Xun Gu

People
Professor
Xun Gu photo

Dr. Gu, Professor. He came to Iowa State University as an Assistant Professor in 1998, and was promoted to Associate Professor (with tenure) in 2002, and to Full Professor (with tenure) in 2006. Dr. Gu serves on the editorial board of “Molecular Phylogenetics and Evolution”, and “Journal of Experimental Zoology B”. Dr. Gu is the 2001 recipient of the prestigious Dupont Young Professor Award. Dr. Gu’s research group has focused on comparative and evolutionary genomics, computational biology, and evolution of systems biology. Dr. Gu and his group have published over 100 papers.

Research Description

His research has been focused on (1) statistical methods for evolutionary genomics for understanding the genome complexity, and (2) high throughput comparative genomics analysis. Achievements of our research group are: Develop statistical methods and bioinformatics software for predicting functional divergence of a protein family, statistical analysis for expression divergence between duplicate genes, and statistical modeling for gene gain and loss during genomic evolution. Analyze across-species model organism genomes, from yeasts, plants, vertebrates to primates. Recently, our research is exploring the new area of Systems Biology and Evolution: Understanding gene pleiotrophy, genetic robustness, genome complexity and gene network evolution.

Publications (since 2004, when GDCB was created)

  • Jiang, C., Gu, J., Gu, X., and T. Peterson (2004) Ordered origin of the typical two- and three-repeat Myb genes.  Gene 326:13-22.
  • Guo J, Zhu P,  Chen S, Chen L, Wu C,  Yu L, Zhao S , Gu X. (2004) In silico analysis indicates a similar gene expression pattern between human brain and testis. Cytogenetic and Genome Research 103:58-62
  • Gu, X* (2004) Statistical framework for phylogenetic analysis of expression profiles. Genetics 167: 531-542.
  • Gu, J and Gu, X* (2004) Further statistical analysis for genome-wide expression evolution in primate brain/liver/fibroblast tissues. Human Genomics 1:247-254.
  • Gu, X*, Zhang H (2004) Genome phylogeny inference based on gene contents. Molecular Biology and Evolution  21:1401-1408.
  • Jiang, C., Gu  X., and T. Peterson (2004) Functional classification and prediction of Myb gene family in Arabidopsis and Rice. Genome Biology 5(7): R46.
  • Zhang, Z, Gu, J and Gu, X* (2004) How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution? Trends in Genetics 20:403-407.
  • Zhang H,  Gu, X* (2004) Maximum Likelihood for Genome Phylogeny on Gene Content. Statsitical Applications in Genetics and Molecular Biology 3:1 Article 31
  • Sen, T*, Kloczkowski, A., Jernigan, R., Yan, C., Honavar, V., Ho, K., Wang, C., Ihm, Y, Cao, H., Gu, X, Dobbs, D.. (2004) Prediction of binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinformatics 5:205
  • Gu, X*, Zhang Z, and Wei Huang (2005) Rapid evolution of expression and regulatory network after yeast gene/genome duplications. PNAS 102:707-712
  • Gu, X*, Huang, W, Xu, D, Zhang H (2005) GeneContent: Software for Whole-Genome Phylogenetic Analysis. Bioinformatics 21(8):1713-1714.
  • Gu X*, Su, ZX (2005) Web-based resources for comparative genomics. Human Genomics Vol.2, No.3, 1-4.
  • Li, W-H, Yang, J and Gu, X (2005) Expression divergence between duplicates. Trends in Genetics. 21:602-607.
  • Gao, X, Kent V Voytas, D, Gu, X* (2005) Tree-based method to identify protein functional domains. BMC Bioinformatics 6:137.
  • Wu, S, Gu, X (2005) Gene Network: Model, dynamics and simulation. Lecture Notes on Computer Science: 3595: pp.12-21.
  • Zheng Y, Xu D, Gu, X* (2006) Functional divergence after the gene duplication and sequence-structure relationship: A case-study of G-protein alpha subunits. Journal of Experimental  Zoology B 306B:1-12.
  • Leebens-Mack, J, VisionT, Brenner E,…Gu X … (2006) Taking the first steps towards a standard for reporting on phylogenies: Minimal Information About a Phylogenetic Analysis (MIAPA). OMIC Integrated Biology. 10:231-237.
  • Lin H, Zhu W, Silva JC, Gu X, and BuellR (2006) Intron turnover of segmentally duplicated genes in rice. Genome Biology 7(5):R41.
