Publications
22 Apr. 2025
Papers

  Times
Cited
60.

Kanako Hisata, Tomofumi Nagata, Megumi Kanai, Frederic Sinniger, Fumihiko Nagata, Mayuki Suwa, Yuki Yoshioka, Saki Harii, Masanori Nonaka, Hironobu Fukami, Seiji Arakaki, Manabu Fujie, Nana Arakaki, Yuna Zayasu, Haruhi Narisoko, Takeshi Noda, Aya Koseki, Koki Nishitsuji, Jun Inoue, Chuya Shinzato and Noriyuki Satoh 2025.
An eDNA metabarcoding system for detecting scleractinian corals to the generic level along the Japanese coast. Galaxea. in press.

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59.

Wilhoit K, Yamanouchi S, Chen BJ, Yamasaki YY, Ishikawa A, Inoue J, Iwasaki W, Kitano J. 2025.
Convergent Evolution and Predictability of Gene Copy Numbers Associated with Diets in Mammals. Genome Biology and Evolution 17: evaf008, 2025.
Convergent evolution and predictability of gene copy numbers associated with diets in mammals. Genome Biology and Evolution. 17. DOI:10.1093/gbe/evaf008.

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58.

Wu Y, Hirai J, Zhou F, Iwataki M, Jiang S, Ogawa H, Inoue J, Hyodo S, Saito H. 2024.
Diversity and biogeography of dinoflagellates in the Kuroshio region revealed by 18S rRNA metabarcoding. Frontiers in Marine Science. Vol.11, 1361452. DOI：10.3389/fmars.2024.1361452

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57.

Yoshioka Y, Kanai M, Gishitomi S, Arakaki N, Koido T, Shinzato C, Inoue J, Nagata T, Satoh, N, 2024.
Extensive mitochondrial genomic analyses reveal dynamic gene order rearrangements in the class Octocorallia (Cnidaria: Anthozoa)
Gene Reports. 389: 102111. doi: https://doi.org/10.1016/j.genrep.2024.102111.

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56.

Inoue J, Shinzato C, Hirai, J. Itoh S, Minegishi Y, Ito S., Hyodo S, 2024.
phyloBARCODER: A web tool for phylogenetic classification of eukaryote metabarcodes using custom reference databases. Molecular Biology and Evolution. 41: msae111. doi: 10.1093/molbev/msae111. 日本語の説明.

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55.

Yu Z, Wong MK-S, Inoue J, Ahmed SI, Higuchi T, Hyodo S, Itoh S, Komatsu K, Saito H and Ito S. 2023.
Environmental DNA in the Kuroshio reveals environment dependent distribution of economically important small pelagic fish. Front. Mar. Sci. 10:1121088. doi: 10.3389/fmars.2023.1121088

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54.

Yu Z., S. Ito*, M. K. Wong, S. Yoshizawa, J. Inoue, S. Itoh, R. Yukami, K. Ishikawa, C. Guo, M. Ijichi and S. Hyodo, 2022.
Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA. PLoS ONE, 17(9): e0273670. doi: 10.1371/journal.pone.0273670

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53.

Isomoto, A., Shoguchi, E., Hisata, K., Inoue, J., Inaba, K., Satoh, N., Ogawa, T., and Shibata, H. 2022.
Active Expression of Genes for Protein Modification Enzymes in Habu Venom Glands. Toxins. 14: 300. doi: 10.3390/toxins14050300.

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52.

Yasuda, Y*., Inoue, J.*, Hall, M.R.*, Nair, M.R., Adjeroud, M., Fortes, M.D., Nishida, M., Tuivavalagi, N., Ravago-Gotanco, R., Forsman, Z.H., Soliman, T.B.H., Koyanagi, R., Hisada, K.,Motti, C.A., Satoh, N. 2022.
Two hidden mtDNA-clades of crown-of-thorns starfish in the Pacific ocean. Frontiers in Marine Science. 9: 831240. *Equally contributed. doi: 10.3389/fmars.2022.831240.

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51.

Inoue, J. 2022.
ORTHOSCOPE*: a phylogenetic pipeline to infer gene histories from genome-wide data. Molecular Biology and Evolution. 39:msab301. doi: 10.1093/molbev/msab301. 日本語の説明.

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50.

Shinzato, C., Narisoko, H., Nishitsuji, N., Nagata, T., Satoh, N., and Inoue, J. 2021.
Novel mitochondrial DNA markers for scleractinian corals and generic-level environmental DNA metabarcoding. Frontiers in Marine Science-Coral Reef Research. 8:758207. Link. doi: https://doi.org/10.3389/fmars.2021.758207

