Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference
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Background and aims - Recent methodological and theoretical advances in community ecology have allowed more robust exploration of complementary facets of biodiversity in plant communities. Focusing on semi-natural permanent grasslands of the French Jura Mo ...
National Botanic Garden of Belgium and Royal Botanical Society of Belgium2014
Background and aims - Recent methodological and theoretical advances in community ecology have allowed more robust exploration of complementary facets of biodiversity in plant communities. Focusing on semi-natural permanent grasslands of the French Jura Mo ...
Background: In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in ...
As many whole genomes are sequenced, comparative genomics is moving from pairwise comparisons to multiway comparisons framed within a phylogenetic tree. A central problem in this process is the inference of data for internal nodes of the tree from data giv ...
The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recomme ...
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions th ...
We study the problem of sorting genomes under an evolutionary model that includes genomic rearrangements and segmental duplications. We propose an iterative algorithm to improve any initial evolutionary trajectory between two genomes in terms of parsimony. ...
Background: Superinfection with drug resistant HIV strains could potentially contribute to compromised therapy in patients initially infected with drug-sensitive virus and receiving antiretroviral therapy. To investigate the importance of this potential ro ...
The evolutionary relationships between organisms or phylogenies are fundamental to biology. They are invaluable as guiding tools to mine, organize and exploit the enormous amounts of biological data in the post-genomic era. The advent of high-throughput se ...
Background: Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have be ...