  • Wu Q, Gu X, Wang Y, Li N, Liu X, Wu C, Yu* L, Gu X*. (2006) Neurotransmitter inactivation is important for the origin of nerve system in animal early evolution: a suggestion from genomic comparison. Prog Neurobiol. 78(6):390-5.
  • Gu, X* (2006) A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences. Molecular Biology and Evolution 23:1937-1945.
  • Su Z, Wang J, Yu J, Huang X and Gu X* (2006) Evolution of Alternative Splicing after Gene Duplications. Genome Research 16:182-189.
  • Gu, X*, and Su, Z (2007) Tissue-driven hypothesis of genomic evolution and sequence-expression correlations. PNAS 104:2279-2784.
  • Guo, H, Weiss R. E., Gu, X, and Suchard, M. A. (2007) Time Squared: Repeated Measures on Phylogenies. Molecular Biology and Evolution. 24:352-362
  • H Zhou, J Gu, S J. Lamont, Gu X * (2007) Evolutionary analysis for functional divergence of Toll-like receptor gene family and altered functional constraints. Journal of Molecular Evolution 65:119-123
  • Su, Z, Huang Y, and Gu, X* (2007) Gene ontology analysis of tissue-driven hypothesis for genomic evolution. Annals of Biomedical Engineering 35:1088-1094.
  • Gu, X*  (2007) Evolutionary framework for protein sequence evolution and gene pleiotropy, Genetics 175:1813-1822.
  • Huang, Y, X Gu* (2007) A bootstrap based analysis pipeline for efficient identification of phylogenetically related animal miRNAs. BMC Genomics 8:66
  • J-Y Sire, T Davit-Béal, S Delgado, X Gu (2007)The Origin and Evolution of Enamel Mineralization Genes. Cells Tissues Organs 186:25-48
  • X Gu, Y Zheng, Y Huang, D Xu (2007) Using ancestral sequence inference to determine the trend of functional divergence. pp117-127 in “Ancestral sequence reconstruction” (DA Liberles ed, ISBN 9780199299188). OUP, New York.
  •  Zhang WJ, Zhou J, Li ZF, Wang L, Gu X, Zhong Y (2007) Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L. Journal of Integrative Plant Biology.  49: 419-425.
  • Gu, X*. (2007) Stabilizing selection of protein function and distribution of selection coefficient among sites. Genetica 130:93-97.
  • H Lin, S Ouyang, A Egan, K Nobuta, B Haas, W Zhu, X Gu, JC Silva, BC Meyers, C R Buell (2008) Characterization of paralogous protein families in rice BMC Plant Biology 8:18.
  • X, Gu*, Yong Huang (2008) Human Transcriptome Evolution. Encyclopedia of Life Sciences. In press.
  • S He, X Gu, R L. Mayden, , W-J Chen, K W. Conway and Y Chen (2008) Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi : Cypriniformes): Evidence from the mitochondrial genome. Molecular Phylogenetics and Evolution. 47:419-425.
  • H Zhang, Y Zhong, B Hao and X Gu* (2009) A simple method for phylogenomic inference using the information of gene content of genomes. Gene  441:163-168
  • Q Cheng, Z Su, Y Zhong and X Gu* (2009) Effect of site-specific heterogeneous evolution on phylogenetic reconstruction: A simple evaluation. Gene 441:156-182
  • X. Gu*(2009) An Evolutionary Model for the Origin of Modularity in a Complex Gene Network. JEZ Part-B: Molecular and Developmental Evolution 312:75-82.
  • Z. Su, and X. Gu* (2008) Predicting the Proportion of Essential Genes in Mouse Duplicates Based on Biased Mouse Knockout Genes. Journal of Molecular Evolution 67:705-709.
  • L Xu, Z Su; Z Gu, and X Gu* (2009) Evolution of RNases in Leaf Monkeys: Being Parallel Gene Duplications or Parallel Gene Conversions is a Problem of Molecular Phylogeny. Molecular Phylogenetics and Evolution 50:397-400.
  • Z Su, L Xu, Z Gu and X Gu* (2009) Origins of digestive RNases in leaf monkeys are an open question.  Molecular Phylogenetics and Evolution53:610-611.
  • X Gu* and Y Huang (2009) Expansion of Duplicated MicroRNAs and Protein-coding Genes during a Broad Time Window of Early Vertebrates. JEZ Part-B: Molecular and Developmental Evolution. 312B:164-170.
  • Blake Mertz,1 Xun Gu, Peter J. Reilly (2009) Analysis of Functional Divergence within Two Structurally Related Glycoside Hydrolase Families. Biopolymer 91:479-495.
  • Y Zou, Z Su, J Yang, Y Zeng and X Gu* (2009)Uncovering Genetic Regulatory Network Divergence between Duplicate Genes Using Yeast eQTL Landscape. JEZ Part B: Molecular and Developmental Evolution. 312B:722-733.
