52 3.1.5.1 Méthodes expérimentales d'´ etude d'interaction protéine-protéine 52 3.1.5.2 Méthodes prédictives d'interaction protéine-protéine ,
106 5.2.1 Données pour l'´ elaboration des r` egles 106 5.2.1.1 Motifs introniques, ., vol.108 ,
125 6.2.1 Cultures cellulaires, Culture, p.125 ,
Validation in vivo des prédictions in silico, p.143 ,
Ces familles sont maintenuesàmaintenuesà jour au fil de l'avancement de l'annotation de nouveaux génomes. En effet, leur compositionétantcompositionétant basée sur des alignements de séquences, 2007. ,
Certaines r` egles sont partie intégrante du système d'annotation semi-automatique MAGUS, utilisé pour la phase Génolevures 3. Cela permet de détecter au plus tôt les erreurs Ce système fait suite au premier système quí etait basé sur le logiciel CAAT-Box, et que nous avions mis en place pour l'annotation des levures de la phase Génolevures 2. Ce premier système d'annotation manuelle permettait de mieux gérer et donc d'accro??treaccro??tre l'efficacité des annotateurs, mais aussi de garantir l'homogénéité de l'annotation réalisée pour les levures C. glabrata, K. lactis, D. hansenii et Y. lipolytica. Par ailleurs, l'´ etude expérimentale des interactions protéine-protéine parélectrophorèseparélectrophorèse BN/SDS chez la levure Y. lipolytica a apporté la preuve biologique de la qualité de la straté Yeast syntaxins Sso1p and Sso2p belong to a family of related membrane proteins that function in vesicular transport, Ceci a permis la détection d'erreurs portant par exemple sur la structure génique, pp.124095-104, 1993. ,
Mining association rules between sets of items in large databases, Proceedings of the 1993 ACM SIGMOD International Conference on Management of Data, pp.28-36, 1993. ,
JIGSAW : integration of multiple sources of evidence for gene prediction, Bioinformatics, vol.21, issue.18, pp.3596-3603, 2005. ,
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
DOI : 10.1016/S0022-2836(05)80360-2
CodonO: codon usage bias analysis within and across genomes, Nucleic Acids Research, vol.35, issue.Web Server, pp.132-136, 2007. ,
DOI : 10.1093/nar/gkm392
UniProt: the Universal Protein knowledgebase, Nucleic Acids Research, vol.32, issue.90001, pp.115-119, 2004. ,
DOI : 10.1093/nar/gkh131
The universal protein resource (UniProt), Nucleic Acids Research, vol.35, pp.193-197, 2007. ,
Applying negative rule mining to improve genome annotation, BMC Bioinformatics, vol.8, issue.1, 2007. ,
DOI : 10.1186/1471-2105-8-261
URL : http://doi.org/10.1186/1471-2105-8-261
Gene ontology : tool for the unification of biology. The Gene Ontology Consortium, Nature Genetics, vol.25, pp.25-29, 2000. ,
Fitting a mixture model by expectation maximization to discover motifs in biopolymers, AAAI Press Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp.28-36, 1994. ,
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment, Genome Biology, pp.7-10, 2006. ,
Non-conventional Yeast in Biotechnology : a Handbook, 1996. ,
Représentation des interactions protéine/protéine dans la cadre d'une méthode de modélisation de réseaux géniques, 2001. ,
Yarrowia lipolytica : a model organism for protein secretion studies, International Microbioly, vol.1, pp.123-130, 1998. ,
Structure and mechanism of DNA topoisomerase II, Nature, vol.379, issue.6562, pp.379225-232, 1996. ,
DOI : 10.1038/379225a0
Spliced segments at the 5??? terminus of adenovirus 2 late mRNA, Proceedings of the National Academy of Sciences, vol.74, issue.8, pp.743171-3175, 1977. ,
DOI : 10.1073/pnas.74.8.3171
The C. elegans genome sequencing project. C. elegans Genome Mapping and Sequencing Consortium., GMSC : Genome Mapping and Sequencing Consortium, pp.99-104, 1995. ,
