Contact

All Stories

  1. Retroviruses and Cancer: Coevolution and Genetic Exchanges Between the Viral and the Host Genomes

    Article • Biology, June 2026, MDPI AG

    Prof. Xuhua Xia

  2. Optimal production of components for the assembly of cellular protein complexes

    Article • Molecular Biology and Evolution, March 2026, Oxford University Press (OUP)

    Prof. Xuhua Xia

  3. Evolution of Translational Machinery in Fast- and Slow-Growing Bacteria

    Article • Microorganisms, February 2026, MDPI AG

    Prof. Xuhua Xia

  4. BLAST, FASTA, and String Algorithms

    Article • January 2026, Springer Science + Business Media

    Prof. Xuhua Xia

  5. Sequence Alignment

    Article • January 2026, Springer Science + Business Media

    Prof. Xuhua Xia

  6. Gibbs Sampler and De Novo Motif Discovery

    Article • January 2026, Springer Science + Business Media

    Prof. Xuhua Xia

  7. Bioinformatics and Translation Initiation

    Article • January 2026, Springer Science + Business Media

    Prof. Xuhua Xia

  8. The Branching Process: A General Conceptual Framework for Addressing Current Ecological and Evolutionary Questions

    Article • Life, December 2025, MDPI AG

    Prof. Xuhua Xia

  9. The Branching Process: A General Conceptual Framework for Addressing Current Ecological and Evolutionary Questions

    Article • November 2025, MDPI AG

    Prof. Xuhua Xia

  10. On Rooting and Dating Viral Trees With a Changing Evolutionary Rate Following Host-Switching

    Article • Genome Biology and Evolution, July 2025, Oxford University Press (OUP)

    Prof. Xuhua Xia

  11. Fake data in NCBI's GenBank

    Article • Microorganisms, October 2024, MDPI AG

    Prof. Xuhua Xia

  12. Phylogeographic Analysis for Understanding Origin, Speciation, and Biogeographic Expansion of Invasive Asian Hornet, Vespa velutina Lepeletier, 1836 (Hymenoptera, Vespidae)

    Article • Life, October 2024, MDPI AG

    Prof. Xuhua Xia

  13. Phylogeographic Analysis to Understand the Origin, Speciation and Biogeographic Expansion of the Invasive Asian Hornet, Vespa velutina

    Article • September 2024, MDPI AG

    Prof. Xuhua Xia

  14. How Trustworthy Are Genomic Sequences of SARS-CoV-2 in GenBank?

    Article • August 2024, MDPI AG

    Prof. Xuhua Xia

  15. Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences

    Article • Algorithms, May 2024, MDPI AG

    Prof. Xuhua Xia

  16. Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species

    Article • Microorganisms, April 2024, MDPI AG

    Prof. Xuhua Xia

  17. Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter

    Article • Emerging Microbes & Infections, March 2024, Taylor & Francis

    Prof. Xuhua Xia

  18. Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species

    Article • March 2024, MDPI AG

    Prof. Xuhua Xia

  19. Phylogeographic Reconstruction to Trace the Source Population of Asian Giant Hornet Caught in Nanaimo in Canada and Blaine in the USA

    Article • Life, February 2024, MDPI AG

    Prof. Xuhua Xia

  20. Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria

    Article • International Journal of Molecular Sciences, February 2024, MDPI AG

    Prof. Xuhua Xia

  21. Computational Design of Novel Griseofulvin Derivatives Demonstrating Potential Antibacterial Activity: Insights from Molecular Docking and Molecular Dynamics Simulation

    Article • International Journal of Molecular Sciences, January 2024, MDPI AG

    Prof. Xuhua Xia

  22. Where did these giant hornets come from?

    Article • January 2024, MDPI AG

    Prof. Xuhua Xia

  23. Cenancestor

    Article • January 2024, Elsevier

    Prof. Xuhua Xia

  24. Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis

    Article • Antibiotics, August 2023, MDPI AG

    Prof. Xuhua Xia

  25. Which of the numerous membrane proteins facilitated viral entry into the cell?

    Article • Frontiers in Microbiology, July 2023, Frontiers

    Prof. Xuhua Xia

  26. Optimizing Protein Production in Therapeutic Phages against a Bacterial Pathogen, Mycobacterium abscessus

    Article • Drugs and Drug Candidates, March 2023, MDPI AG

    Prof. Xuhua Xia

  27. In Silico Exploration of Microtubule Agent Griseofulvin and Its Derivatives Interactions with Different Human β-Tubulin Isotypes