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49. Satoh, N., Tominaga, H, Kiyomoto, M., Hisata, K. Inoue, J., and Nishitsuji, K. 2021
A Preliminary single-cell RNA-Seq analysis of embryonic cells that express Brachyury in the Amphioxus, Branchiostoma japonicum. Frontiers Cell and Developmental Biology 9:696875. doi: 10.3389/fcell.2021.696875		 0
48. Inoue, J. 2021.
Commentary on ORTHOSCOPE: a web tool for genome comparisons. Journal of Genetics and Genomes, 5 1. Link.		  
47. Inoue, J., Saitou, N. 2021.
dbCNS: a new database for conserved noncoding sequences. Molecular Biology and Evolution 38: 1665–1676. Link. https://doi.org/10.1093/molbev/msaa296		 0
46. Shinzato C, Khalturin K, Inoue, J, Zayasu Y, Kanda M, Kawamitsu M, Yoshioka Y, Yamashita H, Suzuki G, Satoh N. 2021.
Eighteen coral genomes reveal the evolutionary origin of Acropora strategies to accommodate environmental changes. Molecular Biology and Evolution 38: 16–30. https://doi.org/10.1093/molbev/msaa216		 18
45. Nishimura, L., Sugimoto, R., Inoue, J., Nakaoka, H., Kanzawa-Kiriyama, H., Shinoda, K., Inoue, I. 2021.
Identification of ancient viruses from metagenomic data of the Jomon people. Journal of Human Genetics. 66: 287-296. https://doi.org/10.1038/s10038-020-00841-6		 0
44. Li Kun-Lung, Nakashima K, Inoue, J, Satoh N. 2020.
Phylogenetic analyses of glycosyl hydrolase family 6 genes in tunicates: possible horizontal transfer. Genes (Basel) 11: 937 10.3390/genes11080937		 1
43. Inoue, J, Hisata K, Yasuda N, Satoh N. 2020.
An investigation into the genetic history of Japanese populations of three Starfish, Acanthaster planci, Linckia laevigata, and Asterias amurensis, based on complete mitochondrial DNA sequences. G3-Genes Genomes Genetics 10: 2519–2528. https://doi.org/10.1534/g3.120.401155		 1
42. Kon, T. Inoue, J. 2019.
An outline of estimation of divergence time and diversification process based on the molecular phylogenetic tree. Fossils 106, 5–17 (in Japanese with English abstract). Link.
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41. Ishikawa, A, Kabeya, N, Ikeya, K, Kakioka, R, Cech, JN, Osada, N, Leal, MC, Inoue, J, Kume, M, Toyoda, A, Tezuka, A, Nagano, AJ, Yamasaki, YY, Suzuki, Y, Kokita, T, Takahashi, H, Lucek, K, Marques, D, Takehana, Y, Naruse, K, Mori, S, Monroig, O, Ladd, N, Schubert, C, Matthews, B, Peichel, CL, Seehausen, O, Yoshizaki, G, Kitano J. 2019.
A key metabolic gene for recurrent freshwater colonization and radiation in fishes
Science 364: 886–9. Link.　DOI: 10.1126/science.aau5656		 54
40. Inoue J, Nakashima K, Satoh, N. 2019.
ORTHOSCOPE analysis reveals the presence of the cellulose synthase gene in all tunicate genomes but not in other animal genomes. Genes 10: 294. Link.　doi.org/10.3390/genes10040294		 8
39. Shiraishi A, Okuda T, Miyasaka N, Osugi T, Okuno Y, Inoue J, and Satake H. 2019.
Repertoires of G protein-coupled receptors for Ciona-specific neuropeptides. Proceedings of the National Academy of Sciences of the United States of America  116: 7847–7856. Link.　doi.org/10.1073/pnas.1816640116		 13
38. Inoue J, Satoh N. 2019.
ORTHOSCOPE: an automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa. Molecular Biology and Evolution 36: 621–631. doi.org/10.1093/molbev/msy226		 12
37. Kim OTP, Nguyen PT, Shoguchi E, Hisata K, Vo TTB,　Inoue J, Shinzato C, Le BTN, Nishitsuji K, Kanda M, et al. 2018.
A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement. BMC Genomics 19: 733.　doi.org/10.1186/s12864-018-5079-x		 12
36. Inoue J, Satoh N. 2018.
Deuterostome genomics: Lineage-specific protein expansions that enabled chordate muscle evolution. Molecular Biology and Evolution 35(4): 914–924. doi.org/10.1093/molbev/msy002		 11
35. Inoue J, Yasuoka Y, Takahashi H, Satoh N. 2017.
The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition. Zoological Letters 3: 4.　doi: 10.1186/s40851-017-0064-9		 7
34. Inoue J, Sato Y, Sinclair R, Tsukamoto K, Nishida M. 2015.
Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling. Proceedings of the National Academy of Sciences of the United States of America 112(48):14918–14923. Link.　doi.org/10.1073/pnas.1507669112. Data download.		 86
33. Miya M., Friedman M, Satoh TP., Takeshima H., Sado T., Iwasaki W., Yamanoue Y., Nakatani M., Mabuchi K., Inoue JG., Poulsen JY., Fukunaga T., Sato Y., Nishida M. 2013.
Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families. Plos One 8(9):e73535. Link. 		117
32. Parham, J.F., Donoghue, P.C.J., Bell, C.J., Calway, T.D., Head, J.J., Holroyd, P.A., Inoue J.G., Irmis, R.B., Joyce, W.G., Ksepka, D.T., Patané, J.S.L., Smith, N.D., Tarver, J.E., van Tuinen, M., Yang, Z., Angielczyk, K.D., Greenwood, J., Hipsley, C.A., Jacobs, L., Makovicky, P.J., Müller, J., Smith, K.T., Theodor, J.M., Warnock, R.C.M., Benton, M.J. 2012.
Best practices for justifying fossil calibrations. Systematic Biology 61: 346-359.		 450
31. Aschliman N.C., Nishida M., Miya M., Inoue J.G., Rosana K.M., Naylor G.J.P. 2011.
Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea). Molecular Phylogenetics and Evolution 63: 28-42.		 116
30. dos Reis M.,Inoue J.G., Hasegawa M., Asher R.J., Donoghue P.C.J. Yang Z. 2012.
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proceedings of the Royal Soceity B 279: 3491-3500. 		323
29. Saitoh, K., Sado, T., Doosey, M.H., Bart, Jr., H.L., Inoue J.G., Nishida, M., Mayden, R.L., Miya, M. 2011.
Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi). Zoological Journal of the Linnean Society, Zoological Journal of the Linnean Society 161: 633–662.		 72
28. Inoue, J.G., Miya, M., Miller, M.J., Sado, T., Hanel, R., Hatooka, K., Aoyama, J., Minegishi, M., Nishida, M., Tsukamoto, K. 2010b.
Deep-ocean origin of the freshwater eels. Biology Letters 6: 363-366. [Open Choice]		 113
27. Inoue, J.G., Miya, M., Lam, K., Tay B.H., Danks, J.A., Bell, J., Walker, T.I., Venkatesh, B. 2010c.
Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective. Molecular Biology and Evolution 27: 2576-2586.		 147
