Publications by authors named "Xun Gu"

100Publications

The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development.

G3 (Bethesda) 2020 Sep 2;10(9):3337-3346. Epub 2020 Sep 2.

Singlera Genomics Inc., Shanghai, 201318, China

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September 2020

DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity.

Front Immunol 2019 1;10:2559. Epub 2019 Nov 1.

Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.

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November 2020

TreeExp2: An Integrated Framework for Phylogenetic Transcriptome Analysis.

Genome Biol Evol 2019 11;11(11):3276-3282

Department of Genetics, Development and Cell Biology, Iowa State University.

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November 2019

Comparative Transcriptome Analyses Reveal the Role of Conserved Function in Electric Organ Convergence Across Electric Fishes.

Front Genet 2019 18;10:664. Epub 2019 Jul 18.

Department of GDC Biology, Iowa State University, Ames, IA, United States.

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July 2019

Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes.

Sci Rep 2019 06 3;9(1):8205. Epub 2019 Jun 3.

Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China.

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June 2019

Estimating the strength of expression conservation from high throughput RNA-seq data.

Bioinformatics 2019 12;35(23):5030-5038

MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China.

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December 2019

Olfactomedin domain-containing proteins: evolution, functional divergence, expression patterns and damaging SNPs.

Mol Genet Genomics 2019 Aug 26;294(4):875-885. Epub 2019 Mar 26.

Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China.

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August 2019

TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome.

Mol Plant 2019 03 23;12(3):447-460. Epub 2019 Feb 23.

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA; Department of Agronomy, Iowa State University, Ames, IA 50011-3260, USA. Electronic address:

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March 2019

Ancestral transcriptome inference based on RNA-Seq and ChIP-seq data.

Methods 2020 04 22;176:99-105. Epub 2018 Nov 22.

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA. Electronic address:

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April 2020

TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis.

Genomics Proteomics Bioinformatics 2018 08 15;16(4):276-282. Epub 2018 Sep 15.

Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address:

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August 2018

Mutation-profile-based methods for understanding selection forces in cancer somatic mutations: a comparative analysis.

Oncotarget 2017 Aug 19;8(35):58835-58846. Epub 2017 Jul 19.

Department of Genetics, Development and Cell Biology, Program of Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, USA.

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August 2017

Evolutionary Origins of Pax6 Control of Crystallin Genes.

Genome Biol Evol 2017 08;9(8):2075-2092

Department of Genetics, Albert Einstein College of Medicine, Bronx, New York.

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August 2017

Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates.

Mol Genet Genomics 2017 Dec 17;292(6):1405-1418. Epub 2017 Aug 17.

State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.

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December 2017

Identification of trunk mutations in gastric carcinoma: a case study.

BMC Med Genomics 2017 07 17;10(1):49. Epub 2017 Jul 17.

College of Pharmaceutical Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China.

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July 2017

Paralog-divergent Features May Help Reduce Off-target Effects of Drugs: Hints from Glucagon Subfamily Analysis.

Genomics Proteomics Bioinformatics 2017 08 20;15(4):246-254. Epub 2017 Jun 20.

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Department of Genetics, Development and Cell Biology, Program of Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA. Electronic address:

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August 2017

Effective estimation of the minimum number of amino acid residues required for functional divergence between duplicate genes.

Mol Phylogenet Evol 2017 08 12;113:126-138. Epub 2017 May 12.

Department of Genetics, Development and Cell Biology, Program of Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA; State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, PR China. Electronic address:

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August 2017

TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection.

R Soc Open Sci 2017 Apr 5;4(4):170050. Epub 2017 Apr 5.

Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China.

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April 2017

Brownian model of transcriptome evolution and phylogenetic network visualization between tissues.

Mol Phylogenet Evol 2017 09 22;114:34-39. Epub 2017 Apr 22.

State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China.

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September 2017

Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization.

Evol Bioinform Online 2016 12;12:303-312. Epub 2016 Dec 12.

School of Life Sciences, Fudan University, Shanghai, China.; Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.

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December 2016

TreeExp1.0: R Package for Analyzing Expression Evolution Based on RNA-Seq Data.

J Exp Zool B Mol Dev Evol 2016 11 26;326(7):394-402. Epub 2016 Oct 26.

State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.

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November 2016

Evolutionary Dynamics of MERS-CoV: Potential Recombination, Positive Selection and Transmission.

Sci Rep 2016 05 4;6:25049. Epub 2016 May 4.

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, PR China.

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May 2016

Model parameters of molecular evolution explain genomic correlations.

