Xuhua Xia - Publications

Affiliations: 
2002- Biology University of Ottawa, Ottawa, ON, Canada 
Area:
Molecular evolution

90 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Kruglikov A, Wei Y, Xia X. Proteins from Thermophilic Often Do Not Fold Correctly in a Mesophilic Expression System Such as . Acs Omega. 7: 37797-37806. PMID 36312379 DOI: 10.1021/acsomega.2c04786  0.591
2022 Aris P, Wei Y, Mohamadzadeh M, Xia X. Griseofulvin: An Updated Overview of Old and Current Knowledge. Molecules (Basel, Switzerland). 27. PMID 36296627 DOI: 10.3390/molecules27207034  0.584
2022 Aris P, Mohamadzadeh M, Wei Y, Xia X. In Silico Molecular Dynamics of Griseofulvin and Its Derivatives Revealed Potential Therapeutic Applications for COVID-19. International Journal of Molecular Sciences. 23. PMID 35805893 DOI: 10.3390/ijms23136889  0.57
2021 Aris P, Yan L, Wei Y, Chang Y, Shi B, Xia X. Conservation of griseofulvin genes in the gsf gene cluster among fungal genomes. G3 (Bethesda, Md.). PMID 34792561 DOI: 10.1093/g3journal/jkab399  0.793
2021 Wei Y, Aris P, Farookhi H, Xia X. Author Correction: Predicting mammalian species at risk of being infected by SARS-CoV-2 from an ACE2 perspective. Scientific Reports. 11: 22016. PMID 34737431 DOI: 10.1038/s41598-021-01576-w  0.562
2021 Tehfe A, Roseshter T, Wei Y, Xia X. Does Require Specific Post-Translational Silencing against Leaky Translation of Hac1up? Microorganisms. 9. PMID 33802931 DOI: 10.3390/microorganisms9030620  0.66
2021 Kruglikov A, Rakesh M, Wei Y, Xia X. Applications of Protein Secondary Structure Algorithms in SARS-CoV-2 Research. Journal of Proteome Research. PMID 33617253 DOI: 10.1021/acs.jproteome.0c00734  0.603
2021 Wei Y, Aris P, Farookhi H, Xia X. Predicting mammalian species at risk of being infected by SARS-CoV-2 from an ACE2 perspective. Scientific Reports. 11: 1702. PMID 33462320 DOI: 10.1038/s41598-020-80573-x  0.602
2020 Wei Y, Silke JR, Aris P, Xia X. Coronavirus genomes carry the signatures of their habitats. Plos One. 15: e0244025. PMID 33351847 DOI: 10.1371/journal.pone.0244025  0.786
2020 Xia X. Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense. Molecular Biology and Evolution. PMID 32289821 DOI: 10.1093/Molbev/Msaa094  0.358
2020 Noah KE, Hao J, Li L, Sun X, Foley B, Yang Q, Xia X. Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates. Evolutionary Bioinformatics Online. 16: 1176934320903735. PMID 32076367 DOI: 10.1177/1176934320903735  0.397
2019 Wei Y, Xia X. Unique Shine-Dalgarno sequences in Cyanobacteria and chloroplasts reveal evolutionary differences in their translation initiation. Genome Biology and Evolution. PMID 31621842 DOI: 10.1093/Gbe/Evz227  0.705
2019 Xia X. RNA-Seq approach for accurate characterization of splicing efficiency of yeast introns. Methods (San Diego, Calif.). PMID 30926533 DOI: 10.1016/J.Ymeth.2019.03.019  0.386
2019 Wei Y, Silke JR, Xia X. An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria. Scientific Reports. 9: 3184. PMID 30816249 DOI: 10.1038/S41598-019-39369-X  0.811
2018 Silke JR, Wei Y, Xia X. RNA-Seq-Based Analysis Reveals Heterogeneity in Mature 16S rRNA 3' Termini and Extended Anti-Shine-Dalgarno Motifs in Bacterial Species. G3 (Bethesda, Md.). PMID 30355764 DOI: 10.1534/G3.118.200729  0.791
2018 Xia X. Is there a mutation gradient along vertebrate mitochondrial genome mediated by genome replication? Mitochondrion. PMID 29909015 DOI: 10.1016/J.Mito.2018.06.004  0.375
2018 Xia X. DAMBE7: New and improved tools for data analysis in molecular biology and evolution. Molecular Biology and Evolution. PMID 29669107 DOI: 10.1093/Molbev/Msy073  0.303
2017 Wei Y, Silke JR, Xia X. Elucidating the 16S rRNA 3' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data. Scientific Reports. 7: 17639. PMID 29247194 DOI: 10.1038/S41598-017-17918-6  0.791