DOI : 10.1101/gr.5.2.99
Identification and comparison of yeast complexomes, ESF-EMBO Symposium Comparative Genomics of Eukaroytic Microorganisms, 2005. ,
Applications of InterPro in protein annotation and genome analysis, Briefings in Bioinformatics, vol.3, issue.3, pp.285-295, 2002. ,
DOI : 10.1093/bib/3.3.285
revisited, FEBS Letters, vol.15, issue.1, pp.31-36, 2000. ,
DOI : 10.1016/S0014-5793(00)02275-4
URL : https://hal.archives-ouvertes.fr/hal-00306551
The Complete Genome Sequence of Escherichia coli K-12, Science, vol.277, issue.5331, pp.2771453-1474, 1997. ,
DOI : 10.1126/science.277.5331.1453
Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns, Nucleic Acids Research, vol.31, issue.4, pp.1121-1135, 2003. ,
DOI : 10.1093/nar/gkg213
URL : https://hal.archives-ouvertes.fr/inria-00339881
GENMARK: Parallel gene recognition for both DNA strands, Computers & Chemistry, vol.17, issue.2, pp.123-133, 1993. ,
DOI : 10.1016/0097-8485(93)85004-V
Detection of new genes in a bacterial genome using Markov models for three gene classes, Nucleic Acids Research, vol.23, issue.17, pp.3554-3562, 1995. ,
DOI : 10.1093/nar/23.17.3554
Genome annotation past, present, and future: How to define an ORF at each locus, Genome Research, vol.15, issue.12, pp.1777-1786, 2005. ,
DOI : 10.1101/gr.3866105
On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA"., Proceedings of the National Academy of Sciences U.S.A, pp.8910706-10710, 1992. ,
DOI : 10.1073/pnas.89.22.10706
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system, Nucleic Acids Research, vol.34, issue.12, pp.3533-3545, 2006. ,
DOI : 10.1093/nar/gkl471
Coevolution of codon usage and transfer RNA abundance, Nature, vol.325, issue.6106, pp.325728-730, 1987. ,
DOI : 10.1038/325728a0
Prediction of complete gene structures in human genomic DNA, Journal of Molecular Biology, vol.268, issue.1, pp.78-94, 1997. ,
DOI : 10.1006/jmbi.1997.0951
Two-dimensional Blue Native/SDS Gel Electrophoresis of Multi-Protein Complexes from Whole Cellular Lysates: A PROTEOMICS APPROACH, Molecular & Cellular Proteomics, vol.3, issue.2, pp.176-182, 2004. ,
DOI : 10.1074/mcp.T300010-MCP200
The evolution of noncoding DNA : how much junk, how much func ?, Trends in Genetics, vol.21, issue.10, pp.533-536, 2005. ,
Mammalian and yeast 14-3-3 isoforms form distinct patterns of dimers in vivo, Biochemical and Biophysical Research Communications, vol.300, issue.3, pp.300679-85, 2003. ,
DOI : 10.1016/S0006-291X(02)02902-9
SGD: Saccharomyces Genome Database, Nucleic Acids Research, vol.26, issue.1, pp.73-80, 1998. ,
DOI : 10.1093/nar/26.1.73
URL : http://doi.org/10.1093/nar/26.1.73
An amazing sequence arrangement at the 5??? ends of adenovirus 2 messenger RNA, Cell, vol.12, issue.1, pp.1-8, 1977. ,
DOI : 10.1016/0092-8674(77)90180-5
A comparative study of duplications in bacteria and eukaryotes: the importance of telomeres, Molecular Biology and Evolution, vol.14, issue.10, pp.141062-1074, 1997. ,
DOI : 10.1093/oxfordjournals.molbev.a025712
Creating the Gene Ontology Resource: Design and Implementation, Genome Research, vol.11, issue.8, pp.1425-1433, 2001. ,
DOI : 10.1101/gr.180801
The Cell : a molecular approach, 2000. ,
Transcriptional analysis of the 69-kb sequence centromeric to HLA-J: A dense and complex structure of five genes, Mammalian Genome, vol.11, issue.12, pp.111127-1131, 2000. ,
DOI : 10.1007/s003350010213
Structural analysis of two genes encoding divergent forms of yeast cytochrome c oxidase subunit V., Molecular and Cellular Biology, vol.7, issue.10, pp.3511-3519, 1987. ,
