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» Detecting recombination in evolving nucleotide sequences
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BMCBI
2006
115views more  BMCBI 2006»
9 years 3 months ago
Detecting recombination in evolving nucleotide sequences
Background: Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent resid...
Cheong Xin Chan, Robert G. Beiko, Mark A. Ragan
BMCBI
2006
92views more  BMCBI 2006»
9 years 3 months ago
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
Background: Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequen...
Anne-Kathrin Schultz, Ming Zhang, Thomas Leitner, ...
NIPS
2008
9 years 5 months ago
A spatially varying two-sample recombinant coalescent, with applications to HIV escape response
Statistical evolutionary models provide an important mechanism for describing and understanding the escape response of a viral population under a particular therapy. We present a ...
Alexander Braunstein, Zhi Wei, Shane T. Jensen, Jo...
BMCBI
2008
114views more  BMCBI 2008»
9 years 3 months ago
Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping
Background: Serotypes of the Foot-and-Mouth disease viruses (FMDVs) were generally determined by biological experiments. The computational genotyping is not well studied even with...
Guohui Lin, Zhipeng Cai, Junfeng Wu, Xiu-Feng Wan,...
BMCBI
2006
100views more  BMCBI 2006»
9 years 3 months ago
Using the nucleotide substitution rate matrix to detect horizontal gene transfer
Background: Horizontal gene transfer (HGT) has allowed bacteria to evolve many new capabilities. Because transferred genes perform many medically important functions, such as conf...
Micah Hamady, M. D. Betterton, Rob Knight
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