2017 Xia X. ARSDA: A New Approach for Storing, Transmitting and Analyzing Transcriptomic Data. G3 (Bethesda, Md.). PMID 29079682 DOI: 10.1534/G3.117.300271  0.336
2017 Xia X. DAMBE6: New tools for microbial genomics, phylogenetics and molecular evolution. The Journal of Heredity. PMID 28379490 DOI: 10.1093/Jhered/Esx033  0.411
2017 Abolbaghaei A, Silke JR, Xia X. How Changes in Anti-SD Sequences Would Affect SD Sequences in Escherichia coli and Bacillus subtilis. G3 (Bethesda, Md.). PMID 28364038 DOI: 10.1534/G3.117.039305  0.787
2017 Vlasschaert C, Cook D, Xia X, Gray DA. The evolution and functional diversification of the deubiquitinating enzyme superfamily. Genome Biology and Evolution. PMID 28177072 DOI: 10.1093/Gbe/Evx020  0.643
2016 Wei Y, Xia X. The Role of +4U as an Extended Translation Termination Signal in Bacteria. Genetics. PMID 27903612 DOI: 10.1534/Genetics.116.193961  0.712
2016 Xia X. PhyPA: phylogenetic method with pairwise sequence alignment outperforms likelihood methods in phylogenetics involving highly diverged sequences. Molecular Phylogenetics and Evolution. PMID 27377322 DOI: 10.1016/J.Ympev.2016.07.001  0.338
2016 Wei Y, Wang J, Xia X. Coevolution between stop codon usage and release factors in bacterial species. Molecular Biology and Evolution. PMID 27297468 DOI: 10.1093/Molbev/Msw107  0.698
2016 Vlasschaert C, Xia X, Gray DA. Selection preserves Ubiquitin Specific Protease 4 alternative exon skipping in therian mammals. Scientific Reports. 6: 20039. PMID 26833277 DOI: 10.1038/Srep20039  0.699
2015 Vlasschaert C, Xia X, Coulombe J, Gray DA. Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11. Bmc Evolutionary Biology. 15: 230. PMID 26503449 DOI: 10.1186/S12862-015-0511-1  0.722
2015 Prabhakaran R, Chithambaram S, Xia X. Escherichia coli and Staphylococcus phages: effect of translation initiation efficiency on differential codon adaptation mediated by virulent and temperate lifestyles. The Journal of General Virology. 96: 1169-79. PMID 25614589 DOI: 10.1099/Vir.0.000050  0.792
2015 Xia X. A major controversy in codon-anticodon adaptation resolved by a new codon usage index. Genetics. 199: 573-9. PMID 25480780 DOI: 10.1534/Genetics.114.172106  0.428
2014 Nikbakht H, Xia X, Hickey DA. The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium. Genome / National Research Council Canada = GéNome / Conseil National De Recherches Canada. 57: 507-11. PMID 25633864 DOI: 10.1139/Gen-2014-0158  0.39
2014 Prabhakaran R, Chithambaram S, Xia X. Aeromonas phages encode tRNAs for their overused codons. International Journal of Computational Biology and Drug Design. 7: 168-82. PMID 24878728 DOI: 10.1504/Ijcbdd.2014.061645  0.782
2014 Chithambaram S, Prabhakaran R, Xia X. Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli. Molecular Biology and Evolution. 31: 1606-17. PMID 24586046 DOI: 10.1093/Molbev/Msu087  0.782
2014 Chithambaram S, Prabhakaran R, Xia X. The effect of mutation and selection on codon adaptation in Escherichia coli bacteriophage. Genetics. 197: 301-15. PMID 24583580 DOI: 10.1534/Genetics.114.162842  0.773
2013 Xia X. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Molecular Biology and Evolution. 30: 1720-8. PMID 23564938 DOI: 10.1093/Molbev/Mst064  0.385
2013 Sun X, Yang Q, Xia X. An improved implementation of effective number of codons (nc). Molecular Biology and Evolution. 30: 191-6. PMID 22915832 DOI: 10.1093/Molbev/Mss201  0.343
2012 Xia X. DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes. Current Genomics. 13: 16-27. PMID 22942672 DOI: 10.2174/138920212799034776  0.322
