Evolution of genetic diversity using networks: the human gut microbiome as a case study.

Marco Fondi, Renato Fani, The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks. Environmental Microbiology. ,vol. 12, pp. 3228- 3242 ,(2010) , 10.1111/J.1462-2920.2010.02295.X

Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, François-Joseph Lapointe, Eric Bapteste, Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli Biology Direct. ,vol. 6, pp. 39- ,(2011) , 10.1186/1745-6150-6-39

Jan-Hendrik Hehemann, Gaëlle Correc, Tristan Barbeyron, William Helbert, Mirjam Czjzek, Gurvan Michel, Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota Nature. ,vol. 464, pp. 908- 912 ,(2010) , 10.1038/NATURE08937

W. F. Doolittle, E. Bapteste, Pattern pluralism and the Tree of Life hypothesis. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 104, pp. 2043- 2049 ,(2007) , 10.1073/PNAS.0610699104

S. Halary, J. W. Leigh, B. Cheaib, P. Lopez, E. Bapteste, Network analyses structure genetic diversity in independent genetic worlds Proceedings of the National Academy of Sciences of the United States of America. ,vol. 107, pp. 127- 132 ,(2010) , 10.1073/PNAS.0908978107

Lucie Bittner, Sébastien Halary, Claude Payri, Corinne Cruaud, Bruno de Reviers, Philippe Lopez, Eric Bapteste, Some considerations for analyzing biodiversity using integrative metagenomics and gene networks Biology Direct. ,vol. 5, pp. 47- 47 ,(2010) , 10.1186/1745-6150-5-47

Eric Bapteste, Maureen A O'Malley, Robert G Beiko, Marc Ereshefsky, J Peter Gogarten, Laura Franklin-Hall, François-Joseph Lapointe, John Dupré, Tal Dagan, Yan Boucher, William Martin, Prokaryotic evolution and the tree of life are two different things Biology Direct. ,vol. 4, pp. 34- 34 ,(2009) , 10.1186/1745-6150-4-34

Ken Kurokawa, Takehiko Itoh, Tomomi Kuwahara, Kenshiro Oshima, Hidehiro Toh, Atsushi Toyoda, Hideto Takami, Hidetoshi Morita, Vineet K. Sharma, Tulika P. Srivastava, Todd D. Taylor, Hideki Noguchi, Hiroshi Mori, Yoshitoshi Ogura, Dusko S. Ehrlich, Kikuji Itoh, Toshihisa Takagi, Yoshiyuki Sakaki, Tetsuya Hayashi, Masahira Hattori, Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes DNA Research. ,vol. 14, pp. 169- 181 ,(2007) , 10.1093/DNARES/DSM018

G. Lima-Mendez, J. Van Helden, A. Toussaint, R. Leplae, Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes Molecular Biology and Evolution. ,vol. 25, pp. 762- 777 ,(2008) , 10.1093/MOLBEV/MSN023

Tal Dagan, William Martin, Getting a better picture of microbial evolution en route to a network of genomes Philosophical Transactions of the Royal Society B. ,vol. 364, pp. 2187- 2196 ,(2009) , 10.1098/RSTB.2009.0040