemoto, N. Kokudo, M. Nagasaki, K. Tokunaga, and M. Nakamura. NELFCD and CTSZ loci are associated with jaundice-stage progression in primary biliary cholangitis in the Japanese population. Sci Rep, 8(1): 8071, 2018.

S. Hirata, K. Kojima, K. Misawa, O. Gervais, Y. Kawai, and M. Nagasaki. Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population. Heliyon, 4(5): e00625, 2018.

M. Nishioka, M. Bundo, J. Ueda, F. Katsuoka, Y. Sato, Y. Kuroki, T. Ishii, W. Ukai, S. Murayama, E. Hashimoto, M. Nagasaki, J. Yasuda, K. Kasai, T. Kato, and K. Iwamoto. Identification of somatic mutations in postmortem human brains by whole genome sequencing and their implications for psychiatric disorders. Psychiatry Clin Neurosci, 72(4): 280-294, 2018.

H. Chiba, Y. Kakuta, Y. Kinouchi, Y. Kawai, K. Watanabe, M. Nagao, T. Naito, M. Onodera, R. Moroi, M. Kuroha, Y. Kanazawa, T. Kimura, H. Shiga, K. Endo, K. Negoro, M. Nagasaki, M. Unno, and T. Shimosegawa. Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease. PLoS One, 13(3): e0194036, 2018.

Y. Yamaguchi-Kabata, J. Yasuda, O. Tanabe, Y. Suzuki, H. Kawame, N. Fuse, M. Nagasaki, Y. Kawai, K. Kojima, F. Katsuoka, S. Saito, I. Danjoh, I.N. Motoike, R. Yamashita, S. Koshiba, D. Saigusa, G. Tamiya, S. Kure, N. Yaegashi, Y. Kawaguchi, F. Nagami, S. Kuriyama, J. Sugawara, N. Minegishi, A. Hozawa, S. Ogishima, H. Kiyomoto, T. Takai-Igarashi, K. Kinoshita, and M. Yamamoto. Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals. J Hum Genet, 63(2): 213-230, 2018.

Y. Shibuya, H. Tokunaga, S. Saito, K. Shimokawa, F. Katsuoka, L. Bin, K. Kojima, M. Nagasaki, M. Yamamoto, N. Yaegashi, and J. Yasuda. Identification of somatic genetic alterations in ovarian clear cell carcinoma with next generation sequencing. Genes Chromosomes Cancer, 57(2): 51-60, 2018.

2017

Y. Shiga, K.M. Nishiguchi, Y. Kawai, K. Kojima, K. Sato, K. Fujita, M. Takahashi, K. Omodaka, M. Araie, K. Kashiwagi, M. Aihara, T. Iwata, F. Mabuchi, M. Takamoto, M. Ozaki, K. Kawase, N. Fuse, M. Yamamoto, J. Yasuda, M. Nagasaki, and T. Nakazawa. Genetic analysis of Japanese primary open-angle glaucoma patients and clinical characterization of risk alleles near CDKN2B-AS1, SIX6 and GAS7. PLoS One, 12(12): e0186678, 2017.

T. Takai-Igarashi, K. Kinoshita, M. Nagasaki, S. Ogishima, N. Nakamura, S. Nagase, S. Nagaie, T. Saito, F. Nagami, N. Minegishi, Y. Suzuki, K. Suzuki, H. Hashizume, S. Kuriyama, A. Hozawa, N. Yaegashi, S. Kure, G. Tamiya, Y. Kawaguchi, H. Tanaka, and M. Yamamoto. Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design. BMC Med Inform Decis Mak, 17(1): 100, 2017.

K. Ueno, T. Iwagawa, G. Ochiai, H. Koso, H. Nakauchi, M. Nagasaki, Y. Suzuki, and S. Watanabe. Analysis of Muller glia specific genes and their histone modification using Hes1-promoter driven EGFP expressing mouse. Sci Rep, 7(1): 3578, 2017.

Y. Hitomi, K. Kojima, M. Kawashima, Y. Kawai, N. Nishida, Y. Aiba, M. Yasunami, M. Nagasaki, M. Nakamura, and K. Tokunaga. Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis. Sci Rep, 7(1): 2904, 2017.

K. Matsuura, H. Sawai, K. Ikeo, S. Ogawa, E. Iio, M. Isogawa, N. Shimada, A. Komori, H. Toyoda, T. Kumada, T. Namisaki, H. Yoshiji, N. Sakamoto, M. Nakagawa, Y. Asahina, M. Kurosaki, N. Izumi, N. Enomoto, A. Kusakabe, E. Kajiwara, Y. Itoh, T. Ide, A. Tamori, M. Matsubara, N. Kawada, K. Shirabe, E. Tomita, M. Honda, S. Kaneko, S. Nishina, A. Suetsugu, Y. Hiasa, H. Watanabe, T. Genda, I. Sakaida, S. Nishiguchi, K. Takaguchi, E. Tanaka, J. Sugihara, M. Shimada, Y. Kondo, Y. Kawai, K. Kojima, M. Nagasaki, K. Tokunaga, and Y. Tanaka. Genome-Wide Association Study Identifies TLL1 Variant Associated With Development of Hepatocellular Carcinoma After Eradication of Hepatitis C Virus Infection. Gastroenterology, 152(6): 1383-1394, 2017.