26. Minegishi, Y., Aoyama, J., Inoue, J.G., Azanza, R.V., Tsukamoto, K. 2010.
Inter- specific and subspecific genetic divergences of freshwater eels, genus Anguilla including a recently described species, A. luzonensis, based on whole mitochondrial genome sequences. Coastal Marine Science 33: 64-77.		 7
25. Inoue, J., Donoghue, P.C.J., Yang, Z. 2010a.
The impact of the representation of fossil calibration on Bayesian estimation of species divergence times. Systematic Biology 59: 74-89. [doi:10.1093/sysbio/syp078 ] [Data		 181
24. Setiamarga, D.H., Miya, M., Inoue, J.G., Ishiguro, N.B., Mabuchi, K., Nishida, M., 2009.
Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biology Letters 23: 812-816.		 75
23. Inoue, J.G., Kumazawa, Y., Miya, M., Nishida, M. 2009.
The historical biogeography of the freshwater knifefishes using mitogenomic approaches: A Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha). Molecular Phylogenetics and Evolution 51: 486-499. [doi:10.1016/j.ympev.2009.01.020]		 49
22. Ma, T., Aoyama, J., Miller, M.J., Minegishi, Y., Inoue, J.G., Tsukamoto, K., 2008. Genetic differentiation in the genus Uroconger in the Indo-Pacific region. Aquatic Biology 2: 29-35.
 8
21. Ma, T., Miller, M. J., Aoyama, J., Minagawa, M., Inoue, J.G., Watanabe, S., Tsukamoto, K. 2008.
Genetic identification of two types of Ariosoma leptocephali. Coastal Marine Science 32: 48-53.		 -
20. Setiamarga, D.H., Miya, M., Yamanoue, Y., Mabuchi, K., Satoh, T.P., Inoue, J.G., Nishida, M., 2008.
Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences. Molecular Phylogenetics and Evolution 49: 598-605. [PubMed]
 86
19. Kawahara, R., Miya, M. Mabuchi, K., Lavoue, S., Inoue, J.G., Satoh, T. P., Kawaguchi, A., Nishida. M. 2008.
Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts. Molecular Phylogenetics and Evolution 46: 224-236. [PubMed]		 104
18. Yamanoue, Y., Miya, M., Inoue, J.G., Matsuura, K., Nishida, M. 2006.
The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. Gene and Genetic Systems 81: 29-39. [PubMed]		 108
17. Minegishi, Y., Aoyama, J., Inoue, J.G., Miya, M., Nishida, M., Tsukamoto, K. 2005.
Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences. Molecular Phylogenetics and Evolution 34: 134-146. [PubMed]		 156
16. Lavoue, S., Miya, M., Inoue, J.G., Saitoh, K., Ishiguro, N. B., Nishida, M. 2005.
Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: Implications for higher-level relationships within the Otocephala. Molecular Phylogenetics and Evolution 37: 165-177. [PubMed]		 97
15. Ishiguro, N. B., Miya, M., Inoue, J.G., Nishida, M. 2005.
Sundasalanx (Sundasalangidae) is a progenetic clupeiform, not a closely-related group of salangids (Osmeriformes): Mitogenomic evidence. Journal of Fish Biology 67: 561-569.		 19
14. Inoue, J.G., Miya, M., Venkatesh, B., Nishida, M. 2005.
The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths. Gene 349: 227-235. [PubMed]		 105
13. Miyai, T., Aoyama, J., Sasai, S., Inoue, J.G., Miller, M. J., Tsukamoto, K. 2004.
Ecological aspects of the downstream migration of introduced European eels in the Uono River, Japan. Environmental Biology of Fishes 71: 105-114.		 23
12. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M. 2004.
Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva. Molecular Phylogenetics and Evolution 32: 274-286. [PubMed]		 97
11. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M. 2003.
Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish." Molecular Phylogenetics and Evolution 26: 110-120. [PubMed]		 265
10. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M. 2003.
Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels. Molecular Biology and Evolution 20: 1917-1924. [PubMed]		 99
9. Miya, M., Takeshima, H., Endo, H., Ishiguro, N. B., Inoue, J.G., Mukai, T., Satoh, T. P., Yamaguchi, M., Kawaguchi, A., Mabuchi, K., Shirai, S. M., Nishida, M. 2003.
Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 26: 121-138. [PubMed]		 660
8. Saitoh, K., Miya, M., Inoue, J.G., Ishiguro, N. B., Nishida, M. 2003.
Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography. Journal of Molecular Evolution 56: 464-472. [PubMed]		 171
7. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M. 2001.
A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences. Molecular Phylogenetics and Evolution 20: 275-285. [PubMed]		 182
6. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M. 2001.
Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families. Journal of Molecular Evolution 52: 311-320. [PubMed]		 86
5. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M. 2001.
Complete mitochondrial DNA sequence of the Japanese anchovy Engraulis japonicus. Fisheries Science 67: 828-835.		 64
4. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M. 2001.
Complete mitochondrial DNA sequence of the Japanese eel Anguilla japonica. Fisheries Science 67: 118-125.		 63
3. Aoyama, J., Ishikawa S., Otake, T., Mochioka, N., Suzuki, Y., Watanabe, S., Shinoda, A., Inoue, J.G., et al. 2001.
Molecular approach to species identification of eggs with respect to determination of the spawning site of the Japanese eel Anguilla japonica. Fisheries Science 67: 761-763.		 21
2. Inoue, J.G., Miya, M. 2001.
Phylogeny of the basal teleosts, with special reference to the Elopomorpha. Japanese Journal of Ichthyology 48: 75-91 (in Japanese with English abstract).
 9
1. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M. 2000.
Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus. Fisheries Science 66: 924-932.		 161
(Only peer reviewed in English are presented), Google scholar
Books
井上 潤．2022. 魚類の進化と多様性．遺伝学の百科事典．日本遺伝学会 編．丸善出版．
井上 潤．2021. 脊椎動物の誕生 (p18-20)．ヒト上科とヒト科で特有なCNS (p104-106)．ヒトゲノム事典．井ノ上逸朗ほか 編．一色出版．
井上 潤．2019. 系統・進化 (p21-25)．ウナギの科学．塚本勝巳 編．朝倉書店．
井上 潤．2018. 古代魚の系統進化 (p60-61)．下位真骨類の系統進化 (p62-63)．魚類学の百科事典．日本魚類学会 編．丸善出版．
井上 潤．2009. 古代魚の進化を探る． 海洋生命系のダイナミクス１：海洋の生命史．西田睦編． 第 6 章．(pp. 102-121)．
井上 潤，宮正樹．2001. ウナギ属 Anguilla の進化的起源． 海洋と生物. 133: 153-159．
 