Authors:
Xun Gu Wenda Tang

Brief Bioinform 2017 01 1;18(1):37-42. Epub 2015 Dec 1.

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January 2017

The evolutionary panorama of organ-specifically expressed or repressed orthologous genes in nine vertebrate species.

PLoS One 2015 13;10(2):e0116872. Epub 2015 Feb 13.

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, PR China; Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, United States of America.

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January 2016

Genepleio software for effective estimation of gene pleiotropy from protein sequences.

Biomed Res Int 2015 5;2015:269150. Epub 2015 Jan 5.

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China ; Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, IA 50011, USA.

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September 2015

Effect of duplicate genes on mouse genetic robustness: an update.

Biomed Res Int 2014 10;2014:758672. Epub 2014 Jul 10.

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China ; Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50010, USA.

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March 2015

Pleiotropy can be effectively estimated without counting phenotypes through the rank of a genotype-phenotype map.

Authors:
Xun Gu

Genetics 2014 Aug 3;197(4):1357-63. Epub 2014 Jun 3.

Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, Iowa 50011, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China.

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August 2014

Asymmetric evolution of human transcription factor regulatory networks.

Mol Biol Evol 2014 Aug 19;31(8):2149-55. Epub 2014 May 19.

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, ChinaDepartment of Genetics, Development and Cell Biology, Program of Bioinformatics and Computational Biology, Iowa State University

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August 2014

Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations.

Mol Genet Genomics 2014 Apr 10;289(2):137-47. Epub 2013 Dec 10.

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Biology Building II 113, Shanghai, 200433, China.

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April 2014

Phylogenomic distance method for analyzing transcriptome evolution based on RNA-seq data.

Genome Biol Evol 2013 ;5(9):1746-53

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.

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April 2014

Identification of functional mutations in GATA4 in patients with congenital heart disease.

PLoS One 2013 23;8(4):e62138. Epub 2013 Apr 23.

Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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November 2013

An update of DIVERGE software for functional divergence analysis of protein family.

Mol Biol Evol 2013 Jul 14;30(7):1713-9. Epub 2013 Apr 14.

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.

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July 2013

[The comparing study between subchronic toxicity and local implantation response of sodium hyaluronan gels for different application].

Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2012 Oct;29(5):919-22

Sichuan Testing Center for Biomaterials and Medical Devices, Sichuan University, Chengdu 610041, China.

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October 2012

A computational analysis framework for molecular cell dynamics: case-study of exocytosis.

PLoS One 2012 11;7(7):e38699. Epub 2012 Jul 11.

School of Life Sciences and Center for Evolutionary Biology, Fudan University, Shanghai, China.

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March 2013

Histone modification pattern evolution after yeast gene duplication.

BMC Evol Biol 2012 Jul 9;12:111. Epub 2012 Jul 9.

Ministry of Education Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China.

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July 2012

Revisit on the evolutionary relationship between alternative splicing and gene duplication.

Authors:
Zhixi Su Xun Gu

Gene 2012 Aug 14;504(1):102-6. Epub 2012 May 14.

MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.

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August 2012

Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis.

BMC Syst Biol 2012 Mar 16;6:19. Epub 2012 Mar 16.

Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA.

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March 2012

A study of the evolution of human microRNAs by their apparent repression effectiveness on target genes.

Authors:
Yong Huang Xun Gu

PLoS One 2011 21;6(9):e25034. Epub 2011 Sep 21.

Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa, United States of America.

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February 2012

Comment on "Positive selection of tyrosine loss in metazoan evolution".

Science 2011 May;332(6032):917; author reply 917

MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.

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May 2011

Predominant gain of promoter TATA box after gene duplication associated with stress responses.

Mol Biol Evol 2011 Oct 22;28(10):2893-904. Epub 2011 Apr 22.

MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.

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October 2011

Highly sensitive dispersion measurement of a high-power passive optical resonator using spatial-spectral interferometry.

Opt Express 2010 Dec;18(25):26184-95

Fraunhofer Institute for Physical Measurement Techniques IPM, Department of Terahertz Measurement and Systems, Erwin-Schroedinger-Str, Building 56, 67663 Kaiserslautern, Germany.

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December 2010

Identification of copy number variation hotspots in human populations.

Am J Hum Genet 2010 Oct;87(4):494-504

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.

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October 2010

A sustainable landscape ecosystem design: a case study.

Ann N Y Acad Sci 2010 May;1195 Suppl 1:E154-63

Department of Environmental Science and Engineering, Fudan University, Shanghai, China.

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May 2010

Genome factor and gene pleiotropy hypotheses in protein evolution.

