Publications

Peer-reviewed publications (corresponding author is marked by *)
  1. Gu X, Xu JG (1987) The diffusion model on the competition among subpopulations under the group selection. Bulletin of Science, Sinica 32:537-540
  2. 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
  3. Gu X *(1988) The stable selection and genetic information threshold in Mendelian population. Bulletin of Science, Sinica 33:1792-1795
  4. Gu X, Li WH (1992) Higher rates of amino acid substitution in rodents than in humans. Molecular Phylogenetics and Evolution 1:211-214
  5. 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
  6. 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
  7. 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
  8. 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.
  9. 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
  10. Li WH, Gu X (1995) Statistical models for studying DNA sequence evolution. Physica A. 221:159-167
  11. Gu X, Li WH (1996) A general additive distance with time-reversibility and rate variation among nucleotide sites. PNAS 93:4671-4676.
  12. Li WH, Gu X (1996) Estimating evolutionary distances. Methods in Enzymology 266:449-459. Academic Press, Inc.
  13. 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.
  14. 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.
  15. 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.
  16. Gu X*(1997) The age of common ancestor of eukaryotes and prokaryotes. Molecular Biology and Evolution 14:861-866.
  17. 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.
  18. 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.
  19. 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.
  20. Gu X, Li WH (1998) Evolutionary distances under stationary and nonstationary models of nucleotide substitutions. PNAS 95: 5899-5905.
  21. Zhang J, Gu X (1998) Correlation between substitution rate and rate variation among sites. Genetics 149:1615-1625
  22. Gu X* (1998) Early metazoan divergence is about 830 million years ago. Journal of Molecular Evolution 47:369-371
  23. Gu X, Hewett-Emmett D, Li WH (1998) Direct mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica 102/103; 383-391
  24. 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.
  25. 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.
  26. Gu X* (1999) Statistical methods for testing functional divergence after gene duplication. Molecular Biology and Evolution 16:1664-1674.
  27. 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.
  28. 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.
  29. Wang Y, Gu X* (2000) Evolutionary patterns of gene families generated in the early stage of vertebrates. Journal of Molecular Evolution. 51:88-96.
  30. Gu X* (2001) Maximum likelihood approach for gene family evolution under functional divergence. Molecular Biology and Evolution. 18: 453-464
  31. 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
  32. 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.
  33. Kumar S, Gadagkar S, Filipski A, Gu, X (2001) Determination of the Number of Conserved Chromosomal Segments between Species. Genetics 157:1387-1395
  34. Wang Y, Gu X* (2001) Functional divergence in the caspase gene family and altered functional constraints: Statistical analysis and prediction. Genetics. 158:1311-1320.
  35. Wu, S, Gu, X* (2001) A greedy algorithm for optimal recombination. Lecture Notes on Computer Science (LNCS). 2108: 86-90.
  36. Gu X* (2001) Mathematical Modeling for Functional Divergence after Gene Duplication. Journal Computational Biology. 8:221-234.
  37. Gu, X* (2001) A simple site-specific measure for the rate-difference between gene family members. Molecular Biology and Evolution 18:2327-2330.
  38. Wu, S, Gu, X* (2002) An Approximation for Multiple Genome Rearrangement By Reversals. Pacific Symposium on Biocomputing (PSB) 7:259-270.
  39. Gu, X*, Vander Velden K (2002) DIVERGE: Phylogeny-based Analysis for Functional-Structural Divergence of a Protein Family. Bioinformatics 18:500-501.
  40. Gu, J, Wang Y, Gu X* (2002) Pattern of Functional divergence in JAK tyrosine protein kinase family. Journal of Molecular Evolution. 54:725-733.
  41. Gu, X*. Huang W (2002) Testing the parsimony test of genome duplications: A counterexample. Genome Research. 12:1-2.
  42. 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.
  43. Wu, S, Gu, X* (2002) Random shuffling permutations of nucleotides. The 6th world Multiconference on Systemics, Cybernetics and Informatics. V 13: 308-313. ISBN: 980-8150-1.
  44. 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.
  45. 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.
  46. 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. Molecule Biology and Evolution 19:1490-1500.
  47. Wang, Y, Gu, X* (2002) Evolutionary analysis for developmental profile of gene family expression in central nervous system. Information Sciences 145:215-223
  48. Gu, J, Gu, X* (2002) Functional divergence in TGF- signaling pathway. Information Sciences. 145:195-204.
  49. 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 Research. 12:1716-1722.
  50. 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.
  51. Gu, X* (2003) Functional divergence in protein (family) sequence evolution. Genetica 118:133-141.
  52. Wu, S, Gu, X* (2003) Algorithms for multiple genome rearrangement by signed reversals. Pacific Symposium on Biocomputing (PSB) 8: 363-374.
  53. 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.