Presentations (International)
2025
Yuan LIN, Zeshu YU, Sk Istiaque AHMED, Xueding WANG, Tomihiko HIGUCHI, Itsuka YABE, Sachihiko ITO, Eisuke TSUTSUMI, Hiroaki, SAITO, Kosei KOMATSU, Atsushi TSUDA, Yusuke KAWAGUCHI, Eitarou OKA, Kyoko OKINO, Hajime OBATA, Yuki MINEGISHI, Hideki FUKUDA, Marty Kwok-Shing WONG, Jun INOUE, Susumu HYODO and Shin-Ichi, ITO .
Quantifying the Front Effect: How Oceanic Fronts Shape Fish Community Distribution around Japan JpGU 2025. Chiba, Japan. (May, 2025).
Zeshu Yu, Marty Kwok-Shing Wong, Jun Inoue, Yuan Lin, Itsuka Yabe, Tomihiko Higuchi, Susumu Hyodo, Sachihiko Itoh, Yuichiro Nishibe, Hajime Obata, Shin-ichi Ito.
Environmental DNA of small pelagic fish in the deep ocean. JpGU 2025. Chiba, Japan. (May, 2025).
2024
AHMED Sk Istiaque, YU Zeshu, HIGUCHI Tomihiko, WANG Xueding, LIN Yuan, INOUE Jun, WONG Marty Kwok-Shing, ITOH Sachihiko, KOMATSU Kosei, KAWAGUCHI Yusuke, TSUTSUMI Eisuke, HYODO Susumu, ITO Shinichi. Assessment of western North Pacific pelagic fish biodiversity using three eDNA meta-barcoding surface-layer sampling techniques: ship-bottom intake, Niskin, and bucket. Can they reel in comparable insights?. JpGU 2024. Chiba, Japan. (May, 2024).
AHMED Sk Istiaque, YU Zeshu, HIGUCHI Tomihiko, INOUE Jun, WONG Marty, YOSHIZAWA Susumu, ITOH Sachihiko, KOMATSU Kosei, KAWAGUCHI Yusuke, TSUTSUMI Eisuke, HYODO Susumu, MORRONGIELLO John, ITO Shin-ichi. Comparison of three surface sampling methods for fish species eDNA detection using MiFish analysis. OSM-2023 (New Orleans, 2024).
Yuan LIN, Tsutsumi EISUKE, Junya HIRAI, Zeshu YU, Sk Istiaque AHMED, Xueding WANG, Itsuka YABE, Sachihiko ITO, Tomihiko HIGUCHI, Marty WONG, Jun INOUE, Susumu HYODO and Shin-Ichi, ITO. eDNA analysis reveals spatiotemporal distribution of fish communities in the coastal-open ocean transition zone. Ocean Sciences Meeting 2024, USA.
Yuan LIN, Zeshu YU, Sk Istiaque AHMED, Xueding WANG, Tomihiko HIGUCHI, Itsuka YABE, Sachihiko ITO, Eisuke TSUTSUMI, Hiroaki, SAITO, Kosei KOMATSU, Atsushi TSUDA, Yusuke KAWAGUCHI, Eitarou OKA, Kyoko OKINO, Hajime OBATA, Yuki MINEGISHI, Hideki FUKUDA, Marty Kwok-Shing WONG, Jun INOUE, Susumu HYODO and Shin-Ichi, ITO. Geographic characteristics of fish community structures around Japan revealed by eDNA survey. JpGU 2024. Chiba, Japan. (May, 2024).
Xueding Wang, Zeshu Yu, Sk Istiaque Ahmed, Zhen Lin, Ziqin Wang, Sachihiko Itoh, Eisuke Tsutsumi, Marty Kwok-Shing Wong, Jun Inoue, Susumu Hyodo, Higuchi Tomihiko and Shin-ichi Ito. Comprising three Environmental DNA (eDNA) sampling methods in terms of small pelagic fish community structures. Ocean sciences meeting 2024.
2023

