Publications

1) Peer-reviewed papers published on international journal

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, 2020.

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.

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. 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.

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.

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.

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.

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 durationin the Japanese population. Sleep, 42(6), 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.

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. 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.

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, 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, 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. Masamune. Correction to: High-resolution melt analysis enables simple genotyping of complicated polymorphisms of codon 18 rendering the NUDT15 diplotype. J Gastroenterol, 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

R. Chia, A. Chio, and B.J. Traynor. Novel genes associated with amyotrophic lateral sclerosis: diagnostic and clinical implications. Lancet Neurol, 17(1): 94-102, 2018.

A. Nicolas, K.P. Kenna, A.E. Renton, N. Ticozzi, F. Faghri, R. Chia, J.A. Dominov, B.J. Kenna, M.A. Nalls, P. Keagle, A.M. Rivera, W. van Rheenen, N.A. Murphy, J. van Vugt, J.T. Geiger, R.A. Van der Spek, H.A. Pliner, Shankaracharya, B.N. Smith, G. Marangi, S.D. Topp, Y. Abramzon, A.S. Gkazi, J.D. Eicher, A. Kenna, G. Mora, A. Calvo, L. Mazzini, N. Riva, J. Mandrioli, C. Caponnetto, S. Battistini, P. Volanti, V. La Bella, F.L. Conforti, G. Borghero, S. Messina, I.L. Simone, F. Trojsi, F. Salvi, F.O. Logullo, S. D’Alfonso, L. Corrado, M. Capasso, L. Ferrucci, C.A.M. Moreno, S. Kamalakaran, D.B. Goldstein, A.D. Gitler, T. Harris, R.M. Myers, H. Phatnani, R.L. Musunuri, U.S. Evani, A. Abhyankar, M.C. Zody, J. Kaye, S. Finkbeiner, S.K. Wyman, A. LeNail, L. Lima, E. Fraenkel, C.N. Svendsen, L.M. Thompson, J.E. Van Eyk, J.D. Berry, T.M. Miller, S.J. Kolb, M. Cudkowicz, E. Baxi, M. Benatar, J.P. Taylor, E. Rampersaud, G. Wu, J. Wuu, G. Lauria, F. Verde, I. Fogh, C. Tiloca, G.P. Comi, G. Soraru, C. Cereda, P. Corcia, H. Laaksovirta, L. Myllykangas, L. Jansson, M. Valori, J. Ealing, H. Hamdalla, S. Rollinson, S. Pickering-Brown, R.W. Orrell, K.C. Sidle, A. Malaspina, J. Hardy, A.B. Singleton, J.O. Johnson, S. Arepalli, P.C. Sapp, D. McKenna-Yasek, M. Polak, S. Asress, S. Al-Sarraj, A. King, C. Troakes, C. Vance, J. de Belleroche, F. Baas, A. Ten Asbroek, J.L. Munoz-Blanco, D.G. Hernandez, J. Ding, J.R. Gibbs, S.W. Scholz, M.K. Floeter, R.H. Campbell, F. Landi, R. Bowser, S.M. Pulst, J.M. Ravits, D.J.L. MacGowan, J. Kirby, E.P. Pioro, R. Pamphlett, J. Broach, G. Gerhard, T.L. Dunckley, C.B. Brady, N.W. Kowall, J.C. Troncoso, I. Le Ber, K. Mouzat, S. Lumbroso, T.D. Heiman-Patterson, F. Kamel, L. Van Den Bosch, R.H. Baloh, T.M. Strom, T. Meitinger, A. Shatunov, K.R. Van Eijk, M. de Carvalho, M. Kooyman, B. Middelkoop, M. Moisse, R.L. McLaughlin, M.A. Van Es, M. Weber, K.B. Boylan, M. Van Blitterswijk, R. Rademakers, K.E. Morrison, A.N. Basak, J.S. Mora, V.E. Drory, P.J. Shaw, M.R. Turner, K. Talbot, O. Hardiman, K.L. Williams, J.A. Fifita, G.A. Nicholson, I.P. Blair, G.A. Rouleau, J. Esteban-Perez, A. Garcia-Redondo, A. Al-Chalabi, E. Rogaeva, L. Zinman, L.W. Ostrow, N.J. Maragakis, J.D. Rothstein, Z. Simmons, J. Cooper-Knock, A. Brice, S.A. Goutman, E.L. Feldman, S.B. Gibson, F. Taroni, A. Ratti, C. Gellera, P. Van Damme, W. Robberecht, P. Fratta, M. Sabatelli, C. Lunetta, A.C. Ludolph, P.M. Andersen, J.H. Weishaupt, W. Camu, J.Q. Trojanowski, V.M. Van Deerlin, R.H. Brown, Jr., L.H. van den Berg, J.H. Veldink, M.B. Harms, J.D. Glass, D.J. Stone, P. Tienari, V. Silani, A. Chio, C.E. Shaw, B.J. Traynor, and J.E. Landers. Genome-wide Analyses Identify KIF5A as a Novel ALS Gene. Neuron, 97(6): 1268-1283.e1266, 2018.

