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Academic Outputs from Our Laboratory

Academic Papers (Peer-reviewed)

Accepted
Jo, T. S., Fukumoto, S., Minamoto, T., Yamashita, Y., Masuda, R. (Accepted) Toward understanding diel changes in environmental DNA detection and quantification patterns in relation to organismal behaviors: A literature review and case study. Water Biology and Security.
Kato-Unoki, Y., Suzawa, T., Thu, T. T., Sugahara, T., Mitani, Y., Masuda, Y., Tsuboi, J., Minamoto, T., Seino, S. (Accepted) Detection assay improvements and distribution analyses of the invasive diatom Cymbella janischii from environmental DNA. Water Biology and Security.
源利文 (印刷中) マクロ生物の環境DNA分析：発展の歴史と将来への展望. 応用生態工学.
2026
Kitani, R. P., Saga, T., Kasada, M., Kiyono, M., Sato, M., Ushimaru, A., Minamoto, T. (2026) Feasibility of an eDNA-based educational program for high school students. Biodiversity and Conservation 35, 85.
Osada, Y., Miya, M., Araki, H., Doi, H., Kasai, A., Masuda, R., Minamoto, T., Seino, S., Takahara, T., Yamamoto, S., Yamanaka, H., Aizu-Hirano, M., Fukaya, K., Fukuchi, T., Gotoh, R.O., Hori, M., Iida, M., Imaizumi, T., Kajita, T., Kanbe, T., Kenta, T., Kobayashi, Y., Matsuura, T., Mizumoto, H., Motomura, H., Murakami, H., Nohara, K., Oka, S., Sado, T., Senou, H., Shibukawa, K., Sunobe, T., Takahashi, H., Takayama, K., Tanaka, K., Yamakawa, H., Yokoyama, S., Yoon, S., Kondoh, M. (2026) Large-scale environmental DNA survey reveals niche axes of a regional coastal fish community. Scientific Reports 16, 3276.
Hunter, M. E., Sepulveda, A., Trujillo-Gonzalez, A., Helbing, C. C., Rees, H. C., Jones-Slobodian, D. N., Miliano, R. C., Minamoto, T., Theroux, S., Wilcox, T., Yamanaka, H., Villacorta-Rath, C., Klymus, K. E. (2026) Best practice guidelines for environmental DNA-based proficiency testing in non-regulatory contexts. Environmental DNA 8, e70189.
2025
Uchiyama, Y., Sato, M., Ushimaru, A., Minamoto, T. (2025) Analysis of integrated studies on ecosystem service, human well-being, and urban planning: Regional trends and recommendations for future studies. Urban Ecosystems 28, 214.
Kuroita, T., Wu, Q., Iwamoto, R., Minamoto, T. (2025) QuickConc: A rapid, efficient, and power-free eDNA concentration method with cationic-assisted capture. Ecology and Evolution 15, e72269.
Hirayama, I. T., Kunimasa, Y., Takeuchi, A., Minamoto, T. (2025) Significant improvement of environmental DNA assay by targeting retrotransposon sequences characteristic to Anguilla eels. Environmental DNA 7, e70197.
Uchiyama, Y., Kyan, A., Sato, M., Ushimaru, A., Minamoto, T., Harada, K., Takakura, M., Kohsaka, R., Kiyono, M., Tsurumi, T., Uchida, A., Saga, T., Yamamoto K. (2025) Association between objective and subjective relatedness to nature and human well-being: key factors for residents and possible measures for inequality in Japan’s megacities. Landscape and Urban Planning 261, 105377.
Ongkulee, J., Suwannapoom, C., Minamoto, T., Osathanunkul, M. (2025) Development of an eDNA-Based qPCR and dPCR method for detecting the spatial distribution and relative abundance of the critically endangered giant barb (Catlocarpio siamensis). Global Ecology and Conservation 59, e03511.
Wu, Q., Nakano, T., Ishida, S., Komai, T., Fujiwara, Y., Yoshida, T., Kawato, M., Oka, S., Fujikura, K., Miya, M., Minamoto, T. (2025) Development of universal PCR primers for the environmental DNA metabarcoding of cephalopod (Mollusca) diversity. Marine Environmental Research 208, 107094.
Takahara, T., Yamagishi, S., Shimoda, R., Nagata, A., Sakata, M. K., Doi H., Minamoto, T. (2025) Seven-year changes in eDNA concentrations of two dominant submerged macrophytes in Lake Shinji: effects of salinity. Estuarine, Coastal and Shelf Science 315, 109165.
Urabe, J., Wakana, I., Ohtsuki, H., Sakata, M. K., Ohtake, Y., Ichige, R., Kuwae, M., Minamoto, T. (2025) Reconstruction of marimo population dynamics over 200 years using molecular markers and fossil plankton remains. Environmental DNA 7, e70085.
Sakata, A., Minamoto, T., Sado, T., Gotoh, R.O., Miya, M. (2025) Influence of homogenization methods on lichen species detection from environmental DNA metabarcoding. Metabarcoding and Metagenomics 9, e144340.
2024
Matsuo, R., Togetani, A., Adisakwattana, P., Yoonuan, T., Phuphisut, O., Limpanont, Y. Sakata, M. K., Sato, M. O., Sato, M., Minamoto, T. (2024) Improved environmental DNA detection sensitivity of Opisthorchis viverrini using a multi-marker assay. Parasitology Research 123, 419.
Uchiyama, Y., Kyan, A., Sato, M., Ushimaru, A., Minamoto, T., Kiyono, M., Harada, K., Takakura, M. (2024) Local environment perceived in daily life and urban green and blue space visits: Uncovering key factors for different age groups to access ecosystem services. Journal of Environmental Management 370, 122676.
Hirayama, I. T., Wu, L., Minamoto, T. (2024) Stability of environmental DNA methylation and its utility in tracing spawning in fish. Molecular Ecology Resources 24, e14011.
Osawa, R., Jo, T. S., Nakamura, R., Futami, K., Itayama, T., Chadeka, E. A., Ngetich, B., Nagi, S., Kikuchi, M., Njenga, S., Ouma, C., Sonye, G. O., Hamano, S., Minamoto, T. (2024) Methodological assessment for efficient collection of Schistosoma mansoni environmental DNA and improved schistosomiasis surveillance in tropical wetlands. Acta Tropica 260, 107402.
Hashimoto, N., Iwata, T., Kihara, N., Nakamura, N., Sakata, M. K., Minamoto, T. (2024) Detection of environmental DNA of finless porpoise (Neophocaena asiaeorientalis) in Osaka Bay, Japan. Conservation Genetics Resources 16, 255-261
Asai, T., Ikushima, S., Sugiyama, M., Morimoto, T., Sudo, A., Minamoto, T. (2024) Application of dietary content analysis using dropped feces to assess damage to fisheries by great cormorants. Ornithological Science 23, 125-128.
Nakagawa, H., Fujiki, D., Numata, H., Wu, L., Mori, T., Minamoto, T. (2024) Regional-scale effects of deer-induced forest degradation on river ecosystem dynamics. Poulation Ecology 66, 196-216.
Kato-Unoki, Y., Mayama, S., Kurihara, A., Minamoto, T. (2024) Development of specific detection assays from environmental DNA of invasive diatom Cymbella janischii in Japan. Limnology 25, 247-254.