  • Yong Huang, Ying Zheng, Zhixi Su, X Gu* (2009) Differences in duplication age distributions between human GPCRs and their downstream genes from a network prospective. BMC Genomics. 10(Suppl 1): S14.
  • Xiujuan Wang, Yong Huang, Dennis V Lavrov* and Xun Gu* (2009) Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications. BMC Evolutionary Biology 9:275
  • Haining Lin, Gaurav Moghe, Shu Ouyang, Amy Iezzoni, Shin-Han Shiu, Xun Gu*, C. Robin Buell* (2010) Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evolutionary Biology. 10:41
  • McGrail M., Batz L., Noack K.E., Pandey S., Huang Y., Gu X., Essner J.J. (2010) Expression of the zebrafish CD133/prominin1 genes in cellular proliferation zones in the embryonic central nervous system and sensory organs. Developmental Dynamics 239(6): 1849-5.
  • Zeng Y, and X. Gu*  (2010) Genome factor and gene pleiotropy hypotheses in protein evolution. Biology Direct 5:37; doi:10.1186/1745-6150-5-37.
  • Su Z, Zeng Y, Gu  X* (2010) A preliminary analysis of gene pleiotropy estimated from protein sequences.  J Exp Zool B Mol Dev Evol, 314B:115-122.
  • Fu W, Zhang F, Wang Y, Gu X, Jin L. (2010) Identification of copy number variation hotspots in human populations. American Journal of Human Genetics. 87: 494-504.
  • Zhang*, H,  Hemasinha, R, Gu, X* (2010) A Statistical Model and Algorithm for Genome Phylogeny Accommodating Lateral Gene Transfer. The International Journal of Systems and Synthetic Biology. Vol. 1: 241-253.
  • Z Su, W Huang, X Gu*  (2011) Comments on ‘Positive selection of tyrosine losses during Metazoan evolution. Science, 332, 917
  • Y Zou, W Huang, Z  Gu, X Gu* (2011) Predominant Gain of Promoter TATA Box after Gene Duplication Associated with Stress Responses. Molecular Biology and Evolution. 28:2893-2904.
  • Y Huang and X, X Gu* (2011) A Study of the Evolution of Human microRNAs by Their Apparent Repression Effectiveness on Target Genes. Plos ONE 6(9): e25034. doi:10.1371/journal.pone.0025034.
  • Chen W, Su, X, Gu, X*. 2012. A Note on Gene Pleiotropy Estimation from Phylogenetic Analysis of Protein Sequences. Journal of Systematics and Evolution (first on-line published in Aug. 2012). DOI: 10.1111/j.1759-6831.2012.00217.x
  • Chen W, Zhou W, Tian X, Gu, X*. 2012. A Computational Analysis Framework for Molecular Cell Dynamics: Case-study of Exocytosis. PLoS ONE7(7): e38699. doi:10.1371/journal.pone.0038699.
  • Su, X, Gu, X*. 2012. Revisit on the Evolutionary Relationship between Alternative Splicing and Gene Duplication. Gene 504 (1): 102-106.
  • Zou, Y, Su, X Huang, W, Gu, X*. 2012. Histone Modification Mediated Regulatory Network Evolution after Yeast Gene Duplication. BMC Evolutionary Biology 12:111 doi:10.1186/1471-2148-12-111.
  • Xia, T, Tong J,  RathoreSS,  Gu, X and DickersonJA (2012) Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis. BMC Systems Biology, 6:19 doi:10.1186/1752-0509-6-19.
  • Gu X*, Zou Y, Su Z (2012)  Gene Duplication and Functional Consequences (Book chapter). Chapter 10 in Translational Bioinformatics Volume 1: Applied Computational Genomics (ed. Yin Yao Shugart), ISBN 978-94-5557-4. Springer.
  • Gu, X* (2012) Statistical methods for detecting functional divergence of gene families. Chapter 10 in Handbook of Statistics 28: Bioinformatics in Human Health and Heredity (ed. C. R. Rao, and Pronab K. Sen) Elsevier, Amsterdam, The Netherlands. ISBN-13: 9780080930985.
  • Wang E, Sun S, Qiao B, Duan W, Huang G, An Y, Xu S, Zheng Y, Su Z, Gu, X, Li J,  Wang H (2013) Identification of Functional Mutations in GATA4 in Patients with Congenital Heart Disease. PLoS ONE 8(4): e62138. doi:10.1371/journal.pone.0062138
  • Gu X*, Zou Y, Su Z, Huang W, Zhou Z, Arendsee Z, Zeng Y (2013) An Update of DIVERGE Software for Functional Divergence Analysis of Protein Family. Molecular Biology and Evolution 30(7) 1713-1719.
  • Gu X*, Zou Y, Huang W, Shen L, Arendsee Z, Su Z (2013) Phylogenomic Distance Method for Analyzing Transcriptome Evolution Based on RNA-seq Data. Genome Biology and Evolution. 5(9):1746-1753.
Area of Expertise: 
Systems Biology and Evolution
Education: 
B.S., Fudan University, China, 1985
M.S., Fudan University, China. 1987
Ph.D., University of Texas, Houston, 1996
Contact
515-294-8075
536 Science Hall ll
Ames
IA
50011-3220