2017

M.A. van Es, O. Hardiman, A. Chio, A. Al-Chalabi, R.J. Pasterkamp, J.H. Veldink, and L.H. van den Berg. Amyotrophic lateral sclerosis. Lancet, 390(10107): 2084-2098, 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.

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.

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.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.

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.

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.

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.

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.

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.

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.

B. Benyamin, J. He, Q. Zhao, J. Gratten, F. Garton, P.J. Leo, Z. Liu, M. Mangelsdorf, A. Al-Chalabi, L. Anderson, T.J. Butler, L. Chen, X.D. Chen, K. Cremin, H.W. Deng, M. Devine, J. Edson, J.A. Fifita, S. Furlong, Y.Y. Han, J. Harris, A.K. Henders, R.L. Jeffree, Z.B. Jin, Z. Li, T. Li, M. Li, Y. Lin, X. Liu, M. Marshall, E.P. McCann, B.J. Mowry, S.T. Ngo, R. Pamphlett, S. Ran, D.C. Reutens, D.B. Rowe, P. Sachdev, S. Shah, S. Song, L.J. Tan, L. Tang, L.H. van den Berg, W. van Rheenen, J.H. Veldink, R.H. Wallace, L. Wheeler, K.L. Williams, J. Wu, X. Wu, J. Yang, W. Yue, Z.H. Zhang, D. Zhang, P.G. Noakes, I.P. Blair, R.D. Henderson, P.A. McCombe, P.M. Visscher, H. Xu, P.F. Bartlett, M.A. Brown, N.R. Wray, and D. Fan. Cross-ethnic meta-analysis identifies association of the GPX3-TNIP1 locus with amyotrophic lateral sclerosis. Nat Commun, 8(1): 611, 2017.

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.

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.

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.

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.

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. 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.

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.

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.

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.

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.

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.

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.

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.

K.C. Arthur, A. Calvo, T.R. Price, J.T. Geiger, A. Chio, and B.J. Traynor. Projected increase in amyotrophic lateral sclerosis from 2015 to 2040. Nat Commun, 7: 12408, 2016.

