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For: DeJesus MA, Zhang YJ, Sassetti CM, Rubin EJ, Sacchettini JC, Ioerger TR. Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. ACTA ACUST UNITED AC 2013;29:695-703. [PMID: 23361328 DOI: 10.1093/bioinformatics/btt043] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Number Cited by Other Article(s)
1
Zhang P, Zhang B, Ji Y, Jiao J, Zhang Z, Tian C. Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome. MLIFE 2024;3:277-290. [PMID: 38948139 PMCID: PMC11211677 DOI: 10.1002/mlf2.12132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/20/2024] [Accepted: 04/24/2024] [Indexed: 07/02/2024]
2
Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy MK, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Eren AM, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. mBio 2024;15:e0283023. [PMID: 38063424 PMCID: PMC10790697 DOI: 10.1128/mbio.02830-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 12/19/2023]  Open
3
Hamami E, Huo W, Neal K, Neisewander I, Geisinger E, Isberg RR. Identification of essential genes that support fitness of Acinetobacter baumannii efflux pump overproducers in the presence of fluoroquinolone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574119. [PMID: 38260615 PMCID: PMC10802289 DOI: 10.1101/2024.01.04.574119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
4
Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024;31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
5
Sharma G, Zee PC, Zea L, Curtis PD. Whole genome-scale assessment of gene fitness of Novosphingobium aromaticavorans during spaceflight. BMC Genomics 2023;24:782. [PMID: 38102595 PMCID: PMC10725011 DOI: 10.1186/s12864-023-09799-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023]  Open
6
Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy M, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Murat Eren A, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540287. [PMID: 37214927 PMCID: PMC10197588 DOI: 10.1101/2023.05.11.540287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
7
Matern WM, Harris HT, Danchik C, McDonald M, Patel G, Srivastava A, Ioerger TR, Bader JS, Karakousis PC. Functional Whole Genome Screen of Nutrient-Starved Mycobacterium tuberculosis Identifies Genes Involved in Rifampin Tolerance. Microorganisms 2023;11:2269. [PMID: 37764112 PMCID: PMC10534295 DOI: 10.3390/microorganisms11092269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023]  Open
8
Matern WM, Harris HT, Danchik C, McDonald M, Patel G, Srivastava A, Ioerger TR, Bader JS, Karakousis PC. Functional whole genome screen of nutrient-starved Mycobacterium tuberculosis identifies genes involved in antibiotic tolerance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536593. [PMID: 37090629 PMCID: PMC10120713 DOI: 10.1101/2023.04.12.536593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
9
Harten T, Nimzyk R, Gawlick VEA, Reinhold-Hurek B. Elucidation of Essential Genes and Mutant Fitness during Adaptation toward Nitrogen Fixation Conditions in the Endophyte Azoarcus olearius BH72 Revealed by Tn-Seq. Microbiol Spectr 2022;10:e0216222. [PMID: 36416558 PMCID: PMC9769520 DOI: 10.1128/spectrum.02162-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/05/2022] [Indexed: 11/24/2022]  Open
10
Bythrow GV, Farhat MF, Levendosky K, Mohandas P, Germain GA, Yoo B, Quadri LEN. Mycobacterium abscessus Mutants with a Compromised Functional Link between the Type VII ESX-3 System and an Iron Uptake Mechanism Reliant on an Unusual Mycobactin Siderophore. Pathogens 2022;11:pathogens11090953. [PMID: 36145386 PMCID: PMC9505556 DOI: 10.3390/pathogens11090953] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/28/2022]  Open
11
Sarsani V, Aldikacti B, He S, Zeinert R, Chien P, Flaherty P. Model-based identification of conditionally-essential genes from transposon-insertion sequencing data. PLoS Comput Biol 2022;18:e1009273. [PMID: 35255084 PMCID: PMC8929702 DOI: 10.1371/journal.pcbi.1009273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 03/17/2022] [Accepted: 02/09/2022] [Indexed: 12/13/2022]  Open
12
