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List of works by Xuhua Xia

18S Ribosomal RNA and Tetrapod Phylogeny

scholarly article by Xuhua Xia et al published 1 June 2003 in Systematic Biology

18S ribosomal RNA and tetrapod phylogeny

scientific article published in June 2003

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

scientific article published in 1993

A comparative study of codon adaptation in ssDNA and dsDNA phages

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

scientific article published on 12 February 2011

A general model of codon bias due to GC mutational bias

scientific article

A major controversy in codon-anticodon adaptation resolved by a new codon usage index

scientific article

A starless bias in the maximum likelihood phylogenetic methods

article

ARSDA: A New Approach for Storing, Transmitting and Analyzing Transcriptomic Data

scientific article published on 27 October 2017

ARSDA: A new approach for storing, transmitting and analyzing high-throughput sequencing data

An Improved Implementation of Codon Adaptation Index

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

article

An extensive study of mutation and selection on the wobble nucleotide in tRNA anticodons in fungal mitochondrial genomes

scientific article published on 10 April 2008

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

scientific article published on 28 February 2019

An improved implementation of effective number of codons (nc).

scientific article published on 21 August 2012

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

An index of substitution saturation and its application

scientific article (publication date: 2003)

Assessing substitution saturation with DAMBE

scholarly article

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

scientific article

Beyond Trees: Regulons and Regulatory Motif Characterization

scientific article published on 25 August 2020

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

Bioinformatics and Drug Discovery

scientific article

Bioinformatics and In Silico 2D Gel Electrophoresis

Bioinformatics and Translation Elongation

Bioinformatics and Translation Initiation

Bioinformatics and Translation Termination in Bacteria

Bioinformatics and the Cell

Bioinformatics and the Cell

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

scientific article

Comparative Genomics

Comparative Genomics

Comparative Genomics and the Comparative Methods

Comparative Viral Genomics: Detecting Recombination

Conflict between translation initiation and elongation in vertebrate mitochondrial genomes

scientific article

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

Cytosine usage modulates the correlation between CDS length and CG content in prokaryotic genomes

scientific article published on 10 May 2006

DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution

scientific article (publication date: July 2013)

DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution

scientific article published on 4 April 2017

DAMBE7: New and improved tools for data analysis in molecular biology and evolution

scientific article published on 14 April 2018

DNA Methylation and Mycoplasma Genomes

article published in 2003

DNA Replication and Strand Asymmetry in Prokaryotic and Mitochondrial Genomes ⬇️

scientific article published on March 1, 2012

Defining global neuroendocrine gene expression patterns associated with reproductive seasonality in fish

scientific article

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

Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage

scientific article

Distance-Based Phylogenetic Methods

scholarly article published 2018

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

scientific article published on 11 August 2020

Effects of GC content and mutational pressure on the lengths of exons and coding sequences

scientific article

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

scientific article published on 2 September 2008

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

scientific article published on 15 December 2017

Factors affecting splicing strength of yeast genes

scientific article

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

scientific article

Fundamentals of Proteomics

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

scientific article published on 11 April 2008

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

scientific article published on 5 September 2006

Genetic evidence of promiscuity in Peromyscus leucopus

article

Genetic variation in clones of Pseudomonas pseudoalcaligenes after ten months of selection in different thermal environments in the laboratory

scientific article

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

Genomic adaptation to acidic environment: evidence from Helicobacter pylori

scientific article published on 4 October 2005

Gibbs sampler

HIV-1 modulates the tRNA pool to improve translation efficiency ⬇️

scientific article

Hidden Markov Models and Protein Secondary Structure Prediction

How Changes in Anti-SD Sequences Would Affect SD Sequences in Escherichia coli and Bacillus subtilis

scientific article

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

scientific article published on 30 August 2020

Imputing missing distances in molecular phylogenetics

scholarly article by Xuhua Xia published 2018 in PeerJ

Infestations of Wild Peromyscus leucopus by Bot Fly Larvae

article by Xuhua Xia & J. S. Millar published 21 May 1990 in Journal of Mammalogy

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

scientific article published on 3 May 2009

MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution

scientific article

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

scientific article published in January 2020

Maximum Likelihood in Molecular Phylogenetics

scholarly article published 2018

Maximum Parsimony Method in Phylogenetics

scholarly article published 2018

Measuring Temporal Variability of Population Density: A Critique

article

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

scientific article published in 2024

Molecular Phylogenetics: Mathematical Framework and Unsolved Problems

scholarly article published 2007

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

article

Morphological changes of Pseudomonas pseudoalcaligenes in response to temperature selection

scientific article

Morphological variation in deer mice in relation to sex and habitat

scientific article published in 1987

Mural granulosa cell gene expression associated with oocyte developmental competence

scientific article

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

scientific article

NeXML: rich, extensible, and verifiable representation of comparative data and metadata

scientific article (publication date: July 2012)

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

Nucleotide Substitution Models and Evolutionary Distances

Offspring Recognition by Male Peromyscus maniculatus

scientific article published in 1988

PGT: Visualizing temporal and spatial biogeographic patterns

scholarly article by Xuhua Xia published 21 April 2019 in Global Ecology and Biogeography

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

scientific article published on July 2016

Phylogenetic analyses: A toolbox expanding towards Bayesian methods

scientific article (publication date: 2008)

Position weight matrix and Perceptron

Preservation of genes involved in sterol metabolism in cholesterol auxotrophs: facts and hypotheses

scientific article

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

scientific article published on 09 June 2009

Protein Isoelectric Point and Helicobacter pylori

Protein Substitution Model and Evolutionary Distance

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

scientific article published in 2022

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

scientific article published on 10 December 2018

Rapid evolution of animal mitochondrial DNA

Revisiting Hamilton's Rule

scientific article published in 1995

Self-Organizing Map and Other Clustering Methods in Transcriptomics

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

Sequence Alignment

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

scientific article published in 1986

String Mathematics, BLAST, and FASTA

Strong eukaryotic IRESs have weak secondary structure

scientific article

The +4G site in Kozak consensus is not related to the efficiency of translation initiation

scientific article

The Role of +4U as an Extended Translation Termination Signal in Bacteria

scientific article

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

scientific article

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

scientific article published on 05 July 2008

The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes ⬇️

scientific article published on March 1, 1998

Thermal adaptation of the small subunit ribosomal RNA gene: a comparative study

scientific article published on 16 June 2006

Transcriptomics and RNA-Seq Data Analysis

scholarly article published 2018

Translation Control of HAC1 by Regulation of Splicing in Saccharomyces cerevisiae

scientific article published on 12 June 2019

Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae

scientific article

Uncertainty of Paternity Can Select Against Paternal Care

scientific article published in 1992

Using generalized procrustes analysis (GPA) for normalization of cDNA microarray data

scientific article

What amino acid properties affect protein evolution?

scientific article

What is Comparative Genomics?

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