W. van Rheenen, A. Shatunov, A.M. Dekker, R.L. McLaughlin, F.P. Diekstra, S.L. Pulit, R.A. van der Spek, U. Vosa, S. de Jong, M.R. Robinson, J. Yang, I. Fogh, P.T. van Doormaal, G.H. Tazelaar, M. Koppers, A.M. Blokhuis, W. Sproviero, A.R. Jones, K.P. Kenna, K.R. van Eijk, O. Harschnitz, R.D. Schellevis, W.J. Brands, J. Medic, A. Menelaou, A. Vajda, N. Ticozzi, K. Lin, B. Rogelj, K. Vrabec, M. Ravnik-Glavac, B. Koritnik, J. Zidar, L. Leonardis, L.D. Groselj, S. Millecamps, F. Salachas, V. Meininger, M. de Carvalho, S. Pinto, J.S. Mora, R. Rojas-Garcia, M. Polak, S. Chandran, S. Colville, R. Swingler, K.E. Morrison, P.J. Shaw, J. Hardy, R.W. Orrell, A. Pittman, K. Sidle, P. Fratta, A. Malaspina, S. Topp, S. Petri, S. Abdulla, C. Drepper, M. Sendtner, T. Meyer, R.A. Ophoff, K.A. Staats, M. Wiedau-Pazos, C. Lomen-Hoerth, V.M. Van Deerlin, J.Q. Trojanowski, L. Elman, L. McCluskey, A.N. Basak, C. Tunca, H. Hamzeiy, Y. Parman, T. Meitinger, P. Lichtner, M. Radivojkov-Blagojevic, C.R. Andres, C. Maurel, G. Bensimon, B. Landwehrmeyer, A. Brice, C.A. Payan, S. Saker-Delye, A. Durr, N.W. Wood, L. Tittmann, W. Lieb, A. Franke, M. Rietschel, S. Cichon, M.M. Nothen, P. Amouyel, C. Tzourio, J.F. Dartigues, A.G. Uitterlinden, F. Rivadeneira, K. Estrada, A. Hofman, C. Curtis, H.M. Blauw, A.J. van der Kooi, M. de Visser, A. Goris, M. Weber, C.E. Shaw, B.N. Smith, O. Pansarasa, C. Cereda, R. Del Bo, G.P. Comi, S. D’Alfonso, C. Bertolin, G. Soraru, L. Mazzini, V. Pensato, C. Gellera, C. Tiloca, A. Ratti, A. Calvo, C. Moglia, M. Brunetti, S. Arcuti, R. Capozzo, C. Zecca, C. Lunetta, S. Penco, N. Riva, A. Padovani, M. Filosto, B. Muller, R.J. Stuit, I. Blair, K. Zhang, E.P. McCann, J.A. Fifita, G.A. Nicholson, D.B. Rowe, R. Pamphlett, M.C. Kiernan, J. Grosskreutz, O.W. Witte, T. Ringer, T. Prell, B. Stubendorff, I. Kurth, C.A. Hubner, P.N. Leigh, F. Casale, A. Chio, E. Beghi, E. Pupillo, R. Tortelli, G. Logroscino, J. Powell, A.C. Ludolph, J.H. Weishaupt, W. Robberecht, P. Van Damme, L. Franke, T.H. Pers, R.H. Brown, J.D. Glass, J.E. Landers, O. Hardiman, P.M. Andersen, P. Corcia, P. Vourc’h, V. Silani, N.R. Wray, P.M. Visscher, P.I. de Bakker, M.A. van Es, R.J. Pasterkamp, C.M. Lewis, G. Breen, A. Al-Chalabi, L.H. van den Berg, and J.H. Veldink. Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis. Nat Genet, 48(9): 1043-1048, 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. 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.

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.

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.

M. Gladman, and L. Zinman. The economic impact of amyotrophic lateral sclerosis: a systematic review. Expert Rev Pharmacoecon Outcomes Res, 15(3): 439-450, 2015.

