Xun Gu

Summary

Affiliation: Iowa State University
Country: USA

Publications

  1. ncbi request reprint Testing the parsimony test of genome duplications: a counterexample
    Xun Gu
    Department of Zoology, Iowa State University, Ames, Iowa 50011, USA
    Genome Res 12:1-2. 2002
  2. ncbi request reprint A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences
    Xun Gu
    Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, USA
    Mol Biol Evol 23:1937-45. 2006
  3. pmc Phylogenomic distance method for analyzing transcriptome evolution based on RNA-seq data
    Xun Gu
    State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
    Genome Biol Evol 5:1746-53. 2013
  4. pmc A computational analysis framework for molecular cell dynamics: case-study of exocytosis
    Wenhai Chen
    School of Life Sciences and Center for Evolutionary Biology, Fudan University, Shanghai, China
    PLoS ONE 7:e38699. 2012
  5. pmc Further statistical analysis for genome-wide expression evolution in primate brain/liver/fibroblast tissues
    Jianying Gu
    Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, IA 50011, USA
    Hum Genomics 1:247-54. 2004
  6. pmc A study of the evolution of human microRNAs by their apparent repression effectiveness on target genes
    Yong Huang
    Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa, United States of America
    PLoS ONE 6:e25034. 2011
  7. pmc Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis
    Tian Xia
    Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA
    BMC Syst Biol 6:19. 2012
  8. doi request reprint An update of DIVERGE software for functional divergence analysis of protein family
    Xun Gu
    State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
    Mol Biol Evol 30:1713-9. 2013
  9. pmc Intron gain and loss in segmentally duplicated genes in rice
    Haining Lin
    The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 7:R41. 2006
  10. pmc Characterization of paralogous protein families in rice
    Haining Lin
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    BMC Plant Biol 8:18. 2008

