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Department of Plant and Microbial Biology



Menardo, F., Gagneux, S., & Freund, F. (2021). Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis. Molecular Biology and Evolution, 38(1), 290-306.

Menardo, F., Rutaihwa, L. K., Zwyer, M., Borrell, S., Comas, I., Conceição, E. C., ... & Gagneux, S. (2021). Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. F1000Research, 10.

Coscolla, M., Gagneux, S., Menardo, F., Loiseau, C., Ruiz-Rodriguez, P., Borrell, S., ... & Brites, D. (2021). Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microbial genomics, 7(2).

Cox, H., Salaam-Dreyer, Z., Goig, G. A., Nicol, M. P., Menardo, F., Dippenaar, A., ... & Warren, R. M. (2021). Potential contribution of HIV during first-line tuberculosis treatment to subsequent rifampicin-monoresistant tuberculosis and acquired tuberculosis drug resistance in South Africa: a retrospective molecular epidemiology study. The Lancet Microbe.


Loiseau, C., Menardo, F., Aseffa, A., Hailu, E., Gumi, B., Ameni, G., ... & Brites, D. (2020). An African origin for Mycobacterium bovis. Evolution, medicine, and public health, 2020(1), 49-59.

Ngabonziza, J. C. S., Loiseau, C., Marceau, M., Jouet, A., Menardo, F., Tzfadia, O., ... & Supply, P. (2020). A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nature communications, 11(1), 1-11.


Menardo, F., Duchêne, S., Brites, D., Gagneux, S. (2019). The molecular clock of Mycobacterium tuberculosis. PLoS Pathogens 15(9): e1008067.

Meehan, C. J., et al. (2019). Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nature Reviews Microbiology, 17, pages533–545.

Payne, J. L., Menardo, F., Trauner, A., Borrell, S., Gygli, S. M., Loiseau, C., Gagneux, S. & Hall, A. R. (2019). Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis. PLoS Biology, 17(5), e3000265.

Rutaihwa, L. K., Menardo, F., Stucki, D., Gygli, S., Ley, S. D., Malla, B., Feldmann, J., Borrel, S., Beisel, C., Middlekoop, K., Carter, E. J., Diero, L., Ballif, M., Jugheli, L., Reither, K., Fenner, L., Brites, D. & Gagneux, S. (2019). Multiple Introductions of Mycobacterium tuberculosis Lineage 2–Beijing into Africa over centuries. Frontiers in Ecology and Evolution, 7, 112. contribution to this study

Bourras, S., Kunz, L., Xue, M., Praz, C. R., Müller, M. C., Kälin, C., Schläfli, M., Ackermann, P., Flückiger, S., Parlange, F., Menardo, F., Schaefer, L. K., Ben-David, R., Roffler, S., Oberhaensli, S., Widrig, V., Lindner, S., Isaksson, J., Wicker, T., Yu, D. & Keller, B. (2019). The AvrPm3-Pm3 effector- NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat. Nature communications, 10(1), 2292.

Müller, M. C., Praz, C. R., Sotiropoulos, A. G., Menardo, F., Kunz, L., Schudel, S., Oberhaensli, S., Poretti, M., Wehrli, A., Bourras, S., Keller, B. & Wicker, T. (2019). A chromosome‐scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew. New Phytologist, 221(4), 2176-2189.


Brites, D., Loiseau, C., Menardo, F., Borrell, S., Boniotti, M. B., Warren, R. M., Dippenaar, A., Parson, S. D. C., Beisel, C., Behr, M. A., Fyfe, J., Coscolla, M. & Gagneux S. (2018). A new phylogenetic framework for the animal-adapted Mycobacterium tuberculosis complex. Frontiers in microbiology, 9, 2820.

Menardo, F., Loiseau, C., Brites, D., Coscolla, M., Gygli, S. M., Rutaihwa, L. K., Trauner, A., Beisel, C., Borrell, S. & Gagneux, S. (2018). Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC bioinformatics, 19(1), 164.

