ArticleNature microbiology2017
A tool named Iris for versatile high-throughput phenotyping in microorganisms.
Article in Nature microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Article
- A Type VII-secreted toxin enables inter-mycobacterial competition.Nature communications · 2026Article
- Synergistic activity of rifampicin and polymyxin B against intracellular Gram-negative ESKAPE pathogens involves bacterial membrane alterations and enhanced oxidative damages.Antimicrobial agents and chemotherapy · 2026Article
- ChemGenXplore: an interactive tool for exploring and analysing chemical genomic data.Bioinformatics (Oxford, England) · 2026Article
- Simple large-scale quantitative phenotyping and antimicrobial susceptibility testing with Q-PHAST.Nature protocols · 2026Review
- High-throughput chemical genomic screening: a step-by-step workflow from plate to phenotype.mSystems · 2025Article
- AlphaDesign: a de novo protein design framework based on AlphaFold.Molecular systems biology · 2025Article
- Antimicrobial efficacy of chlorhexidine-treated surfaces against clinical isolates implicated in nosocomial infections.Journal of medical microbiology · 2025Article
- Uncovering nitroxoline activity spectrum, mode of action and resistance across Gram-negative bacteria.Nature communications · 2025Article
- Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics.Nature microbiology · 2025Article
- TAC-TIC, a high-throughput genetics method to identify triggers or blockers of bacterial toxin-antitoxin systems.Nature protocols · 2024Review
- Systematic Evaluation of Biotic and Abiotic Factors in Antifungal Microorganism Screening.Microorganisms · 2024Article
- Article
- Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations.Communications biology · 2024Article
- High-throughput functional genomics: A (myco)bacterial perspective.Molecular microbiology · 2023Review
- Review
- Epistasis decreases with increasing antibiotic pressure but not temperature.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Article
- ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling.Bioinformatics (Oxford, England) · 2023Article
- A Deep Learning Approach to Capture the Essence of Candida albicans Morphologies.Microbiology spectrum · 2022Article
- Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advances in our ability to systematically introduce and track controlled genetic variance in microorganisms have, in the past decade, fuelled high-throughput reverse genetics approaches. When coupled to quantitative readouts, such approaches are extremely powerful at elucidating gene function and providing insights into the underlying pathways and the overall cellular network organization. Yet, until now, all efforts to quantify microbial macroscopic phenotypes have been restricted to monitoring growth in a small number of model microorganisms. We have developed an image analysis software named Iris, which allows for systematic exploration of a number of orthogonal-to-growth processes, including biofilm formation, colony morphogenesis, envelope biogenesis, sporulation and reporter activity. In addition, Iris provides more sensitive growth measurements than currently available software and is compatible with a variety of different microorganisms, as well as with endpoint or kinetic data. We used Iris to reanalyse existing chemical genomics data in Escherichia coli and to perform proof-of-principle screens on colony biofilm formation and morphogenesis of different bacterial species and the pathogenic fungus Candida albicans. We thereby recapitulated existing knowledge but also identified a plethora of additional genes and pathways involved in both processes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.