ArticleNucleic acids research2019
BACTOME-a reference database to explore the sequence- and gene expression-variation landscape of Pseudomonas aeruginosa clinical isolates.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- MiaA-mediated tRNA modifications couple tryptophan attenuation and changes in tRNA abundance to complex phenotypes in Pseudomonas aeruginosa.Nucleic acids research · 2026Article
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- Extracellular vesicles released by host epithelial cells during Pseudomonas aeruginosa infection function as homing beacons for neutrophils.Cell communication and signaling : CCS · 2024Article
- tRNA epitranscriptome determines pathogenicity of the opportunistic pathogenProceedings of the National Academy of Sciences of the United States of America · 2024Article
- An expanded CRISPR-Cas9-assisted recombineering toolkit for engineering genetically intractable Pseudomonas aeruginosa isolates.Nature protocols · 2023Review
- Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia.mSystems · 2023Article
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- Repetitive Exposure to Bacteriophage Cocktails againstViruses · 2023Article
- Challenges in using transcriptome data to study the c-di-GMP signaling network inFEMS microbes · 2023Article
- Evolution of Habitat-Dependent Antibiotic Resistance in Pseudomonas aeruginosa.Microbiology spectrum · 2022Article
- Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates.NPJ biofilms and microbiomes · 2022Article
- What Makes Pseudomonas aeruginosa a Pathogen?Advances in experimental medicine and biology · 2022Article
- Effects of the Sex Steroid Hormone Estradiol on Biofilm Growth of Cystic FibrosisFrontiers in cellular and infection microbiology · 2022Article
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- RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection.Nature communications · 2021Article
- Compensatory evolution of Pseudomonas aeruginosa's slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis.Nature communications · 2021Article
- The Genomic Basis of Rapid Adaptation to Antibiotic Combination Therapy in Pseudomonas aeruginosa.Molecular biology and evolution · 2021Article
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11 authors.
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Abstract
Extensive use of next-generation sequencing (NGS) for pathogen profiling has the potential to transform our understanding of how genomic plasticity contributes to phenotypic versatility. However, the storage of large amounts of NGS data and visualization tools need to evolve to offer the scientific community fast and convenient access to these data. We introduce BACTOME as a database system that links aligned DNA- and RNA-sequencing reads of clinical Pseudomonas aeruginosa isolates with clinically relevant pathogen phenotypes. The database allows data extraction for any single isolate, gene or phenotype as well as data filtering and phenotypic grouping for specific research questions. With the integration of statistical tools we illustrate the usefulness of a relational database structure for the identification of phenotype-genotype correlations as an essential part of the discovery pipeline in genomic research. Furthermore, the database provides a compilation of DNA sequences and gene expression values of a plethora of clinical isolates to give a consensus DNA sequence and consensus gene expression signature. Deviations from the consensus thereby describe the genomic landscape and the transcriptional plasticity of the species P. aeruginosa. The database is available at https://bactome.helmholtz-hzi.de.
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