Research Grants

Collaborators

Detail Information

Publications73

  1. ncbi request reprint Testing the parsimony test of genome duplications: a counterexample
    Xun Gu
    Department of Zoology, Iowa State University, Ames, Iowa 50011, USA
    Genome Res 12:1-2. 2002
  2. ncbi request reprint A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences
    Xun Gu
    Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, USA
    Mol Biol Evol 23:1937-45. 2006
    ....
  3. pmc Phylogenomic distance method for analyzing transcriptome evolution based on RNA-seq data
    Xun Gu
    State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
    Genome Biol Evol 5:1746-53. 2013
    ..Using mammalian RNA-seq data as example, we demonstrated that this expression distance is useful in phylogenomic analysis. ..
  4. pmc A computational analysis framework for molecular cell dynamics: case-study of exocytosis
    Wenhai Chen
    School of Life Sciences and Center for Evolutionary Biology, Fudan University, Shanghai, China
    PLoS ONE 7:e38699. 2012
    ..Finally, we discuss the potential of this approach to explain experimental observations and to make testable hypotheses for further experimentation...
  5. pmc Further statistical analysis for genome-wide expression evolution in primate brain/liver/fibroblast tissues
    Jianying Gu
    Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, IA 50011, USA
    Hum Genomics 1:247-54. 2004
    ....
  6. pmc A study of the evolution of human microRNAs by their apparent repression effectiveness on target genes
    Yong Huang
    Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa, United States of America
    PLoS ONE 6:e25034. 2011
    ..This feature of miRNAs offers an unprecedented vantage point for evolutionary analysis of gene regulation...
  7. pmc Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis
    Tian Xia
    Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA
    BMC Syst Biol 6:19. 2012
    ..Network motifs, recurring subnetwork patterns, provide significant insight into the biological networks which are believed to govern cellular processes...
  8. doi request reprint An update of DIVERGE software for functional divergence analysis of protein family
    Xun Gu
    State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
    Mol Biol Evol 30:1713-9. 2013
    ..In addition, we have made efforts to improve software design and produce a well-written software manual for the general user...
  9. pmc Intron gain and loss in segmentally duplicated genes in rice
    Haining Lin
    The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 7:R41. 2006
    ..The recent completion of the rice genome in which segmental duplication has been documented has allowed us to investigate intron evolution within rice, a diploid monocotyledonous species...
  10. pmc Characterization of paralogous protein families in rice
    Haining Lin
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    BMC Plant Biol 8:18. 2008
    ..This, coupled with other genetic events such as tandem duplications, has resulted in a substantial number of its genes, and resulting proteins, occurring in paralogous families...
  11. pmc Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana
    Haining Lin
    Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA
    BMC Evol Biol 10:41. 2010
    ..While genes conserved among taxa provide insight into the core processes among species, lineage-specific genes provide insights into evolutionary processes and biological functions that are likely clade or species specific...
  12. ncbi request reprint Genome phylogenetic analysis based on extended gene contents
    Xun Gu
    Department of Genetics, Development, and Cell Biology, Iowa State University, Iowa, USA
    Mol Biol Evol 21:1401-8. 2004
    ..The example of 35 microbial complete genomes demonstrates that it is useful not only to study the universal tree of life but also to explore the evolutionary pattern of genomes...
  13. pmc Statistical framework for phylogenomic analysis of gene family expression profiles
    Xun Gu
    Department of Genetics, Development and Cell Biology GDCB, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011, USA
    Genetics 167:531-42. 2004
    ..Potential applications in evolutionary genomics are discussed...
  14. ncbi request reprint GeneContent: software for whole-genome phylogenetic analysis
    Xun Gu
    Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
    Bioinformatics 21:1713-4. 2005
    ..GeneContent can also be used to explore the genome-wide evolutionary pattern of gene loss and proliferation...
  15. pmc Web-based resources for comparative genomics
    Xun Gu
    Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
    Hum Genomics 2:187-90. 2005
    ..A few currently 'hot' topics have therefore been selected and a brief review of the availability of web-based databases and software is given...
  16. pmc Tissue-driven hypothesis of genomic evolution and sequence-expression correlations
    Xun Gu