DOI : 10.1128/MCB.7.10.3511
A high-resolution map of transcription in the yeast genome, Proceedings of the National Acadademy of Sciences U.S.A, pp.5320-5325, 2006. ,
DOI : 10.1073/pnas.0601091103
Novel Transporters from Hemiascomycete Yeasts, Journal of Molecular Microbiology and Biotechnology, vol.6, issue.1, pp.19-28, 2003. ,
DOI : 10.1159/000073405
Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae, Functional & Integrative Genomics, vol.2, issue.4-5, pp.4-5154, 2002. ,
DOI : 10.1007/s10142-002-0060-8
The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome, Science, vol.304, issue.5668, pp.304304-307, 2004. ,
DOI : 10.1126/science.1095781
The paradox of functional heterochromatin, BioEssays, vol.303, issue.1, pp.29-41, 2005. ,
DOI : 10.1002/bies.20158
Exogean : a framework for annotating protein-coding genes in eukaryotic genomic DNA, Genome Biology, pp.7-7, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00339592
Computational approaches to gene prediction, Journal of Microbiology, vol.44, issue.2, pp.137-144, 2006. ,
Complete DNA sequence of yeast chromosome XI, Nature, vol.369, issue.6479, pp.369371-378, 1994. ,
DOI : 10.1038/369371a0
Genome evolution in yeasts, Nature, issue.6995, pp.43035-43079, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00104411
Sequence Ontology, Genome Biology, vol.6, issue.5, p.44, 2005. ,
DOI : 10.1007/978-1-4419-9863-7_1107
Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology, Science, vol.282, issue.5396, pp.2822012-2018, 1998. ,
DOI : 10.1126/science.282.5396.2012
Protein Molecular Function Prediction by Bayesian Phylogenomics, PLoS Computational Biology, vol.91, issue.5, p.45, 2005. ,
DOI : 10.1371/journal.pcbi.0010045.sd001
URL : http://doi.org/10.1371/journal.pcbi.0010045
[8] SRS: Information retrieval system for molecular biology data banks, Methods Enzymol, vol.266, pp.114-128, 1996. ,
DOI : 10.1016/S0076-6879(96)66010-8
Yeast molecular biology : a short compedium on basis features and novels apsects, Yeast Biol, 2005. ,
Identifying potential tRNA genes in genomic DNA sequences, Journal of Molecular Biology, vol.220, issue.3, pp.659-671, 1991. ,
DOI : 10.1016/0022-2836(91)90108-I
Finding genes by computer: the state of the art, Trends in Genetics, vol.12, issue.8, pp.316-320, 1996. ,
DOI : 10.1016/0168-9525(96)10038-X
A novel genetic system to detect protein???protein interactions, Nature, vol.340, issue.6230, pp.245-246, 1989. ,
DOI : 10.1038/340245a0
Homology, Trends in Genetics, vol.16, issue.5, pp.227-231, 2000. ,
DOI : 10.1016/S0168-9525(00)02005-9
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, vol.269, issue.5223, pp.269496-512, 1995. ,
DOI : 10.1126/science.7542800
CAAT-Box, contigs-Assembly and Annotation Tool-Box for genome sequencing projects, Bioinformatics, vol.20, issue.5, pp.790-797, 2004. ,
DOI : 10.1093/bioinformatics/btg490
The Minimal Gene Complement of Mycoplasma genitalium, Science, vol.270, issue.5235, pp.397-403, 1995. ,
DOI : 10.1126/science.270.5235.397
Functional and structural genomics using PEDANT, Bioinformatics, vol.17, issue.1, pp.44-57, 2001. ,
DOI : 10.1093/bioinformatics/17.1.44
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.25.752
MAGPIE/EGRET Annotation of the 2.9-Mb Drosophila melanogaster Adh Region, Genome Research, vol.10, issue.4, pp.502-510, 2000. ,
DOI : 10.1101/gr.10.4.502
Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture, Biochimie, vol.78, issue.5, pp.78302-310, 1996. ,
DOI : 10.1016/0300-9084(96)84761-4
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.24.6859
