1. Mitochondrial evolution: going, going, gone.
Burki F. (2016). Current Biology, vol. 26, ss. 410-412

2. Functional relationship between a dinoflagellate host and its diatom endosymbiont.
Hehengerger E, Burki F, Kolisko M, Keeling PJ. (2016). Molecular Biology and Evolution, Advance Access publication

3. Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista.
Burki F, Kaplan M, Tikhonenkov DV, Zlatogursky V, Minh BQ, Radaykina LV, Smirnov A, Mylnikov AP, Keeling PJ. (2016). Proceedings of the Royal Society B, vol. 283, ss. 20152802-10.

4. Evolutionary origins of rhizarian parasites.
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). Molecular Biology and Evolution, vol. 33, ss. 980-983.

5. Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives.
Janouškovec J, Tikhonenkov D. V, Burki F, Howe A. T, Kolísko M, Mylnikov A. P, Keeling P. J. (2015). PNAS, vol. 112, ss. 10200-10207.

6. Single-cell transcriptomics for microbial eukaryotes.
Kolísko M, Boscaro V, Burki F, Lynn D. H, Keeling P. J. (2014). Current Biology, vol. 24, ss. 1081-1082.

7. The eukaryotic tree of life from a global phylogenomic perspective.
Burki F. (2014). In: Origin and Evolution in Eukaryotes. Cold Spring Harb Perspect Biol. 6:a016147.

8. Rhizaria.
Burki F and Keeling P.J. (2014). Current Biology, vol. 24, ss. 104.

9. Evidence for the retention of two evolutionary distinct plastids in dinoflagellates with diatom endosymbionts.
Hehenberger E, Imanian B, Burki F, Keeling P. J. (2014). Genome Biology and Evolution, Vol. 6, ss. 2321–2334.

10. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.
Keeling P. J, Burki F,  et al. (81 authors). (2014). PLoS Biology, Vol. 12, ss. e1001889.

11. Endosymbiotic Gene Transfer in Tertiary Plastid-Containing Dinoflagellates.
Burki F, Imanian B, Hehenberger E, Hirakawa Y, Maruyama S, Keeling P. J. (2014). Eukaryotic Cell, vol. 13, ss. 246-255.

12. Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in Rhizaria.Burki F, Corradi N, Sierra R, Pawlowski J, Meyer G. R, Abbott C. L, Keeling P. J. (2013). Current Biology, vol. 23, ss. 1-7.

13. Cthulhu macrofasciculumque n. g., n. sp. and Cthylla microfasciculumque n. g., n. sp., a newly identified lineage of parabasalian termite symbionts.
James E. R, Okamoto N, Burki F, Scheffrahn R. H, Keeling P. J. (2013). PLoS ONE, vol. 8. ss. e58509.

14. Molecular characterization of parabasalian symbionts Coronympha clevelandii and Trichonympha subquasilla from the Hawaiian lowland tree termite Incisitermes immigrans.
James E. R, Burki F, Harper T. J, Scheffrahn R. H, Keeling P. J. (2013).  Journal of Eukaryotic Microbiology, vol. 60, ss. 313-316.

15. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.
Curtis B. A, Tanifuji G, Burki F, et al. (73 authors). (2012). Nature, vol. 492, ss. 59-65.

16. The Revised Classification of Eukaryotes.
Adl S. M et al. (25 authors; Burki F in 8th position). (2012). Journal of Eukaryotic Microbiology, vol. 59, ss. 429-493.

17. Dual targeting of aminoacyl-tRNA synthetases to the mitochondrion and complex plastid in chlorarachniophytes.
Hirakawa Y, Burki F, Keeling P. J. (2012). Journal of Cell Science, vol. 125, ss. 6176-6184.

18. Tertiary endosymbiosis in two dinotoms has generated little change in the mitochondrial genomes of their dinoflagellate hosts and diatom endosymbionts.
Imanian B, Pombert JF, Dorrell R. G, Burki F, Keeling P. J. (2012). PLoS ONE, vol. 7(8), ss. e43763.

19. Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites.
Pombert JF, Selman M, Burki F, Bardell F. T, Farinelli L, Solter L. F, Whitman D. W, Weiss L. M, Corradi N, Keeling P. J. (2012). PNAS, vol. 109, ss. 12638-12643.

20. Re-evaluating the green versus red signal in eukaryotes with secondary plastid of red algal origin.
Burki F*, Flegontov P*, Oborník M, Cihlář J, Pain A, Lukeš J, Keeling P. J. (2012). Genome Biology and Evolution, vol. 4, ss.626-635. *Equally contributed to work

21. Intragenomic spread of plastid-targeting presequences in the coccolithophore Emiliania huxleyi.
Burki F, Hirakawa Y, Keeling P. J. (2012). Molecular Biology and Evolution, vol. 29, ss. 2109-2112.