T. Hamanaka, M. Kimura, T. Sakurai, N. Ishida, J. Yasuda, M. Nagasaki, N. Nariai, A. Endo, K. Homma, F. Katsuoka, Y. Matsubara, M. Yamamoto, and N. Fuse. A Histologic Categorization of Aqueous Outflow Routes in Familial Open-Angle Glaucoma and Associations With Mutations in the MYOC Gene in Japanese Patients. Invest Ophthalmol Vis Sci, 58(5): 2818-2831, 2017.

T. Hachiya, R. Furukawa, Y. Shiwa, H. Ohmomo, K. Ono, F. Katsuoka, M. Nagasaki, J. Yasuda, N. Fuse, K. Kinoshita, M. Yamamoto, K. Tanno, M. Satoh, R. Endo, M. Sasaki, K. Sakata, S. Kobayashi, K. Ogasawara, J. Hitomi, K. Sobue, and A. Shimizu. Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies. NPJ Genom Med, 2: 11, 2017.

M. Ueta, H. Sawai, R. Shingaki, Y. Kawai, C. Sotozono, K. Kojima, K.C. Yoon, M.K. Kim, K.Y. Seo, C.K. Joo, M. Nagasaki, S. Kinoshita, and K. Tokunaga. 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, 62(4): 485-489, 2017.

T.C. Liu, T. Naito, Z. Liu, K.L. VanDussen, T. Haritunians, D. Li, K. Endo, Y. Kawai, M. Nagasaki, Y. Kinouchi, D.P. McGovern, T. Shimosegawa, Y. Kakuta, and T.S. Stappenbeck. LRRK2 but not ATG16L1 is associated with Paneth cell defect in Japanese Crohn’s disease patients. JCI Insight, 2(6): e91917, 2017.

M. Kawashima, Y. Hitomi, Y. Aiba, N. Nishida, K. Kojima, Y. Kawai, H. Nakamura, A. Tanaka, M. Zeniya, E. Hashimoto, H. Ohira, K. Yamamoto, M. Abe, K. Nakao, S. Yamagiwa, S. Kaneko, M. Honda, T. Umemura, T. Ichida, M. Seike, S. Sakisaka, M. Harada, O. Yokosuka, Y. Ueno, M. Senju, T. Kanda, H. Shibata, T. Himoto, K. Murata, Y. Miyake, H. Ebinuma, M. Taniai, S. Joshita, T. Nikami, H. Ota, H. Kouno, H. Kouno, M. Nakamuta, N. Fukushima, M. Kohjima, T. Komatsu, T. Komeda, Y. Ohara, T. Muro, T. Yamashita, K. Yoshizawa, Y. Nakamura, M. Shimada, N. Hirashima, K. Sugi, K. Ario, E. Takesaki, A. Naganuma, H. Mano, H. Yamashita, K. Matsushita, K. Yamauchi, F. Makita, H. Nishimura, K. Furuta, N. Takahashi, M. Kikuchi, N. Masaki, T. Tanaka, S. Tamura, A. Mori, S. Yagi, K. Shirabe, A. Komori, K. Migita, M. Ito, S. Nagaoka, S. Abiru, H. Yatsuhashi, M. Yasunami, S. Shimoda, K. Harada, H. Egawa, Y. Maehara, S. Uemoto, N. Kokudo, H. Takikawa, H. Ishibashi, K. Chayama, M. Mizokami, M. Nagasaki, K. Tokunaga and M. Nakamura. Genome-wide association studies identify PRKCB as a novel genetic susceptibility locus for primary biliary cholangitis in the Japanese population. Hum Mol Genet, 26(3): 650-659, 2017.

X. Pan, N. Nariai, N. Fukuhara, S. Saito, Y. Sato, F. Katsuoka, K. Kojima, Y. Kuroki, I. Danjoh, R. Saito, S. Hasegawa, Y. Okitsu, A. Kondo, Y. Onishi, F. Nagami, H. Kiyomoto, A. Hozawa, N. Fuse, M. Nagasaki, R. Shimizu, J. Yasuda, H. Harigae, and M. Yamamoto. Monitoring of minimal residual disease in early T-cell precursor acute lymphoblastic leukaemia by next-generation sequencing. Br J Haematol, 176(2): 318-321, 2017.

2016

K. Kojima, Y. Kawai, K. Misawa, T. Mimori, and M. Nagasaki. STR-realigner: a realignment method for short tandem repeat regions. BMC Genomics, 17(1): 991, 2016.

H. Koso, A. Tsuhako, C.Y. Lai, Y. Baba, M. Otsu, K. Ueno, M. Nagasaki, Y. Suzuki, and S. Watanabe. Conditional rod photoreceptor ablation reveals Sall1 as a microglial marker and regulator of microglial morphology in the retina. Glia, 64(11): 2005-2024, 2016.

A. Masamune, E. Nakano, T. Niihori, S. Hamada, M. Nagasaki, Y. Aoki, and T. Shimosegawa. Variants in the UBR1 gene are not associated with chronic pancreatitis in Japan. Pancreatology, 16(5): 814-818, 2016.

T. Hasegawa, K. Kojima, Y. Kawai, K. Misawa, T. Mimori, and M. Nagasaki. AP-SKAT: highly-efficient genome-wide rare variant association test. BMC Genomics, 17(1): 745, 2016.