2011 Ma P, Xia X. Factors affecting splicing strength of yeast genes. Comparative and Functional Genomics. 2011: 212146. PMID 22162666 DOI: 10.1155/2011/212146  0.768
2011 Xia X, MacKay V, Yao X, Wu J, Miura F, Ito T, Morris DR. Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae. Genetics. 189: 469-78. PMID 21840854 DOI: 10.1534/Genetics.111.132068  0.763
2011 van Weringh A, Ragonnet-Cronin M, Pranckeviciene E, Pavon-Eternod M, Kleiman L, Xia X. HIV-1 modulates the tRNA pool to improve translation efficiency. Molecular Biology and Evolution. 28: 1827-34. PMID 21216840 DOI: 10.1093/Molbev/Msr005  0.733
2010 Palidwor GA, Perkins TJ, Xia X. A general model of codon bias due to GC mutational bias. Plos One. 5: e13431. PMID 21048949 DOI: 10.1371/Journal.Pone.0013431  0.732
2010 Jiang JY, Xiong H, Cao M, Xia X, Sirard MA, Tsang BK. Mural granulosa cell gene expression associated with oocyte developmental competence. Journal of Ovarian Research. 3: 6. PMID 20205929 DOI: 10.1186/1757-2215-3-6  0.752
2009 Zhang D, Popesku JT, Martyniuk CJ, Xiong H, Duarte-Guterman P, Yao L, Xia X, Trudeau VL. Profiling neuroendocrine gene expression changes following fadrozole-induced estrogen decline in the female goldfish. Physiological Genomics. 38: 351-61. PMID 19509080 DOI: 10.1152/Physiolgenomics.00051.2009  0.748
2009 Zhang D, Xiong H, Mennigen JA, Popesku JT, Marlatt VL, Martyniuk CJ, Crump K, Cossins AR, Xia X, Trudeau VL. Defining global neuroendocrine gene expression patterns associated with reproductive seasonality in fish. Plos One. 4: e5816. PMID 19503831 DOI: 10.1371/Journal.Pone.0005816  0.754
2009 Xia X. Information-theoretic indices and an approximate significance test for testing the molecular clock hypothesis with genetic distances. Molecular Phylogenetics and Evolution. 52: 665-76. PMID 19416757 DOI: 10.1016/J.Ympev.2009.04.017  0.318
2009 Xia X, Holcik M. Strong eukaryotic IRESs have weak secondary structure. Plos One. 4: e4136. PMID 19125192 DOI: 10.1371/Journal.Pone.0004136  0.305
2009 Cong P, Xia X, Yang Q. 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. DOI: 10.1016/J.Pnsc.2009.03.005  0.312
2009 Li H, Liu G, Xia X. Correlations between recombination rate and intron distributions along chromosomes of C. elegans Progress in Natural Science. 19: 517-522. DOI: 10.1016/J.Pnsc.2008.06.019  0.312
2008 Zhang D, Xiong H, Shan J, Xia X, Trudeau VL. 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. PMID 19032786 DOI: 10.1186/1745-6150-3-48  0.734
2008 Mennigen JA, Martyniuk CJ, Crump K, Xiong H, Zhao E, Popesku J, Anisman H, Cossins AR, Xia X, Trudeau VL. Effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus). Physiological Genomics. 35: 273-82. PMID 18765858 DOI: 10.1152/Physiolgenomics.90263.2008  0.741
2008 Vinci G, Xia X, Veitia RA. Preservation of genes involved in sterol metabolism in cholesterol auxotrophs: facts and hypotheses. Plos One. 3: e2883. PMID 18682733 DOI: 10.1371/Journal.Pone.0002883  0.398
2008 Popesku JT, Martyniuk CJ, Mennigen J, Xiong H, Zhang D, Xia X, Cossins AR, Trudeau VL. The goldfish (Carassius auratus) as a model for neuroendocrine signaling. Molecular and Cellular Endocrinology. 293: 43-56. PMID 18657592 DOI: 10.1016/J.Mce.2008.06.017  0.738
2008 Xia X. The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses. Bmc Evolutionary Biology. 8: 211. PMID 18638409 DOI: 10.1186/1471-2148-8-211  0.34
2008 Marín A, Xia X. 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: 508-13. PMID 18486155 DOI: 10.1016/J.Jtbi.2008.04.004  0.374
2008 Carullo M, Xia X. An extensive study of mutation and selection on the wobble nucleotide in tRNA anticodons in fungal mitochondrial genomes. Journal of Molecular Evolution. 66: 484-93. PMID 18401633 DOI: 10.1007/S00239-008-9102-8  0.381
