Papers citing EukRef

del Campo J., Kolisko M., Boscaro V., Santoferrara LF., Nenarokov S., Massana R., Guillou L., Simpson A., Berney C., de Vargas C., Brown MW., Keeling PJ., Wegener Parfrey L. 2018. EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLOS Biology 16:e2005849. DOI: 10.1371/journal.pbio.2005849.

Number of papers citing EukRef: 29


Dias, R., P. de Souza, M. Rossi, et al. (2021). “Ciliates as bioindicators of water quality: A case study in the neotropical region and evidence of phylogenetic signals (18S-rDNA)”. In: Environmental Pollution 268. cited By 0. DOI: 10.1016/j.envpol.2020.115760.

Dumack, K. and M. Bonkowski (2021). “Protists in the plant microbiome: an untapped field of research”. In: Methods in Molecular Biology 2232. cited By 0, pp. 77-84. DOI: 10.1007/978-1-0716-1040-4_8.

Lavrinienko, A., T. Jernfors, J. Koskimäki, et al. (2021). “Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?” In: Trends in Microbiology 29.1. cited By 3, pp. 19-27. DOI: 10.1016/j.tim.2020.05.019.

Mann, D., R. Trobajo, S. Sato, et al. (2021). “Ripe for reassessment: A synthesis of available molecular data for the speciose diatom family Bacillariaceae”. In: Molecular Phylogenetics and Evolution 158. cited By 0. DOI: 10.1016/j.ympev.2020.106985.

Obertegger, U., M. Pindo, and G. Flaim (2021). “Do inferences about freshwater phytoplankton communities change when based on microscopy or high-throughput sequencing data?” In: Freshwater Biology 66.4. cited By 0, pp. 640-655. DOI: 10.1111/fwb.13667.

Rajter, I. Ewers, N. Graupner, et al. (2021). “Colpodean ciliate phylogeny and reference alignments for phylogenetic placements”. In: European Journal of Protistology 77. cited By 0. DOI: 10.1016/j.ejop.2020.125747.

Schiwitza, S. and F. Nitsche (2021). “A Needle in the Haystack – Mapping Sequences to Morphology Exemplified by the Loricate Choanoflagellate Enibas thessalia sp. nov. (Acanthoecida, Acanthoecidae)”. In: Protist 172.1. cited By 0. DOI: 10.1016/j.protis.2020.125782.


Djemiel, C., D. Plassard, S. Terrat, et al. (2020). “µgreen-db: A reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria”. In: Scientific Reports 10.1. cited By 1. DOI: 10.1038/s41598-020-62555-1.

Fawley, M. and K. Fawley (2020). “Identification of eukaryotic microalgal strains”. In: Journal of Applied Phycology 32.5. cited By 2, pp. 2699-2709. DOI: 10.1007/s10811-020-02190-5.

Fiore-Donno, A., T. Richter-Heitmann, and M. Bonkowski (2020). “Contrasting Responses of Protistan Plant Parasites and Phagotrophs to Ecosystems, Land Management and Soil Properties”. In: Frontiers in Microbiology 11. cited By 4. DOI: 10.3389/fmicb.2020.01823.

Gottschling, M., J. Chacón, A. Žerdoner ÄŒalasan, et al. (2020). “Phylogenetic placement of environmental sequences using taxonomically reliable databases helps to rigorously assess dinophyte biodiversity in Bavarian lakes (Germany)”. In: Freshwater Biology 65.2. cited By 8, pp. 193-208. DOI: 10.1111/fwb.13413.

Irion, S., L. Jardillier, I. Sassenhagen, et al. (2020). “Marked spatiotemporal variations in small phytoplankton structure in contrasted waters of the Southern Ocean (Kerguelen area)”. In: Limnology and Oceanography 65.11. cited By 1, pp. 2835-2852. DOI: 10.1002/lno.11555.

Kolisko, M., O. Flegontova, A. Karnkowska, et al. (2020). “EukRef-excavates: Seven curated SSU ribosomal RNA gene databases”. In: Database 2020. cited By 0. DOI: 10.1093/database/baaa080.