S. Kuriyama, N. Yaegashi, F. Nagami, T. Arai, Y. Kawaguchi, N. Osumi, M. Sakaida, Y. Suzuki, K. Nakayama, H. Hashizume, G. Tamiya, H. Kawame, K. Suzuki, A. Hozawa, N. Nakaya, M. Kikuya, H. Metoki, I. Tsuji, N. Fuse, H. Kiyomoto, J. Sugawara, A. Tsuboi, S. Egawa, K. Ito, K. Chida, T. Ishii, H. Tomita, Y. Taki, N. Minegishi, N. Ishii, J. Yasuda, K. Igarashi, R. Shimizu, M. Nagasaki, S. Koshiba, K. Kinoshita, S. Ogishima, T. Takai-Igarashi, T. Tominaga, O. Tanabe, N. Ohuchi, T. Shimosegawa, S. Kure, H. Tanaka, S. Ito, J. Hitomi, K. Tanno, M. Nakamura, K. Ogasawara, S. Kobayashi, K. Sakata, M. Satoh, A. Shimizu, M. Sasaki, R. Endo, K. Sobue, T. Tohoku Medical Megabank Project Study Group, and M. Yamamoto. The Tohoku Medical Megabank Project: Design and Mission. J Epidemiol, 26(9): 493-511, 2016.

K. Kojima, Y. Kawai, N. Nariai, T. Mimori, T. Hasegawa, and M. Nagasaki. Short tandem repeat number estimation from paired-end reads for multiple individuals by considering coalescent tree. BMC Genomics, 17 Suppl 5: 494, 2016.

S. Koshiba, I. Motoike, K. Kojima, T. Hasegawa, M. Shirota, T. Saito, D. Saigusa, I. Danjoh, F. Katsuoka, S. Ogishima, Y. Kawai, Y. Yamaguchi-Kabata, M. Sakurai, S. Hirano, J. Nakata, H. Motohashi, A. Hozawa, S. Kuriyama, N. Minegishi, M. Nagasaki, T. Takai-Igarashi, N. Fuse, H. Kiyomoto, J. Sugawara, Y. Suzuki, S. Kure, N. Yaegashi, O. Tanabe, K. Kinoshita, J. Yasuda, and M. Yamamoto. The structural origin of metabolic quantitative diversity. Sci Rep, 6: 31463, 2016.

Y. Sun, A. Irwanto, L. Toyo-Oka, M. Hong, H. Liu, A.K. Andiappan, H. Choi, Y. Hitomi, G. Yu, Y. Yu, F. Bao, C. Wang, X. Fu, Z. Yue, H. Wang, H. Zhang, M. Kawashima, K. Kojima, M. Nagasaki, M. Nakamura, S.K. Yang, B.D. Ye, Y. Denise, O. Rotzschke, K. Song, K. Tokunaga, F. Zhang, and J. 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, 6: 31429, 2016.

K. Ueno, T. Iwagawa, H. Kuribayashi, Y. Baba, H. Nakauchi, A. Murakami, M. Nagasaki, Y. Suzuki, and S. Watanabe. Transition of differential histone H3 methylation in photoreceptors and other retinal cells during retinal differentiation. Sci Rep, 6: 29264, 2016.

J. Yamagishi, Y. Sato, N. Shinozaki, B. Ye, A. Tsuboi, M. Nagasaki, and R. Yamashita. Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes. PLoS One, 11(4): e0154389, 2016.

M. Nagasaki, Y. Kawai, K. Kojima, T. Mimori, and Y. Yamaugchi-Kabata. [Construction of 1070 Whole-genome Japanese Reference Panel and Bioinformatics]. Seikagaku, 88(1): 15-24, 2016.

N. Nariai, K. Kojima, T. Mimori, Y. Kawai, and M. Nagasaki. A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes. BMC Genomics, 17 Suppl 1: 2, 2016.

M. Kohda, Y. Tokuzawa, Y. Kishita, H. Nyuzuki, Y. Moriyama, Y. Mizuno, T. Hirata, Y. Yatsuka, Y. Yamashita-Sugahara, Y. Nakachi, H. Kato, A. Okuda, S. Tamaru, N.N. Borna, K. Banshoya, T. Aigaki, Y. Sato-Miyata, K. Ohnuma, T. Suzuki, A. Nagao, H. Maehata, F. Matsuda, K. Higasa, M. Nagasaki, J. Yasuda, M. Yamamoto, T. Fushimi, M. Shimura, K. Kaiho-Ichimoto, H. Harashima, T. Yamazaki, M. Mori, K. Murayama, A. Ohtake, and Y. Okazaki. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies. PLoS Genet, 12(1): e1005679, 2016.

2015

Y. Yamaguchi-Kabata, N. Nariai, Y. Kawai, Y. Sato, K. Kojima, M. Tateno, F. Katsuoka, J. Yasuda, M. Yamamoto, and M. Nagasaki. iJGVD: an integrative Japanese genome variation database based on whole-genome sequencing. Hum Genome Var, 2: 15050, 2015.

Y. Kawai, T. Mimori, K. Kojima, N. Nariai, I. Danjoh, R. Saito, J. Yasuda, M. Yamamoto, and M. Nagasaki. Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals. J Hum Genet, 60(10): 581-587, 2015.

T. Mori, M. Sumii, F. Fujishima, K. Ueno, M. Emi, M. Nagasaki, C. Ishioka and N. Chiba. Somatic alteration and depleted nuclear expression of BAP1 in human esophageal squamous cell carcinoma. Cancer Sci, 106(9): 1118-29, 2015.