MAGPIE: automated genome interpretation, Trends in Genetics, vol.12, issue.2, pp.76-78, 1996. ,
DOI : 10.1016/0168-9525(96)81406-5
Structural analyses of a hypothetical minimal metabolism, Philosophical transactions of the Royal Society of London, Series B, Biological sciences, pp.1751-1762, 2007. ,
DOI : 10.1126/science.299.5609.1006
Structure of a split yeast gene: complete nucleotide sequence of the actin gene in Saccharomyces cerevisiae., Proceedings of the National Academy of Sciences, vol.77, issue.5, pp.2546-50, 1980. ,
DOI : 10.1073/pnas.77.5.2546
Sources of systematic error in functional annotation of genomes : domain rearrangement, non-orthologous gene displacement and operon disruption, In Silico Biology, vol.1, issue.1, pp.55-67, 1998. ,
ScanProsite : a reference implementation of a PROSITE scanning tool, Applied Bioinformatics, vol.1, issue.2, pp.107-108, 2002. ,
Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature, vol.415, issue.6868, pp.141-147, 2002. ,
DOI : 10.1038/415141a
Functional profiling of the Saccharomyces cerevisiae genome, Nature, vol.57, issue.6896, pp.418387-391, 2002. ,
DOI : 10.1073/pnas.95.25.14863
A novel arrangement of the 18S and 28S sequences in a repeating unit of drosophila melanogaster rDNA, Cell, vol.10, issue.2, pp.167-176, 1977. ,
DOI : 10.1016/0092-8674(77)90212-4
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica), Science, vol.296, issue.5565, pp.29692-100, 2002. ,
DOI : 10.1126/science.1068275
Codon catalog usage and the genome hypothesis, Nucleic Acids Research, vol.8, issue.1, pp.49-62, 1980. ,
DOI : 10.1093/nar/8.1.197-c
URL : https://hal.archives-ouvertes.fr/hal-00697923
Modern Genetic analysis : integrating genes and genomes, page 299, Freeman, W.H. and Compagny, 2002. ,
Distinctive Sequence Features in Protein Coding Genic Non-coding, and Intergenic Human DNA, Journal of Molecular Biology, vol.253, issue.1, pp.51-60, 1995. ,
DOI : 10.1006/jmbi.1995.0535
EGASP : the human ENCODE genome annotation assessment project, Genome Biology, vol.7, issue.Suppl 1, pp.2-3, 2006. ,
DOI : 10.1186/gb-2006-7-s1-s2
GENCODE : producing a reference annotation for ENCODE, Genome Biology, vol.7, 2006. ,
The HUPO PSI's Molecular Interaction format???a community standard for the representation of protein interaction data, Nature Biotechnology, vol.22, issue.2, pp.177-83, 2004. ,
DOI : 10.1038/nbt926
IntAct: an open source molecular interaction database, Nucleic Acids Research, vol.32, issue.90001, pp.452-455, 2004. ,
DOI : 10.1093/nar/gkh052
URL : https://hal.archives-ouvertes.fr/hal-00306577
CLUSTAL W : improving the sensitivity of progressivemultiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, pp.4673-4680, 1994. ,
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry, Nature, vol.415, issue.6868, pp.415180-183, 2002. ,
DOI : 10.1038/415180a
Crystal structure determination, refinement and molecular model of creatine amidinohydrolase from Pseudomonas putida, Journal of Molecular Biology, vol.204, pp.417-433, 1988. ,
A novel nucleoskeletal-like protein located at the nuclear periphery is required for the life cycle of Saccharomyces cerevisiae, EMBO Journal, vol.7, issue.13, pp.4323-4334, 1988. ,
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, issue.6814, pp.408796-815, 2000. ,
Pathways conservation, 2006. ,
Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonsaccharomyces yeasts, FEMS Yeast Research, 2007. ,
URL : https://hal.archives-ouvertes.fr/inria-00202723
A comprehensive two-hybrid analysis to explore the yeast protein interactome, Proceedings of the National Acadademy of Sciences U.S.A, pp.984569-4574, 2001. ,
