Link to Google Scholar
2023​
  • Onut-Brännström I, Stairs CW, Iveth Aguilera Campos K, Hiltunen Thorén M, Ettema TJG, Keeling PJ, Bass D, Burki F. 2023. A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea). Genome Biol. Evol., 15(3), evad022.
2022
  • Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez S, Wideman JG, Burki F, de Vargas C. 2022. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community Journal 2:e56.
  • Hocke EF, Jamy M, Burki F , Clark CG, Stensvold CR. 2022. Unravelling the Phylogeny of a Common
    Intestinal Protist: Intra-generic Diversity of Endolimax. Protist.     173(5):125908.
  • Jamy M, Biwer C, Vaulot D, Obiol A, Jing H, Peura S, Massana R, Burki F. 2022. Global patterns and rates of habitat transitions across the eukaryotic tree of life. Nat. Ecol. Evol. 6(10):1458-1470.
  • Xiao L, Johansson S, Rughöft S, Burki F, Mendez Sandin M, Tenje M, Behrendt L. 2022. Photophysiological response of Symbiodiniaceae single cells to temperature stress. ISME J. 16:2060–2064.
  • Tikhonenkov DV,  Jamy M, Borodina AS, Belyaev AO, Zagumyonnyi DG, Prokina KI, Mylnikov AP, Burki F, Karpov SA. 2022. On the origin of TSAR: morphology, diversity, and phylogeny of Telonemia. Open Biol. 12: 210325.
  • Irisarri I, Strassert JFH, Burki F. 2022. Phylogenomic Insights into the Origin of Primary Plastids. Syst. Biol. 71(1):105–120.
2021
  • Schön ME, Zlatogursky VV, Singh RP, Poirier C, Wilken S, Mathur V, Strassert JFH, Pinhassi J, Worden AZ, Keeling PJ, Ettema TJG, Wideman JG, Burki F. 2021. Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae. Nat. Commun. 12:6651.
  • Burki F, Sandin MM, Jamy M. 2021. Diversity and ecology of protists revealed by metabarcoding. Curr. Biol. 31(19):R1267-R1280.
  • Tice AK, Žihala D, Pánek T, Jones RE, Salomaki ED, Nenarokov S, Burki F, Eliáš M, Eme L, Roger AJ, Rokas A, Shen XX, Strassert JFH, Kolísko M, Brown MW. 2021. PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. PLoS Biol. 19(8): e3001365. 
  • ​Zlatogursky VV, Shishkin Y, Drachko D, Burki F. 2021. The long-time orphan protist Meringosphaera mediterranea Lohmann, 1902 [1903] is a centrohelid heliozoan. J. Euk. Microbiol. 68(5):e12860.
  • Strassert JFH, Irisarri I, Williams TA, Burki F. 2021. A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids. Nat. Commun. 12:1879.
  • Irisarri I, Burki F, Whelan S. 2021. Automated Removal of Non-homologous Sequence Stretches with PREQUAL. In: Katoh K. (eds) Multiple Sequence Alignment. Methods in Molecular Biology, vol 2231. Humana, New York, NY. 
2020
  • Santoferrara L, Burki F, Filker S, Logares R, Dunthorn M, McManus GB. 2020. Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding. J. Euk. Microbiol. 67(5):612-622.
  • Tikhonenkov D, Strassert JFH, Janouškovec J, Mylnikov A, Aleoshin V, Burki F, Keeling P. 2020. Predatory colponemids are the sister group to all other alveolates. Mol. Phyl. Evol. 149, 106839.
  • ​Jamy M, Foster R, Barbera P, Czech L, Kozlov A, Stamatakis A, Bass D, Burki F. 2020. Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity. Mol. Ecol. Ressourc. 20(2):429-443
  • Burki F, Roger AJ, Brown MW, Simpson AGB. 2020. The New Tree of Eukaryotes. Trends. Ecol. Evol. 35(1):43-55.
2019
  • Keeling PJ, Burki F. 2019. Progress towards the Tree of Eukaryotes. Curr. Biol. 29(16):R808-R817.
  • Strassert JFH, Jamy M, Mylnikov AP, Tikhonenkov DV, Burki F. 2019. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life. Mol. Biol. Evol. 36(4):757–765.
  • Bass D, Ward GM, Burki F. 2019. Ascetosporea. Curr. Biol. 29(1):R7-R8.
  • Adl SM et al. (47 authors; Burki F in 10th position). 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. J. Eukaryot. Microbiol. 66(1):4-119.
2018
  • Whelan S, Irisarri I, Burki F. 2018. PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences. Bioinformatics. 34(22):3929-3930.
  • Irwin NAT, Tikhonenkov DV, Hehenberger E, Janouškovec J, Mylnikov AP, Burki F, Keeling PJ. 2018. Phylogenomics supports the monophyly of the Cercozoa. Mol. Phyl. Evol. 130:416-423.
