Name: 

• Shohei Komaki (ResearchGate, Google Scholar)

Institution: 

• Tohoku Medical Megabank Organization, Tohoku University, Japan

Research Interest:

• Genome/Transcriptome/Epigenome data analysis

• Epigenetic age

• Biogeography

• Longitudinal transcriptomic and epigenetic change

• Hybridization and introgression of amphibians

Articles (Google Scholar):

1. 1. Komaki S, Kurabayashi A, Islam MM, Tojo K and Sumida M (2012) Distributional change and epidemic introgression in overlapping areas of Japanese pond frog species over 30 years. Zoological Science. 29(6):351-358. [Jun 2012] https://doi.org/10.2108/zsj.29.351

   2. Komaki S, Igawa T, Nozawa M, Lin S-M, Oumi S and Sumida M (2014) Development and characterization of 14 microsatellite markers for Buergeria japonica (Amphibia, Anura, Rhacophoridae). Genes & Genetic Systems. 89(1):35-39. [May 2014] https://doi.org/10.1266/ggs.89.35

   3. Igawa T, Nozawa M, Naganoka M, Komaki S, Oumi S, Fujii T, Sumida M (2014) Microsatellite marker development by multiplex ion torrent PGM sequencing: a case study of the endangered Odorrana narina complex of frogs. Journal of Heredity. 106(1):131-137. [Feb 2015] https://doi.org/10.1093/jhered/esu071

   4. Igawa T, Komaki S, Takahara T, Sumida M (2015) Development and validation of PCR-RFLP assay to identify three brown frogs of the true frog genus Rana. Current Herpetology. 34(1):89-94. [Jan 2015] https://doi.org/10.5358/hsj.34.89

   5. Komaki S, Igawa T, Lin S-M, Tojo K, Min M-S, Sumida M (2015) Robust molecular phylogeny and palaeodistribution modelling resolve a complex evolutionary history: glacial cycling drove recurrent mtDNA introgression among Pelophylax frogs in East Asia. Journal of Biogeography. 42(11):2159-2171. [Aug 2015] https://doi.org/10.1111/jbi.12584

   6. Komaki S, Igawa T, Lin S-M, Sumida M (2016) Salinity and thermal tolerance of Japanese stream tree frog (Buergeria japonica) tadpoles from island populations. Herpetological Journal. 26:207-211. [July 2016] Link

   7. Sultana N, Igawa T, Hasan M, Alam MS, Islam MM, Komaki S, Kawamura K, Khan MMR, Sumida M (2017)  Inter- and intra-specific genetic divergence of Asian tiger frogs (genus Hoplobatrachus), with special reference to the population structure of H. tigerinus in Bangladesh. Genes & Genetic Systems. 91(4):217-227. [Mar 2016] https://doi.org/10.1266/ggs.16-00006

   8. Komaki S, Lau Q, Igawa T (2016) Living in a Japanese onsen: field observations and physiological measurements of hot spring amphibian tadpoles, Buergeria japonica. Amphibia-Reptilia. 37(3):311-314. [Sep 2016] https://doi.org/10.1163/15685381-00003052

   9. Lau Q, Igawa T, Komaki S, Satta Y (2016) Characterisation of major histocompatibility complex class I genes in Japanese Ranidae frogs. Immunogeneis. 68(10):797-806. [Nov 2016] https://dx.doi.org/10.1007%2Fs00251-016-0934-x

   10. Komaki S, Lin S-M, Nozawa M, Oumi S, Sumida M, Igawa T (2017) Fine-scale demographic processes resulting from multiple overseas colonization events of the Japanese stream tree frog, Buergeria japonica. Journal of Biogeography. 44(7):1586-1597. [Jul 2017] https://doi.org/10.1111/jbi.12922

   11. Tojo K, Sekiné K, Takenaka M, Isaka Y, Komaki S, Suzuki T, Schoville S (2017) Species diversity of insects in Japan: Their origins and diversification processes. Entomological Science. 20(1):357-381. [Jan/Dec 2017] https://doi.org/10.1111/ens.12261