Rahman ASMZ, Timmerman L, Gallardo F, Cardona ST. Identification of putative essential protein domains from high-density transposon insertion sequencing. Sci Rep 2022;12:962. [PMID: 35046497 PMCID: PMC8770471 DOI: 10.1038/s41598-022-05028-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/29/2021] [Indexed: 12/24/2022]  Open
13
Ioerger TR. Analysis of Gene Essentiality from TnSeq Data Using Transit. Methods Mol Biol 2022;2377:391-421. [PMID: 34709629 PMCID: PMC8941984 DOI: 10.1007/978-1-0716-1720-5_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
14
Li Y, Jiang B, Dai W. A large-scale whole-genome sequencing analysis reveals false positives of bacterial essential genes. Appl Microbiol Biotechnol 2021;106:341-347. [PMID: 34889987 DOI: 10.1007/s00253-021-11702-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 11/26/2022]
15
Immanuel SRC, Arrieta-Ortiz ML, Ruiz RA, Pan M, Lopez Garcia de Lomana A, Peterson EJR, Baliga NS. Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME. NPJ Syst Biol Appl 2021;7:43. [PMID: 34873198 PMCID: PMC8648758 DOI: 10.1038/s41540-021-00205-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 11/02/2021] [Indexed: 12/04/2022]  Open
16
Choudhery S, Brown AJ, Akusobi C, Rubin EJ, Sassetti CM, Ioerger TR. Modeling Site-Specific Nucleotide Biases Affecting Himar1 Transposon Insertion Frequencies in TnSeq Data Sets. mSystems 2021;6:e0087621. [PMID: 34665010 PMCID: PMC8525568 DOI: 10.1128/msystems.00876-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/27/2021] [Indexed: 11/20/2022]  Open
17
3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme. Commun Biol 2021;4:684. [PMID: 34083757 PMCID: PMC8175468 DOI: 10.1038/s42003-021-02222-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/14/2021] [Indexed: 11/16/2022]  Open
18
De novo histidine biosynthesis protects Mycobacterium tuberculosis from host IFN-γ mediated histidine starvation. Commun Biol 2021;4:410. [PMID: 33767335 PMCID: PMC7994828 DOI: 10.1038/s42003-021-01926-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023]  Open
19
Le Breton Y, Belew AT, McIver KS. Protocols for Tn-seq Analyses in the Group A Streptococcus. Methods Mol Biol 2021;2136:33-57. [PMID: 32430812 DOI: 10.1007/978-1-0716-0467-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
20
Dammann AN, Chamby AB, Catomeris AJ, Davidson KM, Tettelin H, van Pijkeren JP, Gopalakrishna KP, Keith MF, Elder JL, Ratner AJ, Hooven TA. Genome-Wide fitness analysis of group B Streptococcus in human amniotic fluid reveals a transcription factor that controls multiple virulence traits. PLoS Pathog 2021;17:e1009116. [PMID: 33684178 PMCID: PMC7971860 DOI: 10.1371/journal.ppat.1009116] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/18/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]  Open
21
Transposon Insertion Sequencing in a Clinical Isolate of Legionella pneumophila Identifies Essential Genes and Determinants of Natural Transformation. J Bacteriol 2021;203:JB.00548-20. [PMID: 33168636 PMCID: PMC7811196 DOI: 10.1128/jb.00548-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/04/2020] [Indexed: 02/07/2023]  Open
22
Identification of Zinc-Dependent Mechanisms Used by Group B Streptococcus To Overcome Calprotectin-Mediated Stress. mBio 2020;11:mBio.02302-20. [PMID: 33173000 PMCID: PMC7667036 DOI: 10.1128/mbio.02302-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
23
Miravet-Verde S, Burgos R, Delgado J, Lluch-Senar M, Serrano L. FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies. Nucleic Acids Res 2020;48:e102. [PMID: 32813015 PMCID: PMC7515713 DOI: 10.1093/nar/gkaa679] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/28/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022]  Open
24
López-Agudelo VA, Mendum TA, Laing E, Wu H, Baena A, Barrera LF, Beste DJV, Rios-Estepa R. A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks. PLoS Comput Biol 2020;16:e1007533. [PMID: 32542021 PMCID: PMC7316355 DOI: 10.1371/journal.pcbi.1007533] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 06/25/2020] [Accepted: 05/08/2020] [Indexed: 01/06/2023]  Open
25
Selection or drift: The population biology underlying transposon insertion sequencing experiments. Comput Struct Biotechnol J 2020;18:791-804. [PMID: 32280434 PMCID: PMC7138912 DOI: 10.1016/j.csbj.2020.03.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/06/2020] [Accepted: 03/22/2020] [Indexed: 01/23/2023]  Open