2008 Xiong H, Zhang D, Martyniuk CJ, Trudeau VL, Xia X. Using generalized procrustes analysis (GPA) for normalization of cDNA microarray data. Bmc Bioinformatics. 9: 25. PMID 18199333 DOI: 10.1186/1471-2105-9-25  0.717
2008 Marlatt VL, Martyniuk CJ, Zhang D, Xiong H, Watt J, Xia X, Moon T, Trudeau VL. Auto-regulation of estrogen receptor subtypes and gene expression profiling of 17β-estradiol action in the neuroendocrine axis of male goldfish Molecular and Cellular Endocrinology. 283: 38-48. PMID 18083300 DOI: 10.1016/J.Mce.2007.10.013  0.729
2007 Xia X. An improved implementation of codon adaptation index. Evolutionary Bioinformatics Online. 3: 53-8. PMID 19461982 DOI: 10.4137/Ebo.S0  0.304
2007 Xia X, Huang H, Carullo M, Betrán E, Moriyama EN. Conflict between translation initiation and elongation in vertebrate mitochondrial genomes. Plos One. 2: e227. PMID 17311091 DOI: 10.1371/Journal.Pone.0000227  0.415
2007 Xia X. The +4G site in Kozak consensus is not related to the efficiency of translation initiation. Plos One. 2: e188. PMID 17285142 DOI: 10.1371/Journal.Pone.0000188  0.361
2007 Khalouei S, Yao X, Mennigen J, Carullo M, Ma P, Song Z, Xiong H, Xia X. Bioinformatic approach to identify penultimate amino acids efficient for N-terminal methionine excision 2007 1st International Conference On Bioinformatics and Biomedical Engineering, Icbbe. 386-389. DOI: 10.1109/ICBBE.2007.102  0.691
2007 Zhang D, Martyniuk C, Xiong H, Popesku J, Duarte P, Xia X, Trudeau V. THE EFFECT OF FADROZOLE-INDUCED ESTROGEN WITHDRAWAL ON GENE EXPRESSION PROFILES IN NEUROENDOCRINE BRAIN IN GOLDFISH (Carassius auratus) Biology of Reproduction. 77: 227-227. DOI: 10.1093/Biolreprod/77.S1.227C  0.733
2006 Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox 2.0: an enhanced version of a MATLAB toolbox for molecular biology and evolution. Evolutionary Bioinformatics Online. 2: 179-82. PMID 19455210 DOI: 10.4137/Ebo.S0  0.642
2006 Martyniuk CJ, Xiong H, Crump K, Chiu S, Sardana R, Nadler A, Gerrie ER, Xia X, Trudeau VL. Gene expression profiling in the neuroendocrine brain of male goldfish (Carassius auratus) exposed to 17alpha-ethinylestradiol. Physiological Genomics. 27: 328-36. PMID 16954407 DOI: 10.1152/Physiolgenomics.00090.2006  0.74
2006 Wang HC, Xia X, Hickey D. Thermal adaptation of the small subunit ribosomal RNA gene: a comparative study. Journal of Molecular Evolution. 63: 120-6. PMID 16786438 DOI: 10.1007/S00239-005-0255-4  0.419
2006 Xia X, Wang H, Xie Z, Carullo M, Huang H, Hickey D. Cytosine usage modulates the correlation between CDS length and CG content in prokaryotic genomes. Molecular Biology and Evolution. 23: 1450-4. PMID 16687416 DOI: 10.1093/Molbev/Msl012  0.371
2005 Xia X, Palidwor G. Genomic adaptation to acidic environment: evidence from Helicobacter pylori. The American Naturalist. 166: 776-84. PMID 16475092 DOI: 10.1086/497400  0.702
2005 Shi B, Xia X. Genetic variation in clones of Pseudomonas pseudoalcaligenes after ten months of selection in different thermal environments in the laboratory. Current Microbiology. 50: 238-45. PMID 15886916 DOI: 10.1007/S00284-004-4449-6  0.762
2005 Xia X, Yuen KY. Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage. Bmc Genetics. 6: 20. PMID 15823202 DOI: 10.1186/1471-2156-6-20  0.376
2005 Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution. Bmc Bioinformatics. 6: 64. PMID 15780146 DOI: 10.1186/1471-2105-6-64  0.637
2005 Xia X. Mutation and selection on the anticodon of tRNA genes in vertebrate mitochondrial genomes. Gene. 345: 13-20. PMID 15716092 DOI: 10.1016/J.Gene.2004.11.019  0.386
2004 Baron D, Cocquet J, Xia X, Fellous M, Guiguen Y, Veitia RA. An evolutionary and functional analysis of FoxL2 in rainbow trout gonad differentiation. Journal of Molecular Endocrinology. 33: 705-15. PMID 15591029 DOI: 10.1677/Jme.1.01566  0.368
