Gu X.*, Zou Y., Su Z., Huang W., Zhou Z., Arendsee A. and Zeng Y. (2013) An update of DIVERGE software for functional divergence analysis of protein family. Mol Biol Evol doi:0.1093/molbev/mst069.
Chen W., Su Z.* and Gu X.* (2012) A note on gene pleiotropy estimation from phylogenetic analysis of protein sequences. J Syst Evol 51:365-369.
Chen W., Zhou W., Xia T. and Gu, X.* (2012) A Computational Analysis Framework for Molecular Cell Dynamics: Case-Study of Exocytosis. PLOS ONE 7: e38699.
Gu X.*, Zou Y. and Su Z. (2012) Gene duplication and functional consequences. Applied Computational Genomics (Translational Bioinformatics) (Shugart Y., eds, Springer), 9th Chapter.
Su Z. and Gu X.* (2012) Revisit on the evolutionary relationship between alternative splicing and gene duplication. Gene 504:102-6.
Zou Y., Su Z., Huang W. and Gu X.*(2012) Histone modification pattern evolution after yeast gene duplication. BMC Evol Biol 12: 111.
Su Z., Huang W. and Gu X.* (2011) Comment on “Positive Selection of Tyrosine Loss in Metazoan Evolution”. Science, 20 May 2011: Vol. 332, no.6032, p. 917.
Zou Y., Huang W., Gu Z. and Gu X.* (2011) Predominant gain of promoter TATA box after gene duplication associated with stress responses. Mol Biol Evol 28(10): 2893-2904.
Hongmei Zhang*, Rohan Hemasinha, Xun Gu* (2010) A Statistical Model and Algorithm for Genome Phylogeny Accommodating Lateral Gene Transfer. International Journal of synthetic and systems biology (IJSSB). in press.
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
Fu W., Zhang F., Wang Y., Gu X. and Jin L. (2010) Identification of copy number variation hotspots in human populations. Am J Hum Genet 87: 494-504.
Zeng Y. and Gu X. (2010) Genome factor and gene pleiotropy hypotheses in protein evolution. Biol Direct 5:37.
Su Z., Zeng Y. and Gu X.* (2010) A preliminary analysis of gene pleiotropy estimated from protein sequences. J Exp Zool B Mol Dev Evol 314: 115-122.
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.
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 Evolution 53:610-611.
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
Gu X.*, Su Z. and Huang Y. (2009) Simultaneous Expansions of MicroRNAs and Protein-coding Genes by Gene/Genome Duplications in Early Vertebrates. J Exp Zool B Mol Dev Evol 312: 164-170.
Cao J., Huang S., Yi P., Qian J., Jin L., Su Z., Yang J. and Liu J. (2009) Evolution of the class C GPCR Venus flytrap modules involved positive selected functional divergence. BMC Evol Biol 9:67.
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.
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.
Chen Q., Su Z., Zhong Y. and Gu X.* 2008. Effect of site-specific heterogeneous evolution on phylogenetic reconstruction: A simple evaluation. Gene 441: 156-162.
Yang J., Zou Y. and Zhu J. (2009) Identifying differentially expressed genes in human acute leukemia and mouse brain microarray datasets utilizing QTModel. Funct Integr Genomics 9: 59-66.
Gu, X*, and Su, Z (2007) Tissue-driven hypothesis of genomic evolution and sequence-expression correlations. PNAS 104:2279-2784.
Su Z., Huang Y. and Gu X.* 2007. Tissue-driven hypothesis with Gene Ontology (GO) Analysis. Ann Biomed Eng 35:1088-1094.
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.
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, Vision T, 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 (in press).
Guo, H, Weiss R. E., Gu, X, and Suchard, M. A. (2006) Time Squared: Repeated Measures on Phylogenies. Molecular Biology and Evolution (in press).
Gu X. (2006) A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences. Mol Biol Evol. Jul 24; [Epub ahead of print]
Lin H, Zhu W, Silva JC, Gu X, Buell CR. (2006) Intron gain and loss in segmentally duplicated genes in rice. Genome Biol. 7(5):R41.
Su Z, Wang J, Yu J, Huang X and Gu X*(2006) Evolution of Alternative Splicing after Gene Duplications. Genome Res. 16(2):182-9.
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 and Su Z (2005) Web-base resources for comparative genomics. Human Genomics, Vol. 2, No. 3, 187-190.
Li, W-H, Yang J, and Gu, X(2005) Expression Divergence between Duplicate Genes. Trends in Genetics 21:602-607.
Gao X, Vander Velden KA, Voytas DF and Gu X* (2005) SplitTester: software to identify domains responsible for functional divergence in protein family BMC Bioinformatics 2005, 6:137
Wu, S, Gu, X (2005) Gene Network: Model, dynamics and simulation. Lecture Notes on Computer Science, 3595: pp.12-21.
Gu, X*, Zhang, Z., Huang, W. (2005) Rapid Evolution of Expression and Regulatory Divergences after Yeast Gene 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.