M. Nagasaki, J. Yasuda, F. Katsuoka, N. Nariai, K. Kojima, Y. Kawai, Y. Yamaguchi-Kabata, J. Yokozawa, I. Danjoh, S. Saito, Y. Sato, T. Mimori, K. Tsuda, R. Saito, X. Pan, S. Nishikawa, S. Ito, Y. Kuroki, O. Tanabe, N. Fuse, S. Kuriyama, H. Kiyomoto, A. Hozawa, N. Minegishi, J. Douglas Engel, K. Kinoshita, S. Kure, N. Yaegashi, and M. Yamamoto. Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nat Commun, 6: 8018, 2015.

Y. Sato, J. Yamagishi, R. Yamashita, N. Shinozaki, B. Ye, T. Yamada, M. Yamamoto, M. Nagasaki, and A. Tsuboi. Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals. PLoS One, 10(6): e0131607, 2015.

N. Nariai, K. Kojima, S. Saito, T. Mimori, Y. Sato, Y. Kawai, Y. Yamaguchi-Kabata, J. Yasuda, and M. Nagasaki. HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data. BMC Genomics, 16 Suppl 2: S7, 2015.

T. Mimori, N. Nariai, K. Kojima, Y. Sato, Y. Kawai, Y. Yamaguchi-Kabata, and M. Nagasaki. Estimating copy numbers of alleles from population-scale high-throughput sequencing data. BMC Bioinformatics, 16 Suppl 1: S4, 2015.

2014

T. Hasegawa, M. Nagasaki, R. Yamaguchi, S. Imoto, and S. Miyano. An efficient method of exploring simulation models by assimilating literature and biological observational data. Biosystems, 121: 54-66, 2014.

T. Fujiwara, N. Fukuhara, R. Funayama, N. Nariai, M. Kamata, T. Nagashima, K. Kojima, Y. Onishi, Y. Sasahara, K. Ishizawa, M. Nagasaki, K. Nakayama, and H. Harigae. Identification of acquired mutations by whole-genome sequencing in GATA-2 deficiency evolving into myelodysplasia and acute leukemia. Ann Hematol, 93(9): 1515-1522, 2014.

T. Hasegawa, R. Yamaguchi, M. Nagasaki, S. Miyano, and S. 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.

I.N. Motoike, M. Matsumoto, I. Danjoh, F. Katsuoka, K. Kojima, N. Nariai, Y. Sato, Y. Yamaguchi-Kabata, S. Ito, H. Kudo, I. Nishijima, S. Nishikawa, X. Pan, R. Saito, S. Saito, T. Saito, M. Shirota, K. Tsuda, J. Yokozawa, K. Igarashi, N. Minegishi, O. Tanabe, N. Fuse, M. Nagasaki, K. Kinoshita, J. Yasuda, and M. Yamamoto. 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.

Y. Sato, K. Kojima, N. Nariai, Y. Yamaguchi-Kabata, Y. Kawai, M. Takahashi, T. Mimori, and M. Nagasaki. SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing. BMC Genomics, 15: 664, 2014.

C. Li, M. Nagasaki, E. Ikeda, Y. Sekiya, and S. Miyano. CSML2SBML: a novel tool for converting quantitative biological pathway models from CSML into SBML. Biosystems, 121: 22-28, 2014.

F. Katsuoka, J. Yokozawa, K. Tsuda, S. Ito, X. Pan, M. Nagasaki, J. Yasuda, and M. Yamamoto. An efficient quantitation method of next-generation sequencing libraries by using MiSeq sequencer. Anal Biochem, 466: 27-29, 2014.

N. Nariai, K. Kojima, T. Mimori, Y. Sato, Y. Kawai, Y. Yamaguchi-Kabata, and M. Nagasaki. TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads. BMC Genomics, 15 Suppl 10: S5, 2014.

K. Kojima, N. Nariai, T. Mimori, Y. Yamaguchi-Kabata, Y. Sato, Y. Kawai, M. Nagasaki. HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads. Algorithms for Computational Biology, 8542: 107-118, 2014.

T. Ohtsuki, N. Nariai, K. Kojima, T. Mimori, Y. Sato, Y. Kawai, Y. Yamaguchi-Kabata, T. Shibuya and M. Nagasaki. SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints. Algorithms for Computational Biology, 8542: 208-219, 2014.

2013

K. Kojima, N. Nariai, T. Mimori, M. Takahashi, Y. Yamaguchi-Kabata, Y. Sato, and M. Nagasaki. A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads. Bioinformatics, 29(22): 2835-2843, 2013.

A. Kon, L.Y. Shih, M. Minamino, M. Sanada, Y. Shiraishi, Y. Nagata, K. Yoshida, Y. Okuno, M. Bando, R. Nakato, S. Ishikawa, A. Sato-Otsubo, G. Nagae, A. Nishimoto, C. Haferlach, D. Nowak, Y. Sato, T. Alpermann, M. Nagasaki, T. Shimamura, H. Tanaka, K. Chiba, R. Yamamoto, T. Yamaguchi, M. Otsu, N. Obara, M. Sakata-Yanagimoto, T. Nakamaki, K. Ishiyama, F. Nolte, W.K. Hofmann, S. Miyawaki, S. Chiba, H. Mori, H. Nakauchi, H.P. Koeffler, H. Aburatani, T. Haferlach, K. Shirahige, S. Miyano, and S. Ogawa. Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat Genet, 45(10): 1232-1237, 2013.

