Publications
Selected publications
- Multi-omics Study of <i>Planobispora rosea</i>, Producer of the Thiopeptide Antibiotic GE2270A (Journal article - 2021)
- Biotechnological application of Streptomyces for the production of clinical drugs and other bioactive molecules. (Journal article - 2022)
- Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships (Journal article - 2019)
- Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters (Journal article - 2019)
- ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0-an improved Bayesian-based method for the annotation of LC-MS/MS untargeted metabolomics data (Journal article - 2023)
2024
An adaptable <i>in silico</i> ensemble model of the arachidonic acid cascade.
Uttley, M., Horne, G., Tsigkinopoulou, A., Del Carratore, F., Hawari, A., Kiezel-Tsugunova, M., . . . Nicolaou, A. (2024). An adaptable <i>in silico</i> ensemble model of the arachidonic acid cascade.. Molecular omics, 20(7), 453-468. doi:10.1039/d3mo00187c
2023
ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0-an improved Bayesian-based method for the annotation of LC-MS/MS untargeted metabolomics data
Del Carratore, F., Eagles, W., Borka, J., & Breitling, R. (2023). ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0-an improved Bayesian-based method for the annotation of LC-MS/MS untargeted metabolomics data. BIOINFORMATICS, 39(7). doi:10.1093/bioinformatics/btad455
2022
Biotechnological application of Streptomyces for the production of clinical drugs and other bioactive molecules.
Del Carratore, F., Hanko, E. K., Breitling, R., & Takano, E. (2022). Biotechnological application of Streptomyces for the production of clinical drugs and other bioactive molecules.. Current opinion in biotechnology, 77, 102762. doi:10.1016/j.copbio.2022.102762
Reference-Grade Genome and Large Linear Plasmid of <i>Streptomyces rimosus</i>: Pushing the Limits of Nanopore Sequencing
Slemc, L., Jakse, J., Filisetti, A., Baranasic, D., Rodriguez-Garcia, A., Del Carratore, F., . . . Tome, M. (2022). Reference-Grade Genome and Large Linear Plasmid of <i>Streptomyces rimosus</i>: Pushing the Limits of Nanopore Sequencing. MICROBIOLOGY SPECTRUM, 10(2). doi:10.1128/spectrum.02434-21
2021
Multi-omics Study of <i>Planobispora rosea</i>, Producer of the Thiopeptide Antibiotic GE2270A
Del Carratore, F., Iorio, M., Perez-Bonilla, M., Schmidt, K., Perez-Redondo, R., Sosio, M., . . . Takano, E. (2021). Multi-omics Study of <i>Planobispora rosea</i>, Producer of the Thiopeptide Antibiotic GE2270A. MSYSTEMS, 6(3). doi:10.1128/mSystems.00341-21
Synthetic biology approaches to actinomycete strain improvement
Breitling, R., Avbelj, M., Bilyk, O., Del Carratore, F., Filisetti, A., Hanko, E. K. R., . . . Takano, E. (2021). Synthetic biology approaches to actinomycete strain improvement. FEMS MICROBIOLOGY LETTERS, 368(10). doi:10.1093/femsle/fnab060
2020
Multi-Omics Analysis of the Effect of cAMP on Actinorhodin Production in <i>Streptomyces coelicolor</i>
Nitta, K., Del Carratore, F., Breitling, R., Takano, E., Putri, S. P., & Fukusaki, E. (2020). Multi-Omics Analysis of the Effect of cAMP on Actinorhodin Production in <i>Streptomyces coelicolor</i>. FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, 8. doi:10.3389/fbioe.2020.595552
2019
Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters
Del Carratore, F., Zych, K., Cummings, M., Takano, E., Medema, M. H., & Breitling, R. (2019). Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters. COMMUNICATIONS BIOLOGY, 2. doi:10.1038/s42003-019-0333-6
Dynamics of the human skin mediator lipidome in response to dietary ω-3 fatty acid supplementation
Kendall, A. C., Pilkington, S. M., Murphy, S. A., Del Carratore, F., Sunarwidhi, A. L., Kiezel-Tsugunova, M., . . . Nicolaou, A. (2019). Dynamics of the human skin mediator lipidome in response to dietary ω-3 fatty acid supplementation. FASEB JOURNAL, 33(11), 13014-13027. doi:10.1096/fj.201901501R
Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships
Del Carratore, F., Schmidt, K., Vinaixa, M., Hollywood, K. A., Greenland-Bews, C., Takano, E., . . . Breitling, R. (2019). Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships. ANALYTICAL CHEMISTRY, 91(20), 12799-12807. doi:10.1021/acs.analchem.9b02354
The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters
Blin, K., Andreu, V. P., de los Santos, E. L. C., Del Carratore, F., Lee, S. Y., Medema, M. H., & Weber, T. (2019). The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters. NUCLEIC ACIDS RESEARCH, 47(D1), D625-D630. doi:10.1093/nar/gky1060
2018
Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery
Pena, A., Del Carratore, F., Cummings, M., Takano, E., & Breitling, R. (2018). Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, 45(7), 615-619. doi:10.1007/s10295-017-1993-1
Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins
Morra, R., Del Carratore, F., Muhamadali, H., Horga, L. G., Halliwell, S., Goodacre, R., . . . Dixon, N. (2018). Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins. MBIO, 9(1). doi:10.1128/mBio.02118-17
2017
<SUP>1</SUP>H NMR spectroscopy-based metabolomics analysis for the diagnosis of symptomatic <i>E</i>. <i>coli</i>-associated urinary tract infection (UTI)
Lussu, M., Camboni, T., Piras, C., Serra, C., Del Carratore, F., Griffin, J., . . . Manzin, A. (2017). <SUP>1</SUP>H NMR spectroscopy-based metabolomics analysis for the diagnosis of symptomatic <i>E</i>. <i>coli</i>-associated urinary tract infection (UTI). BMC MICROBIOLOGY, 17. doi:10.1186/s12866-017-1108-1
Metabolomics As a Tool for the Characterization of Drug-Resistant Epilepsy
Murgia, F., Muroni, A., Puligheddu, M., Polizzi, L., Barberini, L., Orofino, G., . . . Marrosu, F. (2017). Metabolomics As a Tool for the Characterization of Drug-Resistant Epilepsy. FRONTIERS IN NEUROLOGY, 8. doi:10.3389/fneur.2017.00459
RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets
Del Carratore, F., Jankevics, A., Eisinga, R., Heskes, T., Hong, F., & Breitling, R. (2017). RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets. BIOINFORMATICS, 33(17), 2774-2775. doi:10.1093/bioinformatics/btx292
2016
Statistical Health Monitoring Applied to a Metabolomic Study of Experimental Hepatocarcinogenesis: An Alternative Approach to Supervised Methods for the Identification of False Positives
Del Carratore, F., Lussu, M., Kowalik, M. A., Perra, A., Griffin, J. L., Atzori, L., & Grosso, M. (2016). Statistical Health Monitoring Applied to a Metabolomic Study of Experimental Hepatocarcinogenesis: An Alternative Approach to Supervised Methods for the Identification of False Positives. ANALYTICAL CHEMISTRY, 88(16), 7921-7929. doi:10.1021/acs.analchem.5b03078
<SUP>1</SUP>H-NMR analysis provides a metabolomic profile of patients with multiple sclerosis
Cocco, E., Murgia, F., Lorefice, L., Barberini, L., Poddighe, S., Frau, J., . . . Marrosu, M. G. (2016). <SUP>1</SUP>H-NMR analysis provides a metabolomic profile of patients with multiple sclerosis. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION, 3(1). doi:10.1212/NXI.0000000000000185