    Article • Molecules, March 2023, MDPI AG

    Prof. Xuhua Xia

  28. Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time

    Article • Viruses, March 2023, MDPI AG

    Prof. Xuhua Xia

  29. Sequence evidence that the D614G clade of SARS-CoV-2 was already circulating in northern Italy in the fall of 2019

    Article • November 2022, Qeios Ltd

    Prof. Xuhua Xia

  30. Griseofulvin: An Updated Overview of Old and Current Knowledge

    Article • Molecules, October 2022, MDPI AG

    Prof. Xuhua Xia

  31. Proteins from Thermophilic Thermus thermophilus Often Do Not Fold Correctly in a Mesophilic Expression System Such as Escherichia coli

    Article • ACS Omega, October 2022, American Chemical Society (ACS)

    Prof. Xuhua Xia

  32. Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.)

    Article • International Journal of Molecular Sciences, July 2022, MDPI AG

    Prof. Xuhua Xia

  33. Testing alternative hypotheses on the origin and speciation of Hawaiian katydids

    Article • BMC Ecology and Evolution, June 2022, Springer Science + Business Media

    Prof. Xuhua Xia

  34. In Silico Molecular Dynamics of Griseofulvin and Its Derivatives Revealed Potential Therapeutic Applications for COVID-19

    Article • International Journal of Molecular Sciences, June 2022, MDPI AG

    Prof. Xuhua Xia

  35. Multiple regulatory mechanisms for pH homeostasis in the gastric pathogen, Helicobacter pylori

    Article • January 2022, Elsevier

    Prof. Xuhua Xia

  36. Post-Alignment Adjustment and Its Automation

    Article • Genes, November 2021, MDPI AG

    Prof. Xuhua Xia

  37. Conservation of griseofulvin genes in thegsfgene cluster among fungal genomes

    Article • G3 Genes Genomes Genetics, November 2021, Oxford University Press (OUP)

    Prof. Xuhua Xia

  38. Author Correction: Predicting mammalian species at risk of being infected by SARS-CoV-2 from an ACE2 perspective

    Article • Scientific Reports, November 2021, Springer Science + Business Media

    Prof. Xuhua Xia

  39. Missing two key parameters in the pooled testing strategy

    Article • October 2021, Research Square

    Prof. Xuhua Xia

  40. Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes

    Article • Viruses, September 2021, MDPI AG

    Prof. Xuhua Xia

  41. Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines

    Article • Vaccines, July 2021, MDPI AG

    Prof. Xuhua Xia

  42. Inheritance of marsh spot disease resistance in cranberry common bean (Phaseolus vulgaris L.)

    Article • The Crop Journal, July 2021, Elsevier

    Prof. Xuhua Xia

  43. Does Saccharomyces cerevisiae Require Specific Post-Translational Silencing against Leaky Translation of Hac1up?

    Article • Microorganisms, March 2021, MDPI AG

    Prof. Xuhua Xia

  44. Applications of Protein Secondary Structure Algorithms in SARS-CoV-2 Research

    Article • Journal of Proteome Research, February 2021, American Chemical Society (ACS)

    Prof. Xuhua Xia

  45. Predicting mammalian species at risk of being infected by SARS-CoV-2 from an ACE2 perspective

    Article • Scientific Reports, January 2021, Springer Science + Business Media

    Prof. Xuhua Xia

  46. Domains and Functions of Spike Protein in SARS-Cov-2 in the Context of Vaccine Design

    Article • Viruses, January 2021, MDPI AG

    Prof. Xuhua Xia

  47. Marsh Spot Disease and Its Causal Factor, Manganese Deficiency in Plants: A Historical and Prospective Review

    Article • Agricultural Sciences, January 2021, Scientific Research Publishing, Inc,

    Prof. Xuhua Xia

  48. Coronavirus genomes carry the signatures of their habitats

    Article • PLOS One, December 2020, PLOS

    Prof. Xuhua Xia

  49. Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration

    Article • Life, August 2020, MDPI AG

    Prof. Xuhua Xia

  50. Beyond Trees: Regulons and Regulatory Motif Characterization

    Article • Genes, August 2020, MDPI AG

    Prof. Xuhua Xia

  51. Drug efficacy and toxicity prediction: an innovative application of transcriptomic data

    Article • Cell Biology and Toxicology, August 2020, Springer Science + Business Media

