Publications

Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid-Proterozoic

Sandin, Miguel M.; Cohen, Phoebe A.; Morlon, Helene; Burki, Fabien

Part of Proceedings of the National Academy of Sciences of the United States of America, 2026

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• DOI for Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid-Proterozoic
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Identification of a deep-branching lineage of algae using environmental plastid genomes

Jamy, Mahwash; Huber, Thomas; Antoine, Thibault; Ruscheweyh, Hans-Joachim et al.

Part of Nature Communications, 2026

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• DOI for Identification of a deep-branching lineage of algae using environmental plastid genomes
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First report of Hexamita nelsoni in blue mussel (Mytilus edulis): morphology, phylogeny, and host-parasite interaction

Alfjorden, Anders; Jerlström-Hultqvist, Jon; Svärd, Staffan; Burki, Fabien

Part of Journal of Invertebrate Pathology, 2026

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• DOI for First report of Hexamita nelsoni in blue mussel (Mytilus edulis): morphology, phylogeny, and host-parasite interaction

Protist genomics: key to understanding eukaryotic evolution

Schoenle, Alexandra; Francis, Ore; Archibald, John M.; Burki, Fabien et al.

Part of Trends in Genetics, p. 868-882, 2025

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• DOI for Protist genomics: key to understanding eukaryotic evolution
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Paulinella acadia sp. nov., a New Photosynthetic Species Isolated From a Brackish Beach in British Columbia (Canada)

Pardasani, Yash; Palka, Maia V.; Leander, Brian S.; Burki, Fabien

Part of Journal of Eukaryotic Microbiology, 2025

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• DOI for Paulinella acadia sp. nov., a New Photosynthetic Species Isolated From a Brackish Beach in British Columbia (Canada)
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Phylogenetic position and mitochondrial genome evolution of "orphan" eukaryotic lineages

Zlatogursky, Vasily; Boscaro, Vittorio; Lax, Gordon; Wanntorp, Matias et al.

Part of iScience, 2025

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• DOI for Phylogenetic position and mitochondrial genome evolution of "orphan" eukaryotic lineages
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Evolution: Untangling the mix of plastid endosymbiosis events

Keeling, Patrick J.; Burki, Fabien

Part of Current Biology, 2025

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• DOI for Evolution: Untangling the mix of plastid endosymbiosis events

Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes

Overgaard, Christina Karmisholt; Jamy, Mahwash; Radutoiu, Simona; Burki, Fabien et al.

Part of Molecular Ecology Resources, 2024

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• DOI for Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes
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Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria

Hiltunen Thorén, Markus; Onuț-Brännström, Ioana; Alfjorden, Anders; Pecková, Hana et al.

Part of BMC Biology, 2024

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• DOI for Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria
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Identification of a new gregarine parasite associated with mass mortality events of freshwater pearl mussels (Margaritifera margaritifera) in Sweden

Alfjorden, Anders; Onut-Brännström, Ioana; Wengström, Niklas; Kristmundsson, Arni et al.

Part of Journal of Eukaryotic Microbiology, 2024

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• DOI for Identification of a new gregarine parasite associated with mass mortality events of freshwater pearl mussels (Margaritifera margaritifera) in Sweden
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A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration

Sorensen, Megan E. S.; Zlatogursky, Vasily V.; Onuţ-Brännström, Ioana; Walraven, Anne et al.

Part of Current Biology, p. 3571-+, 2023

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• DOI for A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration
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Contrasting outcomes of genome reduction in mikrocytids and microsporidians

Zarsky, Vojtech; Karnkowska, Anna; Boscaro, Vittorio; Trznadel, Morelia et al.

Part of BMC Biology, 2023

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• DOI for Contrasting outcomes of genome reduction in mikrocytids and microsporidians
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A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea)

Onuţ-Brännström, Ioana; Stairs, Courtney W.; Aguilera Campos, Karla Iveth; Hiltunen Thorén, Markus et al.

Part of Genome Biology and Evolution, 2023

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• DOI for A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea)
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EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes

Richter, Daniel J.; Berney, Cédric; Strassert, Jürgen F.H.; Poh, Yu Ping et al.

Part of Peer Community Journal, 2022

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• DOI for EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes

EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes

Richter, Daniel J.; Berney, Cedric; Strassert, Jurgen F. H.; Poh, Yu-Ping et al.

Part of Peer Community Journal, 2022

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• DOI for EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes
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Unravelling the Phylogeny of a Common Intestinal Protist: intrageneric Diversity of Endolimax

Hocke, Emma Filtenborg; Jamy, Mahwash; Burki, Fabien; Clark, C. Graham et al.

Part of Protist, 2022

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• DOI for Unravelling the Phylogeny of a Common Intestinal Protist: intrageneric Diversity of Endolimax

Photophysiological response of Symbiodiniaceae single cells to temperature stress

Xiao, Linhong; Johansson, Sofia; Rughöft, Saskia; Burki, Fabien et al.

Part of The ISME Journal, p. 2060-2064, 2022

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• DOI for Photophysiological response of Symbiodiniaceae single cells to temperature stress
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On the origin of TSAR: morphology, diversity and phylogeny of Telonemia

Tikhonenkov, Denis, V; Jamy, Mahwash; Borodina, Anastasia S.; Belyaev, Artem O. et al.

Part of Open Biology, 2022

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• DOI for On the origin of TSAR: morphology, diversity and phylogeny of Telonemia
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Global patterns and rates of habitat transitions across the eukaryotic tree of life

Jamy, Mahwash; Biwer, Charlie; Vaulot, Daniel; Obiol, Aleix et al.