S.R. Razak, K. Ueno, N. Takayama, N. Nariai, M. Nagasaki, R. Saito, H. Koso, C.Y. Lai, M. Murakami, K. Tsuji, T. Michiue, H. Nakauchi, M. Otsu, and S. Watanabe. Profiling of microRNA in human and mouse ES and iPS cells reveals overlapping but distinct microRNA expression patterns. PLoS One, 8(9): e73532, 2013.

N. Nariai, O. Hirose, K. Kojima, and M. Nagasaki. TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference. Bioinformatics, 29(18): 2292-2299, 2013.

T. Hiramoto, Y. Ebihara, Y. Mizoguchi, K. Nakamura, K. Yamaguchi, K. Ueno, N. Nariai, S. Mochizuki, S. Yamamoto, M. Nagasaki, Y. Furukawa, K. Tani, H. Nakauchi, M. Kobayashi, and K. Tsuji. Wnt3a stimulates maturation of impaired neutrophils developed from severe congenital neutropenia patient-derived pluripotent stem cells. Proc Natl Acad Sci U S A, 110(8): 3023-3028, 2013.

M. Nagasaki, A. Fujita, Y. Sekiya, A. Saito, E. Ikeda, C. Li, and S. Miyano. XiP: a computational environment to create, extend and share workflows. Bioinformatics, 29(1): 137-139, 2013.

T. Mimori, N. Nariai, K. Kojima, M. Takahashi, A. Ono, Y. Sato, Y. Yamaguchi-Kabata, and M. Nagasaki. iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. BMC Syst Biol, 7 Suppl 6: S8, 2013.

2012

H. Koso, H. Takeda, C.C. Yew, J.M. Ward, N. Nariai, K. Ueno, M. Nagasaki, S. Watanabe, A.G. Rust, D.J. Adams, N.G. Copeland, and N.A. Jenkins. Transposon mutagenesis identifies genes that transform neural stem cells into glioma-initiating cells. Proc Natl Acad Sci U S A, 109(44): E2998-3007, 2012.

S. Kawano, T. Shimamura, A. Niida, S. Imoto, R. Yamaguchi, M. Nagasaki, R. Yoshida, C. Print, and S. Miyano. Identifying gene pathways associated with cancer characteristics via sparse statistical methods. IEEE/ACM Trans Comput Biol Bioinform, 9(4): 966-972, 2012.

S. Fujimori, N. Hirai, K. Masuoka, T. Oshikubo, T. Yamashita, T. Washio, A. Saito, M. Nagasaki, S. Miyano, and E. Miyamoto-Sato. IRView: a database and viewer for protein interacting regions. Bioinformatics, 28(14): 1949-1950, 2012.

M. Yamamoto, R. Yamaguchi, K. Munakata, K. Takashima, M. Nishiyama, K. Hioki, Y. Ohnishi, M. Nagasaki, S. Imoto, S. Miyano, A. Ishige, and K. Watanabe. 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.

A. Fujimoto, Y. Totoki, T. Abe, K.A. Boroevich, F. Hosoda, H.H. Nguyen, M. Aoki, N. Hosono, M. Kubo, F. Miya, Y. Arai, H. Takahashi, T. Shirakihara, M. Nagasaki, T. Shibuya, K. Nakano, K. Watanabe-Makino, H. Tanaka, H. Nakamura, J. Kusuda, H. Ojima, K. Shimada, T. Okusaka, M. Ueno, Y. Shigekawa, Y. Kawakami, K. Arihiro, H. Ohdan, K. Gotoh, O. Ishikawa, S. Ariizumi, M. Yamamoto, T. Yamada, K. Chayama, T. Kosuge, H. Yamaue, N. Kamatani, S. Miyano, H. Nakagama, Y. Nakamura, T. Tsunoda, T. Shibata, and H. Nakagawa. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet, 44(7): 760-764, 2012.

M. Yamauchi, R. Yamaguchi, A. Nakata, T. Kohno, M. Nagasaki, T. Shimamura, S. Imoto, A. Saito, K. Ueno, Y. Hatanaka, R. Yoshida, T. Higuchi, M. Nomura, D.G. Beer, J. Yokota, S. Miyano, and N. Gotoh. Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma. PLoS One, 7(9): e43923, 2012.

2011

S. Suzuki, T. Yasuda, Y. Shiraishi, S. Miyano, and M. Nagasaki. ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinformatics, 12 Suppl 14: S7, 2011.

G. Chalkidis, M. Nagasaki, and S. Miyano. High performance hybrid functional Petri net simulations of biological pathway models on CUDA. IEEE/ACM Trans Comput Biol Bioinform, 8(6): 1545-1556, 2011.

H. Matsuno, M. Nagasaki, S. Miyano. Hybrid Petri net based modeling for biological pathway simulation. Nat. Comput, 10:1099-1120, 2011.

