I am a marine biologist studying zooplankton. Zooplankton play a very important ecological role in the aquatic environment, transfer energy and material to higher trophic levels. They are also fascinating animals in the ocean. I use a lot of molecular techniques to study zooplankton ecology, evolution, and diversity.

I am also providing DNA sequence reference database, which can be used as mitochondrial sequence taxonomic assignment reference (MIDORI 2).

期刊論文

1. Mark Louie D. Lopez,Ya-ying Lin,Stephan Q Schneider,Chih-hao Hsieh,Fuh-Kwo Shiah,Ryuji J. Machida*, 2023, “Allometric scaling of interspecific RNA transcript abundance to extend the use of metatranscriptomics in characterizing complex communities”, Molecular Ecology Resources, 23(1), 52-63. (SCIE) (IF: 7.09; SCI ranking: 16.5%,7.2%,12%)
2. Wye‐Lup Kong,Ryuji J. Machida*, 2022, “Development of transcriptomics‐based growth rate indices in two model eukaryotes and relevance to metatranscriptomic datasets”, Molecular Ecology Resources, 22(7), 2627-2639. (SCIE) (IF: 7.09; SCI ranking: 16.5%,7.2%,12%)
3. Matthieu Leray,Nancy Knowlton,Ryuji J Machida*, 2022, “MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences”, Environmental DNA, 4(4), 894-907. (SCIE, Scopus) (IF: 　; 　)
4. Mark Louie D. Lopez, Ya-ying Lin, Mitsuhide Sato, Chih-hao Hsieh, Fuh-Kwo Shiah, Ryuji J. Machida*, 2022, “Using metatranscriptomics to estimate the diversity and composition of zooplankton communities”, Molecular Ecology Resources, 22(2), 638-652. (SCIE) (IF: 7.09; SCI ranking: 16.5%,7.2%,12%)
5. Bucklin A*, Peijnenburg KTCA, Kosobokova K, Machida RJ, 2021, “New insights into biodiversity, biogeography, ecology, and evolution of marine zooplankton based on molecular approaches”, ICES Journal of Marine Science, 79 (9), 3281-3287. (SCIE) (IF: 3.593; SCI ranking: 16.4%,13.5%,13.8%)
6. KJH Wong, YF Tsao, PC Tsai, WP Hsieh, HR Li, RJ Machida, BKK Chan, 2021, “To the light side: molecular diversity and morphology of stomatopod larvae and juveniles (Crustacea: Malacostraca: Stomatopoda) from crustose coralline algal reefs in Taiwan”, MARINE BIODIVERSITY, 51(2), 1-31. (SCIE) (IF: 1.533; SCI ranking: 66.7%,62.2%)
7. Machida RJ*, Kurihara H, Nakajima R, Sakamaki T, Lin YY, Furusawa K, 2021, “Comparative analysis of zooplankton diversities and compositions estimated from complement DNA and genomic DNA amplicons, metatranscriptomics, and morphological identifications”, ICES JOURNAL OF MARINE SCIENCE, 78(9), 3428-3443. (SCIE) (IF: 3.593; SCI ranking: 16.4%,13.5%,13.8%)
8. Leray M, Knowlton N*, Ho SL, Nguyen BN, Machida RJ*, 2020, “Reply to Locatelli et al.: Evaluating species-level accuracy of GenBank metazoan sequences will require experts’ effort in each group”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117(51), 32213-32214. (SCIE) (IF: 11.205; SCI ranking: 11%)
9. Leray M, Machida RJ*, 2020, “Seabed mining could come at a high price for a unique fauna”, MOLECULAR ECOLOGY, 29(23), 4506-4509. (SCIE) (IF: 6.185; SCI ranking: 20.9%,9.6%,14%)
10. Makino W, Machida RJ, Okitsu J, Nisikawa U, 2019, “Underestimated species diversity and hidden habitat preference in Moina (Crustacea, Cladocera) revealed by integrative taxonomy”, HYDROBIOLOGIA, 847, 857–878. (SCIE) (IF: 2.694; SCI ranking: 26.1%)
11. Leray M, Knowlton N, Ho SL, Nguyen BN, Machida RJ*, 2019, “GenBank is a reliable resource for 21st century biodiversity research”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116 (45), 22651-22656. (SCIE) (IF: 11.205; SCI ranking: 11%)
12. Kong WL, Miki T, Lin YY, Makino W, Urabe J, Gu SH, Machida RJ*, 2019, “Nuclear and mitochondrial ribosomal ratio as an index of animal growth rate”, LIMNOLOGY AND OCEANOGRAPHY-METHODS, 17, 575-584. (SCIE) (IF: 2.634; SCI ranking: 23.8%,40%)
13. Pearman JK, Leray M, Villalobos R, Machida RJ, Berumen ML, Knowlton N, Carvalho S, 2018, “Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority”, Scientific Reports, 8(1), 8090. (SCIE) (IF: 4.38; SCI ranking: 23.3%)
14. White KN, Machida RJ*, 2018, “Taiwanese Leucothoidae (Crustacea: Amphipoda), Including Three New Species from Dongsha Atoll”, ZOOLOGICAL STUDIES, 57, 47. (SCIE) (IF: 2.058; SCI ranking: 30.3%)
15. Leray M, Ho SL, Lin IJ, Machida RJ*, 2018, “MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database ”, BIOINFORMATICS, 34(21), 3753-3754. (SCIE) (IF: 6.937; SCI ranking: 7.7%,11.3%,5.2%)