Kamrad, S. et al. Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens. eLife. 9, e55160 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kritikos, G. et al. A tool named Iris for versatile high-throughput phenotyping in microorganisms. Nat. Microbiol. 2, 17014 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Barton, D. B. H. et al. PHENOS: a high-throughput and flexible tool for microorganism growth phenotyping on solid media. BMC Microbiol. 18, 9 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Wagih, O. et al. SGAtools: one-stop analysis and visualization of array-based genetic interaction screens. Nucleic Acids Res. 41, 591–596 (2013).

Article  Google Scholar 

Holland, I. & Davies, J. A. Automation in the life science research laboratory. Front. Bioeng. Biotechnol. 8, 571777 (2020).

Article  PubMed  PubMed Central  Google Scholar 

del Olmo, V. et al. Origin of fungal hybrids with pathogenic potential from warm seawater environments. Nat. Commun. 14, 6919 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Mixão, V. et al. Evolution of loss of heterozygosity patterns in hybrid genomes of Candida yeast pathogens. BMC Biol. 21, 105 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Ksiezopolska, E., Schikora-Tamarit, M. À., Nunez-Rodriguez, J. C. & Gabaldón, T. Long-term stability of acquired drug resistance and resistance associated mutations in the fungal pathogen Nakaseomyces glabratus (Candida glabrata). Front. Cell. Infect. Microbiol. 14, 1416509 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Addinall, S. G. et al. Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects. PLoS Genet. 7, e1001362 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Klemm, C., Howell, R. S. M. & Thorpe, P. H. ScreenGarden: a shinyR application for fast and easy analysis of plate-based high-throughput screens. BMC Bioinformatics 23, 60 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Zackrisson, M. et al. Scan-o-matic: high-resolution microbial phenomics at a massive scale. G3 6, 3003–3014 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wagih, O. & Parts, L. gitter: a robust and accurate method for quantification of colony sizes from plate images. G3 4, 547–552 (2014).

Article  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bischof, L. et al. Spotsizer: high-throughput quantitative analysis of microbial growth. Biotechniques 61, 191–201 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Levin-Reisman, I., Fridman, O. & Balaban, N. Q. ScanLag: high-throughput quantification of colony growth and lag time. J. Vis. Exp 2014, 51456 (2014).

Google Scholar 

Tegally, H., San, J. E., Giandhari, J. & de Oliveira, T. Unlocking the efficiency of genomics laboratories with robotic liquid-handling. BMC Genomics 21, 729 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Lawless, C., Wilkinson, D. J., Young, A., Addinall, S. G. & Lydall, D. A. Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. BMC Bioinformatics 11, 287 (2010).

Article  PubMed  PubMed Central  Google Scholar 

Banks, A. P., Lawless, C. & Lydall, D. A. A quantitative fitness analysis workflow. J. Vis. Exp. 2012, 4018 (2012).

Google Scholar 

Narayanan, S. et al. Quantitative fitness analysis identifies exo1Δ and other suppressors or enhancers of telomere defects in Schizosaccharomyces pombe. PLoS ONE 10, e0132240 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Berman, J. & Krysan, D. J. Drug resistance and tolerance in fungi. Nat. Rev. Microbiol. 18, 319–331 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ksiezopolska, E. et al. Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata. Curr. Biol. 31, 5314–5326 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Daniel, B. & Lawless, C. Modeling competition for nutrients between microbial populations growing on a solid agar surface. Preprint at bioRxiv https://www.biorxiv.org/content/10.1101/086835v1 (2017).