Research Topics
| Xun GuSummaryAffiliation: Iowa State University Country: USA Publications
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Publications
Testing the parsimony test of genome duplications: a counterexampleXun Gu
Department of Zoology, Iowa State University, Ames, Iowa 50011, USA
Genome Res 12:1-2. 2002- A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequencesXun 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.... - Intron gain and loss in segmentally duplicated genes in riceHaining 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... - Characterization of paralogous protein families in riceHaining 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... - Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thalianaHaining 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... - An evolutionary model for the origin of modularity in a complex gene networkXun 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)... - Evolution of duplicate genes versus genetic robustness against null mutationsXun 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 - Functional divergence in protein (family) sequence evolutionXun 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... - Genome phylogenetic analysis based on extended gene contentsXun 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... - Statistical framework for phylogenomic analysis of gene family expression profilesXun 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... - Evolutionary framework for protein sequence evolution and gene pleiotropyXun 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... - GeneContent: software for whole-genome phylogenetic analysisXun Gu
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
Bioinformatics 21:1713-4. 2005..AVAILABILITY: Distribution packages of GeneContent for both Microsoft Windows and Linux operating systems are available at http://xgu.zool.iastate.edu CONTACT: xgu@iastate.edu... - Rapid evolution of expression and regulatory divergences after yeast gene duplicationXun 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... - Simultaneous expansions of microRNAs and protein-coding genes by gene/genome duplications in early vertebratesXun 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... - Tissue-driven hypothesis of genomic evolution and sequence-expression correlationsXun 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... - Web-based resources for comparative genomicsXun 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... - Locus specificity of polymorphic alleles and evolution by a birth-and-death process in mammalian MHC genesX Gu
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, USA
Mol Biol Evol 16:147-56. 1999.... - Statistical methods for testing functional divergence after gene duplicationX Gu
Department of Zoology Genetics, Iowa Computational Molecular Biology Laboratory, Iowa State University, Ames 50011, USA
Mol Biol Evol 16:1664-74. 1999.... - Maximum-likelihood approach for gene family evolution under functional divergenceX 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... - Stabilizing selection of protein function and distribution of selection coefficient among sitesXun 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... - Mathematical modeling for functional divergence after gene duplicationX 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... - DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein familyXun Gu
Department of Zoology and Genetics, Program of Bioinformatics and Computational Biology, Iowa State University, IA 50011, USA
Bioinformatics 18:500-1. 2002..AVAILABILITY: DIVERGE is available free of charge from http://xgu1.zool.iastate.edu/. Distribution packages for both Linux and Microsoft Windows operating systems are available, including manual and example files... - Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolutionXun 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... - SplitTester: software to identify domains responsible for functional divergence in protein familyXiang Gao
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
BMC Bioinformatics 6:137. 2005.... - A preliminary analysis of gene pleiotropy estimated from protein sequencesZhixi 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.... - Predominant gain of promoter TATA box after gene duplication associated with stress responsesYangyun 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.... - Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplicationsXiujuan Wang
Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA
BMC Evol Biol 9:275. 2009.... - A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAsYong 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... - Predicting binding sites of hydrolase-inhibitor complexes by combining several methodsTaner Z Sen
L H Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
BMC Bioinformatics 5:205. 2004.... - Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indicaCizhong Jiang
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
Genome Biol 5:R46. 2004..ssp. indica)... - Identification of copy number variation hotspots in human populationsWenqing 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.... - Differences in duplication age distributions between human GPCRs and their downstream genes from a network prospectiveYong 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.... - Tissue-driven hypothesis with Gene Ontology (GO) analysisZhixi 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... - Ordered origin of the typical two- and three-repeat Myb genesCizhong 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... - Effect of site-specific heterogeneous evolution on phylogenetic reconstruction: a simple evaluationQiqun Cheng
Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
Gene 441:156-62. 2009.... - Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscapeYangyun 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... - A study of the evolution of human microRNAs by their apparent repression effectiveness on target genesYong 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... - Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraintsHuaijun 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.... - Functional divergence after gene duplication and sequence-structure relationship: a case study of G-protein alpha subunitsYing 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... - Natural history and functional divergence of protein tyrosine kinasesJianying 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... - 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... - Further statistical analysis for genome-wide expression evolution in primate brain/liver/fibroblast tissuesJianying Gu
Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, IA 50011, USA
Hum Genomics 1:247-54. 2004.... - Induced gene expression in human brain after the split from chimpanzeeJianying Gu
Dept of Zoology and Genetics, 332 Science II Hall, Iowa State University, Ames, IA 50011, USA
Trends Genet 19:63-5. 2003.... - 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... - Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genesJianying 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... - Genome factor and gene pleiotropy hypotheses in protein evolutionYanwu 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... - Analysis of functional divergence within two structurally related glycoside hydrolase familiesBlake 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... - Neurotransmitter inactivation is important for the origin of nerve system in animal early evolution: a suggestion from genomic comparisonQi 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... - Predicting the proportion of essential genes in mouse duplicates based on biased mouse knockout genesZhixi Su
Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
J Mol Evol 67:705-9. 2008.... - Expression of the zebrafish CD133/prominin1 genes in cellular proliferation zones in the embryonic central nervous system and sensory organsMaura 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... - Correlation between the substitution rate and rate variation among sites in protein evolutionJ 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... - Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and predictionY 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... - A simple method for estimating the parameter of substitution rate variation among sitesX 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... - 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... - The age of the common ancestor of eukaryotes and prokaryotes: statistical inferencesX 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... - Role of duplicate genes in genetic robustness against null mutationsZhenglong 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... - Evolution of alternative splicing after gene duplicationZhixi 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... - The origin and evolution of enamel mineralization genesJean 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... - Expression divergence between duplicate genesWen 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... - Time squared: repeated measures on phylogeniesHua 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... - Predicting functional divergence in protein evolution by site-specific rate shiftsEric 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... - Identification of essential amino acid changes in paired domain evolution using a novel combination of evolutionary analysis and in vitro and in vivo studiesHongmin 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... - Novel PAX6 binding sites in the human genome and the role of repetitive elements in the evolution of gene regulationYi-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... - Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genomeShunping 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 Grants
- METHODS FOR FUNCTIONAL/COMPARATIVE GENOMICSXun Gu; Fiscal Year: 2003..abstract_text> ..