2017
  • ​Strassert JFH, Karnkowska A, Hehenberger E, del Campo J, Kolisko M, Okamoto N, Burki F, Janouškovec J, Poirier C, Leonard G, Hallam SJ, Richards TA, Worden AZ, Santoro AE, Keeling PJ. 2017. Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. ISME J. 12(1):304-308.
  • Janouškovec J, Tikhonenkov DV, Burki F, Howe AT, Rohwer FL, Mylnikov AP, Keeling PJ. 2017. A new Lineage of Eukaryotes Illuminates Eraly Mitochondrial Genome Reduction. Curr. Biol. 27(23):3717-3724​.
  • Burki F. 2017. The Convoluted Evolution of Eukaryotes With Complex Plastids. Advances in Botanical Research. 84:1-30.
  • Janouškovec J, Gavelis GS, Burki F, Dinh D, Bachvaroff TR, Gornik SG, Bright KJ, Imanian B, Strom SL, Delwiche CF, Waller RF, Fensome RA, Leander BS, Rohwer FL, Saldarriaga JF. 2017. Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics. Proc. Natl. Acad. Sci. USA. 114(2):E171-E180.
2016
  • Burki F. 2016. Mitochondrial Evolution: Going, Going, Gone. Curr. Biol. 26(10):R410-412.
  • Hehenberger E, Burki F, Kolisko M, Keeling PJ. 2016. Functional relationship between a dinoflagellate host and its diatom endosymbiont. Mol. Biol. Evol. 33(9):2376-2390.
  • Burki F, Kaplan M, Tikhonenkov DV, Zlatogursky V, Minh BQ, Radaykina LV, Smirnov A, Mylnikov AP, Keeling PJ. 2016. Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. Proc. R. Soc. B. 283:20152802.
2015
  • Sierra R, Cañas-Duarte SJ, Burki F, Schwelm A, Fogelqvist J, Dixelius C, González-García LN, Gile GH, Slamovits C, Klopp C, Restrepo S, Arzul I, Pawlowski J. 2016. Evolutionary origins of rhizarian parasites. Mol. Biol. Evol. 33(4):980-983.
  • Janouškovec J, Tikhonenkov DV, Burki F, Howe AT, Kolisko M, Mylnikov AP, Keeling PJ. 2015. Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives. Proc. Natl. Acad. Sci. USA. 12(33):10200-10207.
2014
  • Kolisko M, Boscaro V, Burki F, Lynn D, Keeling PJ. 2014. Single-cell transcriptomics for microbial eukaryotes. Curr. Biol. 24(22):R1081-1082
  • Hehenberger E, Imanian B, Burki F, Keeling PJ. 2014. Evidence for the retention of two evolutionary distinct plastids in dinoflagellates with diatom endosymbionts. Genome Biol. Evol. 6(9):2321-2334.
  • Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, et al. (81 authors). 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol 12(6): e1001889.
  • Burki F. 2014. The Eukaryotic Tree of Life from a Global Phylogenomic Perspective. Cold Spring Harb. Perspect. Biol. 6:a016147.
  • Burki F, Keeling PJ. 2014. Rhizaria. Curr. Biol. 24(3):R103-107.
  • Burki F*, Imanian B*, Hehenberger E, Hirakawa Y, Maruyama S, Keeling P J. 2014. Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates. Eukaryot. Cell. 13(2):246-255.  *Equally contributed to work
2013
  • Burki F, Corradi N, Sierra R, Pawlowski J, Meyer G R, Abbott C L, Keeling PJ. 2013. Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in Rhizaria. Curr. Biol. 23:1541-1547.
            [See also the Dispatch in the same issue of Current Biology by Mark van der Giezen]
  • James ER, Okamoto N, Burki F, Scheffrahn RH, Keeling PJ. 2013. Cthulhu macrofasciculumque n. g., n. sp. and Cthylla microfasciculumque n. g., n. sp., a newly identified lineage of parabasalian termite symbionts. PLoS ONE. 8(3): e58509.
  • James ER, Burki F, Harper TJ, Scheffrahn RH, Keeling PJ. 2013. Molecular characterization of parabasalian symbionts Coronympha clevelandii and Trichonympha subquasilla from the Hawaiian lowland tree termite Incisitermes immigrans. J. Eukaryot. Microbiol. 60:313-316.
2012
  • Curtis BA, Tanifuji G, Burki F, et al. (73 authors). 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature. 492:59-65.
  • Hirakawa Y, Burki F, Keeling PJ. 2012. Dual targeting of aminoacyl-tRNA synthetases to the mitochondrion and complex plastid in chlorarachniophytes. J. Cell Sci. 125:6176-6184.
  • Adl SM et al. (25 authors; Burki F in 8th position). 2012. The Revised Classification of Eukaryotes. J. Eukaryot. Microbiol. 59:429-493.
  • Imanian B, Pombert JF, Dorrell RG, Burki F, Keeling PJ. 2012. Tertiary endosymbiosis in two dinotoms has generated little change in the mitochondrial genomes of their dinoflagellate hosts and diatom endosymbionts. PLoS ONE. 7(8): e43763.
