Tohoku University Tohoku Medical Megabank Organization (Kengo Kinoshita)
2019.09.20

1.   Sugawara Junichi, Ochi Daisuke, Yamashita Riu, et al. Maternity Log study: a longitudinal lifelog monitoring and multiomics analysis for the early prediction of complicated pregnancy. BMJ Open. 2019; 9 (2): bmjopen-2018-025939. doi:10.1136/bmjopen-2018-025939  
2.   Mori Minako, Hira Asuka, Yoshida Kenichi, et al. Pathogenic mutations identified by a multimodality approach in 117 Japanese Fanconi anemia patients. Haematologica. 2019; : haematol.2018.207241. doi:10.3324/haematol.2018.207241  
3.   Yamaguchi-Kabata Yumi, Yasuda Jun, Uruno Akira, et al. Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals. Human Genetics. 2019; 138 (4): 389-409. doi:10.1007/s00439-019-01998-7  
4.   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  
5.   Sato Tomonori, Kawasaki Yoshihide, Maekawa Masamitsu, et al. Value of global metabolomics in association with diagnosis and clinicopathological factors of renal cell carcinoma. International journal of cancer. 2019; 145 (2): 484-493. doi:10.1002/ijc.32115  
6.   Kuriyama Shinichi, Metoki Hirohito, Kikuya Masahiro, et al. Cohort Profile: Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study (TMM BirThree Cohort Study): Rationale, Progress and Perspective. International Journal of Epidemiology. 2019; : . doi:10.1093/ije/dyz169  
7.   Sakurai Rieko, Ueki Masao, Makino Satoshi, et al. Outlier detection for questionnaire data in biobanks. International Journal of Epidemiology. 2019; : . doi:10.1093/ije/dyz012  
8.   Kiniwa Yukiko, Yasuda Jun, Saito Sakae, et al. Identification of genetic alterations in extramammary Paget disease using whole exome analysis. Journal of Dermatological Science. 2019; 94 (1): 229-235. doi:10.1016/j.jdermsci.2019.03.006  
9.   Mizuguchi Takeshi, Suzuki Takeshi, Abe Chihiro, et al. A 12-kb structural variation in progressive myoclonic epilepsy was newly identified by long-read whole-genome sequencing. Journal of human genetics. 2019; 64 (5): 359-368. doi:10.1038/s10038-019-0569-5  
10.   Obayashi Takeshi, Kagaya Yuki, Aoki Yuichi, et al. COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference. Nucleic acids research. 2019; 47 (D1): D55-D62. doi:10.1093/nar/gky1155  
11.   Yasuda Jun, Kinoshita Kengo, Katsuoka Fumiki, et al. Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare. The Journal of Biochemistry. 2019; 165 (2): 139-158. doi:10.1093/jb/mvy096  
12.   Mimori Takahiro, Yasuda Jun, Kuroki Yoko, et al. Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing. The Pharmacogenomics Journal. 2019; 19 (2): 136-146. doi:10.1038/s41397-017-0010-4  
13.   Yamada Kazunori D., Kinoshita Kengo. De novo profile generation based on sequence context specificity with the long short-term memory network. BMC Bioinformatics. 2018; 19 (1): 272. doi:10.1186/s12859-018-2284-1  
14.   Yamada Kazunori D, Kinoshita Kengo. De novo profile generation based on sequence context specificity with the long short-term memory network. BMC bioinformatics. 2018; 19 (1): 272. doi:10.1186/s12859-018-2284-1  
15.   Okamura Yasunobu, Kinoshita Kengo. Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data. BMC bioinformatics. 2018; 19 (1): 266. doi:10.1186/s12859-018-2279-y  
16.   Yasuda Jun, Katsuoka Fumiki, Danjoh Inaho, et al. Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project. BMC Genomics. 2018; 19 (1): 551. doi:10.1186/s12864-018-4942-0  