2003 Shi B, Xia X. Changes in growth parameters of Pseudomonas pseudoalcaligenes after ten months culturing at increasing temperature. Fems Microbiology Ecology. 45: 127-34. PMID 19719623 DOI: 10.1016/S0168-6496(03)00129-6  0.763
2003 Cocquet J, De Baere E, Gareil M, Pannetier M, Xia X, Fellous M, Veitia RA. Structure, evolution and expression of the FOXL2 transcription unit. Cytogenetic and Genome Research. 101: 206-11. PMID 14684984 DOI: 10.1159/000074338  0.387
2003 Xia X, Xie Z, Kjer KM. 18S ribosomal RNA and tetrapod phylogeny. Systematic Biology. 52: 283-95. PMID 12775520 DOI: 10.1080/10635150390196948  0.419
2003 Xia X, Xie Z, Li WH. Effects of GC content and mutational pressure on the lengths of exons and coding sequences. Journal of Molecular Evolution. 56: 362-70. PMID 12612839 DOI: 10.1007/S00239-002-2406-1  0.37
2003 Shi B, Xia X. Morphological changes of Pseudomonas pseudoalcaligenes in response to temperature selection. Current Microbiology. 46: 120-3. PMID 12520367 DOI: 10.1007/S00284-002-3824-4  0.755
2003 Xia X, Xie Z, Salemi M, Chen L, Wang Y. An index of substitution saturation and its application. Molecular Phylogenetics and Evolution. 26: 1-7. PMID 12470932 DOI: 10.1016/S1055-7903(02)00326-3  0.347
2002 Cocquet J, Pailhoux E, Jaubert F, Servel N, Xia X, Pannetier M, De Baere E, Messiaen L, Cotinot C, Fellous M, Veitia RA. Evolution and expression of FOXL2. Journal of Medical Genetics. 39: 916-21. PMID 12471206 DOI: 10.1136/Jmg.39.12.916  0.395
2000 Xia X. Phylogenetic relationship among horseshoe crab species: Effect of substitution models on phylogenetic analyses Systematic Biology. 49: 87-100. PMID 12116485 DOI: 10.1080/10635150050207401  0.346
1996 Xia X, Hafner MS, Sudman PD. On transition bias in mitochondrial genes of pocket gophers. Journal of Molecular Evolution. 43: 32-40. PMID 8660427 DOI: 10.1007/Bf02352297  0.789
1995 Xia X. Body temperature, rate of biosynthesis, and evolution of genome size Molecular Biology and Evolution. 12: 834-842. PMID 7476129 DOI: 10.1093/Oxfordjournals.Molbev.A040260  0.309
1992 Xia X, Boonstra R. Measuring temporal variability of population density: a critique. The American Naturalist. 140: 883-92. PMID 19426047 DOI: 10.1086/285446  0.392
1991 Millar JS, Xia X, Norrie MB. Relationships among reproductive status, nutritional status, and food characteristics in a natural population of Peromyscus maniculatus Canadian Journal of Zoology. 69: 555-559. DOI: 10.1139/Z91-083  0.393
1991 Xia X, Millar JS. Genetic evidence of promiscuity in Peromyscus leucopus Behavioral Ecology and Sociobiology. 28: 171-178. DOI: 10.1007/Bf00172168  0.477
1990 Xia X, Millar JS. Infestations of Wild Peromyscus leucopus by Bot Fly Larvae Journal of Mammalogy. 71: 255-258. DOI: 10.2307/1382179  0.423
1989 Xia X, Millar JS. Dispersion of adult male Peromyscus leucopus in relation to female reproductive status Canadian Journal of Zoology. 67: 1047-1052. DOI: 10.1139/Z89-145  0.393
1988 El-Haddad M, Millar JS, Xia X. Offspring Recognition by Male Peromyscus maniculatus Journal of Mammalogy. 69: 811-813. DOI: 10.2307/1381635  0.386
1988 Xia X, Millar JS. Paternal behavior by Peromyscus leucopus in enclosures Canadian Journal of Zoology. 66: 1184-1187. DOI: 10.1139/Z88-173  0.407
1987 Xia X, Millar JS. Morphological variation in deer mice in relation to sex and habitat Canadian Journal of Zoology. 65: 527-533. DOI: 10.1139/Z87-082  0.479
1986 Xia X, Millar JS. Sex-related dispersion of breeding deer mice in the Kananaskis Valley, Alberta Canadian Journal of Zoology. 64: 933-936. DOI: 10.1139/Z86-141  0.403
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