Publications
Books:
  1. Xia, X. 2007. Bioinformatics and the cell: modern computational approaches in genomics, proteomics and transcriptomics. Springer. 361 pp.
  2. Xia, X. 2000. Data Analysis in Molecular Biology and Evolution. Kluwer Academic Publishers. Find the book in a library near you. See publications that have cited the book
Book chapters:
  1. Xia, X. 2012. Cenancestor. In: S Maloy, K Hughes, editors. Encyclopedia of Genetics, 2nd edition: Elsevier.
  2. Xia, X. 2012. Codominance. In: S Maloy, K Hughes, editors. Encyclopedia of Genetics, 2nd edition: Elsevier.
  3. Xia, X., C.R. Primmer. 2012. Genotypic Frequency In: S Maloy, K Hughes, editors. Encyclopedia of Genetics, 2nd edition: Elsevier.
  4. Xia, X. 2012. Wobble hypothesis. In: S Maloy, K Hughes, editors. Encyclopedia of Genetics, 2nd edition: Elsevier.
  5. Xia, X. 2012. Rapid evolution in animal mitochondria. Pp. 73-82 In R S. Singh, J. Xu and R. J. Kulathinal (eds.) Evolution In The Fast Lane: Rapidly Evolving Genes and Genetic Systems . Oxford University Press.
  6. Xia, X. 2011. Comparative genomics. Pp. 567-600 in H. H-S Lu, B. Schölkopf, H. Zhao, eds. Handbook of Computational Statistics: Statistical Bioinformatics. Springer.
  7. Xia, X. and Lemey, P. 2009. Assessing substitution saturation with DAMBE. Pp. 615-630 in Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme, eds. The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. 2nd edition. Cambridge University Press
  8. Xia, X. 2007. Molecular phylogenetics: mathematical framework and unsolved problems. Pp. 169-189 in U. Bastolla, M. Porto, H. E. Roman and M. Vendruscolo, eds. Structural approaches to sequence evolution. Springer-Verlag.
  9. Xia, X. Kumar, S. 2006. Codon-based detection of positive selection can be biased by heterogeneous distribution of polar amino acids along protein sequences. In: Markstein P, Xu Y (eds) COMPUTATIONAL SYSTEMS BIOINFORMATICS: Proceedings of the Conference CSB 2006. Imperial College Press, pp. 335-340.
  10. Xia, X. 2005. Content sensors based on codon structure and dna methylation for gene finding in vertebrate genomes. Pp. 21-29 in N. Kolchanov and R. Hofestadt (eds) Bioinformatics of Genome Regulation And Structure II. Springer Science+Business Media, Inc.
  11. Xia, X., Li, C., Yang, Q. 2003. Routine analysis of molecular data with software DAMBE. Pp. 149-167 in Yang, Q. ed. Fundamental concepts and methodology in molecular palaeontology. Science Publishers, China.
  12. Xia, X. and Z. Xie. 2003. Data exploration and tetrapod phylogeny. Pp. 329-347 in Marco Salemi and Anne-Mieke Vandamme, eds. The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. Cambridge University Press June, 2003.
  13. Xia, X. 1999. Estimating the frequency of litters with multiple paternity by using molecular data. in The application, methods and theories in molecular ecology, eds. Zhu, Y. G, Sun, M, Le, K. CHEP-Springer. Pp. 136-151.
My papers in PubMed
Refereed papers (My students and postdoctoral fellows in red italics)
  1. Xia, X. 2012. DNA Replication and Strand Asymmetry in Prokaryotic and Mitochondrial Genomes. Current Genomics 13, 16-27
  2. Vos, R. A., Balhoff, J. P., Caravas, J. A., Holder, M. T., Lapp, H., Maddison, W. P., Midford, P. E., Priyam, A., Sukumaran, S. Xia, X., Stoltzfus, A. 2012. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology. doi:10.1093/sysbio/sys025
  3. Xia, X. , MacKay, V., Yao, X., Wu, J., Miura, F. Ito, T. Morris, D. R. 2011. Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae. Genetics 189:469-478
  4. Ma, P.,Ma, P., Xia X. 2011. Factors affecting splicing strength of yeast genes. Comparative and Functional Genomics. Article ID 212146, 13 pages
  5. Xia, X. , Yang, Q. 2011. A Distance-based Least-square Method for Dating Speciation Events. Molecular Phylogenetics and Evolution 59:342-353.
  6. van Weringh, A, M. Ragonnet-Cronin, E. Pranckeviciene, M. Pavon-Eternod, L. Kleiman, X. Xia. 2011. HIV-1 modulates the tRNA pool to improve translation efficiency. Molecular Biology and Evolution 28:1827-1834
  7. Xia, X. 2010. The Effect of Probe Length and GC% on Microarray Singal Intensity: Characterizing the Functional Relationship. International Journal of Systems and Synthetic Biology 1:171-183.
