Systems biology: a brief overview. Science, pp.1662-1666, 2002. ,
DOI : 10.1126/science.1069492
URL : http://www.physics.unc.edu/~rsuper/UNCSysBio/images/kitano.sysbiooverview.science2002.pdf
Towards building the silicon cell: A modular approach, Biosystems, vol.83, issue.2-3, pp.2-3, 2006. ,
DOI : 10.1016/j.biosystems.2005.07.006
Systems biology and the virtual physiological human. Molecular Systems Biology, Jul, vol.5, 2009. ,
DOI : 10.1038/msb.2009.51
URL : http://msb.embopress.org/content/msb/5/1/292.full.pdf
Integrating systems biology models and biomedical ontologies, BMC Systems Biology, vol.5, issue.1, 2011. ,
DOI : 10.1186/1752-0509-5-124
URL : https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-5-124?site=bmcsystbiol.biomedcentral.com
A framework for evolutionary systems biology, BMC Systems Biology, vol.3, issue.1, p.27, 2009. ,
DOI : 10.1186/1752-0509-3-27
URL : https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-3-27?site=bmcsystbiol.biomedcentral.com
Genomes, phylogeny, and evolutionary systems biology, Proceedings of the National Academy of Sciences, vol.99, issue.17, pp.6630-6635, 2005. ,
DOI : 10.1073/pnas.172390199
URL : http://www.pnas.org/content/102/suppl_1/6630.full.pdf
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions, Nucleic Acids Research, vol.39, issue.Database, pp.556-60, 2011. ,
DOI : 10.1093/nar/gkq1109
The evolution of molecular genetic pathways and networks, BioEssays, vol.155, issue.113, pp.479-84, 2004. ,
DOI : 10.1093/oxfordjournals.molbev.a026108
Genomes, phylogeny, and evolutionary systems biology, Proceedings of the National Academy of Sciences, vol.99, issue.17, pp.6630-6635, 2005. ,
DOI : 10.1073/pnas.172390199
URL : http://www.pnas.org/content/102/suppl_1/6630.full.pdf
Evolution of biomolecular networks ??? lessons from metabolic and protein interactions, Nature Reviews Molecular Cell Biology, vol.103, issue.11, pp.791-803, 2009. ,
DOI : 10.1186/gb-2002-3-12-research0088
An integrated view of protein evolution, Nature Reviews Genetics, vol.7, issue.5, pp.337-385, 2006. ,
Making the right connections: biological networks in the light of evolution, BioEssays, vol.3, issue.10, pp.1080-90, 2009. ,
DOI : 10.1038/msb4100162
Evolutionary systems biology: links between gene evolution and function, Current Opinion in Biotechnology, vol.17, issue.5, pp.481-488, 2006. ,
DOI : 10.1016/j.copbio.2006.08.003
Converging on a general model of protein evolution, Trends in Biotechnology, vol.23, issue.10, pp.485-492, 2005. ,
DOI : 10.1016/j.tibtech.2005.07.009
Lethality and centrality in protein networks, Nature, vol.28, issue.6833, pp.41-43, 2001. ,
DOI : 10.1093/nar/28.1.73
Gene essentiality, gene duplicability and protein connectivity in human and mouse, Trends in Genetics, vol.23, issue.8, pp.375-383, 2007. ,
DOI : 10.1016/j.tig.2007.04.005
Expression breadth and expression abundance behave differently in correlations with evolutionary rates, BMC Evolutionary Biology, vol.10, issue.1, p.241, 2010. ,
DOI : 10.1186/1471-2148-10-241
URL : https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/1471-2148-10-241?site=bmcevolbiol.biomedcentral.com
Unifying measures of gene function and evolution, Proceedings of the Royal Society B: Biological Sciences, vol.22, issue.4, pp.1507-1522, 1593. ,
DOI : 10.1093/molbev/msi101
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560323/pdf
Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi, Genome Biology and Evolution, vol.3, issue.0, pp.75-86, 2011. ,
DOI : 10.1093/gbe/evq083
Visualization of multiple alignments, phylogenies and gene family evolution, Nature Methods, vol.294, issue.3s, pp.16-25, 2010. ,
DOI : 10.1186/gb-2002-3-12-research0077
URL : https://hal.archives-ouvertes.fr/hal-00530522