K. Yoshida, M. Sanada, Y. Shiraishi, D. Nowak, Y. Nagata, R. Yamamoto, Y. Sato, A. Sato-Otsubo, A. Kon, M. Nagasaki, G. Chalkidis, Y. Suzuki, M. Shiosaka, R. Kawahata, T. Yamaguchi, M. Otsu, N. Obara, M. Sakata-Yanagimoto, K. Ishiyama, H. Mori, F. Nolte, W.K. Hofmann, S. Miyawaki, S. Sugano, C. Haferlach, H.P. Koeffler, L.Y. Shih, T. Haferlach, S. Chiba, H. Nakauchi, S. Miyano, and S. Ogawa. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature, 478(7367): 64-69, 2011.

E. Jeong, M. Nagasaki, E. Ikeda, Y. Sekiya, A. Saito, and S. Miyano. CSO validator: improving manual curation workflow for biological pathways. Bioinformatics, 27(17): 2471-2472, 2011.

M. Nagasaki, A. Saito, A. Fujita, G. Tremmel, K. Ueno, E. Ikeda, E. Jeong, and S. Miyano. Systems biology model repository for macrophage pathway simulation. Bioinformatics, 27(11): 1591-1593, 2011.

Y. Tamada, S. Imoto, H. Araki, M. Nagasaki, C. Print, D.S. Charnock-Jones, and S. Miyano. Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers. IEEE/ACM Trans Comput Biol Bioinform, 8(3): 683-697, 2011.

C. Li, M. Nagasaki, C.H. Koh, and S. Miyano. Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension. Mol Biosyst, 7(5): 1576-1592, 2011.

Y. Tamada, R. Yamaguchi, S. Imoto, O. Hirose, R. Yoshida, M. Nagasaki, and S. Miyano. SiGN-SSM: open source parallel software for estimating gene networks with state space models. Bioinformatics, 27(8): 1172-1173, 2011.

C.H. Koh, M. Nagasaki, A. Saito, C. Li, L. Wong, and S. Miyano. MIRACH: efficient model checker for quantitative biological pathway models. Bioinformatics, 27(5): 734-735, 2011.

E. Jeong, M. Nagasaki, K. Ueno, and S. Miyano. Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinformatics, 12 Suppl 1: S8, 2011.

M. Yamauchi, I. Yoshino, R. Yamaguchi, T. Shimamura, M. Nagasaki, S. Imoto, A. Niida, F. Koizumi, T. Kohno, J. Yokota, S. Miyano, and N. Gotoh. N-cadherin expression is a potential survival mechanism of gefitinib-resistant lung cancer cells. Am J Cancer Res, 1(7): 823-833, 2011.

Y. Tamada, T. Shimamura, R. Yamaguchi, S. Imoto, M. Nagasaki, and S. Miyano. Sign: large-scale gene network estimation environment for high performance computing. Genome Inform, 25(1): 40-52, 2011.

T. Shimamura, S. Imoto, Y. Shimada, Y. Hosono, A. Niida, M. Nagasaki, R. Yamaguchi, T. Takahashi, and S. Miyano. A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition. PLoS One, 6(6): e20804, 2011.

M. Nagasaki, A. Saito, E. Jeong, C. Li, K. Kojima, E. Ikeda, and S. Miyano. Cell illustrator 4.0: a computational platform for systems biology. Stud Health Technol Inform, 162: 160-181, 2011.

K. Kaufmann, M. Nagasaki, and R. Jauregui. Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis thaliana. Stud Health Technol Inform, 162: 279-297, 2011.

A. Doi, M. Nagasaki, H. Matsuno, and S. Miyano. Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net. Stud Health Technol Inform, 162: 130-142, 2011.

A. Doi, S. Fujita, H. Matsuno, M. Nagasaki, and S. Miyano. Constructing biological pathway models with hybrid functional petri nets. Stud Health Technol Inform, 162: 92-112, 2011.

2010

A. Niida, S. Imoto, R. Yamaguchi, M. Nagasaki, A. Fujita, T. Shimamura, and S. Miyano. Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinformatics, 26(24): 3090-3097, 2010.

S. Kawano, T. Shimamura, A. Niida, S. Imoto, R. Yamaguchi, M. Nagasaki, R. Yoshida, C. Print and S. Miyano. Discovering Functional Gene Pathways Associated with Cancer Heterogeneity via Sparse Supervised Learning. 2010 Ieee International Conference on Bioinformatics and Biomedicine, 253-258, 2010.

A. Fujimoto, H. Nakagawa, N. Hosono, K. Nakano, T. Abe, K.A. Boroevich, M. Nagasaki, R. Yamaguchi, T. Shibuya, M. Kubo, S. Miyano, Y. Nakamura, and T. Tsunoda. Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet, 42(11): 931-936, 2010.

S. Tasaki, M. Nagasaki, H. Kozuka-Hata, K. Semba, N. Gotoh, S. Hattori, J. Inoue, T. Yamamoto, S. Miyano, S. Sugano, and M. Oyama. Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling. PLoS One, 5(11): e13926, 2010.

C.H. Koh, M. Nagasaki, A. Saito, L. Wong, and S. Miyano. DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics, 26(14): 1794-1796, 2010.

J.H. Do, M. Nagasaki, and S. Miyano. The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. Biosystems, 100(3): 178-184, 2010.

K. Kojima, M. Nagasaki, and S. Miyano. An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinformatics, 11: 335, 2010.

A. Niida, S. Imoto, R. Yamaguchi, M. Nagasaki, and S. Miyano. Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues. PLoS One, 5(6): e10910, 2010.

T. Shimamura, S. Imoto, R. Yamaguchi, M. Nagasaki, and S. Miyano. Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics, 26(8): 1064-1072, 2010.

