S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

L. Koski and G. Golding, The Closest BLAST Hit Is Often Not the Nearest Neighbor, Journal of Molecular Evolution, vol.51, issue.6, pp.540-542, 2001.
DOI : 10.1007/s002390010184

J. Eisen, Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary???Analysis, Genome Research, vol.8, issue.3, pp.163-167, 1998.
DOI : 10.1101/gr.8.3.163

L. Abi-rached, A. Gilles, T. Shiina, P. Pontarotti, and H. Inoko, Evidence of en bloc duplication in vertebrate genomes, Nature Genetics, vol.31, issue.1, pp.100-105, 2002.
DOI : 10.1038/ng855

O. Madsen, M. Scally, C. Douady, D. Kao, R. Debry et al., Parallel adaptive radiations in two major clades of placental mammals, Nature, vol.409, issue.6820, pp.610-614, 2001.
DOI : 10.1038/35054544

W. Murphy, E. Eizirik, W. Johnson, Y. Zhang, O. Ryder et al., Molecular phylogenetics and the origins of placental mammals, Nature, vol.409, issue.6820, pp.614-618, 2001.
DOI : 10.1038/35054550

S. Ohno, Gene duplication and the uniqueness of vertebrate genomes circa 1970???1999, Seminars in Cell & Developmental Biology, vol.10, issue.5, pp.517-522, 1999.
DOI : 10.1006/scdb.1999.0332

D. Sankoff, Gene and genome duplication, Current Opinion in Genetics & Development, vol.11, issue.6, pp.681-684, 2001.
DOI : 10.1016/S0959-437X(00)00253-7

O. Shmueli, S. Horn-saban, V. Chalifa-caspi, M. Shmoish, R. Ophir et al., GeneNote: whole genome expression profiles in normal human tissues, Comptes Rendus Biologies, vol.326, issue.10-11, pp.1067-1072, 2003.
DOI : 10.1016/j.crvi.2003.09.012

Y. Zhang, D. Eberhard, G. Frantz, P. Dowd, T. Wu et al., GEPIS--quantitative gene expression profiling in normal and cancer tissues, Bioinformatics, vol.20, issue.15, 2004.
DOI : 10.1093/bioinformatics/bth256

L. Huminiecki and K. Wolfe, Divergence of Spatial Gene Expression Profiles Following Species-Specific Gene Duplications in Human and Mouse, Genome Research, vol.14, issue.10a, pp.1870-1879, 2004.
DOI : 10.1101/gr.2705204

I. Yanai, D. Graur, and R. Ophir, Incongruent Expression Profiles between Human and Mouse Orthologous Genes Suggest Widespread Neutral Evolution of Transcription Control, OMICS: A Journal of Integrative Biology, vol.8, issue.1, pp.15-24, 2004.
DOI : 10.1089/153623104773547462

P. Gouret, V. Vitiello, N. Balandraud, A. Gilles, P. Pontarotti et al., FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform, BMC Bioinformatics, vol.6, issue.1, p.198, 2005.
DOI : 10.1186/1471-2105-6-198

G. Alarcon, Epidemiology of rheumatoid arthritis, Rheum Dis Clin North Am, vol.21, pp.589-604, 1995.

E. Harris, Rheumatoid arthritis. Pathophysiology and implications for therapy, N Engl J Med, vol.322, pp.1277-1289, 1990.

A. Ishigami, T. Ohsawa, H. Asaga, K. Akiyama, M. Kuramoto et al., Human peptidylarginine deiminase type II: molecular cloning, gene organization, and expression in human skin, Archives of Biochemistry and Biophysics, vol.407, issue.1, pp.25-31, 2002.
DOI : 10.1016/S0003-9861(02)00516-7

A. Suzuki, R. Yamada, X. Chang, S. Tokuhiro, T. Sawada et al., Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis, Nature Genetics, vol.34, issue.4, pp.395-402, 2003.
DOI : 10.1038/ng1206

A. Barton, J. Bowes, S. Eyre, K. Spreckley, A. Hinks et al., A functional haplotype of thePADI4 gene associated with rheumatoid arthritis in a Japanese population is not associated in a United Kingdom population, Arthritis & Rheumatism, vol.111, issue.4, pp.1117-1121, 2004.
DOI : 10.1002/art.20169