    Prof. Xuhua Xia

  52. Coronavirus genomes carry the signatures of their habitats

    Article • June 2020, Cold Spring Harbor Laboratory Press

    Prof. Xuhua Xia

  53. Extreme Genomic CpG Deficiency in SARS-CoV-2 and Evasion of Host Antiviral Defense

    Article • Molecular Biology and Evolution, April 2020, Oxford University Press (OUP)

    Prof. Xuhua Xia

  54. Distance-Based Phylogenetic Methods

    Article • April 2020, Taylor & Francis

    Prof. Xuhua Xia

  55. Sequence Alignment Algorithms

    Article • April 2020, Taylor & Francis

    Prof. Xuhua Xia

  56. Introduction to Molecular Phylogenetics

    Article • April 2020, Taylor & Francis

    Prof. Xuhua Xia

  57. Phylogeny-Based Comparative Methods

    Article • April 2020, Taylor & Francis

    Prof. Xuhua Xia

  58. Maximum Likelihood Methods in Phylogenetics

    Article • April 2020, Taylor & Francis

    Prof. Xuhua Xia

  59. Substitution Rate Heterogeneity Over Sites

    Article • April 2020, Taylor & Francis

    Prof. Xuhua Xia

  60. Maximum Parsimony Method in Phylogenetics

    Article • April 2020, Taylor & Francis

    Prof. Xuhua Xia

  61. Nucleotide Substitution Models and Evolutionary Distances

    Article • April 2020, Taylor & Francis

    Prof. Xuhua Xia

  62. Editorial for the special issue “RNA-Seq: Methods and applications”

    Article • Methods, April 2020, Elsevier

    Prof. Xuhua Xia

  63. RNA-Seq approach for accurate characterization of splicing efficiency of yeast introns

    Article • Methods, April 2020, Elsevier

    Prof. Xuhua Xia

  64. Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates

    Article • Evolutionary Bioinformatics, January 2020, SAGE Publications

    Prof. Xuhua Xia

  65. Unique Shine–Dalgarno Sequences in Cyanobacteria and Chloroplasts Reveal Evolutionary Differences in Their Translation Initiation

    Article • Genome Biology and Evolution, October 2019, Oxford University Press (OUP)

    Prof. Xuhua Xia

  66. Translation Control of HAC1 by Regulation of Splicing in Saccharomyces cerevisiae

    Article • International Journal of Molecular Sciences, June 2019, MDPI AG

    Prof. Xuhua Xia

  67. Is there a mutation gradient along vertebrate mitochondrial genome mediated by genome replication?

    Article • Mitochondrion, May 2019, Elsevier

    Prof. Xuhua Xia

  68. PGT: Visualizing temporal and spatial biogeographic patterns

    Article • Global Ecology and Biogeography, April 2019, Wiley

    Prof. Xuhua Xia

  69. An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria

    Article • Scientific Reports, February 2019, Springer Science + Business Media

    Prof. Xuhua Xia

  70. RNA-Seq-Based Analysis Reveals Heterogeneity in Mature 16S rRNA 3′ Termini and Extended Anti-Shine-Dalgarno Motifs in Bacterial Species

    Article • G3 Genes Genomes Genetics, December 2018, Oxford University Press (OUP)

    Prof. Xuhua Xia

  71. Starless bias and parameter-estimation bias in the likelihood-based phylogenetic method

    Article • AIMS Genetics, December 2018, Thieme Publishing Group

    Prof. Xuhua Xia

  72. A starless bias in the maximum likelihood phylogenetic methods

    Article • October 2018, Cold Spring Harbor Laboratory Press

    Prof. Xuhua Xia

  73. Imputing missing distances in molecular phylogenetics

    Article • PeerJ, July 2018, PeerJ

    Prof. Xuhua Xia

  74. DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution

    Article • Molecular Biology and Evolution, April 2018, Oxford University Press (OUP)

    Prof. Xuhua Xia

  75. An improved method for fitting gamma distribution to substitution rate variation among sites

    Article • March 2018, Cold Spring Harbor Laboratory Press

    Prof. Xuhua Xia

  76. Bioinformatics and In Silico 2D Gel Electrophoresis

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  77. Bioinformatics and Translation Elongation

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  78. Bioinformatics and Translation Initiation

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  79. Bioinformatics and Translation Termination in Bacteria

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  80. Advanced algorithms, simple language, beautifully illustrated numerically

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  81. Distance-Based Phylogenetic Methods

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  82. Fundamentals of Proteomics