Sen, T*, Kloczkowski, A., Jernigan, R., Yan, C., Honavar, V., Ho, K., Wang, C., Ihm, Y. Cao, H., Dobbs, D.,Gu, X. (2004) Prediction of binding sites of hydrolase-inhibitor complexes by combining several methods.BMC Bioinformatics. 5:205.
Zhang, H, and Gu, X* (2004) Maximum Likelihood for Genome Phylogeny on Gene Content. Statistical Applications in Genetics and Molecular Biology.
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.
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. Mol Biol Evol 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.


Gu, X (2003) Functional divergence in protein (family) sequence evolution. Genetica 118:133-141.
Gu, J, Gu, X* (2003) Induced gene expression in human brain after the split from chimpanzee. Trend in Genetics 19:63-65.
Gu, Z, Steinmetz, LM, Gu, X, Scharfe, C., Davis RD, Li, WH (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421:63-66.
Gu, J, Gu, X (2003) Natural history and functional divergence of protein tyrosine kinases. Gene 317:49-57.
Gu, X. 2003. Genetic buffering, gene duplication, and evolution. Trend in Genetic 19:354-356.
Wu, S, Gu, X (2003) Algorithms for multiple genome rearrangement by signed reversals. Pacific Symposium on Biocomputing (PSB) 8:363-374

Huang, W, Nattleton D, Gu, X (2002) Expression pattern of yeast sporulation: A case study for regulatory changes after yeast genome duplication. Information Sciences 145:261-269.
Zhou, Y. H., Zheng, J.B., Gu, X, Saunders, G. F., Yung W-K F (2002) Novel PAX6 binding sites in human genome and the role of SINE in the evolution of gene regulation. Genome Res 12:1716-1722.
Gu, J, Gu, X (2002) Functional divergence in TGF-b signaling pathway. Information Sciences 145:195-204.
Wang, Y, Gu, X (2002) Evolutionary analysis for developmental profile of gene family expression in central nervous system. Information Sciences 145:215-223.
Sun, H., Merugu S., Gu, X. Kang, Y. Dickinson, DP., Callaerts, P. and Li W-H. (2002) Identification of essential amino acid changes in paired domain evolution using a novel combination of evolutionary analysis and in vitro and in vivo studies. Mol. Biol. Evol. 19:1490-1500.
Gu, X, Wang Y, Gu, J (2002) Age-distribution of human gene families showing equal roles of large and small-scale duplications in vertebrate evolution. Nature Genetics 31:205-209.
Gaucher EA, Gu X, Miyamoto, M, Benner, S. (2002) Predicting functional divergence in protein evolution by site-specific rate shifts. Trend in Biochemical Sciences (TiBS) 27:315-321.
Wu, S, Gu, X (2002) Random shuffling permutations of nucleotides. Journal of Systemics, Cybernetics and Informatics. V1 N4: 308-313. ISBN: 980-8150-1.
Gu, X, Wang Y, Gu, J, Vander Velden K (2002) Evolutionary perspective for functional divergence of gene families and applications in functional genomics. Current Genomics. 3:201-212.
Gu, X. Huang W (2002) Testing the parsimony test of genome duplications: A counterexample. Genome Research. 12:1-2.
Gu, J, Wang Y, Gu X (2002) Pattern of Functional divergence in JAK tyrosine protein kinase family. Journal of Molecular Evolution. 54:725-733.
Gu, X, Vander Velden K (2002) DIVERGE: Phylogeny-based Analysis for Functional-Structural Divergence of a Protein Family. Bioinformatics 18:500-501.
Wu, S, Gu, X (2002) Multiple Genome Rearrangement By Reversals. Pacific Symposium on Biocomputing (PSB) 7:259-270.

Gu, X (2001) A site-specific measure for rate-difference after gene duplication or speciation. Mol Biol Evol 18:2327-2330.
Gu X (2001) Mathematical Modeling for Functional Divergence after Gene Duplication. Journal Computational Biology. 8:221-234.
Wu, S, Gu, X (2001) A greedy algorithm for optimal recombination. Lecture Notes on Computer Science (LNCS). 2108: 86-90.
Wang Y, Gu X (2001) Predicting functional divergence of caspase gene family. Genetics. 158:1311-1320.
Kumar S, Gadagkar S, Filipski A, Gu, X (2001) Determination of the Number of Conserved Chromosomal Segments between Species. Genetics 157:1387-1395
Wang Y, Gu J, Gu X (2001) Patterns of Functional Divergence after Gene Duplications in Vertebrate Gene Families: Altered Functional Constraints. In: Proceedings of the Atlantic Symposium on Computational Biology, Genome Information Systems & Technology. Pp.181-185.
Gu. J, Wang Y , Gu X (2001) Statistical Testing for Protein Functional Divergence after Major Evolutionary Events. In: Proceedings of the Atlantic Symposium on Computational Biology, Genome Information Systems & Technology. Pp.176-180
Gu X (2001) Maximum likelihood approach for gene family evolution under functional divergence. Molecular Biology and Evolution. 18: 453-464

