Elizabeth Skippington: Difference between revisions

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* ''impact of LGT on genome structure and protein networks''
* ''impact of LGT on genome structure and protein networks''
* ''LGT in the context of cellular networks and protein-protein interactions''
* ''LGT in the context of cellular networks and protein-protein interactions''
* gene expressivity, evolutionary rate and protein connectivity





Revision as of 01:57, 8 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]

  • genes intergrate slowly into protein-protein interaction networks

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]

  • impact of LGT on genome structure and protein networks
  • LGT in the context of cellular networks and protein-protein interactions
  • gene expressivity, evolutionary rate and protein connectivity


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]

Pál C, Papp B, Lercher MJ: Adaptive evolution of bacterial metabolic networks by horizontal gene transfer Nature Genetics 2005 37:1372 - 1375 [11]


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. [12]

Lawrence JG: Selfish operons and speciation by gene transfer. Trends in Microbiology 1997 5(9):355-359 [13]

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 [14]

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 [15]


Networks

Oltvai ZN and Barabási AL SYSTEMS BIOLOGY: Life's Complexity Pyramid Science, 2002 298(5594):763-764 [16]

Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization Nature Reviews Genetics, 2004 5:101-113 [17]


Pan-genome

Lefébure T & Stanhope MJ: Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition Genome Biology, 2007 8:R71 [18]

  • relative role of selection vs recombination in the diversification of the core-genome of Streptococcus

Gregory C. Kettler, Adam C. Martiny, Katherine Huang, Jeremy Zucker, Maureen L. Coleman, Sebastien Rodrigue, Feng Chen, Alla Lapidus, Steven Ferriera, Justin Johnson, Claudia Steglich, George M. Church, Paul Richardson, Sallie W. Chisholm: Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus PLoS Genetics 3(12): e231 [19]

  • defined core and flexible genomes
  • patterns of gain and loss of non-core genes
  • functions assocaited with core and felxible genomes and metabolic pathways

Sources

Reed JL, Vo TD, Schilling CH and Bernhard O Palsson BO: An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Genome Biology 2003, 4:R54 [20]

  • reconstructed metabolic network of Escherichia coli K-12