Sato, T., Uemura, K., Yasuda, M., Maeda, A., Minamoto, T., Harada, K., Sugiyama, M., Ikushima, S., Yokota, S., Horiuchi, M., Takahashi, S., Asai, T. (2024) Traces of pandemic fluoroquinolone-resistant Escherichia coli clone ST131 transmitted from human society to aquatic environments and wildlife in Japan. One Health 18, 199715.
Hidaka, S., Jo, T. S., Yamamoto, S., Katsuhara, K. R., Tomita, S., Miya, M., Ikegami,M., Ushimaru, A., Minamoto, T. (2024) Sensitive and efficient surveillance of Japanese giant salamander (Andrias japonicus) distribution in western Japan using multi-copy nuclear DNA marker. Limnology 25, 189-198.
Oyabu, A., Wu, L., Matsumoto, T., Kihara, N., Yamanaka, H., Minamoto, T. (2024) The effect of artificial light at night on wild fish community: manipulative field experiment and species composition analysis using environmental DNA. Environmental Advances 15, 100457
Wu, L., Osugi, T., Inagawa, T., Okitsu, J., Sakamoto, S., Minamoto, T. (2024) Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons. Molecular Ecology Resources 24, e13875.
2023
Hashizume, H., Taga, S., Sakata, M. K., Hussein, M., Siddig, E. E., Minamoto, T., Fahal, A. H., Kaneko, S. (2023) Environmental detection of eumycetoma pathogens using multiplex real-time PCR for soil DNA in Sennar State, Sudan. Tropical Medicine and Health 51, 71.
赤塚真依子, 飯村浩太郎, 高山百合子, 源利文 (2023) 藻場を対象とした環境DNAの分布傾向と採水範囲の検討方法について. 土木学会論文集 79, 23-27158.
Yano, N., Minamoto, T., Yamaguchi, H., Goto, T., Nishikata, T. (2023) Comparison of evolutionary relationships between Branchiostoma floridae, Ciona intestinalis, and Homo sapiens globins provide evidence of gene cooption and convergent evolution. International Journal of Molecular Sciences, 24, 16009.
Takahara, T., Doi, H., Kosuge, T., Nomura, N., Maki, N., Minamoto, T., Watanabe, K. (2023) Effective environmental DNA collection for an endangered catfish species: testing for habitat and daily periodicity. Ichthyological Research, 70, 409-418.　
Kanamori, A., Kitani, R., Oota, A., Hirano. K., Myosho, T., Kobayashi, T., Kawamura, K., Kato, N., Ansai, S., Kinoshita, M. (2023) Wnt4a is indispensable for genital duct elongation but not for gonadal sex differentiation in the Medaka, Oryzias latipes. Zoological Science, 40, 348-359.
Wu, Q., Zhou, J., Komoto, T., Ishikawa, T., Goto, N., Sakata, M. K., Kitazawa, D., Minamoto, T. (2023) Opposite trends in environmental DNA distributions of two freshwater species under climate change. Ecosphere 14, e4651.
Miki, T., Yamanaka, H., Sogabe, A., Omori, K., Saito, Y., Minamoto, T., Uchii, K., Honjo, M. N., Suzuki, A. A., Kohmatsu, Y., Kawabata, Z. (2023) Spatial epidemiology model can explain the seasonal dynamics of infectious disease Cyprinid herpesvirus 3 (CyHV-3) by thermoregulation behavior of the host, common carp (Cyprinus carpio). Theoretical Ecology 16, 195-208.
Sato, M., Minamoto, T., Ushimaru, A. (2023) An interdisciplinary approach to environmental conservation policy: A case of Satoyama re-development in the peri-urban area. International Journal of Economic Policy Studies 17, 403-419.
Doi, H., Matsuoka, S., Matsuzaki, S. S., Nagano, M., Sato, H., Yamanaka, H., Matsuhashi, S., Yamamoto, S., Minamoto, T., Araki, H., Ikeda, K., Kato, A., Kamei, K., Maki, N., Mitsuzuka, T., Takahara, T., Toki, K., Ueda, N., Watanabe, T., Yamazoe, K., Miya, M. (2023) Species traits and ecosystem characteristics affect species detection by eDNA metabarcoding in lake fish communities. Freshwater Biology 68, 1346-1358.　
Mori, K., Imamura, A., Hirayama, I., Minamoto, T. (2023) Detection of Echinococcus multilocularis in repurposed environmental DNA samples from river water. PeerJ 11, e15431.
Sakata, M. K., Takeshita, D., Nishizawa, R., Sato, T., Minamoto, T. (2023) An efficient environmental DNA detection method for rare species: a case study of a small salamander (Hynobius boulengeri). Analytical Sciences 39, 721-728.
Wu, Q., Minamoto, T. (2023) Improvement of recovery yield of macro-organismal environmental DNA from seawater samples. Analytical Sciences 39, 713-720.
Souma, R., Katano, I., Doi, H., Takahara, T., Minamoto, T. (2023) Comparing environmental DNA with whole pond survey to estimate the total biomass of fish species in ponds. Freshwater Biology 68, 727-736.
Aoshima, I., Nakao, R., Minamoto, T., Ushimaru, A., Sato, M. (2023) Heterogeneous preference for biodiversity in Japanese urban blue spaces based on people's nature experiences: Analysis using eDNA and satisfaction data. City and Environment Interactions 18, 100101.
Okanishi, M., Kohtsuka, H., Wu, Q., Shinji, J., Shibata, N., Tamada, T., Nakano, T., Minamoto, T. (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Mebarcoding and Metagenomics 7, e94298.
Takahara, T., Fukui, K., Hiramatsu, D., Doi, H., Fujii, M., Minamoto, T. (2023) Development of primer-probe sets for environmental DNA-based monitoring of pond smelt Hypomesus nipponensis and Japanese icefish Salangichthys microdon. Landscape and Ecological Engineering 19. 11-19.
Nishizawa, R., Nakao, R., Ushimaru, A., Minamoto, T. (2023) Development of environmental DNA detection assays for snakes in paddy fields in Japan. Landscape and Ecological Engineering 19, 3-10.
Wu, L., Wu, Q., Inagawa, T., Okitsu, J., Sakamoto, S., Minamoto, T. (2023) Estimating the spawning activity of fish species using nuclear and mitochondrial environmental DNA concentrations and their ratios. Freshwater Biology 68, 103-114.
2022
Nakagawa, H., Fukushima, K., Sakai, M., Wu, L., Minamoto, T. (2022) Relationships between the eDNA concentration obtained from metabarcoding and stream fish abundance estimated by the removal method under field conditions. Environmental DNA 4, 1369-1380.
赤塚真依子, ムチェブエ エドウィン, 高山百合子, 織田幸伸, 源利文 (2022) 環境DNAを活用した藻場モニタリングにおける流れの影響について. 土木学会論文集B2(海岸工学) 78, I_865─I_870.