    School of Life Sciences, Institutes of Biomedical Sciences, Center for Evolutionary Biology, Fudan University, Shanghai 200433, China
    Proc Natl Acad Sci U S A 104:2779-84. 2007
    ..g., hormone-related). We conclude that tissue factors should be considered as an important component in shaping the pattern of genomic evolution and correlations...
  17. pmc Rapid evolution of expression and regulatory divergences after yeast gene duplication
    Xun Gu
    State Key Laboratory of Genetic Engineering, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
    Proc Natl Acad Sci U S A 102:707-12. 2005
    ..Our study highlights the crucial role of early rapid evolution after gene/genome duplication for continuously increasing the complexity of the yeast regulatory network...
  18. ncbi request reprint Stabilizing selection of protein function and distribution of selection coefficient among sites
    Xun Gu
    Department of Genetics, Development and Cell Biology Center for Bioinformatics and Biological Statistics, Iowa State University, 536 Science II Hall, Ames, IA 50011, USA
    Genetica 130:93-7. 2007
    ..These results are helpful for having a better understanding of the underlying evolutionary mechanism of protein sequences, as well as human disease-related mutations...
  19. pmc Evolutionary framework for protein sequence evolution and gene pleiotropy
    Xun Gu
    Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
    Genetics 175:1813-22. 2007
    ..Case studies of vertebrate proteins indicate that K(e) is typically approximately 6-9. We demonstrate that the newly developed SM model of protein evolution may provide a basis for exploring genomic evolution and correlations...
  20. doi request reprint An evolutionary model for the origin of modularity in a complex gene network
    Xun Gu
    Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011, USA
    J Exp Zool B Mol Dev Evol 312:75-82. 2009
    ..Data analysis has shown that, roughly, the rate of gene network evolution can be described as a 2-2-1 pattern (adding two new genes and two new links with the cost of one link-loss)...
  21. ncbi request reprint Evolution of duplicate genes versus genetic robustness against null mutations
    Xun Gu
    Department of Genetics, Development and Cell Biology, Centre for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
    Trends Genet 19:354-6. 2003
  22. ncbi request reprint Locus specificity of polymorphic alleles and evolution by a birth-and-death process in mammalian MHC genes
    X Gu
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, USA
    Mol Biol Evol 16:147-56. 1999
    ....
  23. ncbi request reprint Statistical methods for testing functional divergence after gene duplication
    X Gu
    Department of Zoology Genetics, Iowa Computational Molecular Biology Laboratory, Iowa State University, Ames 50011, USA
    Mol Biol Evol 16:1664-74. 1999
    ....
  24. ncbi request reprint Maximum-likelihood approach for gene family evolution under functional divergence
    X Gu
    Department of Zoology Genetics, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames 50011, USA
    Mol Biol Evol 18:453-64. 2001
    ..The cost of this feasibility is the approximation when frequencies of amino acids are very skewed. The potential bias and correction are discussed...
  25. ncbi request reprint Mathematical modeling for functional divergence after gene duplication
    X Gu
    Department of Zoology Genetics, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
    J Comput Biol 8:221-34. 2001
    ..Our study may have great potential for functional genomics because it is cost-effective, and these predictions can be further tested by biological experimentation...
  26. ncbi request reprint DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family
    Xun Gu
    Department of Zoology and Genetics, Program of Bioinformatics and Computational Biology, Iowa State University, IA 50011, USA
    Bioinformatics 18:500-1. 2002
    ..These results can then be mapped on the 3D protein structure if available...
  27. ncbi request reprint Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution
    Xun Gu
    Department of Zoology and Genetics and Iowa State University, Ames, Iowa 50011, USA
    Nat Genet 31:205-9. 2002
    ..Further analysis indicated that large- and small-scale gene duplications both make a significant contribution during the early stage of vertebrate evolution to build the current hierarchy of the human proteome...
  28. doi request reprint Simultaneous expansions of microRNAs and protein-coding genes by gene/genome duplications in early vertebrates
    Xun Gu
    Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011, USA
    J Exp Zool B Mol Dev Evol 312:164-70. 2009
    ..We further speculate that genetically lying behind the evolution of vertebrate complexity may be the proteome doubling and alterations of the epigenetic (including miRNA) machinery...
  29. ncbi request reprint Functional divergence in protein (family) sequence evolution
    Xun Gu
    Department of Zoology and Genetics, LHB Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
    Genetica 118:133-41. 2003