McNally, K. E., Menardo, F., Lüthi, L., Praz, C. R., Müller, M. C., Kunz, L., Ben-David, R., Chandrasekhar, K., Dinoor, A., Cowger, C., Meyers, E., Xue, M., Zeng, F., Gong, S., Yu, D., Bourras, S. & Keller, B. (2018). Distinct domains of the AVRPM 3A2/F2 avirulence protein from wheat powdery mildew are involved in immune receptor recognition and putative effector function. New Phytologist, 218(2), 681-695.

Praz, C. R., Menardo, F., Robinson, M. D., Müller, M. C., Wicker, T., Bourras, S., & Keller, B. (2018). Non-parent of origin expression of numerous effector genes indicates a role of gene regulation in host adaption of the hybrid triticale powdery mildew pathogen. Frontiers in plant science, 9, 49. )

Sucher, J., Menardo, F., Praz, C. R., Boni, R., Krattinger, S. G., & Keller, B. (2018). Transcriptional profiling reveals no response of fungal pathogens to the durable, quantitative Lr34 disease resistance gene of wheat. Plant pathology, 67(4), 792-798.


Menardo, F., Praz, C. R., Wicker, T., & Keller, B. (2017). Rapid turnover of effectors in grass powdery mildew (Blumeria graminis). BMC evolutionary biology, 17(1), 223.

Zeng, F. S., Menardo, F., Xue, M. F., Zhang, X. J., Gong, S. J., Yang, L. J., Shi, W. & Yu, D. (2017). Transcriptome analyses shed new insights into primary metabolism and regulation of Blumeria graminis f. sp. tritici during conidiation. Frontiers in Plant Science, 8, 1146.

Menardo, F., Wicker, T., & Keller, B. (2017). Reconstructing the evolutionary history of powdery mildew lineages (Blumeria graminis) at different evolutionary time scales with NGS data. Genome biology and evolution, 9(2), 446-456.

Praz, C. R., Bourras, S., Zeng, F., Sánchez‐Martín, J., Menardo, F., Xue, M., Yang, L., Roffler, S., Böni, R., Herre, G., McNally, K. E., Ben-David, R., Parlange, F., Oberhaensli, S., Flückiger, S., Schaefer, L. K., Wicker, T., Yu, D., & Keller, B. (2017). AvrPm2 encodes an RNase like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus. New Phytologist, 213(3), 1301-1314.


Menardo, F., Praz, C. R., Wyder, S., Ben-David, R., Bourras, S., Matsumae, H., McNally, K. E., Parlange, F., Riba, A., Roffler, S., Schaefer, L. K., Shimizu, K. K., Valenti, L., Zbinden, H., Wicker, T. & Keller, B. (2016). Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species. Nature Genetics, 48(2), 201.


Roffler, S., Menardo, F., & Wicker, T. (2015). The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants. Mobile DNA, 6(1), 23.

Bourras, S., McNally, K. E., Ben-David, R., Parlange, F., Roffler, S., Praz, C. R., Oberhaensli, S., Menardo, F., Stirnweis, D., Frenkel, Z., Schaefer, L. K., Flückiger, S., Treier, G., Herren G., Korol, A. B., Wicker, T. & Keller, B. (2015). Multiple avirulence loci and allele-specific effector recognition control the Pm3 race-specific resistance of wheat to powdery mildew. The Plant Cell, 27(10), 2991-3012.

Parlange, F., Roffler, S., Menardo, F., Ben-David, R., Bourras, S., McNally, K. E., Oberhaensli, S., Stirnweis, D., Buchman, G., Wicker, T. & Keller, B. (2015). Genetic and molecular characterization of a locus involved in avirulence of Blumeria graminis f. sp. tritici on wheat Pm3 resistance alleles. Fungal Genetics and Biology, 82, 181-192.



Borovec, R.*, Menardo, F., & Meregalli, M. (2013). A new genus of Entiminae from North Africa, supported by a phylogenetic analysis (Coleoptera: Curculionidae: Entiminae). Zoological Journal of the Linnean Society, 167(2), 243-258.

Meregalli, M., Menardo, F., Klass, K. D., & Cervella, P. (2013). Phylogeny of the Saxifraga-associated species of Dichotrachelus (Insecta: Coleoptera: Curculionidae), with remarks on their radiation in the Alps. Arthropod Systematics & Phylogeny, 71(1), 43-68.