   12. Wang YH, Hsiao YW, Lee KH, Tseng HY, Lin YP, Komaki S, Lin SM (2017) Acoustic differentiation and behavioral response reveals cryptic species within Buergeria treefrogs (Anura, Rhacophoridae) from Taiwan. PLOS ONE. e0184005. [Sep 2017] https://doi.org/10.1371/journal.pone.0184005 (Correction: https://doi.org/10.1371/journal.pone.0193040)

   13. (Komaki S, Igawa T (2017) The widespread misconception about the Japanese major biogeographic boundary, the Watase line (Tokara gap), revealed by bibliographic and beta diversity analyses. bioRxiv. [Sep 2017] https://doi.org/10.1101/186775) -> Published in Journal of Biogeography

   14. Hachiya T, Komaki S, Hasegawa Y, Ohmomo H, Tanno K, Hozawa A, Tamiya G, Yamamoto M, Ogasawara K, Nakamura M, Hitomi J, Ishigaki Y, Sasaki M, Shimizu A (2017) Genome-wide meta-analysis in Japanese populations identifies novel variants at the TMC6-TMC8 and SIX3-SIX2 loci associated with HbA1c. Scientific Reports. 7:16147. [Nov 2017] https://doi.org/10.1038/s41598-017-16493-0

   15. Komaki S, Ohmomo H, Hachiya T, Furukawa R, Shiwa Y, Satoh M, Endo R, Doita M, Sasaki M, Shimizu A (2017) An epigenome-wide association study based on cell type-specific whole-genome bisulfite sequencing: Screening for DNA methylation signatures associated with bone mass. Integrative Molecular Medicine. 4. [Oct 2017] https://doi.org/10.15761/IMM.1000307

   16. Yang SF, Komaki S, Brown RM, Lin SM (2018) Riding the Kuroshio Current: stepping stone dispersal of the Okinawa tree lizard across the East Asian Island Arc. Journal of Biogeography. 45(1):37-50. [Jan 2018] https://doi.org/10.1111/jbi.13111

   17. Komaki S#, Shiwa Y#, Furukawa R, Hachiya T, Ohmomo H, Otomo R, Satoh M, Hitomi J, Sobue K, Sasaki M, Shimizu A (2018) iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation. Human Genome Variation. 5:18008. (# Contributed equally to this work) [Mar 2018] https://doi.org/10.1038/hgv.2018.8

   18. Igawa T*, Takahara T, Lau Q, Komaki S (2019) An application of PCR-RFLP species identification assay for environmental DNA detection. PeerJ. 7:7597. [Oct 2019] https://doi.org/10.7717/peerj.7597

   19. Lau Q, Igawa T, Komaki S, Satta Y (2020) Expression changes of MHC and other immune genes in frog skin during ontogeny. Animals. 10(1):91. [Jan 2020] https://doi.org/10.3390/ani10010091

   20. Nasu T, Satoh M, Ohmomo H, Shiwa Y, Komaki S, Ono K, Shimizu A, Taguchi S, Takahashi Y, Osaki T, Morino Y, Sobue K, Sasaki M (2020) Epigenome-wide association study identifies a novel DNA methylation in patients with severe aortic valve stenosis. Circulation: Genomic and Precision Medicine. 13(1):e002649. [Jan 2020] https://doi.org/10.1161/circgen.119.002649

   21. Komaki S, Sutoh Y, Kobayashi K, Saito S, Saito Tanaka C, Igawa T, Lau Q (2020) Hot spring frogs (Buergeria japonica) prefer cooler water to hot water. Ecology and Evolution. 10(17):9466-9473. [Sep 2020] https://dx.doi.org/10.1002%2Fece3.6637

   22. Wang YH, Hsiao YW, Le KH, Tseng HY, Lin YP, Komaki S, Lin SM (2020) Renaming a new Buergeria species from Taiwan—correction of a nomenclatural act not available to ICZN. Nature Conservation Quarterly. [Sep 2020] 111:4-13. Link

   23. Sutoh Y, Hachiya T, Suzuki Y, Komaki S, Ohmomo H, Kakisaka K, Wang T, Takikawa Y, Shimizu A (2020) ALDH2 genotype modulates the association between alcohol consumption and AST/ALT ratio among middle-aged Japanese men: a genome-wide G × E interaction analysis. Scientific Reports. 10(1):16227. [Oct 2020] https://doi.org/10.1038/s41598-020-73263-1

