| Issue Date | Title | Author(s) | Relation | scopus | WOS | Fulltext/Archive link |
| 2023 | Allometric scaling of interspecific RNA transcript abundance to extend the use of metatranscriptomics in characterizing complex communities | Mark Louie D. Lopez; Ya-ying Lin; Stephan Q Schneider; Chih-hao Hsieh; Fuh-Kwo Shiah; Ryuji J. Machida | Molecular Ecology Resources 23(1), 52-63 | | | |
| 2021 | Comparative analysis of zooplankton diversities and compositions estimated from complement DNA and genomic DNA amplicons, metatranscriptomics, and morphological identifications | Machida, RJ ; Kurihara, H; Nakajima, R; Sakamaki, T; Lin, YY; Furusawa, K | ICES Journal of Marine Science 78(9), 3428-3443 | | | |
| 2022 | Development of transcriptomics-based growth rate indices in two model eukaryotes and relevance to metatranscriptomics datasets | Wye-Lup Kong; Ryuji J. Machida | Molecular Ecology Resources 22(7), 2627-2639 | | | |
| 2022 | Erratum to: New insights into biodiversity, biogeography, ecology, and evolution of marine zooplankton based on molecular approaches | Bucklin, A; Peijnenburg, KTCA; Kosobokova, K; Machida, RJ | ICES Journal of Marine Science 79(1), 245-245 | | | |
| 2019 | GenBank is a reliable resource for 21st century biodiversity research | Leray, M; Knowlton, N; Ho, SL; Nguyen, BN; Machida, RJ | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 116 (45), 22651-22656 | | | |
| 2023 | Insights on the connectivity, genetic diversity, and population structure of Arctodiaptomus dorsalis (Marsh, 1907) (Copepoda: Calanoida: Diaptomidae) in the Philippines | Guinto, SKP; Machida, RJ ; Papa, RDS | JOURNAL OF CRUSTACEAN BIOLOGY 43(4), ruad070 | | | |
| 2017 | Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples | Machida, RJ ; Leray, M; Ho, SL; Knowlton, N | Scientific Data 4, 170027 | | | |
| 2022 | MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences | Matthieu Leray; Nancy Knowlton; Ryuji J Machida | Environmental DNA 4(4), 894-907 | | | |
| 2023 | Molecular characterization of the nearly complete nuclear ribosomal DNA sequence of the Neotropical freshwater copepod Arctodiaptomus dorsalis (Marsh, 1907) (Copepoda, Calanoida, Diaptomidae) | Guinto, SKP; Machida, RJ ; Papa, RDS | Crustaceana 96(5), 407-421 | | | |
| 2021 | New insights into biodiversity, biogeography, ecology, and evolution of marine zooplankton based on molecular approaches | Bucklin, A; Peijnenburg, KTCA; Kosobokova, K; Machida, RJ | ICES Journal of Marine Science 78(9), 3281-3287 | | | |
| 2022 | Novel molecular resources for single-larva barcoding of enigmatic crustacean y-larvae | Dreyer, N; Palero, F; Grygier, M; Savchenko, A; Kolbasov, G; Machida, R ; Chan, B ; Olesen, J | Authorea Preprints | | | |
| 2019 | Nuclear and mitochondrial ribosomal ratio as an index of animal growth rate | Kong, WL; Miki, T; Lin, YY; Makino, W; Urabe, J; Gu, SH; Machida, RJ | LIMNOLOGY AND OCEANOGRAPHY-METHODS 17(11), 575-584 | | | |
| 2017 | Occurrence of Mitochondrial CO1 Pseudogenes in Neocalanus plumchrus (Crustacea: Copepoda): Hybridization Indicated by Recombined Nuclear Mitochondrial Pseudogenes | Machida, RJ ; Lin, YY | PLOS ONE 12(2), e0172710 | | | |
| 2023 | Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller-size coral reef zooplankton by metatranscriptomics | Mattos, FMG; Dreyer, N; Fong, CL; Wen, YHV; Jain, D; De Vivo, M; Huang, YS; Mwihaki, JK; Wang, TY ; Ho, MJ ; Tsai, IJ ; Wang, J ; Chan, BKK ; Machida, RJ | MOLECULAR ECOLOGY RESOURCES 24(3), e13911 | | | |
| 2020 | Reply to Locatelli et al.: Evaluating species-level accuracy of GenBank metazoan sequences will require experts’ effort in each group | Leray, M; Knowlton, N; Ho, SL; Nguyen, BN; Machida, RJ | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 117(51), 32213-32214 | | | |
| 2020 | Seabed mining could come at a high price for a unique fauna | Leray, M; Machida, RJ | MOLECULAR ECOLOGY 29(23), 4506-4509 | | | |
| 2023 | The mitochondrial genome of Isognomon nucleus and mitogenomics of pteriomorphia (Bivalvia: Autobranchia) | Dreyer, N; de Mattos, FMG; Jain, D; Fong, C-L; De Vivo, M; Wen, YV; Huang, Y-S; Mwihaki, JK; Lee, H-H; Tsai, P-C; Tsao, Y-F; Chan, BKK ; Tsai, IJ ; Machida, RJ ; Wang, T-Y ; Wang, J | Journal of Molluscan Studies 89(1), eyad003 | | | |
| 2021 | To the light side: molecular diversity and morphology of stomatopod larvae and juveniles (Crustacea: Malacostraca: Stomatopoda) from crustose coralline algal reefs in Taiwan | KJH Wong; YF Tsao; PC Tsai; WP Hsieh; HR Li; RJ Machida ; BKK Chan | Marine Biodiversity 51, 20 | | | |
| 2019 | Underestimated species diversity and hidden habitat preference in Moina (Crustacea, Cladocera) revealed by integrative taxonomy | Makino, W; Machida, RJ ; Okitsu, J; Nisikawa, U | HYDROBIOLOGIA 847, 857-878 | | | |
| 2021 | Using metatranscriptomics to estimate the diversity and composition of zooplankton communities | Lopez, MLD; Lin, Y; Sato, M; Hsieh, CH; Shiah, FK ; Machida, RJ | MOLECULAR ECOLOGY RESOURCES 22(2), 638-652 | | | |
