• Publications
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Statistical methods for testing functional divergence after gene duplication.
  • X. Gu
  • Biology, Medicine
  • Molecular biology and evolution
  • 1 December 1999
TLDR
A site-specific profile based on the hidden Markov model is developed to identify critical amino acid residues that are responsible for these functional differences between two gene clusters, which may have great potential in functional genomics. Expand
Maximum-likelihood approach for gene family evolution under functional divergence.
  • X. Gu
  • Biology, Medicine
  • Molecular biology and evolution
  • 1 April 2001
TLDR
The subtree likelihood provides a solution that is computationally feasible and robust against the uncertainty of the phylogeny in the large gene family with many member genes (clusters), which appears to be a normal case in postgenomics. Expand
Role of duplicate genes in genetic robustness against null mutations
TLDR
A genome-wide evaluation of the role of duplicate genes in genetic robustness against null mutations shows that there is a significantly higher probability of functional compensation for a duplicate gene than for a singleton, a high correlation between the frequency of compensation and the sequence similarity of two duplicates, and a higher probability for a severe fitness effect when the duplicate copy that is more highly expressed is deleted. Expand
Evolution by the birth-and-death process in multigene families of the vertebrate immune system.
TLDR
The results show that the evolutionary pattern of these families is quite different from that of concerted evolution but is in agreement with the birth-and-death model of evolution in which new genes are created by repeated gene duplication and some duplicate genes are maintained in the genome for a long time but others are deleted or become nonfunctional by deleterious mutations. Expand
An update of DIVERGE software for functional divergence analysis of protein family.
TLDR
An updated version of DIVERGE is released with the following improvements: a feasible approach to examining functional divergence in nearly complete sequences by including deletions and insertions (indels); the calculation of the false discovery rate of functionally diverging sites; estimation of the effective number of functional divergence-related sites that is reliable and insensitive to cutoffs. Expand
DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family
SUMMARY DetectIng Variability in Evolutionary Rates among GEnes (DIVERGE) is a software system to study functional divergence of a protein family by detecting site-specific change in evolutionaryExpand
A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences.
  • X. Gu
  • Medicine, Biology
  • Molecular biology and evolution
  • 1 October 2006
TLDR
This paper approaches the issue of how to statistically identify cluster-specific amino acid residues that are related to the functional divergence after gene duplication using a framework based on site-specific shift of amino acid property ( type-II functional divergence), as opposed to site- specific shift of evolutionary rate (type-I functional divergence). Expand
Evolution of alternative splicing after gene duplication.
TLDR
It is concluded that alternative splicing and gene duplication may not evolve independently, and young duplicates may take over a certain amount of protein function diversity that previously was carried out by the alternative splice mechanism in the early stage. Expand
Predicting functional divergence in protein evolution by site-specific rate shifts.
TLDR
This work applies the "non-homogeneous gamma model" to multiple gene families to identify sites that are likely to be involved in changing function within the gene family, highlighting the widespread divergence of functional behavior among proteins to generate paralogs and orthologs. Expand
Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction.
TLDR
The pattern of type I functional divergence (i.e., altered functional constraints or site-specific rate difference) in the caspase gene family that is important for apoptosis (programmed cell death) and cytokine maturation is explored. Expand
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