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For: Lin YF, A DR, Guan S, Mamanova L, McDowall KJ. A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease. BMC Genomics 2013;14:620. [PMID: 24034785 PMCID: PMC3848588 DOI: 10.1186/1471-2164-14-620] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 09/11/2013] [Indexed: 01/07/2023]  Open
Number Cited by Other Article(s)
1
Chaignaud P, Gruffaz C, Borreca A, Fouteau S, Kuhn L, Masbou J, Rouy Z, Hammann P, Imfeld G, Roche D, Vuilleumier S. A Methylotrophic Bacterium Growing with the Antidiabetic Drug Metformin as Its Sole Carbon, Nitrogen and Energy Source. Microorganisms 2022;10:2302. [PMID: 36422372 PMCID: PMC9699525 DOI: 10.3390/microorganisms10112302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 08/31/2023]  Open
2
Genome-Wide Transcription Start Sites Mapping in Methylorubrum Grown with Dichloromethane and Methanol. Microorganisms 2022;10:microorganisms10071301. [PMID: 35889020 PMCID: PMC9320726 DOI: 10.3390/microorganisms10071301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023]  Open
3
Tang Y, Wang Y, Wang J, Li M, Peng L, Wei G, Zhang Y, Li J, Gao Z. TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification. BMC Bioinformatics 2020;21:532. [PMID: 33208106 PMCID: PMC7672179 DOI: 10.1186/s12859-020-03869-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/09/2020] [Indexed: 12/30/2022]  Open
4
Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies. Microorganisms 2019;7:microorganisms7050128. [PMID: 31086023 PMCID: PMC6560440 DOI: 10.3390/microorganisms7050128] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/25/2022]  Open
5
Plágaro AH, Pearman PB, Kaberdin VR. Defining the transcription landscape of the Gram-negative marine bacterium Vibrio harveyi. Genomics 2018;111:1547-1556. [PMID: 30423347 DOI: 10.1016/j.ygeno.2018.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/13/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022]
6
Determination of the Genome and Primary Transcriptome of Syngas Fermenting Eubacterium limosum ATCC 8486. Sci Rep 2017;7:13694. [PMID: 29057933 PMCID: PMC5651825 DOI: 10.1038/s41598-017-14123-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/03/2017] [Indexed: 01/05/2023]  Open
7
Hücker SM, Ardern Z, Goldberg T, Schafferhans A, Bernhofer M, Vestergaard G, Nelson CW, Schloter M, Rost B, Scherer S, Neuhaus K. Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome. PLoS One 2017;12:e0184119. [PMID: 28902868 PMCID: PMC5597208 DOI: 10.1371/journal.pone.0184119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/20/2017] [Indexed: 12/29/2022]  Open
8
Grüll MP, Peña-Castillo L, Mulligan ME, Lang AS. Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA. RNA Biol 2017;14:914-925. [PMID: 28296577 PMCID: PMC5546546 DOI: 10.1080/15476286.2017.1306175] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]  Open
9
Kwon HH, Suh DH. Recent progress in the research aboutPropionibacterium acnesstrain diversity and acne: pathogen or bystander? Int J Dermatol 2016;55:1196-1204. [DOI: 10.1111/ijd.13282] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/10/2015] [Accepted: 12/05/2015] [Indexed: 12/25/2022]
10
Sass AM, Van Acker H, Förstner KU, Van Nieuwerburgh F, Deforce D, Vogel J, Coenye T. Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315. BMC Genomics 2015;16:775. [PMID: 26462475 PMCID: PMC4603805 DOI: 10.1186/s12864-015-1993-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/06/2015] [Indexed: 12/20/2022]  Open
11
Bischler T, Tan HS, Nieselt K, Sharma CM. Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori. Methods 2015;86:89-101. [PMID: 26091613 DOI: 10.1016/j.ymeth.2015.06.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 06/07/2015] [Accepted: 06/09/2015] [Indexed: 12/29/2022]  Open
12
Creecy JP, Conway T. Quantitative bacterial transcriptomics with RNA-seq. Curr Opin Microbiol 2014;23:133-40. [PMID: 25483350 DOI: 10.1016/j.mib.2014.11.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 02/06/2023]
13
Clarke JE, Kime L, Romero A D, McDowall KJ. Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli. Nucleic Acids Res 2014;42:11733-51. [PMID: 25237058 PMCID: PMC4191395 DOI: 10.1093/nar/gku808] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 12/20/2022]  Open
14
Romero DA, Hasan AH, Lin YF, Kime L, Ruiz-Larrabeiti O, Urem M, Bucca G, Mamanova L, Laing EE, van Wezel GP, Smith CP, Kaberdin VR, McDowall KJ. A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing. Mol Microbiol 2014;94:963-987. [PMID: 25266672 PMCID: PMC4681348 DOI: 10.1111/mmi.12810] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2014] [Indexed: 12/12/2022]
15
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli. J Bacteriol 2014;197:18-28. [PMID: 25266388 DOI: 10.1128/jb.02096-14] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
16
Sharma CM, Vogel J. Differential RNA-seq: the approach behind and the biological insight gained. Curr Opin Microbiol 2014;19:97-105. [PMID: 25024085 DOI: 10.1016/j.mib.2014.06.010] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 06/15/2014] [Accepted: 06/19/2014] [Indexed: 01/14/2023]
17
Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing. mBio 2014;5:e01442-14. [PMID: 25006232 PMCID: PMC4161252 DOI: 10.1128/mbio.01442-14] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
18
Neshat A, Mentz A, Rückert C, Kalinowski J. Transcriptome sequencing revealed the transcriptional organization at ribosome-mediated attenuation sites in Corynebacterium glutamicum and identified a novel attenuator involved in aromatic amino acid biosynthesis. J Biotechnol 2014;190:55-63. [PMID: 24910972 DOI: 10.1016/j.jbiotec.2014.05.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/02/2014] [Accepted: 05/14/2014] [Indexed: 11/27/2022]
19
Mirauta B, Nicolas P, Richard H. Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models. ACTA ACUST UNITED AC 2014;30:1409-16. [PMID: 24470570 DOI: 10.1093/bioinformatics/btu042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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