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  83. Genomic Features: Content Sensors, Nucleotide Skew Plot, Strand Asymmetry, and DNA Methylation

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  84. Gibbs sampler

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  85. Hidden Markov Models and Protein Secondary Structure Prediction

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  86. Maximum Likelihood in Molecular Phylogenetics

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  87. Maximum Parsimony Method in Phylogenetics

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  88. Nucleotide Substitution Models and Evolutionary Distances

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  89. Position weight matrix and Perceptron

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  90. Protein Isoelectric Point and Helicobacter pylori

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  91. Protein Substitution Model and Evolutionary Distance

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  92. Self-Organizing Map and Other Clustering Methods in Transcriptomics

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  93. Sequence Alignment

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  94. String Mathematics, BLAST, and FASTA

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  95. Transcriptomics and RNA-Seq Data Analysis

    Article • January 2018, Springer Science + Business Media

    Prof. Xuhua Xia

  96. Deriving Transition Probabilities and Evolutionary Distances from Substitution Rate Matrix by Probability Reasoning

    Article • Journal of Genetics and Genome Research, December 2017, ClinMed International Library

    Prof. Xuhua Xia

  97. Elucidating the 16S rRNA 3′ boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data

    Article • Scientific Reports, December 2017, Nature

    Prof. Xuhua Xia

  98. Analyzing RNA-Seq Data, correctly.

    Article • G3 Genes Genomes Genetics, October 2017, Genetics Society of America

    Prof. Xuhua Xia

  99. Self-Organizing Map for Characterizing Heterogeneous Nucleotide and Amino Acid Sequence Motifs

    Article • Computation, September 2017, MDPI AG

    Prof. Xuhua Xia

  100. Drugs are expensive. Can it be made cheaper?

    Article • Current Topics in Medicinal Chemistry, April 2017, Bentham Science Publishers

    Prof. Xuhua Xia

  101. A good workbench for molecular and evolutionary biologists

    Article • Journal of Heredity, April 2017, Oxford University Press (OUP)

    Prof. Xuhua Xia

  102. Signals and decoders in bacterial translation initiation

    Article • G3 Genes Genomes Genetics, March 2017, Genetics Society of America

    Prof. Xuhua Xia

  103. Analyzing RNA-Seq Data, correctly.

    Article • March 2017, Cold Spring Harbor Laboratory Press

    Prof. Xuhua Xia

  104. Ying and Yang: where is the Yang side?

    Article • Genome Biology and Evolution, March 2017, Oxford University Press (OUP)

    Prof. Xuhua Xia

  105. The working of an extended translation stop signal in bacteria

    Article • Genetics, November 2016, Genetics Society of America

    Prof. Xuhua Xia

  106. PhyPA: Phylogenetic method with pairwise sequence alignment outperforms likelihood methods in phylogenetics involving highly diverged sequences

    Article • Molecular Phylogenetics and Evolution, September 2016, Elsevier

    Prof. Xuhua Xia

  107. A fascinating tale of two partners in the translation machinery

    Article • Molecular Biology and Evolution, June 2016, Oxford University Press (OUP)

    Prof. Xuhua Xia

  108. Exon-skipping is caused by weak splicing signals flanking the exon.

    Article • Scientific Reports, February 2016, Nature

    Prof. Xuhua Xia

  109. How USP4, USP15 and USP11 evolved and functionally diversified

    Article • BMC Evolutionary Biology, October 2015, Springer Science + Business Media

    Prof. Xuhua Xia

  110. Escherichia coli and Staphylococcus phages: effect of translation initiation efficiency on differential codon adaptation mediated by virulent and temperate lifestyles

    Article • Journal of General Virology, May 2015, Society for General Microbiology

    Prof. Xuhua Xia

  111. Dating the origin of the major lineages of Branchiopoda

    Article • Palaeoworld, February 2015, Elsevier

    Prof. Xuhua Xia

  112. A Major Controversy in Codon-Anticodon Adaptation Resolved by a New Codon Usage Index

    Article • Genetics, December 2014, Genetics Society of America

    Prof. Xuhua Xia

  113. The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium

    Article • Genome, September 2014, Canadian Science Publishing

    Prof. Xuhua Xia

  114. The Effect of Mutation and Selection on Codon Adaptation in Escherichia coli Bacteriophage

    Article • Genetics, May 2014, Oxford University Press (OUP)