Part of Nature Ecology & Evolution, p. 1458-1470, 2022

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• DOI for Global patterns and rates of habitat transitions across the eukaryotic tree of life
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Automated Removal of Non-homologous Sequence Stretches with PREQUAL

Irisarri, Iker; Burki, Fabien; Whelan, Simon

Part of Multiple Sequence Alignment, p. 147-162, Humana Press, 2021

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• DOI for Automated Removal of Non-homologous Sequence Stretches with PREQUAL

The long-time orphan protist Meringosphaera mediterranea Lohmann, 1902 [1903] is a centrohelid heliozoan

Zlatogursky, Vasily V.; Shishkin, Yegor; Drachko, Daria; Burki, Fabien

Part of Journal of Eukaryotic Microbiology, 2021

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• DOI for The long-time orphan protist Meringosphaera mediterranea Lohmann, 1902 [1903] is a centrohelid heliozoan

Phylogenomic Insights into the Origin of Primary Plastids

Irisarri, Iker; Strassert, Jürgen F. H.; Burki, Fabien

Part of Systematic Biology, p. 105-120, 2021

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• DOI for Phylogenomic Insights into the Origin of Primary Plastids

Diversity and ecology of protists revealed by metabarcoding

Burki, Fabien; Sandin, Miguel Mendez; Jamy, Mahwash

Part of Current Biology, 2021

Article, review/survey

• DOI for Diversity and ecology of protists revealed by metabarcoding
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PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

Tice, Alexander K.; Zihala, David; Panek, Tomas; Jones, Robert E. et al.

Part of PLoS biology, 2021

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• DOI for PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
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Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae

Schön, Max Emil; Zlatogursky, Vasily V.; Singh, Rohan P.; Poirier, Camille et al.

Part of Nature Communications, 2021

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• DOI for Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae
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A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids

Strassert, Jürgen F. H.; Irisarri, Iker; Williams, Tom A.; Burki, Fabien

Part of Nature Communications, 2021

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• DOI for A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids
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Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding

Santoferrara, Luciana; Burki, Fabien; Filker, Sabine; Logares, Ramiro et al.

Part of Journal of Eukaryotic Microbiology, p. 612-622, 2020

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• DOI for Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding

Predatory colponemids are the sister group to all other alveolates

Tikhonenkov, Denis, V; Strassert, Juergen F. H.; Janouskovec, Jan; Mylnikov, Alexander P. et al.

Part of Molecular Phylogenetics and Evolution, 2020

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• DOI for Predatory colponemids are the sister group to all other alveolates

Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

Jamy, Mahwash; Foster, Rachel; Barbera, Pierre; Czech, Lucas et al.

Part of Molecular Ecology Resources, p. 429-443, 2020

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• DOI for Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

The New Tree of Eukaryotes

Burki, Fabien; Roger, Andrew J.; Brown, Matthew W.; Simpson, Alastair G. B.

Part of Trends in Ecology & Evolution, p. 43-55, 2020

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• DOI for The New Tree of Eukaryotes
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Progress towards the Tree of Eukaryotes

Keeling, Patrick J.; Burki, Fabien

Part of Current Biology, 2019

Article, review/survey

• DOI for Progress towards the Tree of Eukaryotes

New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

Strassert, Jürgen F. H.; Jamy, Mahwash; Mylnikov, Alexander P.; Tikhonenkov, Denis V. et al.

Part of Molecular biology and evolution, p. 757-765, 2019

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• DOI for New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Adl, Sina M.; Bass, David; Lane, Christopher E.; Lukes, Julius et al.

Part of Journal of Eukaryotic Microbiology, p. 4-119, 2019

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• DOI for Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
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Ascetosporea

Bass, David; Ward, Georgia M.; Burki, Fabien

Part of Current Biology, 2019

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• DOI for Ascetosporea

Phylogenomics supports the monophyly of the Cercozoa

Irwin, Nicholas; Tikhonenkov, Denis; Hehenberger, Elisabeth; Mylnikov, Alexander et al.

Part of Molecular Phylogenetics and Evolution, p. 416-423, 2019

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• DOI for Phylogenomics supports the monophyly of the Cercozoa

PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences

Whelan, Simon; Irisarri, Iker; Burki, Fabien

Part of Bioinformatics, p. 3929-3930, 2018

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• DOI for PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences

Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates

Strassert, Jürgen F H; Karnkowska, Anna; Hehenberger, Elisabeth; del Campo, Javier et al.

Part of The ISME Journal, p. 304-308, 2018

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• DOI for Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates

A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction

Janouskovec, Jan; Tikhonenkov, Denis V.; Burki, Fabien; Howe, Alexis T. et al.

Part of Current Biology, p. 3717-372400000, 2017

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• DOI for A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction

The Convoluted Evolution of Eukaryotes With Complex Plastids

Burki, Fabien

Part of Secondary Endosymbioses, p. 1-30, Elsevier, 2017

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• DOI for The Convoluted Evolution of Eukaryotes With Complex Plastids

A new Lineage of Eukaryotes Illuminates Eraly Mitochondrial Genome Reduction

Burki, Fabien

Part of Current Biology, 2017

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Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics

Janouškovec, Jan; Gavelis, Gregory S; Burki, Fabien; Dinh, Donna et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, 2017

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• DOI for Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics

Functional Relationship between a Dinoflagellate Host and Its Diatom Endosymbiont

Hehenberger, Elisabeth; Burki, Fabien; Kolisko, Martin; Keeling, Patrick J.

Part of Molecular biology and evolution, p. 2376-2390, 2016

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• DOI for Functional Relationship between a Dinoflagellate Host and Its Diatom Endosymbiont

Mitochondrial Evolution: Going, Going, Gone

Burki, Fabien

Part of Current Biology, 2016

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• DOI for Mitochondrial Evolution: Going, Going, Gone