E.T. Cirulli, B.N. Lasseigne, S. Petrovski, P.C. Sapp, P.A. Dion, C.S. Leblond, J. Couthouis, Y.F. Lu, Q. Wang, B.J. Krueger, Z. Ren, J. Keebler, Y. Han, S.E. Levy, B.E. Boone, J.R. Wimbish, L.L. Waite, A.L. Jones, J.P. Carulli, A.G. Day-Williams, J.F. Staropoli, W.W. Xin, A. Chesi, A.R. Raphael, D. McKenna-Yasek, J. Cady, J.M. Vianney de Jong, K.P. Kenna, B.N. Smith, S. Topp, J. Miller, A. Gkazi, A. Al-Chalabi, L.H. van den Berg, J. Veldink, V. Silani, N. Ticozzi, C.E. Shaw, R.H. Baloh, S. Appel, E. Simpson, C. Lagier-Tourenne, S.M. Pulst, S. Gibson, J.Q. Trojanowski, L. Elman, L. McCluskey, M. Grossman, N.A. Shneider, W.K. Chung, J.M. Ravits, J.D. Glass, K.B. Sims, V.M. Van Deerlin, T. Maniatis, S.D. Hayes, A. Ordureau, S. Swarup, J. Landers, F. Baas, A.S. Allen, R.S. Bedlack, J.W. Harper, A.D. Gitler, G.A. Rouleau, R. Brown, M.B. Harms, G.M. Cooper, T. Harris, R.M. Myers, and D.B. Goldstein. Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways. Science, 347(6229): 1436-1441, 2015.

C.C. Chang, C.C. Chow, L.C. Tellier, S. Vattikuti, S.M. Purcell, and J.J. Lee. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 4: 7, 2015.

P.R. Loh, G. Tucker, B.K. Bulik-Sullivan, B.J. Vilhjalmsson, H.K. Finucane, R.M. Salem, D.I. Chasman, P.M. Ridker, B.M. Neale, B. Berger, N. Patterson, and A.L. Price. Efficient Bayesian mixed-model analysis increases association power in large cohorts. Nat Genet, 47(3): 284-290, 2015.

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.

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.

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.

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.

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.

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.

A.E. Renton, A. Chio, and B.J. Traynor. State of play in amyotrophic lateral sclerosis genetics. Nat Neurosci, 17(1): 17-23, 2014.

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.

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. 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.

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.

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.

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.

2012

R. Ohkawa, T. Kishimoto, M. Kurano, T. Dohi, K. Miyauchi, H. Daida, M. Nagasaki, K. Uno, N. Hayashi, N. Sakai, N. Matsuyama, T. Nojiri, K. Nakamura, S. Okubo, H. Yokota, H. Ikeda, and Y. Yatomi. Development of an enzymatic assay for sphingomyelin with rapid and automatable performances: Analysis in healthy subjects and coronary heart disease patients. Clin Biochem, 45(16-17): 1463-1470, 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.

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.

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.

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.

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.

T. Yasuda, S. Suzuki, M. Nagasaki, and S. Miyano. ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. BMC Bioinformatics, 13: 279, 2012.

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.

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.
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.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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

C.J. Willer, Y. Li, and G.R. Abecasis. METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics, 26(17): 2190-2191, 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.

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.

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.

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.

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.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.

2008

Y. Watanabe, M. Okamoto, T. Ishii, S. Takatsuka, H. Taniguchi, M. Nagasaki, and A. Saito. Long-lasting anti-emetic effect of T-2328, a novel NK(1) antagonist. J Pharmacol Sci, 107(2): 151-158, 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.

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.

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.

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.

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

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 transduction. BMC Bioinformatics, 8: 15, 2007.

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

D. Hirtz, D.J. Thurman, K. Gwinn-Hardy, M. Mohamed, A.R. Chaudhuri, and R. Zalutsky. How common are the “common” neurologic disorders? Neurology, 68(5): 326-337, 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 activity. Genome 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 net. In 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 nets. In Silico Biol, 4(3): 271-291, 2004.

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 network. Pac Symp Biocomput: 341-352, 2000.

B.R. Brooks, R.G. Miller, M. Swash, and T.L. Munsat. El Escorial revisited: revised criteria for the diagnosis of amyotrophic lateral sclerosis. Amyotroph Lateral Scler Other Motor Neuron Disord, 1(5): 293-299, 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.

D.R. Rosen, T. Siddique, D. Patterson, D.A. Figlewicz, P. Sapp, A. Hentati, D. Donaldson, J. Goto, J.P. O’Regan, H.X. Deng, and et al. Mutations in Cu/Zn superoxide dismutase gene are associated with familial amyotrophic lateral sclerosis. Nature, 362(6415): 59-62, 1993.

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)