   24. Ohmomo H, Komaki S, Ono K, Sutoh Y, Hachiya T, Arai E, Fujimoto H, Yoshida T, Kanai Y, Sasaki M, Shimizu A (2020) Evaluation of clinical formalin‐fixed paraffin‐embedded tissue quality for targeted‐bisulfite sequencing. Pathology International. 71(2):135-140.  [Feb 2021] https://doi.org/10.1111/pin.13054

   25. Tadaka S, Hishinuma E, Komaki S, Motoike N I, Kawashima J, Saigusa D, Inoue J, Takayama J, Okamura Y, Aoki Y, Shirota M, Otsuki A, Katsuoka F, Shimizu A, Tamiya G, Koshiba S, Sasaki M, Yamamoto M, Kinoshita K (2021) jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population. Nucleic Acids Research. 49(D1):D536-D544. [Jan 2021] https://doi.org/10.1093/nar/gkaa1034

   26. Komaki S (2021) Widespread misperception about a major East Asian biogeographic boundary exposed through bibliographic survey and biogeographic meta-analysis. Journal of Biogeography. 48(9):2375-2386. [Jun 2021] https://doi.org/10.1111/jbi.14210

   27. Komaki S, Matsunami M, Lin J-W, Lee K-H, Lee Y, Lin S-M, Igawa T (2022) Transcriptomic changes in hot spring frog tadpoles (Buergeria otai) in response to heat stress. Frontiers in Ecology and Evolution. 9:706887. [Oct 2021] https://doi.org/10.3389/fevo.2021.706887

   28. Ohmomo H, Harada S, Komaki S, Ono K, Sutoh Y, Otomo R, Umekage S, Hachiya T, Katanoda K, Takebayashi T, Shimizu A (2021) DNA methylation abnormalities and altered whole transcriptome profiles after switching from combustible tobacco smoking to heated tobacco products. Cancer Epidemiology, Biomarkers & Prevention. 31(1):269-279. [Jan 2022] https://doi.org/10.1158/1055-9965.epi-21-0444

   29. Sutoh Y, Komaki S, Yamaji T, Suzuki S, Katagiri R, Sawada N, Ono K, Ohmomo H, Hachiya T, Otsuka-Yamasaki Y, Takashima A, Umekage S, Iwasaki M, Shimizu A (2022) Low MICA gene expression confers an increased risk of Graves' disease: A Mendelian randomization study. Thyroid. 32(2):188-195. [Feb 2022] https://doi.org/10.1089/thy.2021.0417

   30. Komaki S, Ohmomo H, Hachiya T, Sutoh Y, Ono K, Furukawa R, Umekage S, Otsuka-Yamasaki Y, Tanno K, Sasaki M, Shimizu A (2021) Longitudinal DNA methylation dynamics as a practical indicator in clinical epigenetics. Clinical Epigenetics. 13:219. [Dec 2021] https://doi.org/10.1186/s13148-021-01202-6

   31. Oka K, Fujioka S, Kawamura Y, Komohara Y, Chujo T, Sekiguchi K, Yamamura Y, Oiwa Y, Omamiuda-Ishikawa N, Komaki S, Sutoh Y, Sakurai S, Tomizawa K, Bono H, Shimizu A, Araki K, Yamamoto T, Yamada Y, Oshiumi H, Miura K (2022) Resistance to chemical carcinogenesis induction via a dampened inflammatory response in naked mole-rats. Communications Biology. 5(1):287 [Mar 2022] https://doi.org/10.1038/s42003-022-03241-y

   32. Ohmomo H, Komaki S, Sutoh Y, Hachiya T, Ono K, Arai E, Fujimoto H, Yoshida T, Kanai Y, Asahi K, Sasaki M, Shimizu A (2022) Potential DNA methylation biomarkers for the detection of clear cell renal cell carcinoma identified by a whole blood-based epigenome-wide association study. Epigenetics Communications. 2:2. [May 2022] https://doi.org/10.1186/s43682-022-00009-7