Jo, T.*, Sato, M.*, Minamoto, T.*, Ushimaru A.* (2022) Valuing the cultural services from urban blue space ecosystems in Japanese megacities during the COVID-19 pandemic. People and Nature 4, 1176-1189. (*equal contribution)
Asai, T., Sugiyama, M., Omatsu, T., Yoshikawa, M., Minamoto, T. (2022) Isolation of extended-spectrum beta-lactamase-producing Escherichia coli from Japanese red fox (Vulpes vulpes japonica). MicrobiologyOpen 11, e1317.
Wakiya, R., Itakura, H., Hirae, T., Igari T., Manabe, M., Matsuya N., Miyata, K., Sakata, M. K., Minamoto, T. (2022) Slower growth of farmed eels stocked into rivers with higher wild eel density. Journal of Fish Biology 101, 613-627.
Sakata, M. K., Sato, M., Sato, M. O., Watanabe, T., Mitsuishi, H., Hikitsuchi, T., Kobayashi, J., Minamoto, T. (2022) Detection and persistence of environmental DNA (eDNA) of the different developmental stages of a vector mosquito, Culex pipiens pallens. PLoS ONE 17, e0272653.
小出水規行, 源利文, 白子智康, 中村匡聡 (2022) 農業水路における環境DNA調査の適用性と環境DNAの拡散距離. 農業農村工学会誌 90, 11-14.
Wu, L., Yamamoto, Y., Yamaguchi, S., Minamoto, T. (2022) Spatiotemporal changes in environmental DNA concentrations caused by fish spawning activity. Ecological Indicators 142, 109213.
Minamoto, T. (2022) Environmental DNA analysis for macro-organisms: Species distribution and more. DNA Research, 29, dsac018.
Jo, T., Takao, K., Minamoto, T. (2022) ing the state of environmental DNA to its application for biomonitoring and stock assessment: targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes. Environmental DNA 4, 271-283.
Hashizume, H., Taga, S., Sakata, M. K., Taha M. H. M., Siddig, E. E., Minamoto, T., Fahal, A. H., Kaneko, S. (2022) Detection of multiple mycetoma pathogens using fungal metabarcoding analysis of soil DNA in an endemic area of Sudan. PLoS Neglected Tropical Diseases 16, e0010274.
Sakata, M. K., Kawata, M. U., Kurabayashi, A., Kurita, T., Nakamura, M., Shirako, T., Kakehashi R., Nishikawa, K., Hossman, M. Y., Nishijima, T., Kawamoto, J., Miya, M., Minamoto, T. (2022) Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. Metabarcoding and Metagenomics 6, 15-26.
Nagayama, S., Oota, M., Fujita, T., Kitamura, J., Minamoto, T., Mori, S., Kato, M., Takeyama, N., Takino, F., Yonekura, R., Yamanaha, H. (2022) Autumn dispersal and limited success of reproduction of the deepbody bitterling (Acheilognathus longipinnis) in terrestrialized floodplain. Knowledge and Management of Aquatic Ecosystems, 423, 4.
Sasano, S., Murakami, H., Suzuki, K. W., Minamoto, T., Yamashita, Y., Masuda R. (2022) Seasonal changes in the distribution of black sea bream Acanthopagrus schlegelii estimated by environmental DNA. Fisheries Science 88, 91-107
Murakami, H., Masuda, R., Yamamoto, S., Minamoto, T., Yamashita, Y. (2022) Environmental DNA emission by two carangid fishes in single and mixed-species tanks. Fisheries Science 88, 55-62.
Tsuji, S., Nakao, R., Saito, M., Minamoto, T., Akamatsu, Y. (2022) Pre-centrifugation before DNA extraction mitigates extraction efficiency reduction of environmental DNA caused by the preservative solution (benzalkonium chloride) remaining in the filters. Limnology 23, 9-16.
2021
瀬口雄一*, 山本義彦*, 竹門康弘, 源利文 (2021) 淀川大堰湛水域における琵琶湖産アユの河川残留個体の存在. 魚類学雑誌 68, 163-172. (*同等貢献)
Jo, T., Sakata, M. K., Murakami, H., Masuda, R., Minamoto, T. (2021) Universal performance of benzalkonium chloride for the preservation of environmental DNA in seawater samples. Limnology and Oceanography: Methods 19, 758-768.
赤塚真依子, 高山百合子, ムチェブエ エドウィン, 伊藤一教, 渡辺謙太, 桑江朝比呂, 源利文 (2021) 藻場モニタリングのための環境DNA分析プロトコル作成に向けた検討. 土木学会論文集B2（海岸工学） 77, I_895-I_900.
Fukuda, A., Usui, M., Uchiyama, K., Shrestha, D., Hashimoto, N., Sakata, M. K., Minamoto, T., Yoshida, O., Murakami, K., Tamura, Y., Asai, T. (2021) Prevalence of antimicrobial-resistant Escherichia coli in the migratory bird (Anser albifrons) and their habitat in Miyajimanuma, Japan. Journal of Wildlife Diseases 57, 954-958.
Osathanunkul, M., Minamoto, T. (2021) eDNA based detection of a vulnerable crocodile newt (Tylototriton uyenoi) to influence government policy and raise public awareness. Diversity and Distributions 27, 1958-1965.
Ogata, M., Masuda, R., Marino, H., Sakata, M. K., Hatakeyama, M., Yokoyama, K., Yamashita, Y., Minamoto, T. (2021) Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami. Scientific Reports 11, 16830. 　プレスリリース
Wu, Q.*, Sakata, M. K.*, Wu, D., Yamanaka, H., Minamoto, T. (2021) Application of environmental DNA metabarcoding in a lake with extensive algal blooms. Limnology 22, 363-370. (*equal contribution)
Fukaya, K., Murakami, H., Yoon, S., Minami, K., Osada, Y., Yamamoto, S., Masuda, R., Kasai, A., Miyahira, K., Minamoto, T., Kondoh, M. (2021) Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modeling. Molecular Ecology 30, 3057-3067. プレスリリース
Jo, T., Ikeda, S., Fukuoka, A., Inagawa, T., Okitsu, J., Katano, I., Doi, H., Nakai, K., Ichiyanagi, H., Minamoto, T. (2021) Utility of environmental DNA analysis for effective monitoring of invasive fish species in reservoirs. Ecosphere 12, e03643.
Jo, T., Minamoto, T. (2021) Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta-analyses. Molecular Ecology Resources 21, 1490-1503.
Osathanunkul, M., Minamoto, T. (2021) Molecular detection of giant snakeheads, Channa micropeltes (Cuvier, 1831), one of the most troublesome fish species. Scientific Reports 11, 9943.
Yasashimoto, T., Sakata, M. K., Sakita, T., Nakajima, S., Ozaki, M., Minamoto, T. (2021) Environmental DNA detection of an invasive ant species (Linepithema humile) from soil samples. Scientific Reports 11, 10712. プレスリリース
Doi, H.*, Minamoto, T.*, Takahara, T., Tsuji, S., Uchii, K., Yamamoto, S., Katano, I., Yamanaka, H. (2021) Compilation of real-time PCR conditions toward the standardization of eDNA methods. Ecological Research, 36 (3), 379-388. (*equal contribution)
Tenma, H., Tsunekawa, K., Fujiyoshi, R., Takai, H., Hirose, M., Masai, N., Sumi, K., Takihana, Y., Yanagisawa, S., Tsuchida, K., Ohara, K., Jo, T., Takagi, M., Ota, A., Iwata, H., Yaoi, Y., Minamoto, T. (2021) Spatio-temporal distribution of Flavobacterium psychrophilum and ayu Plecoglossus altivelis in rivers revealed by environmental DNA analysis. Fisheries Science 87, 321-330. プレスリリース
Sakata, M. K., Watanabe, T., Maki, N., Ikeda, K., Kosuge, T., Okada, H., Yamanaka, H., Sado, T., Miya, M., Minamoto, T. (2021) Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river. Limnology 22, 221-235. プレスリリース
Hoshino, T., Nakao, R., Doi, H., Minamoto, T. (2021) Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique. Scientific Reports 11, 4372.