C. Li, M. Nagasaki, A. Saito, and S. Miyano. Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. BMC Syst Biol, 4: 39, 2010.

A. Niida, S. Imoto, M. Nagasaki, R. Yamaguchi, and S. Miyano. A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells. Genome Inform, 22: 121-131, 2010.

K. Kojima, R. Yamaguchi, S. Imoto, M. Yamauchi, M. Nagasaki, R. Yoshida, T. Shimamura, K. Ueno, T. Higuchi, N. Gotoh, and S. Miyano. A state space representation of VAR models with sparse learning for dynamic gene networks. Genome Inform, 22: 56-68, 2010.

A. Fujita, M. Nagasaki, S. Imoto, A. Saito, E. Ikeda, T. Shimamura, R. Yamaguchi, Y. Hayashizaki, and S. Miyano. Comparison of gene expression profiles produced by CAGE, illumina microarray and real time RT-PCR. Genome Inform, 24: 56-68, 2010.

K. Kaufmann, M. Nagasaki, and R. Jauregui. Modelling the molecular interactions in the flower developmental network of Arabidopsis thaliana. In Silico Biol, 10(1): 125-143, 2010.

K. Kojima, S. Imoto, M. Nagasaki, and S. Miyano. Gene regulatory network clustering for graph layout based on microarray gene expression data. Genome Inform, 24: 84-95, 2010.

T. Shimamura, S. Imoto, M. Nagasaki, M. Yamauchi, R. Yamaguchi, A. Fujita, Y. Tamada, N. Gotoh, and S. Miyano. Collocation-based sparse estimation for constructing dynamic gene networks. Genome Inform, 24: 164-178, 2010.

M. Nagasaki, A. Saito, E. Jeong, C. Li, K. Kojima, E. Ikeda, and S. Miyano. Cell Illustrator 4.0: a computational platform for systems biology. In Silico Biol, 10(1): 5-26, 2010.

2009

N. Yoshikawa, M. Nagasaki, M. Sano, S. Tokudome, K. Ueno, N. Shimizu, S. Imoto, S. Miyano, M. Suematsu, K. Fukuda, C. Morimoto, and H. Tanaka. Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism. Am J Physiol Endocrinol Metab, 296(6): E1363-1373, 2009.

C. Li, M. Nagasaki, K. Ueno, and S. Miyano. Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Syst Biol, 3: 42, 2009.

T. Shimamura, S. Imoto, R. Yamaguchi, A. Fujita, M. Nagasaki, and S. Miyano. Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst Biol, 3: 41, 2009.

T.B. Hashimoto, M. Nagasaki, K. Kojima, and S. Miyano. BFL: a node and edge betweenness based fast layout algorithm for large scale networks. BMC Bioinformatics, 10: 19, 2009.

H. Araki, Y. Tamada, S. Imoto, B. Dunmore, D. Sanders, S. Humphrey, M. Nagasaki, A. Doi, Y. Nakanishi, K. Yasuda, Y. Tomiyasu, K. Tashiro, C. Print, D.S. Charnock-Jones, S. Kuhara, and S. Miyano. Analysis of PPARalpha-dependent and PPARalpha-independent transcript regulation following fenofibrate treatment of human endothelial cells. Angiogenesis, 12(3): 221-229, 2009.

T. Yamamoto, H. Bannai, M. Nagasaki and S. Miyano. Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality. Discovery Science, 5808: 465-472, 2009.

S. Miyano, R. Yamaguchi, Y. Tamada, M. Nagasaki and S. Imoto. Gene Networks Viewed through Two Models. International Conference on Bioinformatics and Computational Biology, 5462: 54-66, 2009.

Y. Watanabe-Fukuda, M. Yamamoto, N. Miura, M. Fukutake, A. Ishige, R. Yamaguchi, M. Nagasaki, A. Saito, S. Imoto, S. Miyano, J. Takeda, and K. Watanabe. Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine. J Gastroenterol, 44(5): 380-389, 2009.

Y. Tamada, H. Araki, S. Imoto, M. Nagasaki, A. Doi, Y. Nakanishi, Y. Tomiyasu, K. Yasuda, B. Dunmore, D. Sanders, S. Humphreys, C. Print, D.S. Charnock-Jones, K. Tashiro, S. Kuhara, and S. Miyano. Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks. Pac Symp Biocomput: 251-263, 2009.

K. Nakamura, R. Yoshida, M. Nagasaki, S. Miyano, and T. Higuchi. Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing. Pac Symp Biocomput: 227-238, 2009.

2008

K. Numata, R. Yoshida, M. Nagasaki, A. Saito, S. Imoto, and S. Miyano. ExonMiner: Web service for analysis of GeneChip Exon array data. BMC Bioinformatics, 9: 494, 2008.

R. Yoshida, M. Nagasaki, R. Yamaguchi, S. Imoto, S. Miyano, and T. Higuchi. Bayesian learning of biological pathways on genomic data assimilation. Bioinformatics, 24(22): 2592-2601, 2008.

M. Nagasaki, A. Saito, C. Li, E. Jeong, and S. Miyano. Systematic reconstruction of TRANSPATH data into cell system markup language. BMC Syst Biol, 2: 53, 2008.

K. Kojima, M. Nagasaki, and S. Miyano. Fast grid layout algorithm for biological networks with sweep calculation. Bioinformatics, 24(12): 1433-1441, 2008.

