Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli
作者： Julie Beauregard-Racine , Cédric Bicep , Klaus Schliep , Philippe Lopez , François-Joseph Lapointe
关键词: Methodological pluralism 、 Gene regulatory network 、 Genetics 、 Computational biology 、 Heuristic 、 Tree of life 、 Biology
摘要: Background We introduce several forest-based and network-based methods for exploring microbial evolution, apply them to the study of thousands genes from 30 strains E. coli. This case illustrates how additional analyses could offer fast heuristic alternatives standard tree life (TOL) approaches.
biomedcentral.com
springer.com
elsevier.com
paperity.org参考文章(69)
Robert G. Beiko, Mark A. Ragan, Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction. Methods of Molecular Biology. ,vol. 532, pp. 241- 256 ,(2009) , 10.1007/978-1-60327-853-9_14
James Tabery, Making Sense of the Nature–Nurture Debate Biology & Philosophy. ,vol. 24, pp. 711- 723 ,(2009) , 10.1007/S10539-009-9152-3
Stéphane Guindon, Frédéric Delsuc, Jean-François Dufayard, Olivier Gascuel, Estimating Maximum Likelihood Phylogenies with PhyML Methods in Molecular Biology. ,vol. 537, pp. 113- 137 ,(2009) , 10.1007/978-1-59745-251-9_6
Sarah Killcoyne, Gregory W. Carter, Jennifer Smith, John Boyle, Cytoscape: A Community-Based Framework for Network Modeling Methods in Molecular Biology. ,vol. 563, pp. 219- 239 ,(2009) , 10.1007/978-1-60761-175-2_12
Daniel H. Huson, Regula Rupp, Celine Scornavacca, Phylogenetic Networks: Algorithms and applications ,(2010) , 10.1017/CBO9780511974076.010
Paul van den IJssel, Marianne Tijssen, Suet-Feung Chin, Paul Eijk, Beatriz Carvalho, Erik Hopmans, Henne Holstege, Dhinoth Kumar Bangarusamy, Jos Jonkers, Gerrit A Meijer, Carlos Caldas, Bauke Ylstra, None, Human and mouse oligonucleotide-based array CGH Nucleic Acids Research. ,vol. 33, ,(2005) , 10.1093/NAR/GNI191
R. G. Beiko, T. J. Harlow, M. A. Ragan, Highways of gene sharing in prokaryotes Proceedings of the National Academy of Sciences of the United States of America. ,vol. 102, pp. 14332- 14337 ,(2005) , 10.1073/PNAS.0504068102
James O. McInerney, James A. Cotton, Davide Pisani, The prokaryotic tree of life: past, present... and future? Trends in Ecology and Evolution. ,vol. 23, pp. 276- 281 ,(2008) , 10.1016/J.TREE.2008.01.008
François-Joseph Lapointe, Philippe Lopez, Yan Boucher, Jeremy Koenig, Eric Bapteste, Clanistics: a multi-level perspective for harvesting unrooted gene trees Trends in Microbiology. ,vol. 18, pp. 341- 347 ,(2010) , 10.1016/J.TIM.2010.03.009
Olga Zhaxybayeva, J Peter Gogarten, Robert L Charlebois, W Ford Doolittle, R Thane Papke, Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events Genome Research. ,vol. 16, pp. 1099- 1108 ,(2006) , 10.1101/GR.5322306