Aratani, T., Koide, N., Hayami, K., Sugiyama, M., Minamoto, T., Asai, T. (2021) Continuous prevalence of VEB-3 extended-spectrum β-lactamase-producing Aeromonas hydrophila in a local river in Gifu City, Japan. Microbiology and Immunology 65, 99-100.
Doi, H., Akamatsu, Y., Goto, M., Inui, R., Komuro, T., Nagano, M., Minamoto, T. (2021) Broad-scale detection of environmental DNA for an invasive macrophyte and the relationship between DNA concentration and coverage in rivers. Biological Invasions 23, 507-520.
Tsuri, K., Ikeda, S., Hirohara, T., Shimada, Y., Minamoto, T., Yamanaka, H. (2021) Messenger RNA-typing of environmental RNA (eRNA): a case study on zebrafish tank water with perspectives for the future development of eRNA analysis on aquatic vertebrates. Environmental DNA 3, 14-21. プレスリリース
Minamoto, T., Miya, M., Sado, T., Seino, S., Doi, H., Kondoh, M., Nakamura, K., Takahara, T., Yamamoto, S., Yamanaka, H., Araki, H., Iwasaki, W., Kasai, A., Masuda, R., Uchii, K. (2021) An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols. Environmental DNA 3, 8-13.
Sugiura, K., Tomita, S., Minamoto, T., Mishina, T., Iwata, A., Abe, T., Yamamoto, S., Watanabe, K. (2021) Characterizing the spatial and temporal occurrence patterns of the endangered botiid loach Parabotia curtus by environmental DNA analysis using a newly developed species-specific primer set. Ichthyological Research 68, 152-157.
Chen J. -W., Chen, Z., Liu S. -S. Guo, W. -J., Li D., Minamoto, T., Gao, T. -X. (2021) Revealing an invasion risk of fish species in Qingdao Underwater World by Eevironmental DNA metabarcoding. Journal of Ocean University of China, 20 (1), 124-136.
Chen, Z., Minamoto, T., Lin, L. -S., Gao, T. -X. (2021) An optional low-cost method of extracting environmental DNA of macro-organisms from filter membranes in large scale eDNA surveys. Pakistan Journal of Zoology, 53 (1), 263-372.
2020
Osathanunkul, M., Minamoto, T. (2020) A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment. PeerJ, 8, e10338.
Matsumoto, T., Arakawa, H., Murakami, T., Yanai, S. (2020) Settlement patterns of two sesarmid megalopae in the Sai River Estuary, Ishikawa Prefecture, Japan. Plankton and Benthos Research 15(4), 306-316.
Jo, T., Tomita, S., Kohmatsu, Y., Osathanunkul, M., Ushimaru, A., Minamoto, T. (2020) Seasonal monitoring of Hida salamander Hynobius kimurae using environmental DNA with a genus-specific primer set. Endangered Species Research 43, 341-352.
Muchebve, E., Takayama, Y., Akatsuka, M., Ito, K., Minamoto, T. (2020) Feasibility study for seagrass beds monitoring using environmental DNA. 土木学会論文集B2(海岸工学), 76(2), I_949-I_954.
赤塚真依子, 高山百合子, Edwin Muchevbe, 伊藤一教, 渡辺謙太, 桑江朝比呂, 源利文 (2020) 海草場を対象とした環境DNAの季節変化と環境DNA分析における採水量の検討. 土木学会論文集B2(海岸工学), 76(2), I_943-I_948.
Imamura, A., Hayami, K., Sakata, M. K., Minamoto, T. (2020) Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout. Biodiversity Data Journal, 8, e56876.
Kudoh, A., Minamoto, T., Yamamoto, S. (2020) Detection of herbivory: eDNA detection from feeding marks on leaves. Environmental DNA, 2, 627-634. プレスリリース
Sakata, M. K., Yamamoto, S., Gotoh, R. O., Miya, M., Yamanaka, H., Minamoto, T. (2020) Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA. Environmental DNA, 2, 505-518.
Kuwae, M., Tamai, H., Doi, H., Sakata, M. K., Minamoto, T., Suzuki, Y. (2020) Sedimentary DNA tracks decadal-centennial changes in fish abundance. Communications Biology, 3, 558.
Tsuji, S., Maruyama, A., Miya, M., Ushio, M., Sato, H., Minamoto, T., Yamanaka, H. (2020) Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population. Molecular Ecology Resources, 20 (5), 1248-1258.
Takahara, T., Taguchi, J., Yamagishi, S., Doi, H., Ogata, S., Yamanaha, H., Minamoto, T. (2020) Suppression of eDNA degradation in water samples associated with different storage temperature and period using benzalkonium chloride. Limnology and Oceanography: Methods 18, 437-445.
Takeshita, D., Terui, S., Ikeda, K., Mitsuzuka, T., Osathanunkul, M., Minamoto, T. (2020) Projection range of eDNA analysis in marshes: a suggestion from the Siberian salamander (Salamandrella keyserlingii) inhabiting the Kushiro marsh, Japan. PeerJ 8, e9764.
Itakura, H., Wakiya, R., Sakata, M. K., Hsu H. -Y., Chen, S, -C., Yang, C. -S., Han, Y. -S., Minamoto, T. (2020) Estimations of riverine distribution, abundance and biomass of anguillid eels in Japan and Taiwan using environmental DNA analysis. Zoological Studies 59, 17.
Hayami, K., Sakata, M. K., Inagawa, T., Okitsu, J., Katano, I., Doi, H., Nakai, K., Ichiyanagi, H., Gotoh, R. O., Miya, M., Sato, H., Yamanaka, H., Minamoto, T. (2020) Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs. Ecology and Evolution 10 (12), 5354-5367.
Jo, T., Murakami, H., Masuda, R., Minamoto, T. (2020) Selective collection of long fragments of environmental DNA using larger pore size filter. Science of the Total Environment 735, 139462.
Takahashi, S., Sakata, M. K., Minamoto, T., Masuda, R. (2020) Comparing the efficiency of open and enclosed filtering systems in fish and jellyfish environmental DNA quantification. PLOS ONE 15 (4), e0231718
Jo, T., Arimoto, M., Murakami, H., Masuda, R., Minamoto, T. (2020) Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass. Environmental DNA 2 (2), 140-151.
Yatsuyanagi, T., Ishida, R., Sakata, M. K., Kanbe, T., Mizumoto, H., Kobayashi, Y., Namba S., Nii H., Minamoto, T., Araki, H. (2020) Environmental DNA monitoring for short-term reproductive migration of endemic anadromous species, Shishamo smelt (Spirinchus lanceolatus). Environmental DNA 2 (2), 130-139.