S. Chavanas, M. Mechin, H. Takahara, A. Kawada, R. Nachat et al., Comparative analysis of the mouse and human peptidylarginine deiminase gene clusters reveals highly conserved non-coding segments and a new human gene, PADI6, Gene, vol.330, pp.19-27, 2004.
DOI : 10.1016/j.gene.2003.12.038

S. Audic and J. Claverie, The significance of digital gene expression profiles, Genome Res, vol.7, pp.986-995, 1997.

B. Lewis, R. Green, and S. Brenner, Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans, Proceedings of the National Academy of Sciences, vol.9, issue.2, pp.189-192, 2003.
DOI : 10.1038/ng0295-184

M. Nakayama-hamada, A. Suzuki, K. Kubota, T. Takazawa, M. Ohsaka et al., Comparison of enzymatic properties between hPADI2 and hPADI4, Biochemical and Biophysical Research Communications, vol.327, issue.1, pp.192-200, 2005.
DOI : 10.1016/j.bbrc.2004.11.152

. Gu, Statistical Framework for Phylogenomic Analysis of Gene Family Expression Profiles, Genetics, vol.167, issue.1, pp.531-542, 2004.
DOI : 10.1534/genetics.167.1.531

X. Gu, Z. Zhang, and W. Huang, Rapid evolution of expression and regulatory divergences after yeast gene duplication, Proceedings of the National Academy of Sciences, vol.16, issue.12, pp.707-712, 2005.
DOI : 10.1093/oxfordjournals.molbev.a026080

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545572

Z. Gu, S. Rifkin, K. White, and W. Li, Duplicate genes increase gene expression diversity within and between species, Nature Genetics, vol.14, issue.6, pp.577-579, 2004.
DOI : 10.1016/S0092-8674(00)80868-5

L. Duret and D. Mouchiroud, Determinants of Substitution Rates in Mammalian Genes: Expression Pattern Affects Selection Intensity but Not Mutation Rate, Molecular Biology and Evolution, vol.17, issue.1, pp.68-74, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026239

URL : https://hal.archives-ouvertes.fr/hal-00427068

L. Zhang and W. Li, Mammalian Housekeeping Genes Evolve More Slowly than Tissue-Specific Genes, Molecular Biology and Evolution, vol.21, issue.2, pp.236-239, 2004.
DOI : 10.1093/molbev/msh010

URL : http://mbe.oxfordjournals.org/cgi/content/short/21/2/236

J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

S. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998.
DOI : 10.1093/bioinformatics/14.9.755

H. Schmidt, K. Strimmer, M. Vingron, and V. Haeseler, TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, vol.18, issue.3, pp.502-504, 2002.
DOI : 10.1093/bioinformatics/18.3.502

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/18/3/502

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, vol.4, pp.406-425, 1987.

X. Gu, Statistical methods for testing functional divergence after gene duplication, Molecular Biology and Evolution, vol.16, issue.12, pp.1664-1674, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026080

J. Felsenstein, Statistical properties of parsimony, in Inferring Phylogenies, pp.97-122, 2004.

J. Felsenstein, Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, vol.24, issue.6, pp.368-376, 1981.
DOI : 10.1007/BF01734359

A. Templeton, Phylogenetic Inference From Restriction Endonuclease Cleavage Site Maps with Particular Reference to the Evolution of Humans and the Apes, Evolution, vol.37, issue.2, pp.221-244, 1983.
DOI : 10.2307/2408332

A. Templeton, Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data. B. Statistical Analysis of DNA Sequence Data, pp.151-179, 1983.

H. Kishino, Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea, Journal of Molecular Evolution, vol.46, issue.2, pp.179-179, 1989.
DOI : 10.1007/BF02100115

C. Zmasek and S. Eddy, A simple algorithm to infer gene duplication and speciation events on a gene tree, Bioinformatics, vol.17, issue.9, pp.821-828, 2001.
DOI : 10.1093/bioinformatics/17.9.821

X. Huang and A. Madan, CAP3: A DNA Sequence Assembly Program, Genome Research, vol.9, issue.9, pp.868-877, 1999.
DOI : 10.1101/gr.9.9.868

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC310812