Ryuji J. Machida

3.7k citations

43 papers · 2.4k indexed · 1 hit paper · h-index 19

Co-authors: Matthieu Leray Nancy KnowltonChris Meyer Joy Yang Suzanne C. Mills Vincent Ranwez J. T. Boehm Shuhei Nishida
Topics: Marine Biology and Ecology Research (19 papers)Environmental DNA in Biodiversity Studies (15 papers)Genomics and Phylogenetic Studies (13 papers)
Cited by: Ecology Ecological Modeling Oceanography
Journals: Proceedings of the National Academy of Sciences Bioinformatics PLoS ONE
Partner nations: Taiwan Japan United States

In The Last Decade

Ryuji J. Machida

40 papers receiving 2.4k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

2013 1.1k citations Matthieu Leray, Joy Yang et al. Frontiers in Zoology profile →

Peers

Countries citing papers authored by Ryuji J. Machida

Since Specialization

Citations

This map shows the geographic impact of Ryuji J. Machida's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Ryuji J. Machida with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Ryuji J. Machida more than expected).

Fields of papers citing papers by Ryuji J. Machida

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Ryuji J. Machida. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Ryuji J. Machida. The network helps show where Ryuji J. Machida may publish in the future.

Co-authorship network of co-authors of Ryuji J. Machida

This figure shows the co-authorship network connecting the top 25 collaborators of Ryuji J. Machida. A scholar is included among the top collaborators of Ryuji J. Machida based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Ryuji J. Machida. Ryuji J. Machida is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