Jo, T., Fukuoka, A., Uchida, K., Ushimaru A., Minamoto, T. (2020) Multiplex real-time PCR enables the simultaneous detection of environmental DNA from freshwater fishes: a case study of three exotic and three threatened native fishes in Japan. Biological Invasions 22 (2), 455-471.
Tsuji, S., Miya, M., Ushio, M., Sato, H., Minamoto, T., Yamanaka, H. (2020) Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water. Environmental DNA 2, 42-52.
陈治, 宋娜, 源利文, 邬倩倩, 高天翔 (2020) 舟山近海水样环境DNA获取方法的建立. 水生生物学報 44, 1-7.
2019
Kakuda, A., Kakuda, A., Doi, H., Souma, R., Nagano, M., Minamoto, T., Katano, I. (2019) Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality. PeerJ 7, e815.
Fornillos, R. J. C, Sato, M. O., Tabios, I. K. B., Sato, M., Leonardo, L. R., Chigusa, Y., Minamoto, T., Kikuchi, M., Legaspi E. R., Fontanilla, I. K. (2019) Detection of Schistosoma japonicum and Oncomelania hupensis quadrasi environmental DNA and its potential utility to schistosomiasis japonica surveillance in the Philippines. PLOS ONE 14, e0224617.
Uchii, K., Doi, H., Okahashi, T., Katano, I., Yamanaka, H., Sakata, M. K., Minamoto, T. (2019) Comparison of inhibition resistance among PCR reagents for detection and quantification of environmental DNA. Environmental DNA 1, 359-367.
赤塚真依子, 高山百合子, 伊藤一教, 渡辺謙太, 桑江朝比呂, 大澤亮介, 森本哲平, 源利文 (2019) 海草場を対象とした環境DNAの季節変化・日変化・形態変化に関する基礎研究. 土木学会論文集B2（海岸工学） 75 (2), I_1075─I_1080
高山百合子, 赤塚真依子, 伊藤一教, 源利文 (2019) 環境DNAを活用した固着性水生生物モニタリング手法の成立性について. 土木学会論文集B2（海岸工学） 75 (2), I_1087─I_1092.
Calata, F. I., Caranguian, C., Mendoza, J. E., Fornillos, R. J., Tabios, I. K., Fontanilla, I. K., Leonardo, L., Sunico, L., Chigusa, Y., Kikuchi, M., Sato, M. O., Minamoto, T., Sato, M., Baoanan, Z. （2019) Analysis of environmental DNA and edaphic factors for the detection of the snail intermediate host Oncomelania hupensis quadrasi. Pathogens 8, 160.
Sakai, Y., Kusakabe, A., Tsuchida, K., Tsuzuku, Y., Okada, S., Kitamura, T., Tomita, S., Mukai, T., Tagami, M., Takagi, M., Yaoi, Y., Minamoto, T. (2019) Discovery of an unrecorded population of Yamato salamander (Hynobius vandenburghi) by GIS and eDNA analysis. Environmental DNA 1, 281-289. 　プレスリリース（神戸大学） 論文の内容が、朝日新聞、中日新聞などで紹介されました。
Horiuchi, T., Masuda, R., Murakami H., Yamamoto, S., Minamoto, T. (2019) Biomass-dependent emission of environmental DNA in jack mackerel Trachurus japonicus juveniles. Journal of Fish Biology 95, 979-981.
Matsuhashi, S., Minamoto, T., Doi, H. (2019) Seasonal change in environmental DNA concentration of a submerged aquatic plant species. Freshwater Science 38, 654-660.
Jo, T., Arimoto, M., Murakami, H., Masuda, R., Minamoto, T. (2019) Particle size distribution of environmental DNA from the nuclei of marine fish. Environmental Science & Technology 53, 9947-9956.
今村彰生・速水花奈・坂田雅之・源利文 (2019) 河川横断構造物とニジマスが北海道のイワナ属の生息に与える影響：環境DNA分析の結果をもとに. 保全生態学研究 24, 71-81
Kano, K., Kudo, M., Yoshizawa, G., Mizumachi, E., Suga, M., Akiya, N., Ebina, K., Goto, T., Itoh, M., Joh, A., Maenami, H., Minamoto, T., Mori, M., Morimura, Y., Motoki, T., Nakayama, A., Takanashi, K. (2019) How science, technology and innovation can be placed in broader visions? -Public opinions from inclusive public engagement activities-. Journal of Science Communication 18, A02.
Wu, Q., Kawano, K., Ishikawa, T., Sakata, M. K., Nakao, R., Hiraiwa, M. K., Tsuji, S., Yamanaka, H., Minamoto, T. (2019) Habitat selection and migration of the common shrimp, Palaemon paucidens in Lake Biwa, Japan – an eDNA-based study. Environmental DNA 1, 54-63.
Sato, Y., Mizuyama, M., Sato, M., Minamoto, T., Kimura, R., Toma, C. (2019) Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan. Scienctific Reports 9, 6575.
Wu, Q., Takami, Y., Minamoto, T., Ishikawa, T. (2019) The life history with seasonal migration of the lacustrine shrimp Palaemon paucidens in an ancient lake in Japan. Ecosphere 10, 4, e02628.
Takahara, T., Ikebuchi, T., Doi, H., Minamoto, T. (2019) Using environmental DNA to estimate the seasonal distribution and habitat preferences of a Japanese basket clam in Lake Shinji, Japan. Estuarine, Coastal and Shelf Science 221, 15-20.
Itakura, H., Wakiya, R., Yamamoto, S., Kaifu, K., Sato, T., Minamoto, T. (2019) Environmental DNA analysis reveals the spatial distribution, abundance and biomass of Japanese eels at the river basin scale. Aquatic Conservation: Marine and Freshwater Ecosystems 29, 361-373.
Murakami, H., Yoon, S., Kasai, A., Minamoto, T., Yamamoto, S., Sakata, M. K., Horiuchi, T., Sawada, H., Kondoh, M., Yamashita, Y., Masuda, R. (2019) Dispersion and degradation of environmental DNA from caged fish in a marine environment. Fisheries Science 85, 327-337.
Jo, T., Murakami, H.,Yamamoto, S., Masuda, R., Minamoto, T. (2019) Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution. Ecology and Evolution 9, 1135-1146.
Minamoto, T., Hayami, K., Sakata M. K., Imamura, A. (2019) Real-time PCR assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: application to winter surveys. Ecological Research 34, 237-242.
Takeuchi, A., Watanabe, S., Yamamoto, S., Miller, M. J., Fukuba, T., Miwa, T., Okino, T., Minamoto, T., Tsukamoto, K. (2019) First use of oceanic environmental DNA to study the spawning ecology of the Japanese eel Anguilla japonica. Marine Ecology Progress Series 609, 187-196.
2018
丹羽英之・坂田雅之・源利文・清野未恵子（2018）河川における流程500m間隔での環境DNA分析と現地採集調査による魚類検出結果の比較. 保全生態学研究 23 (2), 257-264.　
