Matthew Spencer,Edward Susko,Andrew J Roger
Matthew Spencer
The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only ...
Assessing the applicability of the GTR nucleotide substitution model through simulations [0.03%]
利用模拟评估GTR核苷酸替代模型的适用性
Laurent Gatto,Daniele Catanzaro,Michel C Milinkovitch
Laurent Gatto
The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny inference methods. The procedure described by Waddell and Steel (1997), for estimating distances and inst...
Using minimum bootstrap support for splits to construct confidence regions for trees [0.03%]
利用分裂的最小引导支持构建树的置信区域
Edward Susko
Edward Susko
Many of the estimated topologies in phylogenetic studies are presented with the bootstrap support for each of the splits in the topology indicated. If phylogenetic estimation is unbiased, high bootstrap support for a split suggests that the...
Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges [0.03%]
系统发育多样性(PD)与生物多样性保护：一些生物信息学挑战
Daniel P Faith,Andrew M Baker
Daniel P Faith
Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, "PD", has been defined as the minimum total length of all the phylogenet...
3'UTR-located ALU elements: donors of potential miRNA target sites and mediators of network miRNA-based regulatory interactions [0.03%]
位于3'UTR的ALU元件：潜在的miRNA作用位点捐赠者及基于miRNA调节相互作用网络的调解者
Evelina Daskalova,Vesselin Baev,Ventsislav Rusinov et al.
Evelina Daskalova et al.
Recent research data reveal complex, network-based interactions between mobile elements and regulatory systems of eukaryotic cells. In this article, we focus on regulatory interactions between Alu elements and micro RNAs (miRNAs). Our resul...
Functionality and the evolution of marginal stability in proteins: inferences from lattice simulations [0.03%]
功能与蛋白质边缘稳定性进化：格点模拟推论
Paul D Williams,David D Pollock,Richard A Goldstein
Paul D Williams
It has been known for some time that many proteins are marginally stable. This has inspired several explanations. Having noted that the functionality of many enzymes is correlated with subunit motion, flexibility, or general disorder, some ...
Ingrid J Burgetz,Salimah Shariff,Andy Pang et al.
Ingrid J Burgetz et al.
In comparative genomic studies, syntenic groups of homologous sequence in the same order have been used as supplementary information that can be used in helping to determine the orthology of the compared sequences. The assumption is that or...
Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes [0.03%]
HIV-1包膜基因祖先序列重建的变异性来源分析
Howard A Ross,David C Nickle,Yi Liu et al.
Howard A Ross et al.
We characterized the variation in the reconstructed ancestor of 118 HIV-1 envelope gene sequences arising from the methods used for (a) estimating and (b) rooting the phylogenetic tree, and (c) reconstructing the ancestor on that tree, from...
Mirco Gerke,Erich Bornberg-Bauer,Xiaoyi Jiang et al.
Mirco Gerke et al.
Protein interactions are an important resource to obtain an understanding of cell function. Recently, researchers have compared networks of interactions in order to understand network evolution. While current methods first infer homologs an...
Coevolution of exploiter specialization and victim mimicry can be cyclic and saltational [0.03%]
"捕食者特化与被捕食者模拟的协同进化可以是周期性和跳跃式的"
Niclas Norrström,Wayne M Getz,Noél M A Holmgren
Niclas Norrström
Darwin's Principle of Divergence explains sympatric speciation as gradual and directional. Contradicting evidence suggests that species' traits evolve saltationally. Here, we model coevolution in exploiter-victim systems. Victims (resource ...