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For: Barquist L, Boinett CJ, Cain AK. Approaches to querying bacterial genomes with transposon-insertion sequencing. RNA Biol 2013;10:1161-9. [PMID: 23635712 PMCID: PMC3849164 DOI: 10.4161/rna.24765] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]  Open
Number Cited by Other Article(s)
101
Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii. J Bacteriol 2015;197:2027-35. [PMID: 25845845 DOI: 10.1128/jb.00131-15] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/31/2015] [Indexed: 02/06/2023]  Open
102
Santiago M, Matano LM, Moussa SH, Gilmore MS, Walker S, Meredith TC. A new platform for ultra-high density Staphylococcus aureus transposon libraries. BMC Genomics 2015;16:252. [PMID: 25888466 PMCID: PMC4389836 DOI: 10.1186/s12864-015-1361-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/19/2015] [Indexed: 01/17/2023]  Open
103
High-throughput analysis of gene essentiality and sporulation in Clostridium difficile. mBio 2015;6:e02383. [PMID: 25714712 PMCID: PMC4358009 DOI: 10.1128/mbio.02383-14] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
104
Garcia-Fraile P, Seaman JC, Karunakaran R, Edwards A, Poole PS, Downie JA. Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere. PLANT AND SOIL 2015;390:251-264. [PMID: 26166901 PMCID: PMC4495286 DOI: 10.1007/s11104-015-2389-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/14/2015] [Indexed: 05/29/2023]
105
Klein BA, Duncan MJ, Hu LT. Defining essential genes and identifying virulence factors of Porphyromonas gingivalis by massively parallel sequencing of transposon libraries (Tn-seq). Methods Mol Biol 2015;1279:25-43. [PMID: 25636611 PMCID: PMC4824196 DOI: 10.1007/978-1-4939-2398-4_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
106
Gardner PP, Eldai H. Annotating RNA motifs in sequences and alignments. Nucleic Acids Res 2015;43:691-8. [PMID: 25520192 PMCID: PMC4333381 DOI: 10.1093/nar/gku1327] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 11/30/2014] [Accepted: 12/05/2014] [Indexed: 11/21/2022]  Open
107
Yamaichi Y, Chao MC, Sasabe J, Clark L, Davis BM, Yamamoto N, Mori H, Kurokawa K, Waldor MK. High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4. Nucleic Acids Res 2015;43:348-60. [PMID: 25477379 PMCID: PMC4288162 DOI: 10.1093/nar/gku1262] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/12/2014] [Accepted: 11/17/2014] [Indexed: 12/20/2022]  Open
108
Perry BJ, Yost CK. Construction of a mariner-based transposon vector for use in insertion sequence mutagenesis in selected members of the Rhizobiaceae. BMC Microbiol 2014;14:298. [PMID: 25433486 PMCID: PMC4255674 DOI: 10.1186/s12866-014-0298-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 11/18/2014] [Indexed: 12/11/2022]  Open
109
ARTIST: high-resolution genome-wide assessment of fitness using transposon-insertion sequencing. PLoS Genet 2014;10:e1004782. [PMID: 25375795 PMCID: PMC4222735 DOI: 10.1371/journal.pgen.1004782] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/26/2014] [Indexed: 12/20/2022]  Open
110
Mobegi FM, van Hijum SAFT, Burghout P, Bootsma HJ, de Vries SPW, van der Gaast-de Jongh CE, Simonetti E, Langereis JD, Hermans PWM, de Jonge MI, Zomer A. From microbial gene essentiality to novel antimicrobial drug targets. BMC Genomics 2014;15:958. [PMID: 25373505 PMCID: PMC4233050 DOI: 10.1186/1471-2164-15-958] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 10/23/2014] [Indexed: 01/12/2023]  Open
111
Lindgreen S, Umu SU, Lai ASW, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP. Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Comput Biol 2014;10:e1003907. [PMID: 25357249 PMCID: PMC4214555 DOI: 10.1371/journal.pcbi.1003907] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/11/2014] [Indexed: 02/03/2023]  Open
112
Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis. PLoS Comput Biol 2014;10:e1003848. [PMID: 25233219 PMCID: PMC4168976 DOI: 10.1371/journal.pcbi.1003848] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 08/07/2014] [Indexed: 01/08/2023]  Open
113
Peng C, Gao F. Protein localization analysis of essential genes in prokaryotes. Sci Rep 2014;4:6001. [PMID: 25105358 PMCID: PMC4126397 DOI: 10.1038/srep06001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 07/22/2014] [Indexed: 01/27/2023]  Open
114
Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains. Appl Environ Microbiol 2014;80:6223-42. [PMID: 25085490 DOI: 10.1128/aem.01542-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
115
McAdam PR, Richardson EJ, Fitzgerald JR. High-throughput sequencing for the study of bacterial pathogen biology. Curr Opin Microbiol 2014;19:106-113. [PMID: 25033019 PMCID: PMC4150483 DOI: 10.1016/j.mib.2014.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 06/02/2014] [Accepted: 06/07/2014] [Indexed: 12/23/2022]
116
Rusmini R, Vecchietti D, Macchi R, Vidal-Aroca F, Bertoni G. A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa. BMC Microbiol 2014;14:24. [PMID: 24499134 PMCID: PMC3922391 DOI: 10.1186/1471-2180-14-24] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 01/23/2014] [Indexed: 12/29/2022]  Open
117
Luo H, Lin Y, Gao F, Zhang CT, Zhang R. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res 2013;42:D574-80. [PMID: 24243843 PMCID: PMC3965060 DOI: 10.1093/nar/gkt1131] [Citation(s) in RCA: 401] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
118
Phan MD, Peters KM, Sarkar S, Lukowski SW, Allsopp LP, Moriel DG, Achard MES, Totsika M, Marshall VM, Upton M, Beatson SA, Schembri MA. The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli clone. PLoS Genet 2013;9:e1003834. [PMID: 24098145 PMCID: PMC3789825 DOI: 10.1371/journal.pgen.1003834] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/12/2013] [Indexed: 01/01/2023]  Open
119
Chao MC, Pritchard JR, Zhang YJ, Rubin EJ, Livny J, Davis BM, Waldor MK. High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data. Nucleic Acids Res 2013;41:9033-48. [PMID: 23901011 PMCID: PMC3799429 DOI: 10.1093/nar/gkt654] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
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