The human proteomics initiative (HPI), Trends in Biotechnology, vol.19, issue.5, pp.178-81, 2001. ,
DOI : 10.1016/S0167-7799(01)01598-0
Ensembl 2009, Nucleic Acids Research, vol.37, issue.Database, pp.690-697, 2009. ,
DOI : 10.1093/nar/gkn828
URL : https://hal.archives-ouvertes.fr/hal-01615160
BLAST: at the core of a powerful and diverse set of sequence analysis tools, Nucleic Acids Research, vol.32, issue.Web Server, pp.20-25, 2004. ,
DOI : 10.1093/nar/gkh435
PipeAlign: a new toolkit for protein family analysis, Nucleic Acids Research, vol.31, issue.13, pp.313829-313861, 2003. ,
DOI : 10.1093/nar/gkg518
URL : https://academic.oup.com/nar/article-pdf/31/13/3829/9487137/gkg518.pdf
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches, Nucleic Acids Research, vol.28, issue.15, pp.2919-2945, 2000. ,
DOI : 10.1093/nar/28.15.2919
URL : https://academic.oup.com/nar/article-pdf/28/15/2919/9904662/282919.pdf
RASCAL: rapid scanning and correction of multiple sequence alignments, Bioinformatics, vol.19, issue.9, pp.1155-61, 2003. ,
DOI : 10.1093/bioinformatics/btg133
URL : https://academic.oup.com/bioinformatics/article-pdf/19/9/1155/801480/btg133.pdf
LEON: multiple aLignment Evaluation Of Neighbours, Nucleic Acids Research, vol.32, issue.4, pp.1298-307, 2004. ,
DOI : 10.1093/nar/gkh294
URL : https://academic.oup.com/nar/article-pdf/32/4/1298/6258592/gkh294.pdf
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, issue.14, pp.3059-66, 2002. ,
DOI : 10.1093/nar/gkf436
URL : https://academic.oup.com/nar/article-pdf/30/14/3059/9488148/gkf436.pdf
MACSIMS: multiple alignment of complete sequences information management system, BMC Bioinformatics, vol.7, issue.1, p.318, 2006. ,
DOI : 10.1186/1471-2105-7-318
URL : https://hal.archives-ouvertes.fr/hal-00188166
Gene Ontology: tool for the unification of biology, Nature Genetics, vol.9, issue.1, pp.25-34, 2000. ,
DOI : 10.1091/mbc.9.12.3273
The Pfam protein families database, Nucleic Acids Research, vol.38, issue.suppl_1, pp.211-233, 2010. ,
DOI : 10.1093/nar/gkp985
URL : https://hal.archives-ouvertes.fr/hal-01294685
Orthologs, Paralogs, and Evolutionary Genomics, Annual Review of Genetics, vol.39, issue.1, pp.309-347, 2005. ,
DOI : 10.1146/annurev.genet.39.073003.114725
OrthoInspector: comprehensive orthology analysis and visual exploration, BMC Bioinformatics, vol.12, issue.1, p.11, 2011. ,
DOI : 10.1186/1471-2105-12-11
URL : https://hal.archives-ouvertes.fr/inserm-00663697
Boxplots and batch comparison, in Understanding Robust and Exploratory Data Analysis, pp.58-96, 1983. ,
The Conditional-Potts Clustering Model ,
-Means and Density Estimation, Journal of Computational and Graphical Statistics, vol.17, issue.3, pp.629-58, 2008. ,
DOI : 10.1198/106186008X318855
GoMiner: a resource for biological interpretation of genomic and proteomic data, Genome Biology, vol.4, issue.4, p.28, 2003. ,
DOI : 10.1186/gb-2003-4-4-r28
The human glucagon receptor encoding gene: structure, cDNA sequence and chromosomal localization, Gene, vol.140, issue.2, pp.203-212, 1994. ,
DOI : 10.1016/0378-1119(94)90545-2
Genes Are Expressed in Pluripotent Cells and Map to Chromosome 12p13, a Hotspot for Teratocarcinoma, Stem Cells, vol.95, issue.2, pp.169-79, 2004. ,
DOI : 10.1634/stemcells.22-2-169
THE RAPID EVOLUTION OF REPRODUCTIVE PROTEINS, Nature Reviews Genetics, vol.15, issue.2, pp.137-181, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a025914
Human POGZ modulates dissociation of HP1?? from mitotic chromosome arms through Aurora B activation, Nature Cell Biology, vol.22, issue.7, pp.719-746, 2010. ,
DOI : 10.1016/j.exphem.2003.07.005
