| 1. | Suzuki Nonoka, Kojima Kaname, Malvica Silvia, et al. Deep learning-based histopathological assessment of tubulo-interstitial injury in chronic kidney diseases. Communications Medicine. 2025; 5 (1): 3. doi:10.1038/s43856-024-00708-3 | ||
| 2. | Kojima Kaname, Tadaka Shu, Okamura Yasunobu, Kinoshita Kengo. Two-stage strategy using denoising autoencoders for robust reference-free genotype imputation with missing input genotypes. Journal of Human Genetics. 2024; 69 (10): 511-518. doi:10.1038/s10038-024-01261-6 | ||
| 3. | Tadaka Shu, Kawashima Junko, Hishinuma Eiji, et al. jMorp: Japanese Multi-Omics Reference Panel update report 2023. Nucleic Acids Research. 2024; 52 (D1): D622-D632. doi:10.1093/nar/gkad978 | ||
| 4. | Yanagisawa Yuta, Shido Kosuke, Kojima Kaname, Yamasaki Kenshi. Convolutional neural network-based skin image segmentation model to improve classification of skin diseases in conventional and non-standardized picture images. Journal of Dermatological Science. 2023; 109 (1): 30-36. doi:10.1016/j.jdermsci.2023.01.005 | ||
| 5. | Yu Zhiqian, Ueno Kazuko, Funayama Ryo, et al. Sex-Specific Differences in the Transcriptome of the Human Dorsolateral Prefrontal Cortex in Schizophrenia. Molecular Neurobiology. 2023; 60 (2): 1083-1098. doi:10.1007/s12035-022-03109-6 | ||
| 6. | Fuse Nobuo, Sakurai Miyuki, Motoike Ikuko N., et al. Genome-wide Association Study of Axial Length in Population-based Cohorts in Japan. Ophthalmology Science. 2022; 2 (1): 100113. doi:10.1016/j.xops.2022.100113 | ||
| 7. | Zempo Hirofumi, Kim Su-Jeong, Fuku Noriyuki, et al. A pro-diabetogenic mtDNA polymorphism in the mitochondrial-derived peptide, MOTS-c. Aging. 2021; 13 (2): 1692-1717. doi:10.18632/aging.202529 | ||
| 8. | Yamada Mitsuhiro, Motoike Ikuko N., Kojima Kaname, et al. Genetic loci for lung function in Japanese adults with adjustment for exhaled nitric oxide levels as airway inflammation indicator. Communications Biology. 2021; 4 (1): 1288. doi:10.1038/s42003-021-02813-8 | ||
| 9. | Shido Kosuke, Kojima Kaname, Shirota Matsuyuki, et al. GWAS Identified IL4R and the Major Histocompatibility Complex Region as the Associated Loci of Total Serum IgE Levels in 9,260 Japanese Individuals. Journal of Investigative Dermatology. 2021; 141 (11): 2749-2752. doi:10.1016/j.jid.2021.02.762 | ||
| 10. | Kojima Kaname, Shido Kosuke, Tamiya Gen, et al. Facial UV photo imaging for skin pigmentation assessment using conditional generative adversarial networks. Scientific Reports. 2021; 11 (1): 1213. doi:10.1038/s41598-020-79995-4 | ||
| 11. | Hitomi Yuki, Aiba Yoshihiro, Kawai Yosuke, et al. rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis. Scientific Reports. 2021; 11 (1): 4557. doi:10.1038/s41598-021-84042-x | ||
| 12. | Shido Kosuke, Kojima Kaname, Yoshida‐Akai Saaya, et al. Ehlers–Danlos syndrome type IV with a novel COL3A1 exon 14 skipping variation confirmed by Tohoku Medical Megabank Organization genomic database. The Journal of Dermatology. 2021; 48 (12): 1918-1922. doi:10.1111/1346-8138.16131 | ||
| 13. | Misawa Kazuharu, Hasegawa Takanori, Mishima Eikan, et al. Contribution of Rare Variants of the SLC22A12 Gene to the Missing Heritability of Serum Urate Levels. Genetics. 2020; 214 (4): 1079-1090. doi:10.1534/genetics.119.303006 | ||
| 14. | Ueno Kazuko, Aiba Yoshihiro, Hitomi Yuki, et al. Integrated GWAS and mRNA Microarray Analysis Identified IFNG and CD40L as the Central Upstream Regulators in Primary Biliary Cholangitis. Hepatology Communications. 2020; 4 (5): 724-738. doi:10.1002/hep4.1497 | ||