Mann, A., F. Mazel, M. Lemay, et al. (2020). “Biodiversity of protists and nematodes in the wild nonhuman primate gut”. In: ISME Journal 14.2. cited By 1, pp. 609-622. DOI: 10.1038/s41396-019-0551-4.

Martini, S., F. Larras, A. Boyé, et al. (2020). “Functional trait-based approaches as a common framework for aquatic ecologists”. In: Limnology and Oceanography. cited By 0. DOI: 10.1002/lno.11655.

Santoferrara, L., F. Burki, S. Filker, et al. (2020). “Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding”. In: Journal of Eukaryotic Microbiology 67.5. cited By 3, pp. 612-622. DOI: 10.1111/jeu.12813.


Adl, S., D. Bass, C. Lane, et al. (2019). “Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes”. In: Journal of Eukaryotic Microbiology 66.1. cited By 242, pp. 4-119. DOI: 10.1111/jeu.12691.

Caron, D. and S. Hu (2019). “Are We Overestimating Protistan Diversity in Nature?” In: Trends in Microbiology 27.3. cited By 20, pp. 197-205. DOI: 10.1016/j.tim.2018.10.009.

Del Campo, J., T. Heger, R. Rodríguez-Martínez, et al. (2019). “Assessing the diversity and distribution of apicomplexans in host and free-living environments using high-throughput amplicon data and a phylogenetically informed reference framework”. In: Frontiers in Microbiology 10.OCT. cited By 7. DOI: 10.3389/fmicb.2019.02373.

Ku, C. and A. Sebé-Pedrós (2019). “Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes”. In: Philosophical Transactions of the Royal Society B: Biological Sciences 374.1786. cited By 5. DOI: 10.1098/rstb.2019.0098.

Linard, B., K. Swenson, and F. Pardi (2019). “Rapid alignment-free phylogenetic identification of metagenomic sequences”. In: Bioinformatics 35.18. cited By 3, pp. 3303-3312. DOI: 10.1093/bioinformatics/btz068.

Lutz, S., L. Procházková, L. Benning, et al. (2019). “Evaluating amplicon high–throughput sequencing data of microalgae living in melting snow: Improvements and limitations”. In: Fottea 19.2. cited By 5, pp. 115-131. DOI: 10.5507/fot.2019.003.

Metz, S., D. Singer, I. Domaizon, et al. (2019). “Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches”. In: Environmental Microbiology 21.10. cited By 3, pp. 3885-3895. DOI: 10.1111/1462-2920.14738.

Morard, R., N. Vollmar, M. Greco, et al. (2019). “Unassigned diversity of planktonic foraminifera from environmental sequencing revealed as known but neglected species”. In: PLoS ONE 14.3. cited By 7. DOI: 10.1371/journal.pone.0213936.

Richardson, E. and J. Dacks (2019). “Microbial Eukaryotes in oil sands environments: Heterotrophs in the spotlight”. In: Microorganisms 7.6. cited By 0. DOI: 10.3390/microorganisms7060178.

Rimet, F., E. Gusev, M. Kahlert, et al. (2019). “Diat.barcode, an open-access curated barcode library for diatoms”. In: Scientific Reports 9.1. cited By 21. DOI: 10.1038/s41598-019-51500-6.

Santoferrara, L. (2019). “Current practice in plankton metabarcoding: Optimization and error management”. In: Journal of Plankton Research 41.5. cited By 7, pp. 571-582. DOI: 10.1093/plankt/fbz041.

Yu, Z. and N. Chen (2019). “Emerging trends in red tide and major research progresses [国内外赤潮的发展趋势与研究热点]”. In: Oceanologia et Limnologia Sinica 50.3. cited By 3, pp. 474-486. DOI: 10.11693/hyhz20190200041.


Duarte, S., L. Nunes, P. Borges, et al. (2018). “A bridge too far? An integrative framework linking classical protist taxonomy and metabarcoding in lower termites”. In: Frontiers in Microbiology 9.NOV. cited By 3. DOI: 10.3389/fmicb.2018.02620.

Daniel Vaulot
NTU, Singapore

Focusing on marine (pico)phytoplankton .