Genome-scale evolution: reconstructing gene orders in the ancestral species.

By Guillaume Bourque, Pavel A. Pevzner. 2002

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Citations in the corpus

Reconstructing contiguous regions of an ancestral genome. (2006, methodology): “(2005) which were mainly based on the MGR algorithm (Bourque and Pevzner 2002), are more or less similar to Froenicke et al.”
Genome Rearrangement Distances and Gene Order Phylogeny in γ-Proteobacteria (2005, background): “The INV distances, estimated in 23 our study, are quite close to the actual number of rearrangements, provided that the number of 24 steps is much smaller than the number of genes (Bourque and Pevzner 2002).”
Comparative Genomics (2007, unknown): “-> (4 5 6 7 8 9 10 11 12 13 14 15 16 [18] [17] 19 20 1 2 3)”
Mauve: multiple alignment of conserved genomic sequence with rearrangements. (2004, background): “Much research has been devoted to inference of rearrangement history that could lead to observed permutations in gene order (Bader et al. 2001; Bourque and Pevzner 2002; Larget et al. 2002; Eichler and Sankoff 2003).”
Perfect sorting by reversals is not always difficult (2006, unknown): “A successful way to deal with this problem has been to use the median approach [9], that still relies on the detection of " good reversals " in the sense of the Hannenhalli-Pevzner theory for computing parsimonious scenarios, but allowing to consider non-optimal reversals.”
A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes (2008, background): “We believe that this three-way comparison indicates that the differences discussed in [16,17] are partly due to the methods themselves, and more precisely to the fact that MGR is a rearrangement-based method, whereas all the others are model-free.”
Probability Models for DNA Sequence Evolution (2002, result): “Our curve is less random, but close to data of Bourque and Pevzner (2002) for k − d(π), indicated in the figure by crosses.”