@article {533,
	title = {Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.},
	journal = {Brief Bioinform},
	volume = {12},
	year = {2011},
	month = {2011 Sep},
	pages = {442-8},
	abstract = {<p>Gene duplication is one of the main mechanisms by which genomes can acquire novel functions. It has been proposed that the retention of gene duplicates can be associated to processes of tissue expression divergence. These models predict that acquisition of divergent expression patterns should be acquired shortly after the duplication, and that larger divergence in tissue expression would be expected for paralogs, as compared to orthologs of a similar age. Many studies have shown that gene duplicates tend to have divergent expression patterns and that gene family expansions are associated with high levels of tissue specificity. However, the timeframe in which these processes occur have rarely been investigated in detail, particularly in vertebrates, and most analyses do not include direct comparisons of orthologs as a baseline for the expected levels of tissue specificity in absence of duplications. To assess the specific contribution of duplications to expression divergence, we combine here phylogenetic analyses and expression data from human and mouse. In particular, we study differences in spatial expression among human-mouse paralogs, specifically duplicated after the radiation of mammals, and compare them to pairs of orthologs in the same species. Our results show that gene duplication leads to increased levels of tissue specificity and that this tends to occur promptly after the duplication event.</p>},
	keywords = {Animals, Conserved Sequence, Evolution, Molecular, Gene Duplication, gene expression, Genome, Humans, Mice, Organ Specificity},
	issn = {1477-4054},
	doi = {10.1093/bib/bbr022},
	author = {Huerta-Cepas, Jaime and Dopazo, Joaquin and Huynen, Martijn A and Gabald{\'o}n, Toni}
}
@article {539,
	title = {Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.},
	journal = {Nucleic Acids Res},
	volume = {39},
	year = {2011},
	month = {2011 Jul},
	pages = {W470-4},
	abstract = {<p>Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.</p>},
	keywords = {Evolution, Molecular, Genomics, Internet, Phylogeny, Sequence Alignment, Software},
	issn = {1362-4962},
	doi = {10.1093/nar/gkr408},
	author = {S{\'a}nchez, Rub{\'e}n and Serra, Fran{\c c}ois and T{\'a}rraga, Joaqu{\'\i}n and Medina, Ignacio and Carbonell, Jos{\'e} and Pulido, Luis and De Maria, Alejandro and Capella-Gut{\'\i}errez, Salvador and Huerta-Cepas, Jaime and Gabald{\'o}n, Toni and Dopazo, Joaquin and Dopazo, Hern{\'a}n}
}
