PUBLICATIONS page

Publication List

Associated content and media coverage are indicated separately – Corresponding/lead authorships are marked with an asterisk (*) – ‘Stairs lab’ members are underlined

45. Boisard, J., Williams S., Roger A.J., Stairs C.W.* (2026). CoMR: an integrative scoring pipeline for Comprehensive Mitochondrial proteome Reconstruction across eukaryotes. Briefings in Bioinformatics, 27(5):bbag474

44. Aguilera-Campos, K.I., Boisard, J., Törnblom, V., Jerlström-Hultqvist, J., Behncké-Serra, A., Cotillas, E.A. and Stairs, C.W.* (2025). Anaerobic protist survival in microcosms is dependent on microbiome metabolic function. ISME Journal, 19(1): wraf171

43. Akdeniz, Z., Havelka, M., Stoklasa, M., Jiménez-González, A., Žárský, V., Xu, F., Stairs, C.W., Jerlström-Hultqvist, J., Kolísko, M., Provazník, J. and Svärd, S. (2025). The expanded genome of Hexamita inflata, a free-living diplomonad. Scientific Data, 12(1), p. 192

42. Richards, T.A., Eme, L., Archibald, J.M., Leonard, G., Coelho, S.M., de Mendoza, A., Dessimoz, C., Dolezal, P., Fritz-Laylin, L.K., Gabaldón, T., Hampl, V., Lopez-Garcia, P., McInerney, J.O., Moreira, D., Muñoz-Gómez, S., Stairs, C.W., Eelco, C. (seven authors), Wideman, J. (2024) – Reconstructing the last common ancestor of all eukaryotes. PLoS Biology, 22(11), p. e3002917

41. Jerlström-Hultqvist, J., Gallot-Lavallée, L., Salas-Leiva, D.E., Curtis, B.A., Záhonová, K., Čepička, I., Stairs, C.W., Pipaliya, S., Dacks, J.B., Archibald, J.M. and Roger, A.J. (2024). A unique symbiosome in an anaerobic single-celled eukaryote. Nature Communications, 15(1), p. 9726

40. Williams, S.K., Jerlström Hultqvist, J., Eglit, Y., Salas-Leiva, D.E., Curtis, B., Orr, R.J., Stairs, C.W., Atalay, T.N., MacMillan, N., Simpson, A.G. and Roger, A.J. (2024). Extreme mitochondrial reduction in a novel group of free-living metamonads. Nature Communications, 15(1): 6805

39. Greening, C., Cabotaje, P.R., Alvarado, L.E.V., Leung, P.M., Land, H., Senger, M., Klamke, M.A., Milton, M., Lappan, R.J., Mullen, S., West-Roberts, J., Mao, J., Song, J., Schoelmerich, M., Stairs, C.W., Grinter, R., Spang, A., Banfield, J.F. and Berggren, G. (2024). Minimal and hybrid hydrogenases are active from archaea. Cell, 187(13): 3357–3372

38. Gallot-Lavallée, L., Jerlström-Hultqvist, J., Zegarra-Vidarte, P., Salas-Leiva, D.E., Stairs, C.W., Čepička, I., Roger, A.J. and Archibald, J.M. (2023). Massive intein content in Anaeramoeba reveals aspects of intein mobility in eukaryotes. Proceedings of the National Academy of Sciences, 120(49), e2306381120

37. Záhonová, K., Füssy, Z., Stairs, C.W., Leger, M.M., Tachezy, J., Čepička, I., Roger, A.J. and Hampl, V. (2023). Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans. Microbial Genomics, 9(11): 001143

36. Motyčková, A., Voleman, L., Najdrová, V., Marková, L., Benda, M., Dohnálek, V., Janowicz, N., Malych, R., Šuťák, R., Ettema, T.J.G., Svärd, S., Stairs, C.W.* and Doležal, P. (2023). Adaptation of the late ISC pathway in the anaerobic mitochondrial organelles of Giardia intestinalis. PLoS Pathogens, 19(10): e1010773

35. Eme, L., Tamarit, D., Caceres, E.F., Stairs, C.W., De Anda, V., Schön, M.E., et al. (2023). Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature, 618(7967): 992–999

34. Brännström, I.O.+, Stairs, C.W.+, Aguilera-Campos, K.I., Ettema, T.J.G., Keeling, P.J., Bass, D. and Burki, F. A mitosome with distinct metabolism in the uncultured protist parasite Paramikrocytos canceri (Rhizaria, Ascetosporea). Genome Biology and Evolution, 15(3): evad022 – Contributed equally to the work (+)

33. Leger, M.L. and Stairs, C.W.* (2022). Eukaryotic evolution: Spatial proteomics sheds light on mitochondrial reduction. Current Biology, 32(23): R1308–R1311 – Corresponding author (*)