26
Budell WC, Germain GA, Janisch N, McKie-Krisberg Z, Jayaprakash AD, Resnick AE, Quadri LEN. Transposon mutagenesis in Mycobacterium kansasii links a small RNA gene to colony morphology and biofilm formation and identifies 9,885 intragenic insertions that do not compromise colony outgrowth. Microbiologyopen 2020;9:e988. [PMID: 32083796 PMCID: PMC7142372 DOI: 10.1002/mbo3.988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/05/2023]  Open
27
Riggs-Shute SD, Falkinham JO, Yang Z. Construction and Use of Transposon MycoTetOP 2 for Isolation of Conditional Mycobacteria Mutants. Front Microbiol 2020;10:3091. [PMID: 32038540 PMCID: PMC6985430 DOI: 10.3389/fmicb.2019.03091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/20/2019] [Indexed: 11/13/2022]  Open
28
Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression. BMC Bioinformatics 2019;20:603. [PMID: 31752678 PMCID: PMC6873424 DOI: 10.1186/s12859-019-3156-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022]  Open
29
Lipowska J, Miks CD, Kwon K, Shuvalova L, Zheng H, Lewiński K, Cooper DR, Shabalin IG, Minor W. Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae. Int J Biol Macromol 2019;136:1176-1187. [PMID: 31207330 PMCID: PMC6686667 DOI: 10.1016/j.ijbiomac.2019.05.149] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/01/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023]
30
Borgers K, Vandewalle K, Festjens N, Callewaert N. A guide to Mycobacterium mutagenesis. FEBS J 2019;286:3757-3774. [PMID: 31419030 DOI: 10.1111/febs.15041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/05/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
31
Minato Y, Gohl DM, Thiede JM, Chacón JM, Harcombe WR, Maruyama F, Baughn AD. Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways. mSystems 2019;4:e00070-19. [PMID: 31239393 PMCID: PMC6593218 DOI: 10.1128/msystems.00070-19] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/07/2019] [Indexed: 11/30/2022]  Open
32
Cardenal-Muñoz E, Barisch C, Lefrançois LH, López-Jiménez AT, Soldati T. When Dicty Met Myco, a (Not So) Romantic Story about One Amoeba and Its Intracellular Pathogen. Front Cell Infect Microbiol 2018;7:529. [PMID: 29376033 PMCID: PMC5767268 DOI: 10.3389/fcimb.2017.00529] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/18/2017] [Indexed: 01/06/2023]  Open
33
Peng C, Lin Y, Luo H, Gao F. A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes. Front Microbiol 2017;8:2331. [PMID: 29230204 PMCID: PMC5711816 DOI: 10.3389/fmicb.2017.02331] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022]  Open
34
Ruiz L, Bottacini F, Boinett CJ, Cain AK, O'Connell-Motherway M, Lawley TD, van Sinderen D. The essential genomic landscape of the commensal Bifidobacterium breve UCC2003. Sci Rep 2017;7:5648. [PMID: 28717159 PMCID: PMC5514069 DOI: 10.1038/s41598-017-05795-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/02/2017] [Indexed: 01/15/2023]  Open
35
Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides. mSystems 2017;2:mSystems00015-17. [PMID: 28744485 PMCID: PMC5513736 DOI: 10.1128/msystems.00015-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/16/2017] [Indexed: 12/14/2022]  Open
36
Hudock TA, Foreman TW, Bandyopadhyay N, Gautam US, Veatch AV, LoBato DN, Gentry KM, Golden NA, Cavigli A, Mueller M, Hwang SA, Hunter RL, Alvarez X, Lackner AA, Bader JS, Mehra S, Kaushal D. Hypoxia Sensing and Persistence Genes Are Expressed during the Intragranulomatous Survival of Mycobacterium tuberculosis. Am J Respir Cell Mol Biol 2017;56:637-647. [PMID: 28135421 PMCID: PMC5449490 DOI: 10.1165/rcmb.2016-0239oc] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/13/2016] [Indexed: 12/22/2022]  Open
37
Majumdar G, Mbau R, Singh V, Warner DF, Dragset MS, Mukherjee R. Genome-Wide Transposon Mutagenesis in Mycobacterium tuberculosis and Mycobacterium smegmatis. Methods Mol Biol 2017;1498:321-335. [PMID: 27709585 DOI: 10.1007/978-1-4939-6472-7_21] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
38