  8. Palidwor GA, Perkins TJ, Xia X. 2010. A General Model of Codon Bias Due to GC Mutational Bias. PLoS ONE 5(10): e13431.
  9. Jiang, J.-Y., H. Xiong, M. Cao, X. Xia, M.-A. Sirard, B Tsang. 2010. Mural granulosa cell gene expression associated with oocyte developmental competence. Journal of Ovarian Research 2010, 3:6.
  10. Zhang, D., J. T. Popesku, C. J. Martyniuk, H. Xiong, P. Duarte-Guterman, L. Yao, Xia, X., and V. L. Trudeau. 2009. Profiling neuroendocrine gene expression changes following fadrozole-induced estrogen decline in the female goldfish. Physiol. Genomics 38:351-361.
  11. Li, H., G. Liu, and X. Xia. 2009. Correlations between recombination rate and intron distributions along chromosomes of C. elegans. Progress in Natural Science 19:517.
  12. Xia, X. 2009. Information-theoretic indices and an approximate significance test for testing the molecular clock hypothesis with genetic distances. Molecular Phylogenetics and Evolution 52:665-676.
  13. Xia, X., Holcik, M., 2009. Strong Eukaryotic IRESs Have Weak Secondary Structure. PLoS ONE 4, e4136.
  14. Cong, P., X. Xia, and Q. Yang. 2009. Monophyly of the ring-forming group in Diplopoda (Myriapoda, Arthropoda) based on SSU and LSU ribosomal RNA sequences. Progress in Natural Science 19:1297-1303
  15. Zhang, D., H. Xiong, J. A. Mennigen, J. T. Popesku, V. L. Marlatt, C. J. Martyniuk, K. Crump, A. R. Cossins, X. Xia, and V. L. Trudeau. 2009. Defining Global Neuroendocrine Gene Expression Patterns Associated with Reproductive Seasonality in Fish. PLoS ONE 4:e5816..
  16. Zhang, D., H. Xiong, J. Shan, X. Xia, and V. Trudeau. 2008. Functional insight into Maelstrom in the germline piRNA pathway: a unique domain homologous to the DnaQ-H 3'-5' exonuclease, its lineage-specific expansion/loss and evolutionarily active site switch. Biology Direct 3:48.
  17. Popesku, J. T., C. J. Martyniuk, J. Mennigen, H. Xiong, D. Zhang, X. Xia, A. R. Cossins, and V. L. Trudeau. 2008. The goldfish (Carassius auratus) as a model for neuroendocrine signaling. Mol Cell Endocrinol. 293(1-2):43-56
  18. Vinci, G., X. Xia, and R. A. Veitia. 2008. Preservation of Genes Involved in Sterol Metabolism in Cholesterol Auxotrophs: Facts and Hypotheses. PLoS ONE 3:e2883.
  19. Xia, X. 2008. The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses. BMC Evolutionary Biology 8:211.
  20. Mennigen, J. A., C. J. Martyniuk, K. Crump, H. Xiong, E. Zhao, J. Popesku, H. Anisman, A. R. Cossins, X. Xia, and V. L. Trudeau. 2008. Effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus). Physiol. Genomics 35:273-282.
  21. Marin, A. and Xia, X. 2008. GC skew in protein-coding genes between the leading and lagging strands in bacterial genomes: new substitution models incorporating strand-bias. Journal of Theoretical Biology 253(3):508-513
  22. Aris-Brosou, S. and Xia, X. 2008 Phylogenetic analyses: a toolbox expanding towards Bayesian methods. International Journal of Plant Genomics Article ID 683509.
  23. Carullo, M. and Xia, X. 2008 An extensive study of mutation and selection on the wobble nucleotide in tRNA anticodons in fungal mitochondrial genomes. Journal of Molecular Evolution 66:484-493 .
  24. Marlatt, V.L., Martyniuk, C. J., Zhang, D., Xiong, H., Watt, J., Xia, X., Moon, T., Trudeau, V.L. 2008. Auto-regulation of estrogen receptor subtypes and gene expression profiling of 17beta-estradiol action in the neuroendocrine axis of male goldfish. Molecular and Cellular Endocrinology 283:38-48.
  25. Xiong, H., Zhang D., Martyniuk, C.J., Trudeau, V.L., Xia, X.. 2008. Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data. BMC Bioinformatics, 9(2008) 25
  26. Khalouei, S., Xia, X.. 2008. Selective pressure against AUG triplets in the 5' untranslated region of human immunodeficiency virus type 1 supports cap-dependent translation initiation mechanism. Retrovirology: Research and Treatment 2:1-8.