    ..The emergence of evolutionary functional genomics is also indicated. The related software DIVERGE can be obtained from http://xgu1.zool.iastate.edu...
  30. pmc SplitTester: software to identify domains responsible for functional divergence in protein family
    Xiang Gao
    Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
    BMC Bioinformatics 6:137. 2005
    ....
  31. doi request reprint A preliminary analysis of gene pleiotropy estimated from protein sequences
    Zhixi Su
    Institutes of Biomedical Sciences, School of Life Sciences, Center for Evolutionary Biology, Fudan University, Shanghai, China
    J Exp Zool B Mol Dev Evol 314:115-22. 2010
    ....
  32. ncbi request reprint Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations
    Gangbiao Liu
    State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Biology Building II 113, Shanghai, 200433, China
    Mol Genet Genomics 289:137-47. 2014
    ..We found that the distribution patterns of the major subcellular localizations were similar to that of the whole genome. This study revealed the whole picture of the evolution patterns of gene functional categories in the human genome. ..
  33. pmc Differences in duplication age distributions between human GPCRs and their downstream genes from a network prospective
    Yong Huang
    Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
    BMC Genomics 10:S14. 2009
    ....
  34. ncbi request reprint Tissue-driven hypothesis with Gene Ontology (GO) analysis
    Zhixi Su
    Institutes of Biomedical Sciences, School of Life Sciences, Center for Evolutionary Biology, Fudan University, Shanghai, China
    Ann Biomed Eng 35:1088-94. 2007
    ..It is also shown that sub-grouping genes into GO categories increased the sensitivity for detecting potential positive factors in expression divergence in the tissues...
  35. pmc Predicting binding sites of hydrolase-inhibitor complexes by combining several methods
    Taner Z Sen
    L H Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
    BMC Bioinformatics 5:205. 2004
    ....
  36. ncbi request reprint Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscape
    Yangyun Zou
    Institutes of Biomedical Sciences, Fudan University, Shanghai, China
    J Exp Zool B Mol Dev Evol 312:722-33. 2009
    ..We conclude that eQTL analysis provides a novel approach to explore the effect of gene duplications on the genetic regulatory network...
  37. doi request reprint Predominant gain of promoter TATA box after gene duplication associated with stress responses
    Yangyun Zou
    MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
    Mol Biol Evol 28:2893-904. 2011
    ....
  38. pmc Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications
    Xiujuan Wang
    Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA
    BMC Evol Biol 9:275. 2009
    ....
  39. pmc Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica
    Cizhong Jiang
    Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
    Genome Biol 5:R46. 2004
    ..ssp. indica)...
  40. pmc A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs
    Yong Huang
    Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
    BMC Genomics 8:66. 2007
    ..Most of the current methods for miRNA classification rely heavily on manual inspection and lack measurements of the reliability of the results...
  41. ncbi request reprint Ordered origin of the typical two- and three-repeat Myb genes
    Cizhong Jiang
    Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
    Gene 326:13-22. 2004
    ..Finally, a small group of ancient Myb paralogs prior to the amplification of current Myb genes is identified. Together, these results support a new model for the ordered evolution of Myb gene family...
  42. doi request reprint Effect of site-specific heterogeneous evolution on phylogenetic reconstruction: a simple evaluation
    Qiqun Cheng
    Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
    Gene 441:156-62. 2009
    ....
  43. ncbi request reprint Induced gene expression in human brain after the split from chimpanzee
    Jianying Gu
    Dept of Zoology and Genetics, 332 Science II Hall, Iowa State University, Ames, IA 50011, USA
    Trends Genet 19:63-5. 2003
    ....
  44. ncbi request reprint Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes
    Jianying Gu
    Department of Zoology and Genetics, Iowa State University, Ames, IA 50011, USA
    J Mol Evol 54:725-33. 2002
    ..The implication of our study for functional genomics is discussed...
  45. pmc Identification of functional mutations in GATA4 in patients with congenital heart disease
    Erli Wang
    Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 8:e62138. 2013
    ..Together with the newly reported mutations, approximately 110 non-synonymous mutations have currently been identified in GATA4. Our future analysis will explore why the evolutionarily conserved GATA4 appears to be hypermutable...
  46. pmc Identification of copy number variation hotspots in human populations
    Wenqing Fu
    State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
