| 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 | | | |
| 2018 | Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority | Pearman, J. K.; Leray, M.; Villalobos, R.; Machida, R. J. ; Berumen, M. L.; Knowlton, N.; Carvalho, S. | Scientific Reports 8(1), 8090 | | | |
| 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 | | | |
| 2015 | Early life history of Neocalanus plumchrus (Calanoida: Copepoda) in the western subarctic Pacific | Fujioka, HA; Machida, RJ ; Tsuda, A | PROGRESS IN OCEANOGRAPHY 137, 196-208 | | | |
| 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 | | | |
| 2012 | Global phylogeography of the deep-sea pelagic chetognath Eukrohnia hamata | Miyamoto, H; Machida, RJ ; Nishida, S | Progress in Oceanography 104, 99-109 | | | |
| 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 | | | |
| 2018 | MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database | Leray, M; Ho, SL; Lin, IJ; Machida, RJ | BIOINFORMATICS 34(21), 3753-3754 | | | |
| 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 | | | |
| 2012 | PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences | Machida, RJ ; Kweskin, M; Knowlton, N | PLoS One 7(4), e35887 | | | |
| 2012 | PCR primers for metazoan nuclear 18S and 28S ribosomal DNA sequences | Machida, RJ ; Knowlton, N | PLoS One 7(9), e46180 | | | |
| 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 | | | |
