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RESOURCE: Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: A tool for identifying differentially regulated genes
- Shawn Lewenza,
- Reza K. Falsafi,
- Geoff Winsor,
- W. James Gooderham,
- Joseph B. McPhee,
- Fiona S.L. Brinkman,
- and Robert E.W. Hancock
Genome Res. April 2005 15: 583-589; doi:10.1101/gr.3513905
.... 2000 . Complete sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406 : 959 -964. ↵ Weinel, C., Ermolaeva, M.D., and Ouzounis, C. 2003 . PseuRECA: Genome annotation and gene context analysis for Pseudomonas aeruginosa PAO1. Bioinformatics 19 : 1457 -1460. ↵ Weissenmayer, B...
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COMMENTARY: Community annotation: Procedures, protocols, and supporting tools
- Christine G. Elsik,
- Kim C. Worley,
- Lan Zhang,
- Natalia V. Milshina,
- Huaiyang Jiang,
- Justin T. Reese,
- Kevin L. Childs,
- Anand Venkatraman,
- C. Michael Dickens,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. November 2006 16: 1329-1333; Published in Advance October 25, 2006, doi:10.1101/gr.5580606
...for an annotation submission was either a protein sequence or, in the case of functional annotation without modifying a gene model, a homolog description. Annotation Web site and database Annotation was supported by a database to store and collect gene coordinates, descriptions, and annotator information, as well...
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LETTER: Comparative Genome Analysis of Vibrio vulnificus, a Marine Pathogen
- Chung-Yung Chen,
- Keh-Ming Wu,
- Yo-Cheng Chang,
- Chuan-Hsiung Chang,
- Hui-Chi Tsai,
- Tsai-Lien Liao,
- Yen-Ming Liu,
- Hsiang-Ju Chen,
- Arthur Bo-Ting Shen,
- Jian-Chiuan Li,
- Teh-Li Su,
- Chung-Ping Shao,
- Chung-Te Lee,
- Lien-I Hor,
- and Shih-Feng Tsai
Genome Res. December 2003 13: 2577-2587; doi:10.1101/gr.1295503
...sequences (VV1754, VV1786)of V. vulnificus YJ016 showed significant homology to that of the Streptococcus pneumoniae R6, Streptococcus pneumonia TIGR4, and P. aeruginosa PA01 ( Fig. 3A ). On the other hand, two types of sequences were found for the four PAS factor genes ( Tokugawa et al. 1994 ; VV1767, VV...
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REVIEW: Many Paths to Many Clones: A Comparative Look at High-Throughput Cloning Methods
- Gerald Marsischky and
- Joshua LaBaer
Genome Res. October 15, 2004 14: 2020-2028; doi:10.1101/gr.2528804
...In-Fusion/Creator cloning systems extensively. HIP has created over 13,000 master clones in Gateway and 5000 in the Creator cloning system representing genes from human, S. cerevisiae , and Pseudomonas aeruginosa ( Brizuela et al. 2002 ; LaBaer and Marsischky 2004 ; LaBaer et al. 2004 ). All...
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RESOURCE: Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae
- Yanhui Hu,
- Andreas Rolfs,
- Bhupinder Bhullar,
- Tellamraju V. S. Murthy,
- Cong Zhu,
- Michael F. Berger,
- Anamaria A. Camargo,
- Fontina Kelley,
- Seamus McCarron,
- Daniel Jepson,
- Aaron Richardson,
- Jacob Raphael,
- Donna Moreira,
- Elena Taycher,
- Dongmei Zuo,
- Stephanie Mohr,
- Michael F. Kane,
- Janice Williamson,
- Andrew Simpson,
- Martha L. Bulyk,
- Edward Harlow,
- Gerald Marsischky,
- Richard D. Kolodner,
- and Joshua LaBaer
Genome Res. April 2007 17: 536-543; Published in Advance February 23, 2007, doi:10.1101/gr.6037607
.... , Mar, W. , Zuo, D. , Murthy, T.V. , Taycher, H. , Halleck, A. , Hainsworth, E. , Lory, S. , et al. ( 2004 ) The Pseudomonas aeruginosa PA01 gene collection . Genome Res. 14 : 2190 – 2200 . ↵ Lee, T. , Rinaldi, N. , Robert, R. , Odom, D. , Bar-Joseph, Z. , Gerber, G. , Hannett, N. , Harbison, C...
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ARTICLE: A Complete Sequence of the T. tengcongensis Genome
- Qiyu Bao,
- Yuqing Tian,
- Wei Li,
- Zuyuan Xu,
- Zhenyu Xuan,
- Songnian Hu,
- Wei Dong,
- Jian Yang,
- Yanjiong Chen,
- Yanfen Xue,
- Yi Xu,
- Xiaoqin Lai,
- Li Huang,
- Xiuzhu Dong,
- Yanhe Ma,
- Lunjiang Ling,
- Huarong Tan,
- Runsheng Chen,
- Jian Wang,
- Jun Yu,
- and Huanming Yang
Genome Res. May 1, 2002 12: 689-700; doi:10.1101/gr.219302
...of the sequenced bacterial s have rhodanese-related sulfurtransferases, the two ACR genes are detectable only in a few other bacterial s, including Methanobacterium thermoautotrophicum ( Smith et al. 1997 ), T. maritime ( Nelson et al. 1999 ), E. coli ( Blattner et al. 1997 ), Pseudomonas aeruginosa ( Stover et al...
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LETTER: Universal patterns of purifying selection at noncoding positions in bacteria
- Nacho Molina and
- Erik van Nimwegen
Genome Res. January 2008 18: 148-160; Published in Advance November 21, 2007, doi:10.1101/gr.6759507
...and found several striking universal patterns. Consistent with selection acting at transcriptional regulatory elements near the transcription start, we find a universal positional profile of selection with respect to gene starts and ends, showing most evidence of selection immediately upstream and least...
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LETTER: Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation
- Pooja Rawal,
- Veera Bhadra Rao Kummarasetti,
- Jinoy Ravindran,
- Nirmal Kumar,
- Kangkan Halder,
- Rakesh Sharma,
- Mitali Mukerji,
- Swapan Kumar Das,
- and Shantanu Chowdhury
Genome Res. May 2006 16: 644-655; doi:10.1101/gr.4508806
...) across 18 prokaryotes show enrichment of G4 motifs in regulatory regions and indicate its predominance within promoters of genes pertaining to transcription, secondary metabolite biosynthesis, and signal transduction. Based on this, we predict that G4 DNA may present regulatory signals. This is supported...
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Methods: Concerted Assembly and Cloning of Multiple DNA Segments Using In Vitro Site-Specific Recombination: Functional Analysis of Multi-Segment Expression Clones
- David L. Cheo,
- Steven A. Titus,
- Devon R.N. Byrd,
- James L. Hartley,
- Gary F. Temple,
- and Michael A. Brasch
Genome Res. October 15, 2004 14: 2111-2120; doi:10.1101/gr.2512204
...-Genoscope ( Castelli et al. 2004 ). Repositories of full-length clones, some of which are in the Gateway format, are available for Xenopus ( http://xgc.nci.nih.gov/ ), zebrafish ( http://zgc.nci.nih.gov/ ), as well as many human, mouse, and rat genes ( http://mgc.nci.nih.gov/ ). Subsets of these collections have been...

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