32. Spang, A., Mahendrarajah, T.A., Offre, P. and Stairs, C.W.* (2022). Evolving perspective on the origin and diversification of cellular life and the virosphere. Genome Biology and Evolution, evac034 – Corresponding author (*) and Cover image

31. Aguilera-Campos, K.I. and Stairs, C.W.* (2021). Hydrogen metabolism: A eukaryote taps into the hydrogen sink. Current Biology, 32(1): R49–R51

30. Stairs, C.W., Táborský, P., Kolisko, M., Pánek, T., Eme, L., Salomaki, E., Hradilova, M., Vicek, C., Jerlström-Hultqvist, J., Roger, A.J. and Cepicka, I. (2021). Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes. Current Biology, 31(24): 208–215

29. Kang, S., Tice, A.K., Stairs, C.W., Lahr, D.J.G., Jones, R.E. and Brown, M. (2021). The integrin-mediated adhesive complex in the ancestor of animals, fungi, and amoebae. Current Biology, 31(14): 3073–3085

28. Sjöberg, S., Yu, C., Stairs, C.W., Allard, B., Hallberg, R., Henriksson, S. and Dupraz, C. (2021). Microbe-mediated Mn oxidation—a proposed model of mineral formation. Minerals, 11(10): 1146

27. Milner, D.S., Wideman, J.G., Stairs, C.W., Dunn, C.D. and Richards, T.A. (2021). A functional bacterial-derived restriction modification system in the mitochondrion of a heterotrophic protist. PLoS Biology, 19(4): e3001126 – Associated content: Nature Reviews Microbiology (2021). https://doi.org/10.1038/s41579-021-00570-3

26. Žárský, V., Klimeš, V., Pačes, J., Vlček, C., Beneš, J., Nývltová, E., Hrdý, I., Pyrih, J., Mach, J., Barlow, L., Stairs, C.W., Eme, L., Hall, N., Eliáš, M., Dacks, J., Roger, A.J. and Tachezy, J. (2021). The Mastigamoeba balamuthi genome and the nature of the free-living ancestor of Entamoeba. Molecular Biology and Evolution, 38(6): 2240–2259

25. Gawryluk, R.M.R. and Stairs, C.W.* (2021). Diversity of electron transport chains in anaerobic protists. Biochimica et Biophysica Acta (BBA) – Bioenergetics, 1862: 148334 – Corresponding author (*)

24. Stairs, C.W., Dharamshi, J.E., Tamarit, D., Eme, L., Jørgensen, S.L., Spang, A. and Ettema, T.J.G. (2020). Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. Science Advances, 6(35): eabb7258 – Media coverage: SciShow (over 250,000 views). https://youtu.be/m2jVc_ACpaE

23. Stairs, C.W. and Ettema, T.J.G. (2020). The archaeal roots of the eukaryotic dynamic actin cytoskeleton. Current Biology, 30(10): R521–R526

22. Sjöberg, S., Stairs, C.W., Allard, B., Homa, F., Martin, T., Sjöberg, V., Ettema, T.J.G. and Dupraz, C. (2020). Microbiomes in a manganese oxide-producing ecosystem in the Ytterby mine, Sweden: Impact on metal mobility. FEMS Microbiology Ecology, 96(11): fiaa169

21. Sjöberg, S., Stairs, C.W., Allard, B., Hallberg, R., Homa, F., Martin, T., Ettema, T.J.G. and Dupraz, C. (2020). Bubble biofilm: Bacterial colonization of air–air interface. Biofilm, 100030

20. Najdrová, V., Stairs, C.W., Vinopalová, M., Voleman, L. and Doležal, P. (2020). The evolution of the Puf superfamily of proteins across the tree of eukaryotes. BMC Biology, 18: 77

19. Dharamshi, J.E., Tamarit, D., Eme, L., Stairs, C.W., Martijn, J., Homa, F., Jørgensen, S.L., Spang, A. and Ettema, T.J.G. (2020). Marine sediments illuminate Chlamydiae diversity and evolution. Current Biology, 30(6): 1032–1048 – Associated content (Dispatch): https://doi.org/10.1016/j.cub.2020.01.086

18. Karnkowska, A., Treitli, S.C., Brzoň, O., Novák, L., Vacek, V., Soukal, P., Barlow, L.D., Herman, E.K., Pipaliya, S.V., Pánek, T., Žihala, D., Petrželková, R., Butenko, A., Eme, L., Stairs, C.W., Roger, A.J., Eliáš, M., Dacks, J.B. and Hampl, V. (2019). The oxymonad genome displays canonical eukaryotic complexity in the absence of a mitochondrion. Molecular Biology and Evolution, 36(10): 2292–2312

17. Spang, A., Stairs, C.W., Dombrowski, N., Eme, L., Lombard, J., Caceres, E.F., Jørgensen, S.L., Baker, B.J. and Ettema, T.J.G. (2019). Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism. Nature Microbiology, 4: 1138 – Associated content (News & Views): https://doi.org/10.1038/s41564-019-0495-5

16. Stairs, C.W.*, Kokla, A., Ástvaldsson, Á., Svärd, S.G. and Ettema, T.J.G. (2019). Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida. BMC Biology, 17: 19 – Corresponding author (*)

15. Narrowe, A.B., Spang, A., Stairs, C.W., Caceres, E.F., Baker, B.J., Miller, C.S. and Ettema, T.J.G. (2018). Complex evolutionary history of Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids. Genome Biology and Evolution, 10(9): 2380.