Sato, M. O., Rafalimanantsoa, A., Ramarokoto, C., Rahetilahy, A. M., Ravoniarimbinina, P., Kawai, S., Minamoto, T., Sato, M., Kirinoki, M., Rasolofo, V., De Calan M., Chigusa, Y. (2018) Usefulness of environmental DNA for detection of Schistosoma mansoni in Madagascar. International Journal of Infectious Diseases 76, 130-136.
赤塚真依子・高山百合子・伊藤一教・森本哲平・源利文（2018）海草場を対象とした環境DNA検出方法と三次元数値解析の適用性に関する検討. 土木学会論文集B2（海岸工学）74 (2), I_1225-I_1230.　
高山百合子・赤塚真依子・伊藤一教・源利文（2018）アマモ場のモニタリング手法における環境DNAの活用について. 土木学会論文集B2（海岸工学）74 (2), I_1231-I_1236.　
Nakagawa, H., Yamamoto, S., Sato, Y., Sado, T., Minamoto, T., Miya, M. (2018) Comparing local- and regional-scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods. Freshwater Biology 63 (6), 569-580.
Wu, Q., Kawano, K., Uehara, Y., Okuda, N., Hongo, M., Tsuji, S., Yamanaka, H., Minamoto, T. (2018) Environmental DNA reveals non-migratory individuals of Palaemon paucidens overwintering in Lake Biwa shallow waters. Freshwater Science 37 (2), 307-314.
Ushio, M., Murakami, H., Masuda, R., Sado, T., Miya, M., Sakurai, S., Yamanaka, H., Minamoto, T., Kondoh, T. (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding & Metagenomics 2, e23297.
2017
Doi, H., Akamatsu, Y., Watanabe, Y., Goto, M., Inui, R., Katano, I., Nagano, M., Takahara, T., Minamoto, T. (2017) Water sampling for environmental DNA surveys by using an unmanned aerial vehicle. Limnology and Oceangraphy: Methods 15, 939-944.
Jo, T., Murakami, H., Masuda, R., Sakata, M. K., Yamamoto, S., Minamoto, T. (2017) Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA. Molecular Ecology Resources 17 (6), e25-e33.
Sakata, M. K., Maki, N., Sugiyama, H., Minamoto, T. (2017) Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan. The Science of Nature - Naturwissenschaften 104, 100. 論文の内容が、NHK、朝日放送、秋田放送、朝日新聞、読売新聞、毎日新聞、日経新聞、神戸新聞、秋田魁新報などで紹介されました。
Sato, M., Ushimaru, A., Minamoto, T. (2017) The effect of different personal histories on valuation of forest ecosystem services in urban areas: a case study of Mt. Rokko, Kobe, Japan. Urban Forestry & Urban Greening 28, 110-117.
Uchii, K., Doi, H., Yamanaka, H., Minamoto, T. (2017) Distinct seasonal migration patterns of Japanese native and non-native genotypes of common carp estimated by environmental DNA. Ecology and Evolution 7(20): 8515-8522.
Kouduka, M., Tanabe, A.S., Yamamoto, S., Yanagawa, K., Nakamura, Y., Akiba, F., Tomaru, H., Toju, H., Suzuki, Y. (2017) Eukaryotic diversity in late Pleistocene marine sediments around a shallow methane hydrate deposit in the Japan Sea. Geobiology 15 (5): 715-727.
Katano, I., Harada, K., Doi, H., Souma, R., Minamoto, T. (2017) Environmental DNA method for estimating salamander distribution in headwater streams, and a comparison of water sampling methods. PLOS ONE 12(5): e0176541.
Hashizume, H., Sato, M., Sato, M. O., Ikeda, S., Yoounan, T., Sanguankiat, S., Pongvongsa, T., Moji, K., Minamoto, T. (2017) Application of environmental DNA analysis for the detection of Opisthorchis viverrini DNA in water samples. Acta Tropica 169, 1-7.
Tsuji, S., Ushio, M., Sakurai, S., Minamoto, T. Yamanaka, H. (2017) Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance. PLOS ONE 12(4): e0176608.
Yamanaka, H., Minamoto, T., Matsuura, J., Sakurai, S., Tsui, S., Motozawa, H., Hongo, M., Sogo, Y., Kakimi, N., Teramura, I., Sugita, M., Baba, M., Kondo, A. (2017) A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant. Limnology 17 (2), 233-241.
Minamoto, T., Uchii, K., Takahara, T., Kitayoshi, T., Tsuji, S., Yamanaka, H., Doi, H. (2017) Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio. Molecular Ecology Resources 17 (2), 324-333.
Minamoto, T., Fukuda, M., Katsuhara, K.R., Fujiwara, A., Hidaka, S., Yamamoto, S., Takahashi, K., Masuda, R. (2017) Environmental DNA reflects spatial and temporal jellyfish distribution. PLOS ONE 12 (2), e0173073.
Doi, H., Uchii, K., Matsuhashi, S., Takahara, T., Yamanaka, H., Minamoto, T. (2017) Isopropanol precipitation method for collecting fish environmental DNA. Limnology and Oceanography: Methods, 15 (2), 212-218.
Yamamoto, S., Masuda, R., Sato, Y., Sado, T., Araki, H., Kondoh, M., Minamoto, T., Miya, M. (2017) Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Scientific Reports 7, 40368.
Tsuji, S., Yamanaka, H., Minamoto, T.(2017) Effects of water pH and proteinase K treatment on the yield of environmental DNA from water samples. Limnology 18 (1), 1-8.
Doi, H., Inui, R., Akamatsu, Y., Kanno, K., Yamanaka, H., Takahara, T., Minamoto, T. (2017) Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshwater Biology 62 (1), 30-39.
2016
Miya, M., Minamoto, T., Yamanaka, H., Oka, S., Sato, K., Yamamoto, S., Sado, T., Doi, H. (2016) Use of a filter cartridge for filtration of water samples and extraction of environmental DNA. Journal of Visualized Experiments 117, e54741.
高原輝彦・山中裕樹・源利文・土居秀幸・内井喜美子 (2016) 環境DNA分析の手法開発の現状〜淡水域の研究事例を中心にして〜. 日本生態学会誌 66 (3), 583-599.
山中裕樹・源利文・高原輝彦・内井喜美子・土居秀幸 (2016) 環境DNA分析の野外調査への展開. 日本生態学会誌 66 (3), 601-611.
福岡有紗・高原輝彦・松本宗弘・兵庫県立農業高校生物部・丑丸敦史・源利文 (2016) 在来希少種カワバタモロコの環境DNAによる検出系の確立. 日本生態学会誌 66 (3), 613-620.
Yamanaka, H., Motozawa, H., Tsuji, S., Miyazawa, R. C., Takahara, T., Minamoto, T. (2016) On-site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation. Ecological Research 31 (6), 963-967.
Matsuhashi, S., Doi, H., Fujiwara, A., Watanabe, S., Minamoto, T. (2016) Evaluation of the environmental DNA method for estimating distribution and biomass of submerged aquatic plants. PLOS ONE 11(6), e0156217.
Fujiwara, A., Matsuhashi, S., Doi, H., Yamamoto, S., Minamoto, T. (2016) Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds. Freshwater Science 35 (2), 748-754.