  54. Gu, J, Gu, X* (2003) Natural history and functional divergence of protein tyrosine kinases. Gene 317:49-57.
  55. Gu, J, Gu, X* (2003) Induced gene expression in human brain after the split from chimpanzee. Trends in Genetics 19:63-65.
  56. Gu, X*. (2003) Genetic buffering, gene duplication, and evolution. Trends in Genetics. 19:354-356.
  57. S Wu, Gu, X (2003) Random Shuffling Permutations of Nucleotides. Journal of
  58. Systemics, Cybernetics and Informatics 1:4 (ISBN 1690-4524).
  59. 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.
  60. 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
  61. Gu, X* (2004) Statistical framework for phylogenetic analysis of expression profiles. Genetics 167: 531-542.
  62. 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.
  63. Gu, X*, Zhang H (2004) Genome phylogeny inference based on gene contents. Molecular Biology and Evolution 21:1401-1408.
  64. 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.
  65. 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.
  66. Zhang H, Gu, X* (2004) Maximum Likelihood for Genome Phylogeny on Gene Content. Statsitical Applications in Genetics and Molecular Biology 3:1 Article 31
  67. 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
  68. Gu, X*, Zhang Z, and Wei Huang (2005) Rapid evolution of expression and regulatory network after yeast gene/genome duplications. PNAS 102:707-712
  69. Gu, X*, Huang, W, Xu, D, Zhang H (2005) GeneContent: Software for Whole-Genome Phylogenetic Analysis. Bioinformatics 21(8):1713-1714.
  70. Gu X*, Su, ZX (2005) Web-based resources for comparative genomics. Human Genomics Vol.2, No.3, 1-4.
  71. Li, W-H, Yang, J and Gu, X (2005) Expression divergence between duplicates. Trends in Genetics. 21:602-607.
  72. Gao, X, Kent V Voytas, D, Gu, X* (2005) Tree-based method to identify protein functional domains. BMC Bioinformatics 6:137.
  73. Wu, S, Gu, X (2005) Gene Network: Model, dynamics and simulation. Lecture Notes on Computer Science: 3595: pp.12-21.
  74. 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.
  75. 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. 10:231-237.
  76. Lin H, Zhu W, Silva JC, Gu X, and Buell R (2006) Intron turnover of segmentally duplicated genes in rice. Genome Biology 7(5):R41.
  77. 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.
  78. 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.
  79. Su Z, Wang J, Yu J, Huang X and Gu X* (2006) Evolution of Alternative Splicing after Gene Duplications. Genome Research 16:182-189.
  80. Gu, X*, and Su, Z (2007) Tissue-driven hypothesis of genomic evolution and sequence-expression correlations. PNAS 104:2279-2784.
  81. 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
  82. 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
  83. 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.
  84. Gu, X* (2007) Evolutionary framework for protein sequence evolution and gene pleiotropy, Genetics 175:1813-1822.
  85. Huang, Y, X Gu* (2007) A bootstrap based analysis pipeline for efficient identification of phylogenetically related animal miRNAs. BMC Genomics 8:66
  86. 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
  87. 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.
  88. 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.
  89. Gu, X*. (2007) Stabilizing selection of protein function and distribution of selection coefficient among sites. Genetica 130:93-97.
  90. 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.
  91. X, Gu*, Yong Huang (2008) Human Transcriptome Evolution. Encyclopedia of Life Sciences. In press.
  92. 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.
  93. 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
  94. 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
  95. 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.
  96. 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.
  97. 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.
  98. 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.
  99. 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.
  100. Blake Mertz,1 Xun Gu, Peter J. Reilly (2009) Analysis of Functional Divergence within Two Structurally Related Glycoside Hydrolase Families. Biopolymer 91:479-495.
  101. 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.
  102. 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.
  103. 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
  104. 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
  105. 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.
  106. 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.
  107. 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.
  108. 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.
  109. 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.
  110. Z Su, W Huang, X Gu* (2011) Comments on ‘Positive selection of tyrosine losses during Metazoan evolution. Science, 332, 917
  111. 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.
  112. 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.
  113. 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
  114. Chen W, Zhou W, Tian X, Gu, X*. 2012. A Computational Analysis Framework for Molecular Cell Dynamics: Case-study of Exocytosis. PLoS ONE 7(7): e38699. doi:10.1371/journal.pone.0038699.
  115. Su, X, Gu, X*. 2012. Revisit on the Evolutionary Relationship between Alternative Splicing and Gene Duplication. Gene 504 (1): 102-106.
  116. 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.
  117. Xia, T, Tong J, Rathore SS, Gu, X and Dickerson JA (2012) Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis. BMC Systems Biology, 6:19 doi:10.1186/1752-0509-6-19.
  118. 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.
  119. 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.
  120. 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
  121. 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.
  122. 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.