| 15. | Kojima Kaname, Tadaka Shu, Katsuoka Fumiki, et al. A genotype imputation method for de-identified haplotype reference information by using recurrent neural network. PLOS Computational Biology. 2020; 16 (10): e1008207. doi:10.1371/journal.pcbi.1008207 | ||
| 16. | Hitomi Yuki, Nakatani Ken, Kojima Kaname, et al. NFKB1 and MANBA Confer Disease Susceptibility to Primary Biliary Cholangitis via Independent Putative Primary Functional Variants. Cellular and Molecular Gastroenterology and Hepatology. 2019; 7 (3): 515-532. doi:10.1016/j.jcmgh.2018.11.006 | ||
| 17. | 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 | ||
| 18. | 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 | ||
| 19. | Nagasaki Masao, Kuroki Yoko, Shibata Tomoko F., et al. Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing. Human Genome Variation. 2019; 6 (1): 27. doi:10.1038/s41439-019-0057-7 | ||
| 20. | Shido Kosuke, Kojima Kaname, Yamasaki Kenshi, et al. Susceptibility Loci for Tanning Ability in the Japanese Population Identified by a Genome-Wide Association Study from the Tohoku Medical Megabank Project Cohort Study. Journal of Investigative Dermatology. 2019; 139 (7): 1605-1608.e13. doi:10.1016/j.jid.2019.01.015 | ||
| 21. | Hitomi Yuki, Ueno Kazuko, Kawai Yosuke, et al. POGLUT1, the putative effector gene driven by rs2293370 in primary biliary cholangitis susceptibility locus chromosome 3q13.33. Scientific Reports. 2019; 9 (1): 102. doi:10.1038/s41598-018-36490-1 | ||
| 22. | Nishiyama Takeshi, Nakatochi Masahiro, Goto Atsushi, et al. Genome-wide association meta-analysis and Mendelian randomization analysis confirm the influence of ALDH2 on sleep durationin the Japanese population. Sleep. 2019; 42 (6): . doi:10.1093/sleep/zsz046 | ||
| 23. | 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 | ||
| 24. | 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 | ||
| 25. | 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 | ||
| 26. | Hirata Satoshi, Kojima Kaname, Misawa Kazuharu, et al. Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population. Heliyon. 2018; 4 (5): e00625. doi:10.1016/j.heliyon.2018.e00625 | ||
| 27. | 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 | ||
| 28. | Shido K., Kojima K., Yamasaki K., et al. 299 A genome-wide association study identifies a novel susceptibility locus for total IgE in a Japanese population from Tohoku Medical Megabank cohort study. Journal of Investigative Dermatology. 2018; 138 (5): S51. doi:10.1016/j.jid.2018.03.305 | ||
| 29. | Nishida Nao, Aiba Yoshihiro, Hitomi Yuki, et al. NELFCD and CTSZ loci are associated with jaundice-stage progression in primary biliary cholangitis in the Japanese population. Scientific Reports. 2018; 8 (1): 8071. doi:10.1038/s41598-018-26369-6 | ||
| 30. | 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 | ||
| 31. | 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 | ||
| 32. | Kawashima Minae, Hitomi Yuki, Aiba Yoshihiro, et al. Genome-wide association studies identify PRKCB as a novel genetic susceptibility locus for primary biliary cholangitis in the Japanese population. Human Molecular Genetics. 2017; 26 (3): ddw406. doi:10.1093/hmg/ddw406 | ||
| 33. | Ueta Mayumi, Sawai Hiromi, Shingaki Ryosei, et al. 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. Journal of Human Genetics. 2017; 62 (4): 485-489. doi:10.1038/jhg.2016.160 | ||
| 34. | Shido K, Kojima K, Hozawa A, et al. 503 Genome-wide association study identifies novel susceptibility loci for tanning ability in Japanese population. Journal of Investigative Dermatology. 2017; 137 (5): S86. doi:10.1016/j.jid.2017.02.523 | ||