AHMED Sk Istiaque, YU Zeshu, Xueding Wang, INOUE Jun, WONG Marty, YOSHIZAWA Susumu, ITOH Sachihiko, HYODO Susumu, ITO Shin-ichi. Comparison of fish species eDNA detection by MiFish analysis between intake-water, surface-water & niskin bottle sampling methods. JpGU 2023 Japan.
Yuan LIN, Tsutsumi EISUKE, Junya HIRAI, Zeshu YU, Sk Istiaque AHMED, Xueding WANG, Itsuka YABE, Sachihiko ITO, Tomihiko HIGUCHI, Marty WONG, Jun INOUE, Susumu HYODO and Shin-Ichi, ITO. eDNA analysis reveals spatiotemporal distribution of fish communities in the coastal-open ocean transition zone. Ocean Science Meeting 2023.

Zeshu Yu, Shin ichi Ito, Marty Kwok Shing Wong, Jun Inoue, Sk. Istiaque Ahemd, Tomihiko Higuchi, Susumu Hyodo, Sachihiko Itoh, Kosei Komatsu, Hiroaki Saito. Open ocean environmental DNA revealed environment dependent distribution pattern of small pelagic fish in the Kuroshio. JpGU 2023.
Xueding Wang, Zeshu Yu, Megumi Enomoto, Marty Kwok-Shing Wong, Jun Inoue, Susumu Hyodo, Higuchi Tomihiko, Atsushi Tsuda1 and Shin-ichi Ito. Exploring environmental effects on small pelagic fish community composition in the open ocean using environmental DNA. 2023 ECCWO-5.
Xueding Wang, Zeshu Yu, Marty Kwok-Shing Wong, Jun Inoue, Susumu Hyodo, Higuchi Tomihiko, Atsushi Tsuda and Shin-ichi Ito. Using environmental DNA to reveal the influence of environmental factors on the forage fish community compositions. PICES-2023 Annual Meeting.
2022
Zeshu Yu, Shin-ichi Ito, Marty Kwok-Shing Wong, Susumu Yoshizawa, Jun Inoue, Sachihiko Itoh, Kazuo Ishikawa, Chenying Guo, Minoru Ijichi, Susumu Hyodo . Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA. JpGU 2022. Xxxx, Japan.
Yubei Wu, Siyu Jiang, Junya Hirai, Fanyu Zhou, Jun Inoue, Susumu Hyodo, and Hiroaki Saito. Diversity and Biogeography of Dinoflagellates in the Kuroshio Region. PICES2022.
2021
Inoue, J. dbCNS: a new database for conserved non-coding sequencess. Genome Concept Centennial Symposium. Numazu (Zoom), Japan (Feb., 2021). Link.

Zeshu Yu, Shin-ichi Ito, Marty Wong, Susumu Yoshizawa, Jun Inoue, Susumu Hyodo. Marine fish distribution in the Kuroshio Extension area observed by OceanDNA. JpGU 2021. Online, Japan. (May, 2021).
2019
Inoue, J., Satoh, N. ORTHOSCOPE: an automatic web tool for estimating the origins and the functions of bilaterian protein-coding genes by comparing gene and species trees. Society for Molecular Biology and Evolution Conference 2019. Manchester, UK (July, 2019).
Inoue, J., Satoh, N. A Genomic survey of muscle structural proteins that enabled the rise of chordates. Society for Molecular Biology and Evolution Conference 2016. Gold Coast, Australia (July, 2016).
Inoue, J., Sato, Y., Sinclair, R., Nishida, M. Identification of phylogenetic marker gene considering whole genome duplication and species tree. Introduction to the analysis of molecular evolution in the genomic era. Shanghai (November, 2015).

Inoue J., Sato, Y., Sinclair, R., Nishida, M. Selecting molecular markers from transcriptome data for fish phylogenetics. Workshop on Methods for Biodiversity Research, Shanghai (March, 2014).
Inoue, J., Donoghue, P.C.J., Yang, Z. The impact of the representation of fossil calibration on Bayesian estimation of species divergence times. Evolution 2009, Moscow (June, 2009).
Miya, M., Inoue, J.G., Mabuchi, K., Nishida, M. Patterns of diversification in modern ray-finned fishes: a mitogenomic overview. Christchurch (June, 2007).
Inoue, J.G., M. Miya, B. Venkatesh, and M. Nishida. Mitochondrial phylogenomics of fishes: estimation of divergence times among basal ray-finned fish lineages. Phylogenomics conference, Montreal (March, 2006).
Inoue, J.G., M. Miya, B. Venkatesh, and M. Nishida. The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths. ASIH Annual Meetings, Tampa (July, 2005).
Lavoue S., Miya, M., Inoue J.G., Saitoh, K., Ishiguro, N. B., Nishida, M. Molecular phylogeny of the Clupeiformes (Teleostei) inferred from whole mitogenome sequences. ASIH Annual Meetings, Tampa (July, 2005).
Inoue, J.G., M. Miya, B. Venkatesh, and M. Nishida. The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths. Seventh Indo-Pacific Fish Conference, Taipei (May 2004).
Inoue, J.G., M. Miya, K. Tsukamoto, and M. Nishida. Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish." Society of Integrative and Comparative Biology Annual Meeting, Sheraton Centre Toronto (January, 2003).
Inoue, J.G. Novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families. International Symposium Advances in Eel Biology. University of Tokyo (September, 2001).
Inoue, J.G., M. Miya, K. Tsukamoto, and M. Nishida. Mitogenomic analysis of elopomorph relationships and origin of leptocephalus larva. International Commemorative Symposium 70th Anniversary of Japanese Society of Fisheries Science, Pacifico Yokohama (October, 2001).
Inoue, J.G., M. Miya, K. Tsukamoto, and M. Nishida. Gene rearrangements in the mitochondrial genomes of the order Anguilliformes (Teleostei: Elopomorpha): phylogenetic implication for the interfamilial relationships. International Symposium on Diversity of Fishes, National Science Museum, Tokyo (February, 2000).
Presentations (Domestic)
2024
西野純子, 井上潤, 浦野明央, 豊田敦, 伊藤武彦, 清本正人, 神田真司, 窪川かおる, 西野敦雄。 ナメクジウオにおけるmyh16のオーソログの探索。日本動物学会・令和6年度東北支部大会。
林元、平井惇也、余沢庶、Ahmed SI、王雪丁、矢部いつか、伊藤幸彦、樋口富彦、Wong MKS、井上潤、兵藤晋、伊藤進一。 eDNA分析による沿岸から外洋への移行域における魚群の時空間的分布の解明。海と地球のシンポジウム2023 (2024) 東京都
王雪丁、余沢庶、Ahmed SI、林珍、王子欽、矢部いつか、伊藤幸彦、Wong MKS、井上潤、兵藤晋、樋口富彦、伊藤進一。小型浮魚群集組成を用いた海洋DNAサンプリング手法の比較研究。海と地球のシンポジウム 2023 (2024 年) 東京都
2023
Ahmed SI, Yu Z, Higuchi T, Inoue J, Wong MKS, Yoshizawa S, Itoh S, Komatsu K, Kawaguchi Y, Hyodo S, Ito SI, Tsutsumi E, Morroniello J. Comparing three surface sampling methods for fish species detection in eDNA metabarcoding: Can ship bottom intake samples substitute the conventional Niskin and bucket samples? 海と地球のシンポジウム 2023 (2024 年) 東京都
AHMED Sk Istiaque1,2, YU Zeshu2, HIGUCHI Tomihiko2, INOUE Jun, WONG Marty2, YOSHIZAWA Susumu2, ITOH Sachihiko2, KOMATSU Kosei2, KAWAGUCHI Yusuke2, TSUTSUMI Eisuke3, HYODO Susumu2, MORRONGIELLO John2,4, ITO Shin-ichi2. Comparison of fish species eDNA detection by MiFish analysis between three surface sampling methods. Oceanographic Society of Japan Fall Meeting 2023。
伊藤進一、余沢庶、樋口富彦、Ahmed SI 、王雪丁、林元、Wong MKS、井上潤、兵藤晋。黒潮の環境DNAから青魚の分布特性を探る黒潮の環境DNAから青魚の分布特性を探る。OceanDNAテック2023 (2023 年)