    Prof. Xuhua Xia

  115. Differential Codon Adaptation between dsDNA and ssDNA Phages in Escherichia coli

    Article • Molecular Biology and Evolution, February 2014, Oxford University Press (OUP)

    Prof. Xuhua Xia

  116. Phylogenetic Bias in the Likelihood Method Caused by Missing Data Coupled with Among-Site Rate Variation: An Analytical Approach

    Article • January 2014, Springer Science + Business Media

    Prof. Xuhua Xia

  117. Aeromonas phages encode tRNAs for their overused codons

    Article • International Journal of Computational Biology and Drug Design, January 2014, Inderscience Publishers

    Prof. Xuhua Xia

  118. DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution

    Article • Molecular Biology and Evolution, April 2013, Oxford University Press (OUP)

    Prof. Xuhua Xia

  119. Comparative Genomics

    Article • January 2013

    Prof. Xuhua Xia

  120. What is Comparative Genomics?

    Article • January 2013, Springer Science + Business Media

    Prof. Xuhua Xia

  121. Comparative Viral Genomics: Detecting Recombination

    Article • January 2013, Springer Science + Business Media

    Prof. Xuhua Xia

  122. Comparative Genomics and the Comparative Methods

    Article • January 2013, Springer Science + Business Media

    Prof. Xuhua Xia

  123. An Improved Implementation of Effective Number of Codons (Nc)

    Article • Molecular Biology and Evolution, August 2012, Oxford University Press (OUP)

    Prof. Xuhua Xia

  124. Rapid evolution of animal mitochondrial DNA

    Article • June 2012, Oxford University Press (OUP)

    Prof. Xuhua Xia

  125. DNA Replication and Strand Asymmetry in Prokaryotic and Mitochondrial Genomes

    Article • Current Genomics, March 2012, Bentham Science Publishers

    Prof. Xuhua Xia

  126. NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

    Article • Systematic Biology, February 2012, Oxford University Press (OUP)

    Prof. Xuhua Xia

  127. Codons and tRNAs dance differently in single-stranded and double-stranded phages

    Article • January 2012, ACM (Association for Computing Machinery)

    Prof. Xuhua Xia

  128. Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction

    Article • Scientifica, January 2012, Hindawi Publishing Corporation

    Prof. Xuhua Xia

  129. Selected Works in Bioinformatics

    Article • October 2011, IntechOpen

    Prof. Xuhua Xia

  130. Translation Initiation: A Regulatory Role for Poly(A) Tracts in Front of the AUG Codon in Saccharomyces cerevisiae

    Article • Genetics, August 2011, Genetics Society of America

    Prof. Xuhua Xia

  131. Non-AUG initiation codon and downstream inframe AUG in Pyrococcus Horikoshii: Evaluating two hypotheses

    Article • May 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Xuhua Xia

  132. A distance-based least-square method for dating speciation events

    Article • Molecular Phylogenetics and Evolution, May 2011, Elsevier

    Prof. Xuhua Xia

  133. Defining Global Neuroendocrine Gene Expression Patterns Associated with Reproductive Seasonality in Fish

    Article • April 2011, Taylor & Francis

    Prof. Xuhua Xia

  134. HIV-1 Modulates the tRNA Pool to Improve Translation Efficiency

    Article • Molecular Biology and Evolution, January 2011, Oxford University Press (OUP)

    Prof. Xuhua Xia

  135. Comparative Genomics

    Article • January 2011, Springer Science + Business Media

    Prof. Xuhua Xia

  136. Factors Affecting Splicing Strength of Yeast Genes

    Article • Comparative and Functional Genomics, January 2011, Hindawi Publishing Corporation

    Prof. Xuhua Xia

  137. A General Model of Codon Bias Due to GC Mutational Bias

    Article • PLOS One, October 2010, PLOS

    Prof. Xuhua Xia

  138. Mural granulosa cell gene expression associated with oocyte developmental competence

    Article • Journal of Ovarian Research, March 2010, Springer Science + Business Media

    Dr Marc Andre Sirard, Prof. Xuhua Xia

  139. Consanguinity, Genetic Drift, and Genetic Diseases in Populations with Reduced Numbers of Founders

    Article • January 2010, Springer Science + Business Media

    Prof. Xuhua Xia

  140. Monophyly of the ring-forming group in Diplopoda (Myriapoda, Arthropoda) based on SSU and LSU ribosomal RNA sequences

    Article • Progress in Natural Science Materials International, October 2009, Elsevier