  27. Xia, X. 2007. An Improved Implementation of Codon Adaptation Index. Evolutionary Bioinformatics 3:53–58.
  28. Xia, X., Huang H.,Carullo, M.,Betran, E.,Moriyama, E. 2007. Conflict between translation initiation and elongation in vertebrate mitochondrial genomes. PLoS ONE 2(2): e227.
  29. Xia, X. 2007. The +4G site in Kozak consensus is not related to the efficiency of translation initiation. PLoS ONE 2(2):e188.
  30. Khalouei, S., X. Yao, J. Mennigen, M. Carullo, P. Ma, Z. Song, H. Xiong, and Xia, X.. 2007. Bioinformatic Approach to Identify Penultimate Amino Acids Efficient for N-Terminal Methionine Excision. Pp. 386-389. Bioinformatics and Biomedical Engineering, 2007, IEEE. The 1st International Conference on Bioinformatics and Biomedical Engineering (ICBBE2007).
  31. Martyniuk, C. J., Xiong H., Crump, K., Chiu, S., Sardana, R., Nadler, A., Gerrie, E. R., Xia, X., Trudeau, V. L. 2006. Gene expression profiling in the neuroendocrine brain of male goldfish (Carassius auratus) exposed to 17-alpha-ethinylestradiol. Physiol. Genomics 27(3):328-336.
  32. Xia, X. 2006. Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances. Evolutionary Bioinformatics 2006: 2 375–387.
  33. Wang, H. C., Xia, X. , D. Hickey. 2006. Thermal adaptation of small ribosomal RNA genes: a comparative study. Journal of Molecular Evolution 63(1):120-126
  34. Xia, X. , Wang, H. C., Z. Xie, M. Carullo, H. Huang, and D. Hickey. 2006. Cytosine usage modulates the correlation between CDS length and CG content in prokaryotic genomes. Molecular Biology and Evolution 23:1450-1454
  35. Cai, J. J., Smith, D. K., Xia, X. , Yuen, K. Y. 2006. MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution. Evolutionary Bioinformatics 2:187-190.
  36. Xia, X. and G. Palidwor. 2005. Genomic Adaptation to Acidic Environment: Evidence from Helicobacter pylori. American Naturalist 166:776-784
  37. Shi, B., and X. Xia. 2005. Genetic variation in clones of Pseudomonas pseudoalcaligenes after ten months of selection in different thermal environments in the laboratory. Curr Microbiol 50:238-45.
  38. Xia. X. and K. Y. Yuen. 2005. Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage. BMC Genetics 6:20.
  39. Cai, J., Smith, D., X. Xia, and K. Y. Yuen. 2005. MBEToolbox: a Matlab toolbox for sequence data analysis of molecular biology and evolution. BMC Bioinformatics 6:64.
  40. Xia, X. 2005. Mutation and Selection on the Anticodon of tRNA Genes in Vertebrate Mitochondrial Genomes. Gene 345:13-20.
  41. Baron, D., J. Cocquet, X. Xia, M. Fellous, Y. Guiguen, and R. A. Veitia. 2004. An evolutionary and functional analysis of FoxL2 in rainbow trout gonad differentiation. J. Mol. Endocrinol. 33:705-715.
  42. Xia, X. 2004. A peculiar codon usage pattern revealed after removing the effect of DNA methylation. Proceedings of the 4th International Conference on Bioinformatics of Genome Regulation and Structure 1:216-220.
  43. Cocquet, J., E. De Baere, M. Gareil, M. Pannetier, X. Xia, M. Fellous, R. Veitia. 2003. Structure, evolution and expression of the FOXL2 transcription unit. Cytogenetic Genome Res 101:206-211.
  44. X. Xia. 2003. DNA methylation and Mycoplasma genomes. Journal of Molecular Evolution 57:S21-S28.
  45. Shi, B., X. Xia. 2003. Changes in growth parameters of Pseudomonas pseudoalcaligenes after ten months culturing at increasing temperature in the laboratory. FEMS Microbiology Ecology 45:127-134.
  46. Xia, X., Z. Xie, K. Kjer. 2003. 18S rRNA and Tetrapod Phylogeny. Systematic Biology 52(3):283-295 (Editor's choice in Science)
  47. Xia, X., Z. Xie, W. H. Li. 2003. Effects of GC Content and Mutational Pressure on the Lengths of Exons and Coding Sequences. Journal of Molecular Evolution 56:362-370.
  48. Shi, B., X. Xia. 2003. Morphological changes of Pseudomonas pseudoalcaligenes in response to temperature selection. Current Microbiology 46:120-123.