王雪丁、余沢庶、Sk Istiaque AHMED、林珍、王子欽、矢部いつか、伊藤幸彦、WONG Marty、井上潤、兵藤晋、樋口富彦、伊藤進一、堤英輔. 小型浮魚群集組成を用いた海洋DNAサンプリング手法の比較研究。海と地球のシンポジウム 2023 東京都
Zeshu Yu, Shin-ichi Ito, Marty Kwok-Shing Wong, Jun Inoue, Sk. Istiaque Ahemd, Tomihiko Higuchi, Susumu Hyodo, Sachihiko Itoh, Kosei Komatsu, Hiroaki Saito. Environmental DNA study on small pelagic fish distributional characteristics in the Kuroshio frontal region. 海洋生物シンポジウム2023 東京。
余沢庶、黄國成、井上潤、樋口富彦、兵藤晋、伊藤幸彦、小松幸生、齊藤宏明、伊藤進一、Ahmed SI。環境DNAを用いた黒潮流系における環境要因に関連した小型浮魚類の分布研究。海と地球のシンポジウム 2023 (2024 年) 東京都
2022
王雪丁、余沢庶、榎本めぐみ, 黄國成、井上潤、兵藤晋、樋口富彦、津田敦、伊藤進一. 環境DNAを用いた外洋域における魚類群集組成と環境要因について.海と地球のシンポジウム 2022 東京都
井上 潤。ORTHOSCOPE* ：ゲノムに存在する全遺伝子の歴史を推定する系統解析パイプライン。日本動物学会・早稲田大会 (2022 年 9 月)。
Kayla Wilhoit, Shun Yamanouchi, Asano Ishikawa, Jun Inoue, Wataru Iwasaki, and Jun Kitano. Convergent change in gene copy number associated with diet and habitat shifts in animals.Ecological Society of Japan in March

余沢庶、伊藤進一、兵藤晋、伊藤幸彦、黄國成、吉澤晋、井上潤、伊知地稔. 海水に含まれるDNAから外洋の小型浮魚類の分布を探る.海と地球のシンポジウム 2022 東京都
Zeshu Yu, Shin-ichi Ito, Marty Kwok-Shing Wong, Susumu Yoshizawa, Jun Inoue, Sachihiko Itoh, Minoru Ijichi, Susumu Hyodo . OceanDNAを用いた黒潮流系における環境要因に関連した小型浮魚類の分布研究. 海洋生物シンポジウム 2022 東京都
井上 潤。系統樹に基づいたゲノム比較。生命科学を支える分子系統学 (2022 年 7 月)。
2021
井上 潤、斎藤成也。dbCNS: 進化的に保存された非コード配列の新たなデータベース。日本動物学会オンライン米子大会 (2021 年 9 月)
井上 潤、Using dbCNS, a database of conserved noncoding sequences. 遺伝研共同研究会「日本列島人の起源と成立をゲノム情報から探る」(2021 年 3 月)
2020
西野純子、井上 潤、神田真司、西野敦雄。脊椎動物の頭部筋肉に特異的なミオシン重鎖遺伝子MYH16 の起源と進化。日本動物学会・東北支部大会 (2020 年 12 月)．

西村瑠佳、杉本竜太、井上 潤、中岡博史、神澤秀明、篠田謙一、井ノ上逸郎。縄文人由来 DNA を用いた古代微生物の配列解析。日本進化学会 第22 回オンライン大会 (2020 年 9 月)．
2018
井上 潤，佐藤 矩行．種の系統樹に基づいて左右相称動物のオーソログを判定するウェブツールの開発． 日本動物学会 第89 回大会 (代替)・本郷 (2018 年 12 月)．
井上 潤．脊索動物の系統進化とゲノム進化．JT生命誌館 (2018 年 10 月)．