Yamamoto, S., Minami, K., Fukaya, K., Takahashi, K., Sawada, H., Murakami, H., Tsuji, S., Hashizume, H., Kubonaga, S., Horiuchi, T., Hongo, M., Nishida, J., Okugawa, Y., Fujiwara, A., Fukuda, M., Hidaka, S., Suzuki, K. W., Miya, M., Araki, H., Yamanaka, H., Maruyama, A., Miyashita, K., Masuda, R., Minamoto, T., and Kondoh, M. (2016) Environmental DNA as a 'snapshot' of fish distribution: a case study of Japanese jack mackerel in Maizuru Bay, Sea of Japan. PLOS ONE 11(3), e1249786.
Toju, H., Yamamoto, S., Tanabe, A.S., Hayakawa, T., Ishii, H.S. (2016) Network modules and hubs in plant-root fungal biome. Journal of the Royal Society Interface 13, 20151097.
Ino, K., Kouduka, M., Hirota, A., Togo, Y., Fukuda, A., Komatsu, D., Tsunogai, U., Tanabe, A.S., Yamamoto, S., Iwatsuki, T., Mizuno, T., Ito, K., Suzuki, Y. (2016) Deep microbial life in high-quality granitic groundwater from geochemically and geographically distinct underground boreholes. Environmental Microbiology Reports 8, 285–294.
源利文・山本哲史・笠井亮秀・近藤倫生 （2016） 環境DNAを用いた沿岸域における魚類モニタリング. 沿岸海洋研究. 53巻2号. pp. 173-178.
Uchii, K., Doi, H., Minamoto, T. (2016) A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes. Molecular Ecology Resources 16 (2), 415-422.
Yamanaka, H., Minamoto, T. (2016) The use of environmental DNA of fishes as an efficient method of determining habitat connectivity. Ecological Indicators 62, 147-153.
Minamoto, T., Naka, T., Moji, K.,Maruyama, A. (2016) Techniques for the practical collection of environmental DNA: filter selection, preservation, and extraction. Limnology 17 (1), 23-32.
Yamamoto, S., Beljaev, E., Sota, T. (2016) Phylogenetic analysis of the winter geometrid genus Inurois reveals repeated reproductive season shifts. Molecular Phylogenetics and Evolution 94 part A, 47-54.
2015
Matsumae, H., Ishiwata, R., Minamoto, T., Ishida, N., Ogishima, S., Tanaka, H. (2015) Detection of periodic patterns in microarray data reveals novel oscillating transcripts of biological rhythms in Ciona intestinalis. Artificial Life and Robotics 20 (4), 347-352.
Miya, M., Sato, Y. Fukunaga, T., Sado, T., Poulsen, J.Y., Sato., K., Minamoto, T., Yamamoto, S., Yamanaka, H., Araki, H., Kondoh, M., Iwasaki, W. (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species. Royal Society Open Science 2, 150088. 　論文の内容が、NHK、日経新聞、千葉日報、琉球新報、沖縄タイムスなどで紹介されました。
Koizumi, N., Takahara, T., Minamoto, T., Doi, H., Mori, Atsushi, Watanabe, K., Takemura, T. (2015) Preliminary experiment for detection method of fish inhabiting agricultural drainage canals using environmental DNA. 農業農村工学会論文集 297 (83-3), IV_7-IV_8.
Doi, H., Takahara, T., Minamoto, T., Matsuhashi, S., Uchii, K., Yamanaka, H. (2015) Droplet digital Polymerase chain reaction (PCR) outperforms real-time PCR in the detection of environmental DNA from an invasive fish species. Environmental Science and Technology 49 (9), 5601-5608.
Doi, H., Uchii, K., Takahara, T., Matsuhashi, S., Yamanaka, H., Minamoto, T. (2015) Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys. PLOS ONE 10(3): e0122763.
Fukumoto S., Ushimaru A., Minamoto T. (2015) A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: A case study of giant salamanders in Japan. Journal of Applied Ecology 52 (2) 358-365. 　論文の内容が、NHK、サンテレビ、読売新聞、朝日新聞、産経新聞、日経新聞、神戸 新聞、共同通信、時事通信などで紹介されました。
Takahara T., Minamoto T., Doi H. (2015) Effects of sample processing on the detection rate of environmental DNA from the Common Carp (Cyprinus carpio). Biological Conservation, 183, 64-69.
Minamoto T., Pu X., Xie J., Dong Y., Wu D., Kong H., Yang X., Takahara T., Honjo M. N., Yamanaka H., Kawabata Z. (2015) Monitoring of fish pathogenic viruses in natural lakes in Yunnan, China. Limnology 16(1), 69-77.
2014
Maruyama, A., Nakamura, K., Yamanaka, H., Kondoh, M., Minamoto, T.. (2014) The release rate of environmental DNA from juvenile and adult fish. PLoS ONE. 9 (12), e114639
水町衣里・加納圭・伊藤真之・源利文・中山晶絵・蛯名邦禎・秋谷直矩（2014）パブリックコメント・ ワークショップの試行　〜「宇宙基本計画（案）」をテーマとしたワークショップの事例報告〜. 科学技術コミュニケーション 15, 123-136.
Takahara T., Honjo M. N. Uchii K., Minamoto T., Doi H., Ito T., Kawabata Z. (2014) Effects of daily temperature fluctuation on the survival of carp infected with Cyprinid herpesvirus 3. Aquaculture 433, 208-213.
Takahara T., Minamoto T., Doi H., Ito T., Kawabata Z. (2014) Differences between domesticated Eurasian and Japanese indigenous strains of the common carp (Cyprinus carpio) in cortisol release following acute stressor. Ichthyological Research 61 (2) 165-168.
Uchii K., Minamoto T., Honjo M.N., Kawabata Z. (2014) Seasonal reactivation enables Cyprinid herpesvirus 3 to persist in a wild host population. FEMS Microbiol. Ecol. 87 (2) 536-542.
2013
Uchii K., Okuda N., Minamoto T., Kawabata Z. (2013) An emerging infectious pathogen endangers an ancient lineage of common carp by acting synergistically with conspecific exotic strains. Animal Conservation 16(3), 324-330.
谢杰・吴德意・陈雪初・孔海南・普孝英・杨晓霞・源利文・山中裕树・本庄三惠・川端善一郎・李梅新　(2013) 滇池和洱海湖滨带水生植被状况与水质的关系研究. 环境科学与技术 36 (2) 61-65.
Takahara T., Minamoto T., Doi H. (2013) Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLOS ONE. 8(2): e56584. 論文の内容が朝日新聞、読売新聞、西日本新聞、共同通信他で紹介されました
2012
Minamoto T.*, Yamanaka H.*, Takahara T., Honjo M. N., Kawabata Z. (2012) Surveillance of fish species composition using environmental DNA. Limnology 13(2), 193-197. (*equal contribution) 　論文の内容が、読売新聞、京都新聞で紹介されました
Minamoto T., Honjo M. N., Yamanaka H., Uchii K., Kawabata Z. (2012) Nationwide Cyprinid herpesvirus 3　contamination in natural rivers of Japan. Res. Vet. Sci. 93 (1) 508-514.
