{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Rees-Garbutt J"],"funding":["Medical Research Council","Biotechnology and Biological Sciences Research Council","Engineering and Physical Sciences Research Council"],"pagination":["836"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC7012841"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["11(1)"],"pubmed_abstract":["In the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept. Minimal genomes are ideal for this purpose as they have a simple functional assay whether the cell replicates or not. We used the first (and currently only published) whole-cell model for the bacterium Mycoplasma genitalium. Our computational design-simulate-test cycles discovered novel in silico minimal genomes which, if biologically correct, predict in vivo genomes smaller than JCVI-Syn3.0; a bacterium with, currently, the smallest genome that can be grown"],"journal":["Nature communications"],"pubmed_title":["Designing minimal genomes using whole-cell models."],"pmcid":["PMC7012841"],"funding_grant_id":["MR/N021444/1","BB/L01386X/1","EP/R041695/1","1793989"],"pubmed_authors":["Grierson C","Chalkley O","Rees-Garbutt J","Marucci L","Purcell O","Landon S"],"additional_accession":[]},"is_claimable":false,"name":"Designing minimal genomes using whole-cell models.","description":"In the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept. Minimal genomes are ideal for this purpose as they have a simple functional assay whether the cell replicates or not. We used the first (and currently only published) whole-cell model for the bacterium Mycoplasma genitalium. Our computational design-simulate-test cycles discovered novel in silico minimal genomes which, if biologically correct, predict in vivo genomes smaller than JCVI-Syn3.0; a bacterium with, currently, the smallest genome that can be grown","dates":{"release":"2020-01-01T00:00:00Z","publication":"2020 Feb","modification":"2025-05-29T22:01:15.02Z","creation":"2025-05-29T22:01:15.02Z"},"accession":"S-EPMC7012841","cross_references":{"pubmed":["32047145"],"doi":["10.1038/s41467-020-14545-0"]}}