  123. Chen W, Su Z, Gu X* (2013) A note on gene pleiotropy estimation from phylogenetic analysis of protein sequences. Journal of Systematics and Evolution 51(3): 365-369.
  124. Gu X* (2014) Pleiotropy can be effectively estimated without counting phenotypes through the rank of a genotype-phenotype map. Genetics 197(4): 1357-1363.
  125. Zhou Z, Zhou J, Su Z*, Gu X* (2014) Asymmetric evolution of human transcription factor regulatory networks. Mol Biol Evol 31(8): 2149-2155.
  126. Liu G, Zou Y, Cheng Q, Zeng Y, Gu X, Su Z*. (2014) Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations. Mol Genet Genomics 289(2): 137-147.
  127. Su Z, Wang J, Gu X* (2014) Effect of duplicate genes on mouse genetic robustness: an update. BioMed research international 2014:758672. doi:10.1155/2014/758672.
  128. Chen W, Chen D, Zhao M, Zou Y, Zeng Y*, Gu X* (2015) Genepleio software for effective estimation of gene pleiotropy from protein sequences. BioMed research international 2015:269150. doi:10.1155/2015/269150
  129. Shen L, Liu G, Zou Y, Zhou Z, Su Z, Gu X* (2015) The evolutionary panorama of organ-specifically expressed or repressed orthologous genes in nine vertebrate species. PloS one 10 (2):e0116872. doi:10.1371/journal.pone.0116872
  130. Gu X* (2016) Statistical detection of differentially expressed genes based on RNA-seq: from biological to phylogenetic replicates. Briefings in bioinformatics 17 (2):243-248. doi:10.1093/bib/bbv035
  131. Gu X* (2016) Understanding tissue expression evolution: from expression phylogeny to phylogenetic network. Briefings in bioinformatics 17 (2):249-254. doi:10.1093/bib/bbv041
  132. Ruan H, Su Z, Gu X* (2016) TreeExp1.0: R Package for Analyzing Expression Evolution Based on RNA-Seq Data. Journal of experimental zoology Part B, Molecular and developmental evolution 326 (7):394-402. doi:10.1002/jez.b.22707
  133. Wang Y, Tao XF, Su ZX, Liu AK, Liu TL, Sun L, Yao Q, Chen KP, Gu X (2016) Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization. Evolutionary bioinformatics online 12:303-312. doi:10.4137/ebo.S40703
  134. Zhang Z, Shen L, Gu X* (2016) Evolutionary Dynamics of MERS-CoV: Potential Recombination, Positive Selection and Transmission. Scientific reports 6:25049. doi:10.1038/srep25049
  135. Cvekl A, Zhao Y, McGreal R, Xie Q, Gu X, Zheng D (2017) Evolutionary Origins of Pax6 Control of Crystallin Genes. Genome biology and evolution 9 (8):2075-2092. doi:10.1093/gbe/evx153
  136. Gu X, Ruan H, Su Z, Zou Y (2017) Brownian model of transcriptome evolution and phylogenetic network visualization between tissues. Molecular phylogenetics and evolution 114:34-39. doi:10.1016/j.ympev.2017.03.027
  137. Gu X, Tang W (2017) Model parameters of molecular evolution explain genomic correlations. Briefings in bioinformatics 18 (1):37-42. doi:10.1093/bib/bbv098
  138. Liu A, He F, Gu X (2017) Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates. Molecular genetics and genomics : MGG 292 (6):1405-1418. doi:10.1007/s00438-017-1356-7
  139. Sa Z, Zhou J, Zou Y, Su Z, Gu X (2017) Paralog-divergent Features May Help Reduce Off-target Effects of Drugs: Hints from Glucagon Subfamily Analysis. Genomics, proteomics & bioinformatics 15 (4):246-254. doi:10.1016/j.gpb.2017.03.004
  140. Zhou J, Liu D, Sa Z, Huang W, Zou Y, Gu X (2017) Effective estimation of the minimum number of amino acid residues required for functional divergence between duplicate genes. Molecular phylogenetics and evolution 113:126-138. doi:10.1016/j.ympev.2017.05.010
  141. Zhou Z, Lyu X, Wu J, Yang X, Wu S, Zhou J, Gu X, Su Z, Chen S (2017) TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection. Royal Society open science 4 (4):170050. doi:10.1098/rsos.170050
  142. Zhou Z, Wu S, Lai J, Shi Y, Qiu C, Chen Z, Wang Y, Gu X, Zhou J, Chen S (2017) Identification of trunk mutations in gastric carcinoma: a case study. BMC medical genomics 10 (1):49. doi:10.1186/s12920-017-0285-y