Authors:
Yanwu Zeng Xun Gu

Biol Direct 2010 May 24;5:37. Epub 2010 May 24.

School of Life Sciences, Fudan University, Shanghai 200433, China.

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May 2010

Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana.

BMC Evol Biol 2010 Feb 12;10:41. Epub 2010 Feb 12.

Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA.

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February 2010

Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications.

BMC Evol Biol 2009 Nov 30;9:275. Epub 2009 Nov 30.

Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA.

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November 2009

A preliminary analysis of gene pleiotropy estimated from protein sequences.

J Exp Zool B Mol Dev Evol 2010 Mar;314(2):115-22

Institutes of Biomedical Sciences, School of Life Sciences, Center for Evolutionary Biology, Fudan University, Shanghai, China.

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March 2010

Differences in duplication age distributions between human GPCRs and their downstream genes from a network prospective.

BMC Genomics 2009 Jul 7;10 Suppl 1:S14. Epub 2009 Jul 7.

Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA.

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July 2009

Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscape.

J Exp Zool B Mol Dev Evol 2009 Nov;312(7):722-33

Institutes of Biomedical Sciences, Fudan University, Shanghai, China.

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November 2009

Simultaneous expansions of microRNAs and protein-coding genes by gene/genome duplications in early vertebrates.

J Exp Zool B Mol Dev Evol 2009 May;312B(3):164-70

Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011, USA.

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May 2009

Analysis of functional divergence within two structurally related glycoside hydrolase families.

Biopolymers 2009 Jun;91(6):478-95

Department of Chemical and Biological Engineering, IA State University, Ames, IA 50011, USA.

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June 2009

An evolutionary model for the origin of modularity in a complex gene network.

Authors:
Xun Gu

J Exp Zool B Mol Dev Evol 2009 Mar;312(2):75-82

Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011, USA.

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March 2009

Evolution of RNases in leaf monkeys: being parallel gene duplications or parallel gene conversions is a problem of molecular phylogeny.

Mol Phylogenet Evol 2009 Feb 13;50(2):397-400. Epub 2008 Nov 13.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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February 2009

Predicting the proportion of essential genes in mouse duplicates based on biased mouse knockout genes.

Authors:
Zhixi Su Xun Gu

J Mol Evol 2008 Dec;67(6):705-9

Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.

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December 2008

Effect of site-specific heterogeneous evolution on phylogenetic reconstruction: a simple evaluation.

Gene 2009 Jul 12;441(1-2):156-62. Epub 2008 Aug 12.

Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China.

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July 2009

A simple method for phylogenomic inference using the information of gene content of genomes.

Gene 2009 Jul 17;441(1-2):163-8. Epub 2008 Jul 17.

Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC 29208, USA.

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July 2009

Characterization of paralogous protein families in rice.

BMC Plant Biol 2008 Feb 19;8:18. Epub 2008 Feb 19.

The Institute for Genomic Research, 9712 Medical Center Dr. , Rockville, MD 20850, USA.

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February 2008

Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genome.

Mol Phylogenet Evol 2008 Apr 22;47(1):419-25. Epub 2007 Oct 22.

Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China.

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April 2008

Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraints.

J Mol Evol 2007 Aug;65(2):119-23

Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, 332 Science II Hall, Ames, IA 50011, USA.

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August 2007

The origin and evolution of enamel mineralization genes.

Cells Tissues Organs 2007 ;186(1):25-48

UMR 7138, Université Pierre et Marie Curie-Paris 6, Paris, France.

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August 2007

Tissue-driven hypothesis with Gene Ontology (GO) analysis.

Ann Biomed Eng 2007 Jun 20;35(6):1088-94. Epub 2007 Mar 20.

Institutes of Biomedical Sciences, School of Life Sciences, Center for Evolutionary Biology, Fudan University, Shanghai, China.

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June 2007

A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs.

Authors:
Yong Huang Xun Gu

BMC Genomics 2007 Mar 6;8:66. Epub 2007 Mar 6.

Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA.

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March 2007

Tissue-driven hypothesis of genomic evolution and sequence-expression correlations.

Authors:
Xun Gu Zhixi Su

Proc Natl Acad Sci U S A 2007 Feb 14;104(8):2779-84. Epub 2007 Feb 14.

School of Life Sciences, Institutes of Biomedical Sciences, Center for Evolutionary Biology, Fudan University, Shanghai 200433, China.

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February 2007

Evolutionary framework for protein sequence evolution and gene pleiotropy.

Authors:
Xun Gu

Genetics 2007 Apr 4;175(4):1813-22. Epub 2007 Feb 4.

Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA.

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April 2007

Functional divergence after gene duplication and sequence-structure relationship: a case study of G-protein alpha subunits.

J Exp Zool B Mol Dev Evol 2007 Jan;308(1):85-96

Department of Genetics, Development & Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Iowa 50011, USA.

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January 2007

Time squared: repeated measures on phylogenies.

Mol Biol Evol 2007 Feb 1;24(2):352-62. Epub 2006 Nov 1.

Department of Biostatistics, School of Public Health, University of California, Los Angeles, USA.

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February 2007

Stabilizing selection of protein function and distribution of selection coefficient among sites.

Authors:
Xun Gu

Genetica 2007 May 1;130(1):93-7. Epub 2006 Nov 1.

Department of Genetics, Development and Cell Biology Center for Bioinformatics and Biological Statistics, Iowa State University, 536 Science II Hall, Ames, IA 50011, USA.

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May 2007

A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences.

Authors:
Xun Gu

Mol Biol Evol 2006 Oct 24;23(10):1937-45. Epub 2006 Jul 24.

Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, USA.

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October 2006

Intron gain and loss in segmentally duplicated genes in rice.

Genome Biol 2006 23;7(5):R41. Epub 2006 May 23.

The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA.

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August 2006

Neurotransmitter inactivation is important for the origin of nerve system in animal early evolution: a suggestion from genomic comparison.

Prog Neurobiol 2006 Apr 2;78(6):390-5. Epub 2006 May 2.

State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China.

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April 2006

Maximum likelihood for genome phylogeny on gene content.

Stat Appl Genet Mol Biol 2004 14;3:Article31. Epub 2004 Nov 14.

University of West Florida, USA.

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May 2006

Evolution of alternative splicing after gene duplication.

Genome Res 2006 Feb 19;16(2):182-9. Epub 2005 Dec 19.

James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China.

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February 2006

Web-based resources for comparative genomics.

Authors:
Xun Gu Zhixi Su

Hum Genomics 2005 Sep;2(3):187-90

Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA.

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September 2005

Expression divergence between duplicate genes.

Trends Genet 2005 Nov 2;21(11):602-7. Epub 2005 Sep 2.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

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November 2005

SplitTester: software to identify domains responsible for functional divergence in protein family.

BMC Bioinformatics 2005 Jun 1;6:137. Epub 2005 Jun 1.

Department of Genetics, Development & Cell Biology, Iowa State University, Ames, Iowa 50011, USA.

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June 2005

Rapid evolution of expression and regulatory divergences after yeast gene duplication.

Proc Natl Acad Sci U S A 2005 Jan 12;102(3):707-12. Epub 2005 Jan 12.

State Key Laboratory of Genetic Engineering, School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.

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January 2005

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods.

BMC Bioinformatics 2004 Dec 17;5:205. Epub 2004 Dec 17.

L.H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA.

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December 2004

GeneContent: software for whole-genome phylogenetic analysis.

Bioinformatics 2005 Apr 14;21(8):1713-4. Epub 2004 Dec 14.

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.

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April 2005

Further statistical analysis for genome-wide expression evolution in primate brain/liver/fibroblast tissues.

Authors:
Jianying Gu Xun Gu

Hum Genomics 2004 May;1(4):247-54

Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, IA 50011, USA.

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May 2004

How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution?

Trends Genet 2004 Sep;20(9):403-7

Department of Genetics, Development & Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, IA 50011, USA.

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September 2004

Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica.

Genome Biol 2004 29;5(7):R46. Epub 2004 Jun 29.

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.

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October 2004

Statistical framework for phylogenomic analysis of gene family expression profiles.

Authors:
Xun Gu

Genetics 2004 May;167(1):531-42

Department of Genetics, Development and Cell Biology (GDCB), Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011, USA.

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May 2004

Genome phylogenetic analysis based on extended gene contents.

Mol Biol Evol 2004 Jul 14;21(7):1401-8. Epub 2004 Apr 14.

Department of Genetics, Development, and Cell Biology, Iowa State University, Iowa, USA.

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July 2004

Ordered origin of the typical two- and three-repeat Myb genes.

Gene 2004 Feb;326:13-22

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.

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February 2004

Natural history and functional divergence of protein tyrosine kinases.

Authors:
Jianying Gu Xun Gu

Gene 2003 Oct;317(1-2):49-57

Department of Zoology and Genetics, Center for Bioinformatics and Biological Statistics, 332 Science II Hall, Iowa State University, Ames, IA 50011, USA.

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October 2003