    Prof. Xuhua Xia

  141. Information-theoretic indices and an approximate significance test for testing the molecular clock hypothesis with genetic distances

    Article • Molecular Phylogenetics and Evolution, September 2009, Elsevier

    Prof. Xuhua Xia

  142. Profiling neuroendocrine gene expression changes following fadrozole-induced estrogen decline in the female goldfish

    Article • Physiological Genomics, June 2009, American Physiological Society

    Prof. Xuhua Xia

  143. Defining Global Neuroendocrine Gene Expression Patterns Associated with Reproductive Seasonality in Fish

    Article • PLOS One, June 2009, PLOS

    Prof. Xuhua Xia

  144. Correlations between recombination rate and intron distributions along chromosomes of C. elegans

    Article • Progress in Natural Science Materials International, April 2009, Elsevier

    Prof. Xuhua Xia

  145. Strong Eukaryotic IRESs Have Weak Secondary Structure

    Article • PLOS One, January 2009, PLOS

    Prof. Xuhua Xia

  146. The goldfish (Carassius auratus) as a model for neuroendocrine signaling

    Article • Molecular and Cellular Endocrinology, October 2008, Elsevier

    Prof. Xuhua Xia

  147. Effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus)

    Article • Physiological Genomics, September 2008, American Physiological Society

    Prof. Xuhua Xia

  148. Preservation of Genes Involved in Sterol Metabolism in Cholesterol Auxotrophs: Facts and Hypotheses

    Article • PLOS One, August 2008, PLOS

    Prof. Xuhua Xia

  149. GC skew in protein-coding genes between the leading and lagging strands in bacterial genomes: New substitution models incorporating strand bias

    Article • Journal of Theoretical Biology, August 2008, Elsevier

    Prof. Xuhua Xia

  150. An Extensive Study of Mutation and Selection on the Wobble Nucleotide in tRNA Anticodons in Fungal Mitochondrial Genomes

    Article • Journal of Molecular Evolution, April 2008, Springer Science + Business Media

    Prof. Xuhua Xia

  151. Auto-regulation of estrogen receptor subtypes and gene expression profiling of 17β-estradiol action in the neuroendocrine axis of male goldfish

    Article • Molecular and Cellular Endocrinology, February 2008, Elsevier

    Prof. Xuhua Xia

  152. Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Prof. Xuhua Xia

  153. The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses

    Article • BMC Evolutionary Biology, January 2008, Springer Science + Business Media

    Prof. Xuhua Xia

  154. 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

    Article • Biology Direct, January 2008, Springer Science + Business Media

    Prof. Xuhua Xia

  155. Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods

    Article • International Journal of Plant Genomics, January 2008, Hindawi Publishing Corporation

    Prof. Xuhua Xia

  156. Internal ribosomal entry site lacks secondary structure

    Article • Nature Precedings, October 2007, Springer Science + Business Media

    Prof. Xuhua Xia

  157. THE EFFECT OF FADROZOLE-INDUCED ESTROGEN WITHDRAWAL ON GENE EXPRESSION PROFILES IN NEUROENDOCRINE BRAIN IN GOLDFISH (Carassius auratus)

    Article • Biology of Reproduction, July 2007, Oxford University Press (OUP)

    Prof. Xuhua Xia

  158. Conflict between Translation Initiation and Elongation in Vertebrate Mitochondrial Genomes

    Article • PLOS One, February 2007, PLOS

    Prof. Xuhua Xia

  159. The +4G Site in Kozak Consensus Is Not Related to the Efficiency of Translation Initiation

    Article • PLOS One, February 2007, PLOS

    Prof. Xuhua Xia

  160. Bioinformatics and the Cell

    Article • January 2007, Springer Science + Business Media

    Prof. Xuhua Xia

  161. Molecular Phylogenetics: Mathematical Framework and Unsolved Problems

    Article • January 2007, Springer Science + Business Media

    Prof. Xuhua Xia

  162. Bioinformatic Approach to Identify Penultimate Amino Acids Efficient for N-Terminal Methionine Excision

    Article • January 2007, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Xuhua Xia

  163. An Improved Implementation of Codon Adaptation Index

    Article • Evolutionary Bioinformatics, January 2007, SAGE Publications

    Prof. Xuhua Xia

  164. Gene expression profiling in the neuroendocrine brain of male goldfish (Carassius auratus) exposed to 17 -ethinylestradiol