17.   Koshiba Seizo, Motoike Ikuko, Saigusa Daisuke, et al. Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project. Genes to Cells. 2018; 23 (6): 406-417. doi:10.1111/gtc.12588  
18.   Yamaguchi-Kabata Yumi, Yasuda Jun, Tanabe Osamu, et al. Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals. Journal of Human Genetics. 2018; 63 (2): 213-230. doi:10.1038/s10038-017-0347-1  
19.   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  
20.   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  
21.   Obayashi Takeshi, Aoki Yuichi, Tadaka Shu, et al. ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index. Plant & cell physiology. 2018; 59 (1): e3. doi:10.1093/pcp/pcx191  
22.   Kondo Hiroko X., Yoshida Norio, Shirota Matsuyuki, Kinoshita Kengo. Molecular Mechanism of Depolarization-Dependent Inactivation in W366F Mutant of Kv1.2. The Journal of Physical Chemistry B. 2018; 122 (48): 10825-10833. doi:10.1021/acs.jpcb.8b09446  
23.   Iwaki Masayo, Takeshita Kohei, Kondo Hiroko X., et al. Zn 2+ -Binding to the Voltage-Gated Proton Channel Hv1/VSOP. The Journal of Physical Chemistry B. 2018; 122 (39): 9076-9080. doi:10.1021/acs.jpcb.8b04890  
24.   Iwaki Masayo, Takeshita Kohei, Kondo Hiroko X, et al. Zn2+-Binding to the Voltage-Gated Proton Channel Hv1/VSOP. The journal of physical chemistry. B. 2018; 122 (39): 9076-9080. doi:10.1021/acs.jpcb.8b04890  
25.   Takai-Igarashi Takako, Kinoshita Kengo, Nagasaki Masao, et al. Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design. BMC Medical Informatics and Decision Making. 2017; 17 (1): 100. doi:10.1186/s12911-017-0494-5  
26.   Tsugita Misato, Morimoto Nobuyuki, Tashiro Manabu, et al. SR-B1 Is a Silica Receptor that Mediates Canonical Inflammasome Activation. Cell Reports. 2017; 18 (5): 1298-1311. doi:10.1016/j.celrep.2017.01.004  
27.   Matsuura Kentaro, Sawai Hiromi, Ikeo Kazuho, et al. Genome-wide Association Study Identifies TLL1 Variant Associated With Development of Hepatocellular Carcinoma After Eradication of Hepatitis C Virus Infection. Gastroenterology. 2017; 152 (6): 1383-1394. doi:10.1053/j.gastro.2017.01.041  
28.   Hachiya Tsuyoshi, Furukawa Ryohei, Shiwa Yuh, et al. Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies. npj Genomic Medicine. 2017; 2 (1): 11. doi:10.1038/s41525-017-0016-5  
29.   Tadaka Shu, Kinoshita Kengo. NCMine: Core-peripheral based functional module detection using near-clique mining. Bioinformatics (Oxford, England). 2016; 32 (22): 3454-3460. doi:10.1093/bioinformatics/btw488  
30.   Yamada Kazunori D, Nishi Hafumi, Nakata Junichi, Kinoshita Kengo. Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins. Biophysics and physicobiology. 2016; 13 : 157-163. doi:10.2142/biophysico.13.0_157  
31.   Shirota Matsuyuki, Kinoshita Kengo. Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population. Database. 2016; 2016 : baw124. doi:10.1093/database/baw124  
32.   Kuriyama Shinichi, Yaegashi Nobuo, Nagami Fuji, et al. The Tohoku Medical Megabank Project: Design and Mission. Journal of Epidemiology. 2016; 26 (9): 493-511. doi:10.2188/jea.JE20150268  
33.   Murakami Yoichi, Omori Satoshi, Kinoshita Kengo. NLDB: a database for 3D protein-ligand interactions in enzymatic reactions. Journal of structural and functional genomics. 2016; 17 (4): 101-110. doi:10.1007/s10969-016-9206-0  
34.   Gojobori Takashi, Ikeo Kazuho, Katayama Yukie, et al. VaProS: a database-integration approach for protein/genome information retrieval. Journal of structural and functional genomics. 2016; 17 (4): 69-81. doi:10.1007/s10969-016-9211-3  