    Am J Hum Genet 87:494-504. 2010
    ....
  47. ncbi request reprint Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraints
    Huaijun Zhou
    Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, 332 Science II Hall, Ames, IA 50011, USA
    J Mol Evol 65:119-23. 2007
    ....
  48. ncbi request reprint Natural history and functional divergence of protein tyrosine kinases
    Jianying Gu
    Department of Zoology and Genetics, Center for Bioinformatics and Biological Statistics, 332 Science II Hall, Iowa State University, Ames, IA 50011, USA
    Gene 317:49-57. 2003
    ..Our results show that site-specific shifted evolutionary rate (altered functional constraint) is a common pattern in PTK gene family evolution...
  49. ncbi request reprint How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution?
    Zhongqi Zhang
    Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, IA 50011, USA
    Trends Genet 20:403-7. 2004
    ..Our observations suggest that, in addition to the cis-regulatory motif structure in the upstream region of the gene, multiple trans-acting factors in the gene network can influence the pattern of gene expression significantly...
  50. ncbi request reprint Functional divergence after gene duplication and sequence-structure relationship: a case study of G-protein alpha subunits
    Ying Zheng
    Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Iowa 50011, USA
    J Exp Zool B Mol Dev Evol 308:85-96. 2007
    ..Finally, these predicted residues are mapped to the protein structures to test whether these residues may have 3D structure or solvent accessibility preference...
  51. pmc Histone modification pattern evolution after yeast gene duplication
    Yangyun Zou
    Ministry of Education Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
    BMC Evol Biol 12:111. 2012
    ..In this study, we conducted detailed analyses on yeast histone modification (HM), the major epigenetics type in this organism, as well as other available functional genomics data to address this issue...
  52. doi request reprint Comment on "Positive selection of tyrosine loss in metazoan evolution"
    Zhixi Su
    MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
    Science 332:917; author reply 917. 2011
    ..We challenge this hypothesis, providing evidence that the high guanine-cytosine (GC) content of metazoan genomes was the primary driver in the loss of tyrosine residues...
  53. doi request reprint Revisit on the evolutionary relationship between alternative splicing and gene duplication
    Zhixi Su
    MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
    Gene 504:102-6. 2012
    ....
  54. pmc Genome factor and gene pleiotropy hypotheses in protein evolution
    Yanwu Zeng
    School of Life Sciences, Fudan University, Shanghai 200433, China
    Biol Direct 5:37. 2010
    ..In this short article, we propose that gene pleiotropy, the capacity for affecting multiple phenotypes, may play a vital role in molecular evolution. We discuss several approaches to testing this hypothesis...
  55. doi request reprint Analysis of functional divergence within two structurally related glycoside hydrolase families
    Blake Mertz
    Department of Chemical and Biological Engineering, IA State University, Ames, IA 50011, USA
    Biopolymers 91:478-95. 2009
    ..Four cluster comparisons between these four main subfamilies again have identified amino acid residues involved in functional divergence between the subfamilies. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 478-495, 2009...
  56. ncbi request reprint Expression of the zebrafish CD133/prominin1 genes in cellular proliferation zones in the embryonic central nervous system and sensory organs
    Maura McGrail
    Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
    Dev Dyn 239:1849-57. 2010
    ..Based on these analyses, the zebrafish prominin1 genes will be useful markers for examining proliferating cell populations in adult organs, tissues, and tumors...
  57. doi request reprint Predicting the proportion of essential genes in mouse duplicates based on biased mouse knockout genes
    Zhixi Su
    Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
    J Mol Evol 67:705-9. 2008
    ....
  58. ncbi request reprint Neurotransmitter inactivation is important for the origin of nerve system in animal early evolution: a suggestion from genomic comparison
    Qi Wu
    State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China
    Prog Neurobiol 78:390-5. 2006
    ..quot; Further experimental evidence is needed to support the suggestion and to explain the importance of neurotransmitter inactivation to metazoan multicellular function...
  59. pmc Correlation between the substitution rate and rate variation among sites in protein evolution
    J Zhang
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Genetics 149:1615-25. 1998
    ..We conclude that the correlation is a general feature of protein evolution and discuss its implications in statistical tests of positive Darwinian selection and molecular time estimation of deep divergences...