   33. Komaki S, Ohmomo H, Hachiya T, Sutoh Y, Ono K, Furukawa R, Umekage S, Otsuka-Yamasaki Y, Minabe S, Takashima A, Tanno K, Sasaki M, Shimizu A (2022) Evaluation of short-term epigenetic age fluctuation. Clinical Epigenetics. 14:76. [Jun 2022]  https://doi.org/10.1186/s13148-022-01293-9

   34. Ogata S, Doi H, Igawa T, Komaki S, Takahara T (Accepted) Environmental DNA methods for detecting two invasive alien species (American bullfrog and red swamp crayfish) in Japanese ponds. Ecological Research. [Jul 2022] https://doi.org/10.1111/1440-1703.12341

   35. Saito S, Saito T C, Igawa T, Takeda N, Komaki S, Ohta T, Tominaga M (2022) Evolutionary tuning of Transient Receptor Potential Ankyrin 1 underlies the variation in heat avoidance behaviors among frog species inhabiting diverse thermal niches. Molecular Biology and Evolution. msac180. [Aug 2022] https://doi.org/10.1093/molbev/msac180

   36. Kaniz Fatema Kanon, Bushratul Jannat, Shohei Komaki, Md Shahanoor Alam, Mohammad Shafiqul Alam (2022) Molecular differentiation between native and Vietnam originated striped snakeheads (Channa striata) in Bangladesh using mitochondrial cytchrome b gene. Journal of Bangladesh Agricultural University. 20:467–476. [Dec 2022]

   37. Komaki S, Nagata M, Arai E, Otomo R, Ono K, Abe Y, Ohmomo H, Umekage S, Shinozaki-O N, Hachiya T, Sutoh Y, Otsuka-Yamasaki Y, Arai Y, Hirose N, Yoneyama A, Okano H, Sasaki M, Kanai Y, Shimizu A (2023) Epigenetic profile of Japanese supercentenarians: a cross-sectional study. The Lancet Healthy Longevity, 4:e83–e90. [Feb 2023] https://doi.org/10.1016/S2666-7568(23)00002-8

   38. Taguchi Y, Komaki S, Sutoh Y, Ohmomo H, Otsuka-Yamasaki Y, Shimizu A (2023) Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction. PLOS ONE, 18(8):e0289029. [Aug 2023] https://doi.org/10.1371/journal.pone.0289029

   39. Tadaka S, Kawashima J, Hishinuma E, Saito S, Okamura Y, Otsuki A, Kojima K, Komaki S, Aoki Y, Kanno T, Saigusa D, Inoue J, Shirota M, Takayama J, Katsuoka F, Shimizu A, Tamiya G, Shimizu R, Hiratsuka M, Motoike IN, Koshiba S, Sasaki M, Yamamoto M, Kinoshita K (2023) jMorp: Japanese Multi-Omics Reference Panel update report 2023. Nucleic Acids Research, gkad978. [Nov 2023] https://doi.org/10.1093/nar/gkad978

   40. Komaki S, Sahoyama Y, Hachiya T, Koseki K, Ogata Y, Hamazato F, Shiozawa M, Nakagawa T, Suda W, Hattori M, Kawakami E (2024) Dimension reduction of microbiome data linked Bifidobacterium and Prevotella to allergic rhinitis. Scientific Reports, 14:7983. [Apr 2024] https://doi.org/10.1038/s41598-024-57934-x

   41. Harada S et al (2024) Study Profile of the Tsuruoka Metabolomics Cohort Study (TMCS).  Journal of Epidemiology, JE20230192 [Jun 2024] https://doi.org/10.2188/jea.JE20230192

   42. Sutou Y et al (2024) Healthy lifestyle practice correlates with decreased obesity prevalence in individuals with high polygenic risk: TMM CommCohort study. Journal of Human Genetics. [Aug 2024] https://doi.org/10.1038/s10038-024-01280-3

   43. Nagata M et al (2024) Influence of physical activity on the epigenetic clock: evidence from a Japanese cross-sectional study. Clinical Epigenetics, 16:142. [Oct 2024] https://doi.org/10.1186/s13148-024-01756-1

   44. Sutoh Y et al (2025) Reference-based standardization approach stabilizing small batch risk prediction via polygenic score. Genetic Epidemiology, e70002. [Mar 2025] https://doi.org/10.1002/gepi.70002