14. Stairs, C.W., Eme, L., Munoz-Gomez, S., Cohen, A.M., Shepperd, J.M., Dellaire, G., Fawcett, J. and Roger, A.J. (2018). Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis. eLife, 7: e34292.

13. Leger, M.M., Eme, L., Stairs, C.W. and Roger, A.J. (2018). Demystifying eukaryote lateral gene transfer. BioEssays, 40(5): e1700242.

12. Eme, L., Spang, A., Lombard, J., Stairs, C.W. and Ettema, T.J.G. (2017). Archaea and the origin of eukaryotes. Nature Reviews Microbiology, 15: 711.

11. Gentekaki, E., Curtis, B., Stairs, C.W., Klimes, V., Elias, M., Salas-Leiva, D., Herman, E.K., Eme, L., Arias, M.C., Henrissat, B., Hilliou, F., Klute, M.J., Suga, H., Malik, S.B., Pightling, A.W., Kolisko, M., Rachubinski, R.A., Schlacht, A., Soanes, D.M., Tsaousis, A.D., Archibald, J.M., Ball, S.G., Dacks, J.B., Clark, C.G., van der Giezen, M. and Roger, A.J. (2017). Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. PLoS Biology, 15(9): e2003769

10. Leger, M.M., Kolisko, M., Kamikawa, R., Stairs, C.W., Kume, K., Čepička, I., Silberman, J., Andersson, J.O., Xu, F., Yabuki, A., Eme, L., Zhang, Q., Takishita, T., Inagaki, Y., Simpson, A.G.B., Hashimoto, T. and Roger, A.J. (2017). Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nature Ecology & Evolution, 1: 0092

9. Gawryluk, R., Kamikawa, R., Stairs, C.W., Silberman, J.D., Brown, M.W. and Roger, A.J. (2016). The earliest stages of mitochondrial adaptation to low oxygen revealed in a novel rhizarian. Current Biology, 26(20): 2729.

8. Novák, L., Zubáčová, Z., Karnkowska, A., Kolisko, M., Hroudová, M., Stairs, C.W., Simpson, A.G.B., Keeling, P.J., Roger, A.J., Čepička, I. and Hampl, V. (2016). Arginine deiminase pathway enzymes: Evolutionary history in metamonads and other eukaryotes. BMC Evolutionary Biology, 16(1): 197

7. Hamann, E., Gruber-Vodicka, H., Kleiner, M., Tegetmeyer, H., Riedel, D., Littmann, S., Chen, J., Milucka, J., Viehweger, B., Becker, K.W., Dong, X., Stairs, C.W., Hinrichs, K., Brown, M.W., Roger, A.J. and Strous, M. (2016). Environmental Breviatea harbour mutualistic Arcobacter epibionts. Nature, 534(7606): 254

6. Karnkowska, A., Vacek, V., Zubáčová, Z., Treitli, S.C., Petrželková, R., Eme, L., Novák, L., Žárský, V., Barlow, L.D., Herman, E.K., Soukal, P., Hroudová, M., Doležal, P., Stairs, C.W., Roger, A.J., Eliáš, M., Dacks, J.B., Vlček, C. and Hampl, V. (2016). A eukaryote without a mitochondrial organelle. Current Biology, 26(10): 1274–1284

5. Stairs, C.W., Leger, M.M. and Roger, A.J. (2015). Diversity and origins of anaerobic metabolism in mitochondria and related organelles. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1678)

4. Nývltová, E., Stairs, C.W., Hrdý, I., Pačes, J., Roger, A.J. and Tachezy, J. (2015). Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes. Molecular Biology and Evolution, 32(4): 1039–1055

3. Stairs, C.W., Eme, L., Brown, M.W., Mutsaers, C., Susko, E., Dellaire, G., Soanes, D., van der Giezen, M. and Roger, A.J. (2014). A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia. Current Biology, 24(11): 1176–1186

2. Hampl, V., Stairs, C.W. and Roger, A.J. (2011). The tangled past of eukaryotic enzymes involved in anaerobic metabolism. Mobile Genetic Elements, 1(1): 71

1. Stairs, C.W., Roger, A.J. and Hampl, V. (2011). Eukaryotic pyruvate formate lyase and its activating enzyme were acquired laterally from a firmicute. Molecular Biology and Evolution, 28(7): 2087