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Li","year":"2006","journal-title":"Bioinformatics"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"D447","DOI":"10.1093\/nar\/gkv1145","article-title":"2016 update of the PRIDE database and its related tools","volume":"44","author":"JA Vizca\u00edno","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.jmb.2011.01.030","article-title":"Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering","volume":"407","author":"JA Sawitzke","year":"2011","journal-title":"J Mol Biol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"2702","DOI":"10.1111\/j.1462-2920.2011.02538.x","article-title":"Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440","volume":"13","author":"E Mart\u00ednez\u2010Garc\u00eda","year":"2011","journal-title":"Environ Microbiol"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"6640","DOI":"10.1073\/pnas.120163297","article-title":"One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products","volume":"97","author":"KA Datsenko","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.1111\/j.1365-2958.2011.07657.x","article-title":"Activation of cryptic aminoglycoside resistance in Salmonella enterica","volume":"80","author":"S Koskiniemi","year":"2011","journal-title":"Mol Microbiol"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/BF00270447","article-title":"Phage P22-mutants with increased or decreased transduction abilities","volume":"119","author":"H. 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