    Article • Physiological Genomics, July 2006, American Physiological Society

    Prof. Xuhua Xia

  165. CODON-BASED DETECTION OF POSITIVE SELECTION CAN BE BIASED BY HETEROGENEOUS DISTRIBUTION OF POLAR AMINO ACIDS ALONG PROTEIN SEQUENCES

    Article • July 2006, World Scientific Pub Co Pte Lt

    Prof. Xuhua Xia

  166. Thermal Adaptation of the Small Subunit Ribosomal RNA Gene: A Comparative Study

    Article • Journal of Molecular Evolution, June 2006, Springer Science + Business Media

    Prof. Xuhua Xia

  167. Cytosine Usage Modulates the Correlation between CDS Length and CG Content in Prokaryotic Genomes

    Article • Molecular Biology and Evolution, May 2006, Oxford University Press (OUP)

    Prof. Xuhua Xia

  168. CODON-BASED DETECTION OF POSITIVE SELECTION CAN BE BIASED BY HETEROGENEOUS DISTRIBUTION OF POLAR AMINO ACIDS ALONG PROTEIN SEQUENCES

    Article • January 2006, World Scientific Pub Co Pte Lt

    Prof. Xuhua Xia

  169. CODON-BASED DETECTION OF POSITIVE SELECTION CAN BE BIASED BY HETEROGENEOUS DISTRIBUTION OF POLAR AMINO ACIDS ALONG PROTEIN SEQUENCES

    Article • January 2006, World Scientific Pub Co Pte Lt

    Prof. Xuhua Xia

  170. Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances

    Article • Evolutionary Bioinformatics, January 2006, SAGE Publications

    Prof. Xuhua Xia

  171. MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution

    Article • Evolutionary Bioinformatics, January 2006, SAGE Publications

    Prof. Xuhua Xia

  172. Genomic Adaptation to Acidic Environment: Evidence fromHelicobacter pylori

    Article • The American Naturalist, December 2005, University of Chicago Press

    Prof. Xuhua Xia

  173. Genetic Variation in Clones of Pseudomonas pseudoalcaligenes After Ten Months of Selection in Different Thermal Environments in the Laboratory

    Article • Current Microbiology, April 2005, Springer Science + Business Media

    Prof. Xuhua Xia

  174. Mutation and selection on the anticodon of tRNA genes in vertebrate mitochondrial genomes

    Article • Gene, January 2005, Elsevier

    Prof. Xuhua Xia

  175. Article • BMC Genetics, January 2005, Springer Science + Business Media

    Prof. Xuhua Xia

  176. Article • BMC Bioinformatics, January 2005, Springer Science + Business Media

    Prof. Xuhua Xia

  177. An evolutionary and functional analysis of FoxL2 in rainbow trout gonad differentiation

    Article • Journal of Molecular Endocrinology, December 2004, Bioscientifica

    Prof. Xuhua Xia

  178. Structure, evolution and expression of the FOXL2 transcription unit

    Article • Cytogenetic and Genome Research, December 2003, Karger Publishers

    Prof. Xuhua Xia

  179. DNA Methylation and Mycoplasma Genomes

    Article • Journal of Molecular Evolution, August 2003, Springer Science + Business Media

    Prof. Xuhua Xia

  180. Changes in growth parameters of Pseudomonas pseudoalcaligenes after ten months culturing at increasing temperature

    Article • FEMS Microbiology Ecology, July 2003, Oxford University Press (OUP)

    Prof. Xuhua Xia

  181. 18S Ribosomal RNA and Tetrapod Phylogeny

    Article • Systematic Biology, June 2003, Oxford University Press (OUP)

    Prof. Xuhua Xia

  182. 18S Ribosomal RNA and Tetrapod Phylogeny

    Article • Systematic Biology, June 2003, Oxford University Press (OUP)

    Prof. Xuhua Xia

  183. Effects of GC Content and Mutational Pressure on the Lengths of Exons and Coding Sequences

    Article • Journal of Molecular Evolution, March 2003, Springer Science + Business Media

    Prof. Xuhua Xia

  184. Morphological Changes of Pseudomonas pseudoalcaligenes in Response to Temperature Selection

    Article • Current Microbiology, February 2003, Springer Science + Business Media

    Prof. Xuhua Xia

  185. An index of substitution saturation and its application

    Article • Molecular Phylogenetics and Evolution, January 2003, Elsevier

    Prof. Xuhua Xia

  186. Evolution and expression of FOXL2

    Article • Journal of Medical Genetics, December 2002, BMJ

    Prof. Xuhua Xia

  187. Protein Structure, Neighbor Effect, and a New Index of Amino Acid Dissimilarities

    Article • Molecular Biology and Evolution, January 2002, Oxford University Press (OUP)