  143. Zhou Z, Zou Y, Liu G, Zhou J, Wu J, Zhao S, Su Z, Gu X (2017) Mutation-profile-based methods for understanding selection forces in cancer somatic mutations: a comparative analysis. Oncotarget 8 (35):58835-58846. doi:10.18632/oncotarget.19371
  144. Wu J, Zhao W, Zhou B, Su Z, Gu X, Zhou Z, Chen S (2018) TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis. Genomics, proteomics & bioinformatics 16 (4):276-282. doi:10.1016/j.gpb.2018.06.003
  145. Gu X, Ruan H, Yang J (2019) Estimating the strength of expression conservation from high throughput RNA-seq data. Bioinformatics (Oxford, England) 35 (23):5030-5038. doi:10.1093/bioinformatics/btz405
  146. He F, Wei R, Zhou Z, Huang L, Wang Y, Tang J, Zou Y, Shi L, Gu X, Davis MJ, Su Z (2019) Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes. Scientific reports 9 (1):8205. doi:10.1038/s41598-019-44489-5
  147. Li Q, Liu A, Gu X, Su Z (2019) Olfactomedin domain-containing proteins: evolution, functional divergence, expression patterns and damaging SNPs. Molecular genetics and genomics : MGG 294 (4):875-885. doi:10.1007/s00438-019-01549-9
  148. Liu A, He F, Zhou J, Zou Y, Su Z, Gu X (2019) Comparative Transcriptome Analyses Reveal the Role of Conserved Function in Electric Organ Convergence Across Electric Fishes. Frontiers in genetics 10:664. doi:10.3389/fgene.2019.00664
  149. Su W, Gu X, Peterson T (2019) TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome. Molecular plant 12 (3):447-460. doi:10.1016/j.molp.2019.02.008
  150. Wu J, Wang W, Zhang J, Zhou B, Zhao W, Su Z, Gu X, Wu J, Zhou Z, Chen S (2019) DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity. Frontiers in immunology 10:2559. doi:10.3389/fimmu.2019.02559
  151. Yang J, Ruan H, Xu W, Gu X (2019) TreeExp2: An Integrated Framework for Phylogenetic Transcriptome Analysis. Genome biology and evolution 11 (11):3276-3282. doi:10.1093/gbe/evz222
  152. Yang J, Ruan H, Zou Y, Su Z, Gu X (2020) Ancestral transcriptome inference based on RNA-Seq and ChIP-seq data. Methods (San Diego, Calif) 176:99-105. doi:10.1016/j.ymeth.2018.11.010
  153. Zhou Y, He F, Pu W, Gu X, Wang J, Su Z (2020) The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development. G3 (Bethesda, Md) 10 (9):3337-3346. doi:10.1534/g3.120.401511
  154. Wu S, Haltom J, Zhao W, Yang J, Zhou Z, Gu X (2021) Evolution and functional divergence of the ERBB receptor family. Pharmacogenomics 22 (8):473-484. doi:10.2217/pgs-2020-0158
  155. Zhao W, Yang J, Wu J, Cai G, Zhang Y, Haltom J, Su W, Dong MJ, Chen S, Wu J, Zhou Z, Gu X (2021) CanDriS: posterior profiling of cancer-driving sites based on two-component evolutionary model. Briefings in bioinformatics 22(5):bbab131. doi:10.1093/bib/bbab131
  156. Zhou Z, Wu J, Ren J, Chen W, Zhao W, Gu X, Chi Y, He Q, Yang B, Wu J, Chen S (2021) TSNAD v2.0: A one-stop software solution for tumor-specific neoantigen detection. Computational and structural biotechnology journal 19:4510-4516. doi:10.1016/j.csbj.2021.08.016
  157. Liu J, Gu X, Li H (2022) Assembly of 97 Novel Bacterial Genomes in the Microbial Community Affiliated with Polyvinyl Alcohol in Soil of Northern China. BioMed research international 2022:2229147. doi:10.1155/2022/2229147
  158. Gu X (2022) A Simple Evolutionary Model of Genetic Robustness After Gene Duplication. J Mol Evol. 90(5):352-361. doi: 10.1007/s00239-022-10065-1.
  159. Gu X (2022) dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution. J Mol Evol. 90(5):342-351. doi: 10.1007/s00239-022-10064-2.
  160. Wu J, Chen W, Zhou Y, Chi Y, Hua X, Wu J, Gu X, Chen S, Zhou Z (2022) TSNAdb v2.0: the Updated Version of Tumor-specific Neoantigen Database. Genomics Proteomics Bioinformatics. S1672-0229(22)00128-0. doi: 10.1016/j.gpb.2022.09.012.
  161. Zhao W, Gu X, Chen S, Wu J, Zhou Z (2022) MODIG: integrating multi-omics and multi-dimensional gene network for cancer driver gene identification based on graph attention network model. Bioinformatics. 38(21):4901-4907. doi: 10.1093/bioinformatics/btac622.