35.   Aoki Yuichi, Okamura Yasunobu, Ohta Hiroyuki, et al. ALCOdb: Gene Coexpression Database for Microalgae. Plant & cell physiology. 2016; 57 (1): e3. doi:10.1093/pcp/pcv190  
36.   Aoki Yuichi, Okamura Yasunobu, Tadaka Shu, et al. ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression. Plant & cell physiology. 2016; 57 (1): e5. doi:10.1093/pcp/pcv165  
37.   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  
38.   Kasahara Kota, Kinoshita Kengo, Schulz R, et al. IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels. PloS one. 2016; 11 (12): e0167524. doi:10.1371/journal.pone.0167524  
39.   Kasahara Kota, Shirota Matsuyuki, Kinoshita Kengo. Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction. PloS one. 2016; 11 (3): e0150716. doi:10.1371/journal.pone.0150716  
40.   Kasahara Kota, Kinoshita Kengo. Landscape of protein-small ligand binding modes. Protein Science. 2016; 25 (9): 1659-1671. doi:10.1002/pro.2971  
41.   Nishi Hafumi, Nakata Junichi, Kinoshita Kengo. Distribution of single-nucleotide variants on protein-protein interaction sites and its relationship with minor allele frequency. Protein science : a publication of the Protein Society. 2016; 25 (2): 316-21. doi:10.1002/pro.2845  
42.   Fujiwara Yuichiro, Kondo Hiroko X., Shirota Matsuyuki, et al. Structural basis for the membrane association of ankyrinG via palmitoylation. Scientific Reports. 2016; 6 (1): 23981. doi:10.1038/srep23981  
43.   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  
44.   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  
45.   Okamura Yasunobu, Aoki Yuichi, Obayashi Takeshi, et al. COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems. Nucleic acids research. 2015; 43 (Database issue): D82-6. doi:10.1093/nar/gku1163  
46.   Okamura Yasunobu, Obayashi Takeshi, Kinoshita Kengo. Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules. PloS one. 2015; 10 (7): e0132039. doi:10.1371/journal.pone.0132039  
47.   Kasahara Kota, Kinoshita Kengo. GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes. BMC Bioinformatics. 2014; 15 (1): 12. doi:10.1186/1471-2105-15-12  
48.   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  
49.   Obayashi Takeshi, Okamura Yasunobu, Ito Satoshi, et al. ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants. Plant & cell physiology. 2014; 55 (1): e6. doi:10.1093/pcp/pct178  
50.   Kasahara Kota, Shirota Matsuyuki, Kinoshita Kengo. Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions. Journal of chemical information and modeling. 2013; 53 (1): 241-8. doi:10.1021/ci300377f  
51.   Obayashi Takeshi, Okamura Yasunobu, Ito Satoshi, et al. COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. Nucleic acids research. 2013; 41 (Database issue): D1014-20. doi:10.1093/nar/gks1014  
52.   Kasahara Kota, Shirota Matsuyuki, Kinoshita Kengo. Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel. PloS one. 2013; 8 (2): e56342. doi:10.1371/journal.pone.0056342  
53.   Shirota Matsuyuki, Kinoshita Kengo. Analyses of the general rule on residue pair frequencies in local amino acid sequences of soluble, ordered proteins. Protein science : a publication of the Protein Society. 2013; 22 (6): 725-33. doi:10.1002/pro.2255  
54.   布施 昇男、清水 愛、木村 雅恵、高野 良真、石 棟、宮澤 晃子、国松 志保、劉 孟林、渡邊 亮、安田 正幸、横山 悠、檜森 紀子、津田 聡、山本 耕太郎、中澤 徹、安田 純、勝岡 史城、小島 要、成相 直樹、松本 光代、元池 育子、長崎 正朗、木下 賢吾、五十嵐 和彦、山本 雅之、新堀 哲也、青木 洋子、松原 洋一、舟山 亮、長嶋 剛史、中山 啓子、眞島 行彦、舟山 智代、田中 光一、原田 高幸、阿部 春樹、福地 健郎、安田 典子、出田 秀尚、鄭 暁東、白石 敦、大橋 祐一、石田 誠夫、原 岳、金森 章. 緑内障のゲノム解析―次世代医療•個別化医療に向けて. 日本眼科学会雑誌. 2013; 118 ((3)): 216-240.