    Prof. Xuhua Xia

  188. DAMBE: Software Package for Data Analysis in Molecular Biology and Evolution

    Article • Journal of Heredity, July 2001, Oxford University Press (OUP)

    Prof. Xuhua Xia

  189. AMADA: analysis of microarray data

    Article • Bioinformatics, June 2001, Oxford University Press (OUP)

    Prof. Xuhua Xia

  190. The genusSchevoderaBorchmann: Phylogeny and historical biogeography, with description of a new species (Coleoptera: Tenebrionidae: Lagriinae)

    Article • Oriental Insects, January 2001, Taylor & Francis

    Prof. Xuhua Xia

  191. Phylogenetic Relationship Among Horseshoe Crab Species: Effect of Substitution Models on Phylogenetic Analyses

    Article • Systematic Biology, January 2000, Oxford University Press (OUP)

    Prof. Xuhua Xia

  192. What Amino Acid Properties Affect Protein Evolution?

    Article • Journal of Molecular Evolution, November 1998, Springer Science + Business Media

    Prof. Xuhua Xia

  193. The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes

    Article • Molecular Biology and Evolution, March 1998, Oxford University Press (OUP)

    Prof. Xuhua Xia

  194. On transition bias in mitochondrial genes of pocket gophers

    Article • Journal of Molecular Evolution, July 1996, Springer Science + Business Media

    Prof. Xuhua Xia

  195. Revisiting Hamilton's Rule

    Article • The American Naturalist, March 1995, University of Chicago Press

    Prof. Xuhua Xia

  196. A Full Sibling is not as Valuable as an Offspring: On Hamilton's Rule

    Article • The American Naturalist, July 1993, University of Chicago Press

    Prof. Xuhua Xia

  197. Mating system of the meadow vole, Microtus pennsylvanicus

    Article • Behavioral Ecology, January 1993, Oxford University Press (OUP)

    Dr Rudy Boonstra, Prof. Xuhua Xia

  198. Measuring Temporal Variability of Population Density: A Critique

    Article • The American Naturalist, November 1992, University of Chicago Press

    Dr Rudy Boonstra, Prof. Xuhua Xia

  199. Uncertainty of Paternity Can Select Against Paternal Care

    Article • The American Naturalist, May 1992, University of Chicago Press

    Prof. Xuhua Xia

  200. Genetic evidence of promiscuity in Peromyscus leucopus

    Article • Behavioral Ecology and Sociobiology, March 1991, Springer Science + Business Media

    Prof. Xuhua Xia

  201. Relationships among reproductive status, nutritional status, and food characteristics in a natural population ofPeromyscus maniculatus

    Article • Canadian Journal of Zoology, March 1991, Canadian Science Publishing

    Prof. Xuhua Xia

  202. Infestations of Wild Peromyscus leucopus by Bot Fly Larvae

    Article • Journal of Mammalogy, May 1990, Oxford University Press (OUP)

    Prof. Xuhua Xia

  203. Dispersion of adult malePeromyscus leucopusin relation to female reproductive status

    Article • Canadian Journal of Zoology, April 1989, Canadian Science Publishing

    Prof. Xuhua Xia

  204. Offspring Recognition by Male Peromyscus maniculatus

    Article • Journal of Mammalogy, November 1988, Oxford University Press (OUP)

    Prof. Xuhua Xia

  205. Paternal behavior byPeromyscus leucopusin enclosures

    Article • Canadian Journal of Zoology, May 1988, Canadian Science Publishing

    Prof. Xuhua Xia

  206. Morphological variation in deer mice in relation to sex and habitat

    Article • Canadian Journal of Zoology, March 1987, Canadian Science Publishing

    Prof. Xuhua Xia

  207. Sex-related dispersion of breeding deer mice in the Kananaskis Valley, Alberta

    Article • Canadian Journal of Zoology, April 1986, Canadian Science Publishing

    Prof. Xuhua Xia

  208. Assessing substitution saturation with DAMBE

    Article • Cambridge University Press

    Prof. Xuhua Xia

  209. Content Sensors Based on Codon Structure and DNA Methylation for Gene Finding in Vertebrate Genomes

    Article • Springer Science + Business Media

    Prof. Xuhua Xia