| 35. | Shiga Yukihiro, Nishiguchi Koji M., Kawai Yosuke, et al. Genetic analysis of Japanese primary open-angle glaucoma patients and clinical characterization of risk alleles near CDKN2B-AS1, SIX6 and GAS7. PLOS ONE. 2017; 12 (12): e0186678. doi:10.1371/journal.pone.0186678 | ||
| 36. | Hitomi Yuki, Kojima Kaname, Kawashima Minae, et al. Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis. Scientific Reports. 2017; 7 (1): 2904. doi:10.1038/s41598-017-03067-3 | ||
| 37. | Nariai Naoki, Kojima Kaname, Mimori Takahiro, et al. A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes. BMC Genomics. 2016; 17 (S1): 2. doi:10.1186/s12864-015-2295-5 | ||
| 38. | Hasegawa Takanori, Kojima Kaname, Kawai Yosuke, et al. AP-SKAT: highly-efficient genome-wide rare variant association test. BMC Genomics. 2016; 17 (1): 745. doi:10.1186/s12864-016-3094-3 | ||
| 39. | Kojima Kaname, Kawai Yosuke, Nariai Naoki, et al. Short tandem repeat number estimation from paired-end reads for multiple individuals by considering coalescent tree. BMC Genomics. 2016; 17 (S5): 494. doi:10.1186/s12864-016-2821-0 | ||
| 40. | Kojima Kaname, Kawai Yosuke, Misawa Kazuharu, et al. STR-realigner: a realignment method for short tandem repeat regions. BMC Genomics. 2016; 17 (1): 991. doi:10.1186/s12864-016-3294-x | ||
| 41. | Sun Yonghu, Irwanto Astrid, Toyo-oka Licht, et al. Fine-mapping analysis revealed complex pleiotropic effect and tissue-specific regulatory mechanism of TNFSF15 in primary biliary cholangitis, Crohn’s disease and leprosy. Scientific Reports. 2016; 6 (1): 31429. doi:10.1038/srep31429 | ||
| 42. | 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 | ||
| 43. | Mimori Takahiro, Nariai Naoki, Kojima Kaname, et al. Estimating copy numbers of alleles from population-scale high-throughput sequencing data. BMC Bioinformatics. 2015; 16 (S1): S4. doi:10.1186/1471-2105-16-S1-S4 | ||
| 44. | 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 (S2): S7. doi:10.1186/1471-2164-16-S2-S7 | ||
| 45. | 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 (1): 15050. doi:10.1038/hgv.2015.50 | ||
| 46. | 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 | ||
| 47. | 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 (1): 8018. doi:10.1038/ncomms9018 | ||
| 48. | Fujiwara Tohru, Fukuhara Noriko, Funayama Ryo, et al. Identification of acquired mutations by whole-genome sequencing in GATA-2 deficiency evolving into myelodysplasia and acute leukemia. Annals of Hematology. 2014; 93 (9): 1515-1522. doi:10.1007/s00277-014-2090-4 | ||
| 49. | 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 | ||
| 50. | 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 (S10): S5. doi:10.1186/1471-2164-15-S10-S5 | ||
| 51. | 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 (1): 673. doi:10.1186/1471-2164-15-673 | ||
| 52. | 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 | ||
| 53. | 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 | ||
| 54. | 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; 29 (22): 2835-2843. doi:10.1093/bioinformatics/btt503 | ||
| 55. | 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. 2013; 29 (18): 2292-2299. doi:10.1093/bioinformatics/btt381 | ||
| 56. | Mimori Takahiro, Nariai Naoki, Kojima Kaname, et al. iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. BMC Systems Biology. 2013; 7 (S6): S8. doi:10.1186/1752-0509-7-S6-S8 | ||
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