Yamanaka H., Minamoto T., Wu D., Kong H., Wei Z.-H., Liu B., Kawabata Z. (2012) Spatial-temporal analysis of water temperatures during spring in Lake Erhai, China: implications for fisheries. Inland Waters 2(3), 129-136. 　関連する写真がInland Waters誌の表紙に採用されました
Takahara T., Minamoto T., Yamanaka H., Doi H., Kawabata Z. (2012) Estimation of fish biomass using environmental DNA. PLOS ONE, 7 (4), e35868. 論文の内容が、読売新聞、毎日新聞、日本経済新聞、西日本新聞、テレビ新広島で紹介されました
Minamoto T., Fuchikawa, T., Shimizu I. (2012) Expression of spliced variants of period mRNA in the Japanese honeybee Apis cerana japonica. Biol. Rhythm Res. 43 (2), 125-135.
Honjo M. N., Minamoto T., Kawabata Z. (2012) Reservoirs of Cyprinid herpesvirus 3 (CyHV-3) DNA in sediments of natural lakes and ponds. Vet. Microbiol. 155 (2-4), 183-190.
Minamoto T., Wada E., Shimizu I. (2012) A new method for random mutagenesis by error-prone polymerase chain reaction　using heavy water. J. Biotech. 157 (1), 71-74.

Other Publications

Others
源利文 (2025) 環境DNAを用いて陸上の動物を調べる. HABATAKI, 2026 WINTER/SPRING, 5.
源利文 (2025) 環境DNA調査の広がりと今後の期待. ミルシル, 18, 15–17.
源利文 (2024) 教科書的には正しくないことがおもしろい. 中等教育資料, 1063, 2-3.
Yamanaka, H., Doi, H., Araki, A., Uchii, K., Minamoto, T. (2024) The eDNA Society International Meeting 2023, “Moving from knowledge into practice”. Environmental DNA 5, 1191-1195.
山本義彦 (2023) 環境DNAを用いた魚類分布調査. 國立公園, 816, 18.
源利文 (2022) 環境DNA入門 漂う遺伝子は何を語るか. 岩波書店.
源利文 (2022) 生息地土壌の環境DNA分析による侵略的外来アリの分布状況把握. ペストコントロール 198, 20-25.
源利文 (2022) 環境DNA分析（澤田嗣郎監修） 先端の分析法第２版, 株式会社エヌ・ティー・エス, pp. 756-765.
坂田雅之・徐寿明・源利文 (2021) 環境DNA分析の概要 （土居秀幸・近藤倫生編）環境DNA−生態系の真の姿を読み解く−. 共立出版, pp 1-35.
源利文 (2021) 環境DNA分析における手法の標準化 （土居秀幸・近藤倫生編）環境DNA−生態系の真の姿を読み解く−. 共立出版, pp 249-253.
源利文 (2020) 環境DNAなどの生体分子を用いた水中生物の情報取得の試み. JMOA レポート No.19, 1-10.
源利文 (2019) 環境DNAを用いた生物調査法の発展とその応用. 科学 89, 1029-1035.
源利文 (2019) 環境DNA：水中の生物相を簡単に把握できるツール. 清流青湖 146, 10-11.
源利文 (2019) 環境DNA分析の概要と希少種の検出~水をくむだけで絶滅危惧種の分布がわかる. 化学と生物 57 (3), 181-186.
源利文 (2018) 環境DNA. （日本魚類学会編）魚類学の百科事典. 丸善, 東京都千代田区, pp. 492-493.
源利文 (2018) 種特異的な環境DNA検出によるマクロ生物の生態調査. 水環境学会誌 41A (4), 123-127.
池田幸資・土居秀幸・源利文 (2018) 水を汲むだけの生物調査〜環境DNA技術の紹介〜. 技術士 30 (3), 20-21.
源利文 (2018) 環境DNAとは何か. 海洋と生物 40 (1), 3-8.
益田玲爾・村上弘章・高橋宏司・源利文・宮正樹 (2018) 環境DNAの有効性：水槽実験とフィールドでの検証. 海洋と生物 40 (1), 17-22.
深谷肇一・長田穣・源利文 (2018) 環境DNAによる個体数・生物量推定の可能性. 海洋と生物 40 (1), 47-53.
源利文 (2017) 水域生態系における環境DNAモニタリング手法開発の現在. 環境技術 46 (12), 624-629.
源利文・内井喜美子・高原輝彦・土居秀幸 (2017) 環境DNAモニタリング手法の課題と展望. 環境技術 46 (12), 648-652.
源利文 (2017) 環境DNAを用いた感染症研究への期待. ウイルス 66, 171-178.
Minamoto, T. (2017) Random Mutagenesis by Error-Prone Polymerase Chain Reaction Using a Heavy Water Solvent in "Methods in Molecular Biology Volume 1498 In Vitro Mutagenesis" (Ed. Andrew Reeves), Springer New York, pp. 491-495.
内井喜美子・源利文土居秀幸・高原輝彦・山中裕樹・片野泉 (2016) 環境DNA分析：新しい水棲生物分布調査法. 日本生態学会誌 66 (3), 581-582.
源利文・内井喜美子・山中裕樹・高原輝彦・片野泉・土居秀幸　(2016) 環境DNA分析のさらなる進展にむけて. 日本生態学会誌 66(3), 621-623.
源利文 (2016) 環境DNAを用いて水中の生物相を知る. BIOINDUSTRY, 33 (6), 60-65.
源利文・伊藤真之・蛯名邦禎 (2016) 環境ＤＮＡ分析手法による高校生研究活動への支援. 日本科学教育学会研究会研究報告 30, 21-24.
蛯名邦禎・伊藤真之・梅村界渡・源利文 (2016) 市民による科学情報読み解きへの支援 -「IPCCレポートを根掘り葉掘り読む会」-. 日本科学教育学会研究会研究報告 30, 17-20.
岩崎渉・佐藤行人・源利文・山中裕樹・荒木仁志・宮正樹 (2016) 環境DNA研究のインパクト. 実験医学 34 (1), 103-107.
源利文 (2014)環境DNA：エコヘルス研究の新しいツール. 医学のあゆみ. 249巻, 12号. pp 1264-1269.
高原輝彦・源利文・土居秀幸(2014) 水を調べるだけで生き物がわかる！環境DNAを利用した生物分布モニタリング法. 日本陸水学会東海支部会編 身近な水の環境科学 実習・測定編. 朝倉書店, 東京都新宿区, pp. 159-161.
源利文・川端善一郎 (2014) 湖の環境改変と感染症. 川端善一郎、孔海南、呉得意、福士由紀、窪田順平編 湖の現状と未来可能性（RIHN-China Study Series No.3）. 松香堂書店, 京都市左京区, pp.75-86. （日中英3カ国語出版：担当箇所は日英2カ国語で記述）
谢强・吴德意・源利文・山中裕树・本庄三惠・川端善一郎 (2014) 水生植物湖滨带改善现场实证性研究. 川端善一郎、孔海南、呉德意、福士由紀、窪田順平編 湖の現状と未来可能性（RIHN-China Study Series No.3）. 松香堂書店, 京都市左京区, pp.139-151. （日中英3カ国語出版：担当箇所は中英2カ国語で記述）
源利文（2014）「環境DNAを用いた水中動物相のモニタリング」（総合地球環境学研究所編：地球環境学マニュアル２ はかる・みせる・読みとく） 朝倉書店（東京） pp.68-69.