#	Work	Indexed citations
1	Taxon‐specific BLAST percent identity thresholds for identification of unknown sequences using metabarcoding 2025 ·Methods in Ecology and Evolution ·Paula Pappalardo,Jan M. Hemmi,Ryuji J. Machida,Matthieu Leray,Allen G. Collins,Karen J. Osborn	0
2	A new species of Pseudodiaptomus (Copepoda, Calanoida, Pseudodiaptomidae) from the coastal waters of northern Taiwan with notes on co-occurring and previously recorded species 2024 ·Crustaceana ·(unknown),Ryuji J. Machida,Jiang‐Shiou Hwang	0
3	The mitochondrial genome ofIsognomon nucleusand mitogenomics of pteriomorphia (Bivalvia: Autobranchia) 2023 ·Journal of Molluscan Studies ·Niklas Dreyer,(unknown),(unknown),(unknown),(unknown),(unknown),(unknown),(unknown),Hsin‐Han Lee,(unknown),(unknown),Benny K. K. Chan,Isheng Jason Tsai,Ryuji J. Machida,Tzi‐Yuan Wang,John Wang	1
4	Allometric scaling of interspecific RNA transcript abundance to extend the use of metatranscriptomics in characterizing complex communities 2022 ·Molecular Ecology Resources ·(unknown),(unknown),Stephan Schneider,Chih‐hao Hsieh,Fuh‐Kwo Shiah,Ryuji J. Machida	5
5	Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum 2022 ·Scientific Reports ·(unknown),Hsin‐Han Lee,(unknown),Niklas Dreyer,(unknown),(unknown),(unknown),(unknown),(unknown),Tzi‐Yuan Wang,Ryuji J. Machida,John Wang,Benny K. K. Chan,Isheng Jason Tsai	15
6	To the light side: molecular diversity and morphology of stomatopod larvae and juveniles (Crustacea: Malacostraca: Stomatopoda) from crustose coralline algal reefs in Taiwan 2021 ·Marine Biodiversity ·(unknown),(unknown),(unknown),(unknown),(unknown),Ryuji J. Machida,Benny K. K. Chan	2
7	Using metatranscriptomics to estimate the diversity and composition of zooplankton communities 2021 ·Molecular Ecology Resources ·(unknown),(unknown),M. Sato,Chih‐hao Hsieh,Fuh‐Kwo Shiah,Ryuji J. Machida	12
8	Nuclear and mitochondrial ribosomal ratio as an index of animal growth rate 2019 ·Limnology and Oceanography Methods ·(unknown),Takeshi Miki,(unknown),Wataru Makino,Jotaro Urabe,Shi‐Hong Gu,Ryuji J. Machida	2
9	Taiwanese Leucothoidae (Crustacea: Amphipoda), Including Three New Species from Dongsha Atoll. 2018 ·PubMed Central ·Kristine N. White,Ryuji J. Machida	3
10	Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority 2018 ·Scientific Reports ·John K. Pearman,Matthieu Leray,Rodrigo Villalobos,Ryuji J. Machida,Michael L. Berumen,Nancy Knowlton,Susana Carvalho	61
11	Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples 2017 ·Scientific Data ·Ryuji J. Machida,Matthieu Leray,(unknown),Nancy Knowlton	128
12	Occurrence of mitochondrial CO1 pseudogenes in Neocalanus plumchrus (Crustacea: Copepoda): Hybridization indicated by recombined nuclear mitochondrial pseudogenes 2017 ·PLoS ONE ·Ryuji J. Machida,(unknown)	8
13	A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contentsbreakdown → 2013 ·Frontiers in Zoology ·Matthieu Leray,Joy Yang,Chris Meyer,Suzanne C. Mills,(unknown),Vincent Ranwez,J. T. Boehm,Ryuji J. Machida	1089
14	PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences 2012 ·PLoS ONE ·Ryuji J. Machida,(unknown),Nancy Knowlton	26
15	PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences 2012 ·PLoS ONE ·Ryuji J. Machida,Nancy Knowlton	96
16	Dissimilarity of Species and Forms of Planktonic Neocalanus Copepods Using Mitochondrial COI, 12S, Nuclear ITS, and 28S Gene Sequences 2010 ·PLoS ONE ·Ryuji J. Machida,Atsushi Tsuda	37
17	Zooplankton diversity analysis through single-gene sequencing of a community sample 2009 ·BMC Genomics ·Ryuji J. Machida,Yasuyuki Hashiguchi,Mutsumi Nishida,Shuhei Nishida	60
18	PCR-Based Approach for Sequencing Mitochondrial Genomes of Decapod Crustaceans, with a Practical Example from Kuruma Prawn (Marsupenaeus japonicus) 2004 ·Marine Biotechnology ·(unknown),Masaki Miya,Ryuji J. Machida,Mutsumi Nishida	50
19	Complete Mitochondrial DNA Sequence of Tigriopus japonicus (Crustacea: Copepoda) 2002 ·Marine Biotechnology ·Ryuji J. Machida,Masaki Miya,Mutsumi Nishida,Shuhei Nishida	130
20	Species variations in the gel-forming characteristics of fish meat paste. 1981 ·Bulletin of the Japanese Society of Scientific Fisheries ·Y. Shimizu,Ryuji J. Machida,(unknown)	71

About Ryuji J. Machida

Ryuji J. Machida is a scholar working on Oceanography, Ecology and Nature and Landscape Conservation, having authored 43 papers that have together received 2.4k indexed citations. Recurring topics across this work include Marine Biology and Ecology Research (19 papers), Environmental DNA in Biodiversity Studies (15 papers) and Genomics and Phylogenetic Studies (13 papers). The work is most often cited by research in Ecology (1.9k citations), Ecological Modeling (144 citations) and Oceanography (380 citations). Ryuji J. Machida has collaborated with scholars based in Taiwan, Japan and United States. Frequent co-authors include Matthieu Leray, Nancy Knowlton, Chris Meyer, Joy Yang, Suzanne C. Mills, Vincent Ranwez, J. T. Boehm, Shuhei Nishida, Mutsumi Nishida and Masaki Miya. Their work appears in journals such as Proceedings of the National Academy of Sciences, Bioinformatics and PLoS ONE.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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