The genome of the early chordate Ciona intestinalis encodes only five cytoplasmic intermediate filament proteins including a single type I and type II keratin and a unique IF???annexin fusion protein, Gene, vol.326, pp.123-132, 2004. ,
DOI : 10.1016/j.gene.2003.10.019
Terrestrial vertebrates have two keratin gene clusters; striking differences in teleost fish, European Journal of Cell Biology, vol.84, issue.6, pp.623-658, 2005. ,
DOI : 10.1016/j.ejcb.2005.01.007
Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair, BMC Evolutionary Biology, vol.8, issue.1, p.241, 2008. ,
DOI : 10.1186/1471-2148-8-241
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny, BMC Genomics, vol.6, issue.7, p.303, 2011. ,
DOI : 10.1038/msb.2010.79
URL : https://hal.archives-ouvertes.fr/hal-00784423
Superparamagnetic Clustering of Data, Physical Review Letters, vol.237, issue.18, pp.3251-3255, 1996. ,
DOI : 10.1016/0370-2693(90)91209-T
Functional connectivity mapping using the ferromagnetic Potts spin model, Human Brain Mapping, vol.8, issue.122, pp.422-462, 2008. ,
DOI : 10.1007/978-1-4899-3324-9
Super-paramagnetic clustering of yeast gene expression profiles. Physica A, pp.1-4, 2000. ,
DOI : 10.1016/s0378-4371(99)00524-5
Gene expression analysis reveals a strong signature of an interferon-induced pathway in childhood lymphoblastic leukemia as well as in breast and ovarian cancer, Oncogene, vol.24, issue.42, pp.6367-75, 2005. ,
DOI : 10.1073/pnas.94.14.7406
Super Paramagnetic Clustering of DNA Sequences, Journal of Biological Physics, vol.7, issue.1, pp.11-25, 2006. ,
DOI : 10.1152/physiolgenomics.00040.2001
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022498/pdf
Super paramagnetic clustering of protein sequences, BMC Bioinformatics, vol.6, 2005. ,
The Conditional-Potts Clustering Model. (submitted), 2011. ,
DOI : 10.1080/10618600.2013.837828
URL : http://www.dms.umontreal.ca/%7Emurua/research/conditionalPotts.pdf
Genomics of Olfactory Receptors, Results Probl Cell Differ, vol.47, pp.25-36, 2009. ,
DOI : 10.1007/400_2008_28
Co-regulation of a large and rapidly evolving repertoire of odorant receptor genes, BMC Neuroscience, vol.8, issue.Suppl 3, p.2, 2007. ,
DOI : 10.1186/1471-2202-8-S3-S2
Structural imperatives impose diverse evolutionary constraints on helical membrane proteins, Proceedings of the National Academy of Sciences, vol.25, issue.17, pp.17747-50, 2009. ,
DOI : 10.1093/nar/25.17.3389
URL : http://www.pnas.org/content/106/42/17747.full.pdf
FactoMineR: An R package for multivariate analysis, Journal of Statistical Software. Mar, vol.25, issue.1, pp.1-18, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00359835
Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5'-methylthioadenosine. IUBMB Life, pp.1132-1174, 2009. ,
The methionine salvage pathway compound 4-methylthio-2-oxobutanate causes apoptosis independent of down-regulation of ornithine decarboxylase, Biochemical Pharmacology, vol.72, issue.7, pp.806-821, 2006. ,
DOI : 10.1016/j.bcp.2006.06.018
Expression, Function of the Human Androgen-Responsive Gene AD11 in Prostate Cancer, Neoplasia, vol.9, issue.8, pp.643-51, 2007. ,
DOI : 10.1593/neo.07415
The novel immunosuppressive enzyme IL4I1 is expressed by neoplastic cells of several B-cell lymphomas and by tumor-associated macrophages, Leukemia, vol.29, issue.5, pp.952-60, 2009. ,
DOI : 10.4049/jimmunol.168.3.996
URL : https://hal.archives-ouvertes.fr/inserm-00392067
Origin and diversification of the L-amino oxidase family in innate immune defenses of animals, Immunogenetics, vol.208, issue.11-12, pp.11-12, 2010. ,
DOI : 10.4049/jimmunol.173.7.4561
Concerted and Birth-and-Death Evolution of Multigene Families, Annual Review of Genetics, vol.39, issue.1, pp.121-52, 2005. ,
DOI : 10.1146/annurev.genet.39.073003.112240
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1464479/pdf