Main publications

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      Real-time identification of epistatic interactions in SARS-CoV-2 from large genome collections

      Innocenti, G., & Galardini, M. (2023). Real-time identification of epistatic interactions in SARS-CoV-2 from large genome collections (p. 2023.08.22.554253). bioRxiv. doi.org/10.1101/2023.08.22.554253

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    • Biorxiv Preprint: 554253

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      Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study

      Galardini M.*, Clermont O., Baron A., Busby B., Dion S., Schubert S., Beltrao P. & Denamur E.* (2020). Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study. PLOS Genetics 16(10): e1009065.

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    • PMID: 33112851
    • PMCID: PMC7592755
    • Biorxiv Preprint: 712034

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      The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae

      Galardini, M.*, Busby, B. P.*, Vieitez, C., Dunham, A. S., Typas, A., & Beltrao, P.* (2019). The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae. Molecular Systems Biology, 15(12).

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    • PMID: 31885205
    • PMCID: PMC6901017
    • Biorxiv Preprint: 487439

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      pyseer: a comprehensive tool for microbial pangenome-wide association studies

      Lees, J. A.*, Galardini, M.*, Bentley, S. D., Weiser, J. N., & Corander, J.* (2018). pyseer: a comprehensive tool for microbial pangenome-wide association studies. Bioinformatics, 34(24), 4310-4312.

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    • PMID: 30535304
    • PMCID: PMC6289128
    • Biorxiv Preprint: 266312

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      Phenotype inference in an Escherichia coli strain panel

      Galardini, M., Koumoutsi, A., Herrera, C. M., Cordero Varela, J. A., Telzerow, A., Wagih O., Wartel M., Clermont O., Denamur E., Typas, A., Beltrao, P.* (2017). Phenotype inference in an Escherichia coli strain panel. eLife, 6.

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    • PMID: 29280730
    • PMCID: PMC5745082
    • Biorxiv Preprint: 141879

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    • All data generated from the E. coli strain panel

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    Other publications

    D’Amato, R., Taxiarchi, C., Galardini, M., Trusso, A., Minuz, R. L., Grilli, S., Somerville, A. G. T., Shittu, D., Khalil, A. S., Galizi, R., Crisanti, A., Simoni, A., & Müller, R. (2024). Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages. Nature Communications, 15(1), Article 1.

    PMID: 38296981
    PMCID: PMC10830555
    Preprint: 10.21203/rs.3.rs-2831470/v1
    Extra: Modelling code

    Royer, G., Clermont, O., Marin, J., Condamine, B., Dion, S., Blanquart, F., … Galardini, M. & Denamur, E. (2023). Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence. Nature Communications, 14(1), 3667.

    PMID: 37339949
    PMCID: PMC10282060
    Biorxiv Preprint: 517969

    Pisciotta, A., Sampino, A. M., Presentato, A., Galardini, M., Manteca, A., & Alduina, R. (2023). The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145. Scientific reports, 13(1), 7038.

    PMID: 37120673
    PMCID: PMC10148868

    Doherty, H. M., Kritikos, G., Galardini, M., Banzhaf, M., & Moradigaravand, D. (2023). ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling. Bioinformatics, 39(4), btad171.

    PMID: 37014365
    PMCID: PMC10085634
    Biorxiv Preprint: 522861
    Extra: Software code

    Mulkern, A. J., Oyama, L. B., Cookson, A. R., Creevey, C. J., Wilkinson, T. J., Olleik, H., … Damaris B. F., … & Huws, S. A.* (2022). Microbiome-derived antimicrobial peptides offer therapeutic solutions for the treatment of Pseudomonas aeruginosa infections. NPJ biofilms and microbiomes, 8(1), 1-15.

    PMID: 36038584
    PMCID: PMC9424236

    Bobonis, J., Mitosch, K., Mateus, A., Karcher, N., Kritikos, G., Selkrig, J., … Galardini, M., … & Typas, A.* (2022). Bacterial retrons encode phage-defending tripartite toxin–antitoxin systems. Nature, 609(7925), 144-150.

    PMID: 35850148
    Biorxiv Preprint: 160168

    Viéitez, C.*, Busby, B. P.*, Ochoa, D., Mateus, A., Memon, D., Galardini, M., … & Beltrao, P.* (2022). High-throughput functional characterization of protein phosphorylation sites in yeast. Nature biotechnology, 40(3), 382-390.

    PMID: 34663920
    PMCID: PMC7612524
    Biorxiv Preprint: 872770

    Annas, G. J., Beisel, C. L., Clement, K., Crisanti, A., Francis, S., Galardini, M., … & Joung, J. K.* (2021). A code of ethics for gene drive research. The CRISPR Journal, 4(1), 19-24.

    PMID: 33571044
    PMCID: PMC7898401

    diCenzo, G. C., Galardini, M., & Fondi, M.* (2021). Tn-Core: Functionally Interpreting Transposon-Sequencing Data with Metabolic Network Analysis. In Computational Methods in Synthetic Biology (pp. 199-215). Humana, New York, NY.

    PMID: 33180303
    Extra: Software code
    Extra: Webserver