van Wyk N, Drancourt M, Henrissat B, Kremer L. Current perspectives on the families of glycoside hydrolases ofMycobacterium tuberculosis: their importance and prospects for assigning function to unknowns. Glycobiology 2016;27:112-122. [DOI: 10.1093/glycob/cww099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 08/28/2016] [Accepted: 09/26/2016] [Indexed: 11/14/2022]  Open
39
Hooven TA, Catomeris AJ, Akabas LH, Randis TM, Maskell DJ, Peters SE, Ott S, Santana-Cruz I, Tallon LJ, Tettelin H, Ratner AJ. The essential genome of Streptococcus agalactiae. BMC Genomics 2016;17:406. [PMID: 27229469 PMCID: PMC4881062 DOI: 10.1186/s12864-016-2741-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/14/2016] [Indexed: 12/22/2022]  Open
40
Chao MC, Abel S, Davis BM, Waldor MK. The design and analysis of transposon insertion sequencing experiments. Nat Rev Microbiol 2016;14:119-28. [PMID: 26775926 DOI: 10.1038/nrmicro.2015.7] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Wivagg CN, Wellington S, Gomez JE, Hung DT. Loss of a Class A Penicillin-Binding Protein Alters β-Lactam Susceptibilities in Mycobacterium tuberculosis. ACS Infect Dis 2016;2:104-10. [PMID: 27624961 DOI: 10.1021/acsinfecdis.5b00119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Glutamate Dehydrogenase Is Required by Mycobacterium bovis BCG for Resistance to Cellular Stress. PLoS One 2016;11:e0147706. [PMID: 26824899 PMCID: PMC4732601 DOI: 10.1371/journal.pone.0147706] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/07/2016] [Indexed: 11/19/2022]  Open
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DeJesus MA, Ioerger TR. Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes. J Bioinform Comput Biol 2016;14:1642004. [PMID: 26932272 DOI: 10.1142/s021972001642004x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Lunardi J, Borges Martinelli LK, Raupp AS, Sacconi Nunes JE, Rostirolla DC, Saraiva Macedo Timmers LF, Villela AD, Pissinate K, Limberger J, Norberto de Souza O, Basso LA, Santos DS, Machado P. Mycobacterium tuberculosis histidinol dehydrogenase: biochemical characterization and inhibition studies. RSC Adv 2016. [DOI: 10.1039/c6ra03020c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
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DeJesus MA, Ambadipudi C, Baker R, Sassetti C, Ioerger TR. TRANSIT--A Software Tool for Himar1 TnSeq Analysis. PLoS Comput Biol 2015;11:e1004401. [PMID: 26447887 PMCID: PMC4598096 DOI: 10.1371/journal.pcbi.1004401] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/10/2015] [Indexed: 02/07/2023]  Open
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van der Beek SL, Le Breton Y, Ferenbach AT, Chapman RN, van Aalten DMF, Navratilova I, Boons GJ, McIver KS, van Sorge NM, Dorfmueller HC. GacA is essential for Group A Streptococcus and defines a new class of monomeric dTDP-4-dehydrorhamnose reductases (RmlD). Mol Microbiol 2015;98:946-62. [PMID: 26278404 PMCID: PMC4832382 DOI: 10.1111/mmi.13169] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2015] [Indexed: 12/29/2022]
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Neglected Tropical Diseases in the Post-Genomic Era. Trends Genet 2015;31:539-555. [DOI: 10.1016/j.tig.2015.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/01/2015] [Accepted: 06/03/2015] [Indexed: 01/22/2023]
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Acetate Dissimilation and Assimilation in Mycobacterium tuberculosis Depend on Carbon Availability. J Bacteriol 2015. [PMID: 26216844 DOI: 10.1128/jb.00259-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
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Le Breton Y, Belew AT, Valdes KM, Islam E, Curry P, Tettelin H, Shirtliff ME, El-Sayed NM, McIver KS. Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes. Sci Rep 2015;5:9838. [PMID: 25996237 PMCID: PMC4440532 DOI: 10.1038/srep09838] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/23/2015] [Indexed: 02/01/2023]  Open
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Characterization of genome-wide ordered sequence-tagged Mycobacterium mutant libraries by Cartesian Pooling-Coordinate Sequencing. Nat Commun 2015;6:7106. [PMID: 25960123 PMCID: PMC4432585 DOI: 10.1038/ncomms8106] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/07/2015] [Indexed: 02/02/2023]  Open
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