Tohoku University Tohoku Medical Megabank Organization (Integrative Genomics)

1.   Tadaka Shu, Katsuoka Fumiki, Ueki Masao, et al. 3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome. Human Genome Variation. 2019; 6 (1): 28. doi:10.1038/s41439-019-0059-5  
2.   Kakuta Yoichi, Kawai Yosuke, Naito Takeo, et al. A Genome-wide Association Study Identifying RAP1A as a Novel Susceptibility Gene for Crohn’s Disease in Japanese Individuals. Journal of Crohn's and Colitis. 2019; 13 (5): 648-658. doi:10.1093/ecco-jcc/jjy197  
3.   Shibuya Yusuke, Tokunaga Hideki, Saito Sakae, et al. Identification of somatic genetic alterations in ovarian clear cell carcinoma with next generation sequencing. Genes, Chromosomes and Cancer. 2018; 57 (2): 51-60. doi:10.1002/gcc.22507  
4.   Tadaka Shu, Saigusa Daisuke, Motoike Ikuko N., et al. jMorp: Japanese Multi Omics Reference Panel. Nucleic Acids Research. 2018; 46 (D1): D551-D557. doi:10.1093/nar/gkx978  
5.   Chiba Hirofumi, Kakuta Yoichi, Kinouchi Yoshitaka, et al. Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease. PLOS ONE. 2018; 13 (3): e0194036. doi:10.1371/journal.pone.0194036  
6.   Pan Xiaoqing, Nariai Naoki, Fukuhara Noriko, et al. Monitoring of minimal residual disease in early T-cell precursor acute lymphoblastic leukaemia by next-generation sequencing. British Journal of Haematology. 2017; 176 (2): 318-321. doi:10.1111/bjh.13948  
7.   Saigusa Daisuke, Okamura Yasunobu, Motoike Ikuko N., et al. Establishment of Protocols for Global Metabolomics by LC-MS for Biomarker Discovery. PLOS ONE. 2016; 11 (8): e0160555. doi:10.1371/journal.pone.0160555  
8.   Koshiba Seizo, Motoike Ikuko, Kojima Kaname, et al. The structural origin of metabolic quantitative diversity. Scientific Reports. 2016; 6 (1): 31463. doi:10.1038/srep31463  
9.   Mimori Takahiro, Nariai Naoki, Kojima Kaname, et al. Estimating copy numbers of alleles from population-scale high-throughput sequencing data. BMC Bioinformatics. 2015; 16 ((Suppl 1):S4): . doi:10.1186/1471-2105-16-S1-S4  
10.   Nariai Naoki, Kojima Kaname, Saito Sakae, et al. HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data. BMC Genomics. 2015; 16 ((Suppl 2):S7): .  
11.   Yamaguchi-Kabata Yumi, Nariai Naoki, Kawai Yosuke, et al. iJGVD: an integrative Japanese genome variation database based on whole-genome sequencing. Human Genome Variation. 2015; 2 : 15050. doi:10.1038/hgv.2015.50  
12.   Kawai Yosuke, Mimori Takahiro, Kojima Kaname, et al. Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals. Journal of Human Genetics. 2015; 60 (10): 581-587. doi:10.1038/jhg.2015.68  
13.   河合 洋介, 三森 隆広, 小島 要, et al. ジャポニカアレイの設計と全ゲノムインピュテーションによる活用. Medical Science Digest. 2015; 41 (5): 34-37.  
14.   Nagasaki Masao, Yasuda Jun, Katsuoka Fumiki, et al. Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nature communications. 2015; 6 : 8018. doi:10.1038/ncomms9018  
15.   Sato Yukuto, Yamagishi Junya, Yamashita Riu, et al. Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals. PLOS ONE. 2015; 10 (6): e0131607. doi:10.1371/journal.pone.0131607  
16.   Katsuoka Fumiki, Yokozawa Junji, Tsuda Kaoru, et al. An efficient quantitation method of next-generation sequencing libraries by using MiSeq sequencer. Analytical Biochemistry. 2014; 466 (466C): 27-29. doi:10.1016/j.ab.2014.08.015  
17.   Sato Yukuto, Kojima Kaname, Nariai Naoki, et al. SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing. BMC genomics. 2014; 15 (1): 664. doi:10.1186/1471-2164-15-664  
18.   Nariai Naoki, Kojima Kaname, Mimori Takahiro, et al. TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads. BMC Genomics. 2014; 15 ((Suppl 10):S5): . doi:10.1186/1471-2164-15-S10-S5  
19.   Motoike Ikuko N, Matsumoto Mitsuyo, Danjoh Inaho, et al. 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. 2014; 15 : 673. doi:10.1186/1471-2164-15-673  
20.   Takezawa Y, Kato K, Oota H, et al. Human genetic research, race, ethnicity and the labeling of populations: recommendations based on an interdisciplinary workshop in Japan. BMC Med Ethics. 2014; 15 : 33. doi:10.1186/1472-6939-15-33  
21.   Kojima Kaname, Nariai Naoki, Mimori Takahiro, et al. HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads. Lecture Notes in Computer Science. 2014; 8542 : 107-118. doi:10.1007/978-3-319-07953-0_9  
22.   Ohtsuki Tomohiko, Nariai Naoki, Kojima Kaname, et al. SVEM: a Structural Variant Estimation Method using Multi-Mapped Reads on Breakpoints. Lecture Notes in Computer Science. 2014; 8542 : 208-219. doi:10.1007/978-3-319-07953-0_17  
23.   Morihara T, Hayashi N, Yokokoji M, et al. Transcriptome analysis of distinct mouse strains reveals kinesin light chain-1 splicing as an amyloid-beta accumulation modifier. Proc Natl Acad Sci U S A. 2014; 111 (7): 2638-2643. doi:10.1073/pnas.1307345111  
24.   Kojima Kaname, Nariai Naoki, Mimori Takahiro, et al. A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads. Bioinformatics. 2013; Nov 15 (29(22)): 2835-43. doi:10.1093/bioinformatics/btt503  
25.   Nariai Naoki, Hirose Osamu, Kojima Kaname, Nagasaki Masao. TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference. Bioinformatics (Oxford, England). 2013; 29 (18): 2292-9. doi:10.1093/bioinformatics/btt381  
26.   Mimori Takahiro, Nariai Naoki, Kojima Kaname, et al. iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. BMC Syst Biol. 2013; 7 (Suppl 6): S8. doi:10.1186/1752-0509-7-S6-S8