Wang Y, Gu X (2000) Evolutionary patterns of gene families generated in the early stage of vertebrates. Journal of Molecular Evolution. 51:88-96.
Gu X (2000) A simple evolutionary model for genome phylogeny inference based on gene content. Comparative genomics (ed. Sankoff and Nadeau) Pp.515-524. Kluwer Academic Publishers.
Zhou YH, Zheng JB, Gu X, Li WH, Saunders GF (2000) A novel Pax-6 binding site in rodent B1 repetitive elements: coevolution between developmental regulation and repeated elements? Gene 245:319-328.

Gu X (1999) Statistical methods for testing functional divergence after gene duplication. Molecular Biology and Evolution 16:1664-1674.
Su C, Jakobsen I, Gu X, Nei M (1999) Diversity and evolution of T-cell receptor variable region genes in mammals and birds. Immunogenetics 50:301-308.
Gu X, Nei M (1999) Locus-specificity of polymorphic alleles and evolution by birth-and-death process in mammalian MHC genes. Molecular Biology and Evolution 16:147-156.

Gu X, Hewett-Emmett D, Li WH (1998) Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica 102/103; 383-391
Gu X (1998) Early metazoan divergence is about 830 million years ago.Journal of Molecular Evolution 47:369-371
Zhang J, Gu X (1998) Correlation between substitution rate and rate variation among sites. Genetics 149:1615-1625
Gu X, Li WH (1998) Evolutionary distances under stationary and nonstationary models of nucleotide substitutions. PNAS 95: 5899-5905.
Huang W, Yun-Xin Fu, Chang B HJ, Gu X, Jorde LB, Li WH (1998) Sequence variation in ZFX introns in human populations. Molecular Biology and Evolution 15:138-142.

Gu X, Zhang J (1997) A simple method for estimating the parameter of substitution rate variation among sites. Molecular Biology and Evolution. 14:1106-1113.
Nei M, Gu X, Stinikova T (1997) Evolution by the birth-and-death process in multigene families of the vertebrate immune systems. PNAS 94:7799-7806.
Gu X(1997) The age of common ancestor of eukaryotes and prokaryotes. Molecular Biology and Evolution 14:861-866.
Huang W, Chang B HJ, Gu X, Hewett-Emmett D, Li WH (1997) Sex differences in mutation rate in higher primates estimated from AMG intron sequences. Journal of Molecular Evolution. 44:463-465.

Gu X, Li WH (1996) Bias-corrected paralinear and LogDet distances and tests of molecular clocks and phylogenies under nonstationary nucleotide frequencies. Molecular Biology and Evolution. 13:1375-1383.
Gu X, Zera AJ (1996) Quantitative genetics of juvenile hormone esterase, juvenile hormone binding and general esterase activity in the cricket, Gryllus assimilis. Heredity. 76:136-142.
Li WH, Gu X (1996) Estimating evolutionary distances. Methods in Enzymology 266:449-459. Academic Press, Inc.
Gu X, Li WH (1996) A general additive distance with time-reversibility and rate variation among nucleotide sites. PNAS 93:4671-4676.

1995 and before
Li WH, Gu X (1995) Statistical models for studying DNA sequence evolution. Physica A. 221:159-167
Gu X, Li WH (1995) The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. Journal of Molecular Evolution 40:464-473
Gu X, Fu YX, Li WH (1995) Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Molecular Biology and Evolution 12: 546-557.
Gu X, Zera AJ (1994) Developmental profiles and characteristics of hemolymph juvenile hormone esterase, general esterase and juvenile hormone binding in the cricket, Gryllus assimilis. Comparative Biochemistry and Physiology 107B:553-560
Gu X, Li WH (1994) A model for the correlation of mutation rate with GC content and the origin GC-rich isochores. Journal of Molecular Evolution 38:468-475
Zera AJ, Gu X, Zeisset M (1992) Characterization of juvenile hormone esterase from genetically-determined wing morphs of the cricket, Gryllus Rubens. Insect Biochemistry and Molecular Biology 22:829-839
Gu X, Li WH (1992) Higher rates of amino acid substitution in rodents than in humans. Molecular Phylogenetics and Evolution 1:211-214
Gu X (1988) The stable selection and genetic information threshold in Mendelian population. Bulletin of Science, Sinica 33:1792-1795
Gu X, Liu TT (1988) The diffusion model of gene in the population with overlapping generations and its heterozygosity. Bulletin of Science, Sinica 33:1641-1645
Gu X, Xu JG (1987) The diffusion model on the competition among subpopulations under the group selection. Bulletin of Science, Sinica 32:537-540