Elizabeth Skippington: Difference between revisions
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= Literature = | = Literature = | ||
==LGT== | ==LGT== | ||
Jain R, Rivera MC, Lake JA: '''Horizontal gene transfer among genomes: the complexity hypothesis.''' Proc. Natl. Acad. Sci. 1999 96:3801-3806 [http://www.pnas.org/cgi/reprint/96/7/3801.pdf] | Jain R, Rivera MC, Lake JA: '''Horizontal gene transfer among genomes: the complexity hypothesis.''' Proc. Natl. Acad. Sci. 1999 96:3801-3806 [http://www.pnas.org/cgi/reprint/96/7/3801.pdf] | ||
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===LGT and regulatory networks=== | ===LGT and regulatory networks=== | ||
McAdams HH, Srinivasan B & Arkin AP: '''The evolution of genetic regulatory systems in bacteria''' | McAdams HH, Srinivasan B & Arkin AP: '''The evolution of genetic regulatory systems in bacteria''' | ||
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Price MN, Dehal PS, Arkin AP: '''Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli.''' Genome Biol 2008, 9(1):R4 [http://genomebiology.com/content/pdf/gb-2008-9-1-r4.pdf] | Price MN, Dehal PS, Arkin AP: '''Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli.''' Genome Biol 2008, 9(1):R4 [http://genomebiology.com/content/pdf/gb-2008-9-1-r4.pdf] | ||
===LGT and metabolic networks=== | ===LGT and metabolic networks=== | ||
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Light S, Kraulis P and Elofsson, A: '''Preferential attachment in the evolution of metabolic networks.''' BMC Genomics 2005, 6:159 [http://www.biomedcentral.com/1471-2164/6/159] | Light S, Kraulis P and Elofsson, A: '''Preferential attachment in the evolution of metabolic networks.''' BMC Genomics 2005, 6:159 [http://www.biomedcentral.com/1471-2164/6/159] | ||
===LGT and operon formation=== | ===LGT and operon formation=== | ||
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Homma K, Fukuchi S, Nakamura Y, Gojobori T, Nishikawa K: '''Gene Cluster Analysis Method Identifies Horizontally Transferred Genes with High Reliability and Indicates that They Provide the Main Mechanism of Operon Gain in 8 Species of {gamma}-Proteobacteria.''' Molecular Biology and Evolution 2007 24(3):805-813 [http://mbe.oxfordjournals.org/cgi/reprint/24/3/805] | Homma K, Fukuchi S, Nakamura Y, Gojobori T, Nishikawa K: '''Gene Cluster Analysis Method Identifies Horizontally Transferred Genes with High Reliability and Indicates that They Provide the Main Mechanism of Operon Gain in 8 Species of {gamma}-Proteobacteria.''' Molecular Biology and Evolution 2007 24(3):805-813 [http://mbe.oxfordjournals.org/cgi/reprint/24/3/805] | ||
===Networks=== | |||
Barabasi AL, Oltvai ZN: '''Network biology: understanding the cell's functional organization''' Nature Reviews Genetics, 2004 5:(101-113) [[http://hydra.icgeb.trieste.it/~pongor/biophys-homepage/ALB/Network-Biology.pdf] | |||
Revision as of 23:51, 6 April 2008
PIC Server [1]
Literature
LGT
Jain R, Rivera MC, Lake JA: Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. 1999 96:3801-3806 [2]
Aris-Brosou S: Determinants of Adaptive Evolution at the Molecular Level: the Extended Complexity Hypothesis Molecular Biology and Evolution 2005 22(2):200-209 [3]
Wellner A and Lurie MN: Complexity, connectivity, and duplicability as barriers to lateral gene transfer. Genome Biology 2007, 8:R156 [4]
Davids W, Zhang Z: The impact of horizontal gene tranfer in shaping operons and protein interaction networks- direct evidence of preferential attachment. BMC Evoutionary Biology 2008, 8:23 [5]
LGT and regulatory networks
McAdams HH, Srinivasan B & Arkin AP: The evolution of genetic regulatory systems in bacteria Nature Reviews Genetics 2004, 5:169-178 [6]
Lercher MJ, and Pál C: Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years. Molecular Biology and Evolution 2008, 25(3):559-567 [7]
Price MN, Dehal PS, Arkin AP: Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol 2008, 9(1):R4 [8]
LGT and metabolic networks
Eisenberg E, Levanon EY: Preferential attachment in the protein network evolution. Phys Rev Lett 2003, 91(13):138701 [9]
Light S, Kraulis P and Elofsson, A: Preferential attachment in the evolution of metabolic networks. BMC Genomics 2005, 6:159 [10]
LGT and operon formation
Lawrence JG & Roth JR: Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics. 1996 143(4): 1843–1860. [11]
Lawrence JG: Selfish operons and speciation by gene transfer. Trends in Microbiology 1997 5(9):355-359 [12]
Omelchenko MV, Makarova KS, Wolf YI, Rogozin IB, Koonin EV: Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol. 2003; 4(9): R55 [13]
Homma K, Fukuchi S, Nakamura Y, Gojobori T, Nishikawa K: Gene Cluster Analysis Method Identifies Horizontally Transferred Genes with High Reliability and Indicates that They Provide the Main Mechanism of Operon Gain in 8 Species of {gamma}-Proteobacteria. Molecular Biology and Evolution 2007 24(3):805-813 [14]
Networks
Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization Nature Reviews Genetics, 2004 5:(101-113) [[15]