井上 潤，佐藤 行人，シンクレア ロバート，塚本 勝巳，西田 睦．海を支配する真骨魚類のゲノム再編と爆発的な多様化の関係．NGS 現場の会 (2017 年 5 月)．
井上 潤，佐藤 行人，シンクレア ロバート，塚本 勝巳，西田 睦．魚類ゲノム進化 3 億年の謎に迫る〜全ゲノム重複と種の系統樹を考慮した系統解析マーカ〜遺伝子の選定〜．中央水産研究所 (2016 年 3 月)．
井上 潤．ウナギの起源と進化．Eel Planet．日本大学 (2015 年 12 月)．
井上 潤，佐藤 行人，シンクレア ロバート，塚本 勝巳，西田 睦．全ゲノム重複と種の系統樹を考慮した系統解析マーカ遺伝子の選定．日本進化学会年会「夏の学校」．中央大学 (2015 年 8 月)．
井上 潤，佐藤 行人，西田 睦．脊椎動物 3 億年のゲノム進化：ゲノム重複に由来する遺伝子の保持と進化に寄与した自然選択項の検出．日本進化学会年会．筑波大学 (2013 年 9 月)．
井上 潤．真骨魚類ゲノムの進化特性: トランスクリプトーム相同遺伝子データベースの構築．日本進化学会年会．首都大学東京 (2012 年 8 月)．
山崎 彩．井上 潤．宗原弘幸．気候変動・分岐年代より推定するツマグロカジカ属の適応放散．日本進化学会年会．首都大学東京 (2012 年 8 月)．

