Publications from the lab

Main publications

microGWAS: a computational pipeline to perform large scale bacterial genome-wide association studies

Burgaya, J., Damaris, B. F., Fiebig, J., & Galardini, M. (2025). microGWAS: A computational pipeline to perform large-scale bacterial genome-wide association studies. Microbial Genomics, 11(2), 001349.

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PMID: 39932497
Biorxiv Preprint: 602456

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Summary blog post (published version)
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Online documentation
Press release (RESIST)
Press release (Twincore, in German)

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A systematic identification of resistance determinants to antisense antibiotics suggests adaptation strategies dependent on the delivery peptide

Mulkern, A. J., Vu, T.-H., Popella, L., Kerrinnes, T., Đurica-Mitić, S., Barquist, L., Vogel, J., & Galardini, M. (2024). A systematic identification of resistance determinants to antisense antibiotics suggests adaptation strategies dependent on the delivery peptide (p. 2024.10.29.620885). bioRxiv. https://doi.org/10.1101/2024.10.29.620885

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Biorxiv Preprint: 620885

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Summary blog post
Analysis repository
Raw sequencing reads

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

Innocenti, G., Obara, M., Costa, B., Jacobsen, H., Katzmarzyk, M., Cicin-Sain, L., Kalinke, U., & Galardini, M. (2024). Real-time identification of epistatic interactions in SARS-CoV-2 from large genome collections. Genome Biology, 25(1), 228.

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PMID: 39175058
PMCID: PMC11342480
Biorxiv Preprint: 554253

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Summary blog post (preprint)
Summary blog post (published version)
Press release (Twincore)

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Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric k-mers

Sommer, H., Djamalova, D., & Galardini, M. (2023). Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric k-mers. Microbial Genomics, 9(11), 001129.

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PMID: 37934071
PMCID: PMC10711318
Biorxiv Preprint: 536385

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Summary blog post
Software repository
conda package
pypi package
Benchmark repository
Twitter summary thread (pre-print)

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The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans

Burgaya, J.*, Marin, J.*, Royer, G., Condamine, B., Gachet, B., Clermont, O., Jaureguy, F., Burdet, C., Lefort, A., Lastours, V. de, Denamur, E.*, Galardini, M.*, Blanquart, F.* (2023). The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans. PLOS Genetics, 19(8), e1010842.

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PMID: 37531401
PMCID: PMC10395866
Biorxiv Preprint: 522367

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Analysis pipeline for the paper
Twitter summary thread
Preprint Mastodon summary thread
Preprint Twitter summary thread
Press release (RESIST)
Press release (MHH, in German)

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Genome wide association study of human bacteremia Escherichia coli isolates identifies genetic determinants for the portal of entry but not fatal outcome

Denamur, E., Condamine, B., Esposito-Farèse, M., Royer, G., Clermont, O., Laouenan, C., … & Galardini, M.* (2022). Genome wide association study of human bacteremia Escherichia coli isolates identifies genetic determinants for the portal of entry but not fatal outcome. PLoS Genet. 2022;18(3):e1010112.

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PMID: 35324915
PMCID: PMC8946752
Medrxiv Preprint: 2021.11.09.21266136

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Analysis pipeline for the paper
Input genome sequences (Colibafi)
Input genome sequences (Septicoli)
Twitter summary thread
Press release (Twincore)

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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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Analysis pipeline for the paper
Input genome sequences

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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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Analysis pipeline for the paper

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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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pyseer docs

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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

Cacace, E., Tietgen, M., Steinhauer, M., Mateus, A., Schultze, T. G., Eckermann, M., … Galardini, M., … & Göttig, S. (2025). Uncovering nitroxoline activity spectrum, mode of action and resistance across Gram-negative bacteria. Nature Communications, 16(1), 3783.

40263263

PMC12015411

597298

Bartolec, T., Mitosch, K., Potel, C., Corona, F., Yang, A. L. J., Burtscher, M. L., … Galardini, M., … & Savitski, M. M. (2024). Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses. bioRxiv, 2024-12.

629319

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.

38296981

PMC10830555

10.21203/rs.3.rs-2831470/v1

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.

37339949

PMC10282060

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.

37120673

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.

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.

36038584

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.

35850148

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.

34663920

PMC7612524

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.

33571044

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.

33180303

Software code

Webserver