R. Yamaguchi, S. Imoto, M. Yamauchi, M. Nagasaki, R. Yoshida, T. Shimamura, Y. Hatanaka, K. Ueno, T. Higuchi, N. Gotoh, and S. Miyano. Predicting differences in gene regulatory systems by state space models. Genome Inform, 21: 101-113, 2008.

E. Jeong, M. Nagasaki, and S. Miyano. Rule-based reasoning for system dynamics in cell systems. Genome Inform, 20: 25-36, 2008.

Y. Hatanaka, M. Nagasaki, R. Yamaguchi, T. Obayashi, K. Numata, A. Fujita, T. Shimamura, Y. Tamada, S. Imoto, K. Kinoshita, K. Nakai, and S. Miyano. A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human. Genome Inform, 20: 212-221, 2008.

2007

K. Kojima, M. Nagasaki, E. Jeong, M. Kato, and S. Miyano. An efficient grid layout algorithm for biological networks utilizing various biological attributesBMC Bioinformatics, 8: 76, 2007.

A. Saito, M. Nagasaki, M. Oyama, H. Kozuka-Hata, K. Semba, S. Sugano, T. Yamamoto, and S. Miyano. AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transductionBMC Bioinformatics, 8: 15, 2007.

R. Yamaguchi, M. Yamamoto, S. Imoto, M. Nagasaki, R. Yoshida, K. Tsuiji, A. Ishige, H. Asou, K. Watanabe, and S. Miyano. Identification of activated transcription factors from microarray gene expression data of Kampo medicine-treated mice. Genome Inform, 18: 119-129, 2007.

E. Jeong, M. Nagasaki, A. Saito, and S. Miyano. Cell system ontology: representation for modeling, visualizing, and simulating biological pathwaysIn Silico Biol, 7(6): 623-638, 2007.

E. Jeong, M. Nagasaki, and S. Miyano. Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway. Genome Inform, 18: 225-236, 2007.

2006

R. Yoshida, K. Numata, S. Imoto, M. Nagasaki, A. Doi, K. Ueno, and S. Miyano. A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST Arrays. Genome Inform, 17(1): 88-99, 2006.

A. Saito, M. Nagasaki, A. Doi, K. Ueno, and S. Miyano. Cell fate simulation model of gustatory neurons with MicroRNAs double-negative feedback loop by hybrid functional Petri net with extension. Genome Inform, 17(1): 100-111, 2006.

M. Nagasaki, R. Yamaguchi, R. Yoshida, S. Imoto, A. Doi, Y. Tamada, H. Matsuno, S. Miyano, and T. Higuchi. Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Inform, 17(1): 46-61, 2006.

A. Doi, M. Nagasaki, K. Ueno, H. Matsuno, and S. Miyano. A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activityGenome Inform, 17(1): 112-123, 2006.

A. Doi, M. Nagasaki, H. Matsuno, and S. Miyano. Simulation-based validation of the p53 transcriptional activity with hybrid functional petri netIn Silico Biol, 6(1-2): 1-13, 2006.

S. Tasaki, M. Nagasaki, M. Oyama, H. Hata, K. Ueno, R. Yoshida, T. Higuchi, S. Sugano, and S. Miyano. Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Inform, 17(2): 226-238, 2006.

2005

M. Nagasaki, A. Doi, and S. Miyano. [Dynamic pathway modeling language: CSML]. Tanpakushitsu Kakusan Koso, 50(16 Suppl): 2269-2274, 2005.

M. Kato, M. Nagasaki, A. Doi, and S. Miyano. Automatic drawing of biological networks using cross cost and subcomponent data. Genome Inform, 16(2): 22-31, 2005.

-2004

M. Nagasaki, A. Doi, H. Matsuno, and S. Miyano. A versatile petri net based architecture for modeling and simulation of complex biological processes. Genome Inform, 15(1): 180-197, 2004.

A. Doi, S. Fujita, H. Matsuno, M. Nagasaki, and S. Miyano. Constructing biological pathway models with hybrid functional Petri netsIn Silico Biol, 4(3): 271-291, 2004.

T. Kono, R. Noda, H. Kitacaze, M. Nagasaki, A. Doi, H. Matsuno, and S. Miyano. Distributed Client-Server System Architecture for High Performance Simulations on Genomic Object Net. Genome Inform, 14: 619-620, 2003.

M. Nagasaki, A. Doi, H. Matsuno, and S. Miyano. Genomic Object Net: I. A platform for modelling and simulating biopathways. Appl Bioinformatics, 2(3): 181-184, 2003.

A. Doi, M. Nagasaki, S. Fujita, H. Matsuno, and S. Miyano. Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension. Appl Bioinformatics, 2(3): 185-188, 2003.

H. Matsuno, A. Doi, M. Nagasaki, and S. Miyano. Hybrid Petri net representation of gene regulatory networkPac Symp Biocomput: 341-352, 2000.

M. Nagasaki, S. Onami, S. Miyano, and H. Kitano. Bio-calculus: Its Concept and Molecular Interaction. Genome Inform Ser Workshop Genome Inform, 10: 133-143, 1999.

V.N. Kuz’menko, and N. Bordiushkov Iu. [Effect of central and peripheral estrogen administration on the indices of immune homeostasis]. Probl Endokrinol (Mosk), 30(3): 45-49, 1984.

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)