  49. Xia, X., Z. Xie, M. Salemi, L. Chen, Y. Wang. 2003. An index of substitution saturation and its application. Molecular Phylogenetics and Evolution 26:1-7.
  50. Cocquet, J., E. Pailhoux, F. Jaubert, N. Servel, X. Xia, M. Pannetier, E. De Baere, L. Messiaen, C. Cotinot, M. Fellous, R. Veitia. 2002. Evolution and expression of FOXL2. Journal of Medical Genetics.39:916-921.
  51. Xia, X., T. Wei, Z. Xie and A. Danchin. 2002. Genomic changes in nucleotide and di-nucleotide frequencies in Pasteurella multocida cultured under high temperature. Genetics 161:1385-94.
  52. Xia, X. and Z. Xie. 2002. Protein Structure, Neighbor Effect, and a New Index of Amino Acid Dissimilarities. Molecular Biology and Evolution 19:58-67.
  53. Xia, X. and Z. Xie. 2001. AMADA: Analysis of microarray data. Bioinformatics 17:569-570.
  54. Xia, X. and Z. Xie. 2001. DAMBE: Data analysis in molecular biology and evoluiton. Journal of Heredity 92:371-373.
  55. Chen, B., and X. Xia, 2001 The genus Schevodera Borchmann: Phylogeny, historic biogeography and new Chinese records, with description of a new species (Coleoptera: Tenebrionidae: Lagriinae). Oriental Insects 35: 3-27.
  56. Xia, X. 2000. Phylogenetic Relationship among Horseshoe Crab Species: The Effect of Substitution Models on Phylogenetic Analyses. Systematic Biology 49:87-100.
  57. Xia, X. and W.-H. Li 1998. What amino acid properties affect protein evolution? Journal of Molecular Evolution 47:557-564.
  58. Xia, X. 1998. How optimized is the translational machinery in E. coli, S. typhimurium, and S. cerevisiae? Genetics 149: 37-44.
  59. Xia, X. 1998. The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes. Molecular Biology and Evolution 15:336-344.
  60. Xia, X. 1996. Maximising transcription efficiency causes codon usage bias. Genetics 144:1309-1320.
  61. Xia, X., Hafner, M. S. and P. D. Sudman. 1996. On transition bias in mitochondrial genes of pocket gophers. Journal of Molecular Evolution 43:32-40.
  62. Xia, X. 1995. Body temperature, rate of biosynthesis, and evolution of genome size. Molecular Biology and Evolution 12:834-842.
  63. Xia, X. 1995. Revisiting Hamilton's rule. American Naturalist 145:483-492.
  64. Xia, X. 1993. A full sibling is not as valuable as an offspring: on Hamilton's rule. American Naturalist 142:174-185.
  65. Boonstra, R., Xia, X. and L. Pavone. 1992. Mating system of the meadow vole, Microtus pennsylvanicus. Behavioral Ecology 4:83-89.
  66. Xia, X. and R. Boonstra. 1992. Measuring temporal variation in population density: a critique. American Naturalist 140:883-892.
  67. Xia, X. 1992. Uncertainty of paternity can select against paternal care. American Naturalist 139:1126-1129.
  68. Xia, X. and J. S. Millar. 1991. Genetic evidence of promiscuity in Peromyscus leucopus. Behavioral Ecology and Sociobiology 28:171-178.
  69. Millar, J. S., Xia, X. and M. B. Norrie. 1991. Relationship among reproductive status, nutritional status and food characteristics in a natural population of Peromyscus maniculatus. Canadian Journal of Zoology 69:555-559.
  70. Xia, X. and J. S. Millar. 1990. Infestation of wild Peromyscus leucopus by bot fly larvae. Journal of Mammalogy 71:255-258.
  71. Xia, X. and J. S. Millar. 1989. Dispersion of adult males in relation to female reproductive status in Peromyscus leucopus. Canadian Journal of Zoology 67:1047-1052.
  72. El-Haddad, M., J. S. Millar and X. Xia. 1989. Offspring recognition by male Peromyscus maniculatus. Journal of Mammalogy 69:811-813.
  73. Xia, X. and J. S. Millar. 1988. Paternal behaviour by Peromyscus leucopus in enclosures. Canadian Journal of Zoology 66:1184-1187.
  74. Xia, X. and J. S. Millar. 1987. Morphological variation in deer mice in relation to sex and habitat. Canadian Journal of Zoology 65:527-533.
  75. Xia, X. and J. S. Millar. 1986. Sex-related dispersion in Peromyscus maniculatus. Canadian Journal of Zoology 64:933-936.
PhD thesis

Xia, X. 1990. Mating system of natural populations of the white-footed mouse, Peromyscus leudocpus. University of Western Ontario.