  60. ncbi request reprint Asymmetric evolution of human transcription factor regulatory networks
    Zhan Zhou
    State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
    Mol Biol Evol 31:2149-55. 2014
    ....
  61. ncbi request reprint A simple method for estimating the parameter of substitution rate variation among sites
    X Gu
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802
    Mol Biol Evol 14:1106-13. 1997
    ..Our method is computationally as fast as the parsimony method, and the estimation accuracy is much higher than that of parsimony and similar to that of the likelihood method...
  62. pmc Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction
    Y Wang
    Department of Zoology and Genetics, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011, USA
    Genetics 158:1311-20. 2001
    ..Our approach can be cost effective in functional genomics to make statistically sound predictions from amino acid sequences...
  63. pmc Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)
    Jim Leebens-Mack
    Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
    OMICS 10:231-7. 2006
    ..Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors...
  64. ncbi request reprint The age of the common ancestor of eukaryotes and prokaryotes: statistical inferences
    X Gu
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
    Mol Biol Evol 14:861-6. 1997
    ..s estimate (approximately 2.0 Ga) seems too recent, and (2) that the traditional view about the divergence time between eukaryotes and prokaryotes (T0 = 3.5 Ga) can be rejected at the 0.1% significance level...
  65. pmc Evolution of alternative splicing after gene duplication
    Zhixi Su
    James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
    Genome Res 16:182-9. 2006
    ..In the late stage, the gain and loss of alternative splicing seem to be independent between duplicates...
  66. ncbi request reprint Expression divergence between duplicate genes
    Wen Hsiung Li
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Trends Genet 21:602-7. 2005
    ..In addition, the relationship between gene duplication and evolution of transcriptional regulatory networks is largely unexplored...
  67. ncbi request reprint Time squared: repeated measures on phylogenies
    Hua Guo
    Department of Biostatistics, School of Public Health, University of California, Los Angeles, USA
    Mol Biol Evol 24:352-62. 2007
    ..To demonstrate PR model applicability more generally, we conclude with a short examination of variation in brain development across 4 primate species...
  68. ncbi request reprint The origin and evolution of enamel mineralization genes
    Jean Yves Sire
    UMR 7138, Universite Pierre et Marie Curie Paris 6, Paris, France
    Cells Tissues Organs 186:25-48. 2007
    ..This suggests that enamel matrix proteins (EMPs) have at least the same age. We review the current data on the origin, evolution and relationships of enamel mineralization genes...
  69. ncbi request reprint Predicting functional divergence in protein evolution by site-specific rate shifts
    Eric A Gaucher
    NASA Astrobiology Institute, University of Florida, Gainesville, FL 32611, USA
    Trends Biochem Sci 27:315-21. 2002
    ..Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs...
  70. ncbi request reprint Role of duplicate genes in genetic robustness against null mutations
    Zhenglong Gu
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA
    Nature 421:63-6. 2003
    ..We estimate that in S. cerevisiae at least a quarter of those gene deletions that have no phenotype are compensated by duplicate genes...
  71. ncbi request reprint Identification of essential amino acid changes in paired domain evolution using a novel combination of evolutionary analysis and in vitro and in vivo studies
    Hongmin Sun
    Human Genetics Center, University of Texas Houston, USA
    Mol Biol Evol 19:1490-500. 2002
    ..Our approach for selecting candidate sites responsible for the functional divergence between genes should also be useful for studying other gene families...
  72. pmc Novel PAX6 binding sites in the human genome and the role of repetitive elements in the evolution of gene regulation
    Yi Hong Zhou
    Department of Neuro Oncology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Genome Res 12:1716-22. 2002
    ..This difference indicates that human and mouse Pax6-regulated gene networks may have evolved through these lineage-specific repeat elements...
  73. ncbi request reprint Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genome
    Shunping He
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
    Mol Phylogenet Evol 47:419-25. 2008

Research Grants4

  1. METHODS FOR FUNCTIONAL/COMPARATIVE GENOMICS
    Xun Gu; Fiscal Year: 2003
    ..abstract_text> ..
  2. METHODS FOR FUNCTIONAL/COMPARATIVE GENOMICS
    Xun Gu; Fiscal Year: 2000
    ..abstract_text> ..
  3. METHODS FOR FUNCTIONAL/COMPARATIVE GENOMICS
    Xun Gu; Fiscal Year: 2001
    ..abstract_text> ..
  4. METHODS FOR FUNCTIONAL/COMPARATIVE GENOMICS
    Xun Gu; Fiscal Year: 2002
    ..abstract_text> ..