22. The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins.
Burki F, Okamoto N, Pombert JF, Keeling P. J. (2012). Proceedings of the Royal Society B, vol. 279, ss. 2246-2254.

23. Genome-based reconstruction of the protein import machinery in the secondary plastid of a chlorarachniophyte alga.
Hirakawa Y, Burki F, Keeling P. J. (2012). Eukaryotic Cell, vol. 11, ss. 324-333.

24. Collodictyon - an ancient lineage in the tree of eukaryotes.
Zhao S*, Burki F*, Brate J, Keeling P. J, Klaveness D, Shalchian-Tabrizi K. (2012). Molecular Biology and Evolution, vol. 29, ss. 1557-1568. *Equally contributed to work

25. Identifying and Characterizing Alternative Molecular Markers for the Symbiotic and Free-Living Dinoflagellate Genus Symbiodinium.
Pochon X, Putnam H. M, Burki F, Gates R. D. (2012). PLoS ONE, vol. 7, ss. e29816.

26. The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape.
Smith D. R., Burki F, Yamada T, Grigoriev I. V., Van Etten J. L., Keeling P. J. (2011). PLoS ONE, vol. 6, ss. e23624.

27. Nucleus- and nucleomorph-targeted histone proteins in a chlorarachniophyte alga.
Hirakawa Y, Burki F, Keeling P. J. (2011). Molecular Microbiology, vol. 80, ss. 1439-1449.

28. Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists.
Burki F, Kudryavtsev A, Matz M. V, Aglyamova G. V, Bulman S, Fiers M, Keeling P. J, Pawlowski J. (2010). BMC Evolutionary Biology, vol. 10, ss. 377.

29. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates.
Burki F, Inagaki Y, Brate J, Archibald J. M, Keeling P. J, Cavalier-Smith T, Sakaguchi M, Hashimoto T, Horak A, Kumar S, Klaveness D, Jakobsen K. S, Pawlowski J, and Shalchian-Tabrizi K. (2009). Genome Biology and Evolution, vol. 1, ss. 231-238.

30. Untangling the phylogeny of amoeboid protists.
Pawlowski J and Burki F. (2009). Journal of Eukaryotic Microbiology, vol. 56, ss. 16-25.

31. Evolutionary position of breviate amoebae and the primary eukaryote divergence.
Minge M, Silberman J. D, Orr R. J. S, Cavalier-Smith T, Shalchian-Tabrizi K, Burki F, Skjæveland A and Jakobsen K. S. (2009). Proceedings of the Royal Society B, vol. 276, ss. 597-604.

32. AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses.
Kumar S, Skjæveland A, Orr R. J. S, Enger P, Ruden T, Mevik B, Burki F, Botnen A, Shalchian-Tabrizi K. (2009). BMC Bioinformatics, vol. 10:357.

33. Phylogenomics reveals a new “megagroup” including most photosynthetic eukaryotes.
Burki F, Shalchian-Tabrizi K and Pawlowski J. (2008). Biology Letters, vol. 4, ss. 366-369.

34. Phylogenomics Reshuffles the Eukaryotic Supergroups.
Burki F, Shalchian-Tabrizi K, Minge M, Skjæveland A, Nikolaev S. I, Jakobsen K. S and Pawlowski J. (2007). PLoS ONE, vol. 2:e790.

35. Monophyly of Rhizaria and Multigene Phlogeny of Unicellular Bikonts.
Burki F and Pawlowski J. (2006). Molecular Biology and Evolution, vol. 23, ss. 1922-1930.

36. Analysis of expressed sequenced tags from a naked foraminiferan Reticulomyxa filosa.
Burki F, Nikolaev S. I, Bolivar I, Guiard J and Pawlowski J. (2006). Genome, vol. 49, ss. 882-887.

37. Birth and adaptive evolution of a hominoid gene supporting high neurotransmitter flux.
Burki F and Kaessmann H. (2004). Nature Genetetics, vol. 10, ss. 1061-1063.

38. Multigene evidence for close evolutionary relations between Gromia and Foraminifera.
Longet D, Burki F, Flakowski J, Berney C, Polet S, Fahrni J and Pawlowski J. (2004). Acta Protozoologica, vol. 43, ss. 303-311.

39. Phylogenetic Position of Gromia oviformis Dujardin inferred from Nuclear-Encoded Small Subunit Ribosomal DNA.
Burki F, Berney C and Pawlowski J. (2002). Protist, vol. 153, ss. 251-260.