  • Pombert JF, Selman M, Burki F, Bardell FT, Farinelli L, Solter LF, Whitman DW, Weiss LM, Corradi N, Keeling PJ. 2012. Gain and loss of multiple functionally-related horizontally transferred genes in the reduced genomes of two microsporidian parasites. Proc. Natl. Acad. Sci. USA. 109:12638-12643.
  • Burki F*, Flegontov P*, Oborník M, Cihlář J, Pain A, Lukeš J, Keeling PJ. 2012. Reevaluating the green  versus red signal in eukaryotes with secondary plastid of red algal origin. Genome Biol. Evol. 4:626-635. *Equally contributed to work
  • Burki F, Hirakawa Y, Keeling PJ. 2012. Intragenomic spread of plastid-targeting presequences in the coccolithophore Emiliania huxleyi. Mol. Biol. Evol. 29:2109-2112.
  • Burki F, Okamoto N, Pombert JF, Keeling PJ. 2012. The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins.  Proc. R. Soc. B. 279:2246-2254.
  • Hirakawa Y, Burki F, Keeling PJ. 2012. Genome-based reconstruction of the protein import machinery in the secondary plastid of a chlorarachniophyte alga. Euk. Cell. 11(3):324-33.
  • Zhao S*, Burki F*, Brate J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K. 2012. Collodictyon - an ancient lineage in the tree of eukaryotes. Mol. Biol. Evol. 29(6):1557-1568. *Equally contributed to work
    [Evaluated by Faculty of 1000: F1000.com/716247803]
  • Pochon X, Putnam HM, Burki F, Gates RD. 2012. Identifying and Characterizing Alternative Molecular Markers for the Symbiotic and Free-Living Dinoflagellate Genus Symbiodinium. PLoS ONE. 7(1): e29816.
2011
  • Smith DR, Burki F, Yamada T, Grimwood J, Grigoriev IV, Van Etten JL, Keeling PJ. 2011. The GC-Rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape. PLoS ONE. 6(8): e23624.
  • Hirakawa Y, Burki F, Keeling PJ. 2011. Nucleus- and nucleomorph-targeted histone proteins in a chlorarachniophyte alga. Mol. Microbiol. 80(6):1439-1449.
2010
  • Burki F, Kudryavtsev A, Matz MV, Aglyamova GV, Bulman S, Fiers M, Keeling PJ, Pawlowski J. 2010. Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. BMC Evol. Biol. 10:377.
2009
  • Burki F, Inagaki Y, Brate J, Archibald JM, Keeling PJ, Cavalier-Smith T, Sakaguchi M, Hashimoto T, Horak A, Kumar S, Klaveness D, Jakobsen KS, Pawlowski J, Shalchian-Tabrizi K. 2009. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol. Evol. 1(1):231-238.
  • Kumar S, Skjaeveland A, Orr RJS, Enger P, Ruden T, Mevik B, Burki F, Botnen A, Shalchian-Tabrizi K. 2009. AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinformatics. 10:357.
  • Pawlowski J and Burki F. 2009. Untangling the phylogeny of amoeboid protists. J. Eukaryot. Microbiol. 56:16-25.
  • Minge M, Silberman JD, Orr RJS, Cavalier-Smith T, Shalchian-Tabrizi K, Burki F, Skjaeveland A, Jakobsen KS. 2009. Evolutionary position of breviate amoebae and the primary eukaryote divergence. P. Roy. Soc. B. 276:597-604.
2008
  • Burki F, Shalchian-Tabrizi K, Pawlowski J. 2008. Phylogenomics reveal a new “megagroup” including most photosynthetic eukaryotes. Biol. Letters. 4:366-369. 
    [See the NEWS FOCUS in Science by E. Pennisi that talked about our work]
2007
  • Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev SI, Jakobsen KS, Pawlowski J. 2007. Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE. 2(8):e790.
2006
  • Burki F and Pawlowski J. 2006. Monophyly of Rhizaria and multigene phylogeny of univellular bikonts. Mol. Biol. Evol. 23(10):1922-1930.
  • Burki F, Nikolaev SI, Bolivar I, Guiard J, Pawlowski J. 2006. Analysis of expressed sequenced tags from a naked foraminiferan Reticulomyxa filosa. Genome. 49:882-887.
2004
  • Longet D, Burki F, Flakowski J, Berney C, Polet S, Fahrni J, Pawlowski J. 2004. Multigene evidence for close evolutionary relations between Gromia and Foraminifera. Acta Protozool. 43:303-311.
  • Burki F and Kaessmann H. 2004. Birth and adaptive evolution of a hominoid gene supporting high neurotransmitter flus. Nature Genet. 10:1061-1063.
2002
  • Burki F, Berney C, Pawlowski J. 2002. Phylogenetic position of Gromia oviformis Dujardin inferred from nuclear-encoded small subunit ribosomal DNA. Protist. 153:251-260.