Jun Inoue, Donoghue, P.C.J., Yang, Z. 化石制約がベイズ年代推定に及ぼす影響．日本進化学会年会．東京工業大学．(2010 年 9 月).
Davin H. E. SETIAMARGA, 宮 正樹, 山野上 祐介, 馬渕 浩司, 佐藤 崇, 井上 潤, 西田 睦. ミトコンドリアゲノム全塩基配列に基づくトウゴロウイワシ系魚類の分子系統．日本魚類学会年会．愛媛大学 (2008 年 9 月)．
馬 涛，青山 潤，MILLER Michael J.，峰岸 有紀，井上 潤，塚本 勝巳．インド-太平洋におけるUroconger (Congridae)の遺伝的分化．日本魚類学会年会．北海道大学 (2007 年 10 月)．
若畑 勇人，淀 太我，井上 潤，吉谷 圭介，北川 えみ，北川 忠生．三重県七色貯水池のオオクチバス2亜種混生集団の遺伝解析．日本魚類学会年会，静岡県コンベンションアーツセンター グランシップ，(2006 年 10 月)．
白井 滋，井上 潤，宮 正樹，西田 睦．ミトゲノム解析による現生板鰓類の系統類縁関係推定．日本魚類学会年会，静岡県コンベンションアーツセンター グランシップ，(2006 年 10 月)．
井上 潤．ミトコンドリアゲノム全長解析に基づく下位条鰭類の系統解析と分岐年代推定．日本魚類学会年会，静岡県コンベンションアーツセンター グランシップ，(2006 年 10 月)．
井上 潤．African and Asian coelacanths: An evolutionary history of the extant two species estimated from complete mitochondrial genome sequences．日本進化学会 2006 年大会，国立オリンピック記念青少年総合センター，(2006 年 8 月)．
Lavoue S., Miya, M., Inoue J.G., Saitoh, K., Ishiguro, N. B., Nishida, M. Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences. 日本魚類学会年会，琉球大学 (2004 年 9 月).
宮 正樹，井上 潤，石黒 直哉，武島 弘彦，佐藤 崇，馬渕 浩司，向井 貴彦， 鈴木 伸明，東 陽一郎，中谷 将典，山野上 祐介，中山 耕至，柳下 直己，白井 滋，斎藤 憲治，遠藤 広光，櫻井 博，西田 睦．条鰭類の大系統：350 種から得られたミトゲノム全長配列に基づく予備的解析その 1．日本魚類学会年会，京都大学，(2003 年 10 月)．
井上 潤，宮 正樹，塚本 勝巳，西田 睦．深海魚フウセンウナギ類のミトコンドリアゲノムにおける大規模な遺伝子配置変動．日本進化学会福岡大会，九州大学，(2003 年 8 月)．
宮 正樹，白井 滋，井上 潤，石黒 直哉，武島 弘彦，佐藤 崇，馬渕 浩司，向井 貴彦，鈴木 伸明，東 陽一郎，中谷 将典，山野上 祐介，中山 耕至，柳下 直己，斎藤 憲治，遠藤 広光，櫻井 博，西田 睦．ミトコンドリアゲノム全塩基配列に基づく "スズキ類" の大系統．魚類学会年会，信州大学，(2002 年 10月)．
井上 潤，宮 正樹，塚本 勝巳，西田 睦．ミトコンドリアゲノム全塩基配列に基づく古代魚の系統解析．魚類学会年会，信州大学，(2002 年 10月)．
井上 潤，宮 正樹，塚本 勝巳，西田 睦．ミトコンドリアゲノム全塩基配列データにもとづく古代魚の系統解析．分子生物学会年会，パシフィコ横浜，(2001 年 12 月)．
井上 潤，宮 正樹，塚本 勝巳，西田 睦．ミトコンドリアゲノミクスによるカライワシ類の系統解析とレプトケファルス幼生の起源．魚類学会年会，鹿児島大学，(2001 年 10 月)．
井上 潤，宮 正樹，塚本 勝巳，西田 睦．魚類のミトゲノミクス- VI：下位真骨類の系統．魚類学会年会，生命の星・地球博物館，(2000 年 10 月)．
井上 潤，宮 正樹，塚本 勝巳，西田 睦．魚類のミトコンドリア・ゲノミクス- II:：ウナギ目内部における顕著な遺伝子配置の変動と系統との関係．魚類学会年会，九州大学，(1999 年 10月)．
井上 潤，西田 睦，塚本 勝巳．ウナギ目魚類における mtDNA 遺伝子配置の変動：系統推定マーカーとしての検討．日本水産学会春期大会，東京水産大学，(1999 年 4 月)．
井上 潤，西田 睦，石川 智士，青山 潤，塚本 勝巳．mtDNA 12S rRNA および cyt b 遺伝子データによるウナギ目魚類の系統解析．日本水産学会秋季大会，広島大学，(1997 年 9 月)．
井上 潤，西田 睦，石川 智士，青山 潤，塚本 勝巳．ウナギ目魚類の系統解析：12S rRNA 遺伝子データの有効性の検討．日本水産学会春季大会，東京水産大学，(1997 年 4 月)．
Proceedings
Tsuchida, S., H. Yamaguchi, J.G.Inoue, A. Shinoda, M., Aoki, N. Togashi, A. So, Y. Matsuura, A. Shiraishi, S. Araki, T. Sugiyama. 2003. Distribution of anguilliform fishes on five seamounts in Mariana Area. JAMSTEC Journal of Deep Sear Research, 23 69-76.
井上 潤・宮 正樹. 2001. ウナギ属 Anguilla の進化的起源．海洋と生物, 133: 153-159.
Ishikawa, S., T. Otake, N. Mochioka, Y.Suzuki, J. Aoyama, S. Watanabe, T. Yoshinaga, J. G. Inoue, A. Shinoda, and T. Miyai. 2000. Sampling of Anguilla japonica eggs around Seamounts area. Preliminary Report of the Hakuho Maru Cruise KH 98-2, 40-44.
Otake, T., N. Mochioka, S. Ishikawa, Y. Suzuki, S. Watanabe, M. Oya, T. Yoshinaga, J. G. Inoue, A. Shinoda, T. Miyai, T. Utou, H. Matsuura, Y. Kurata, T. Yoshida, P. M. Lokman, A. Torii, H. Katayama, T. W. Lee, and K. Fujii. 2000. Distribution of Anguilla japonica leptocephali around Arakane and Pathfinder Seamounts. Preliminary Report of the Hakuho Maru Cruise KH 98-2, 45-47.
Dissertations
2001年 3月 29日 ミトコンドリアゲノム分析に基づくカライワシ類 (Elopomorpha) の系統に関する研究. 東京大学博士論文．博農第 2252 号
1998年 3月 30日 ウナギ目魚類の進化に関する分子系統学的研究. 東京大学修士論文．修農第 3784 号
External funds
2021 年 科研究費補助金　基盤研究（A）　(21H04922)
「亜熱帯化する海への布石：高精度な環境 DNA 解析による海洋生物分布マップの開発」
Grant-in-Aid for Scientific Research (A) (General)
“Laying the Groundwork for Subtropical Seas: Development of High-Precision Environmental DNA Analysis-Based Marine Organism Distribution Maps”
2018 年 科研究費補助金　基盤研究（C）　(18K06396)
「核ゲノム解析による進化速度の速い種の系統的位置決定：尾索動物オタマボヤ類を例に」
Grant-in-Aid for Scientific Research (C) (General)
“Determining phylogenetic positions of species with accelerated evolutionary rates by genome-wide analyses: a case study on urochordate Larvaceans”
2015 年 科研究費補助金　基盤研究（C）　(15K07172)
「脊椎動物の全ゲノム比較解析を可能にする統合オーソログ判定パイプラインの構築」
Grant-in-Aid for Scientific Research (C) (General)
“Development of an integrated pipeline of ortholog identification for comparative genome analysis of vertebrates”
2012 年 科研究費補助金　若手研究（B）　(24770070)
「核ゲノムデータを用いた条鰭類の系統解析に向けて：相同遺伝子選定パイプラインの構築」
Grant-in-Aid for Young Scientists (B)
“Phylogenetic analysis of ray-finned fish using genome-wide data: development of identification pipeline for homologous genes”．研究成果報告書．
2005 年 日本学術振興会　海外特別研究員・研究活動費
「脊椎動物ミトコンドリアゲノムの新たな分子進化モデル開発: より正確な系統推定の試み」
2003 年 日本学術振興会　特別研究員・特別研究員奨励費
「ミトゲノミクスに基づく下位条鰭類大分類群の再考」
Honors
2016 年 8月 27日 日本進化学会・研究奨励賞
「魚類の系統進化とゲノム進化」
2014 年 10月 3日 ライフサイエンス統合データベースセンター，オープン・サイエンス・アワード，ウェブサイト部門 (3位)
2011年 7月 30日　
　
 日本進化学会・教育啓蒙賞
「ホームページ（http://www.geocities.jp/ancientfishtree）を通じた広範な情報発信」
2006 年 10月 8日 日本魚類学会・奨励賞　
「ミトコンドリアゲノム全長配列に基づく下位条鰭類の系統解析と分岐年代推定」
Lectures
2016 年〜 分子進化・系統解析の方法:実演と実習．ゲノム多様性ワークショップ．北海道大学．Web.(2.0 時間)．
2013 年〜 Bayesian estimation of divergence time. Summer School on “Computational Biology Based on Tree of Life: Methods and Applications” held at Fudan University, Shanghai. Contents (3 hours)．
2010 年〜 分岐年代のベイズ推定．農林交流センターセミナー・ワークショップ．Web. 講義内容 (1.5 時間)．