DOI : 10.1073/pnas.061034498
Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models, Nucleic Acids Research, vol.31, issue.8, pp.312242-2251, 2003. ,
DOI : 10.1093/nar/gkg306
Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII, Science, vol.265, issue.5181, pp.2652077-2082, 1994. ,
DOI : 10.1126/science.8091229
Estimating the annotation error rate of curated GO database sequence annotations, BMC Bioinformatics, vol.8, issue.1, pp.364-373, 2007. ,
DOI : 10.1186/1471-2105-8-170
From genomics to chemical genomics: new developments in KEGG, Nucleic Acids Research, vol.34, issue.90001, pp.34-354, 2006. ,
DOI : 10.1093/nar/gkj102
Genome comparisons and analysis, Current Opinion in Structural Biology, vol.13, issue.3, pp.344-352, 2003. ,
DOI : 10.1016/S0959-440X(03)00073-3
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae, Nature, vol.428, issue.6983, pp.428617-624, 2004. ,
DOI : 10.1038/nature02424
Broadening the horizon ??? level 2.5 of the HUPO-PSI format for molecular interactions, BMC Biology, vol.5, issue.1, p.44, 2007. ,
DOI : 10.1186/1741-7007-5-44
URL : https://hal.archives-ouvertes.fr/hal-00306554
Systematic Discovery of New Genes in the Saccharomyces cerevisiae Genome, Genome Research, vol.13, issue.2, 2003. ,
DOI : 10.1101/gr.232903
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT, Bioinformatics, vol.17, issue.10, pp.17920-926, 2001. ,
DOI : 10.1093/bioinformatics/17.10.920
High-Definition Macromolecular Composition of Yeast RNA-Processing Complexes, Molecular Cell, vol.13, issue.2, pp.225-264, 2004. ,
DOI : 10.1016/S1097-2765(04)00003-6
Gene relics in the genome of the yeast Saccharomyces cerevisiae, Gene, vol.335, p.335, 2004. ,
DOI : 10.1016/j.gene.2004.03.028
Nouveau procédé pour l'analyse de l'ensemble des complexes protéiques d'une cellule, SFEAP 2005 I er Symposium de Chimie et Biologie Analytiques, 2005. ,
A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis, Electrophoresis, issue.16, pp.273306-3321, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00306561
Protein???protein interaction maps: a lead towards cellular functions, Trends in Genetics, vol.17, issue.6, pp.346-352, 2001. ,
DOI : 10.1016/S0168-9525(01)02323-X
Apollo : a sequence annotation editor, Genome Biol, vol.3, issue.12, p.82, 2002. ,
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence, Nucleic Acids Research, vol.25, issue.5, pp.955-964, 1997. ,
DOI : 10.1093/nar/25.5.0955
Efficient decoding algorithms for generalized hidden Markov model gene finders, BMC Bioinformatics, vol.6, issue.1, p.16, 2005. ,
DOI : 10.1186/1471-2105-6-16
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders, Bioinformatics, vol.20, issue.16, pp.202878-2879, 2004. ,
DOI : 10.1093/bioinformatics/bth315
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.150.4492
Comparative analysis of 1 196 orthologous mouse and human full-length mRNA and protein sequences, 1996. ,
Detecting protein function and protein-protein interactions from genome sequences, Science, issue.5428, pp.285751-753, 1999. ,
FROST: A filter-based fold recognition method, Proteins: Structure, Function, and Genetics, vol.34, issue.4, pp.493-509, 2002. ,
DOI : 10.1002/prot.10231
Current methods of gene prediction, their strengths and weaknesses, Nucleic Acids Research, vol.30, issue.19, pp.304103-4117, 2002. ,
DOI : 10.1093/nar/gkf543
Induction of instability at selected loci in maize, Genetics, vol.38, issue.6, pp.579-599, 1953. ,
A method for measuring the non-random bias of a codon usage table, Nucleic Acids Research, vol.12, issue.24, pp.9567-9575, 1984. ,
DOI : 10.1093/nar/12.24.9567
Imagene: an integrated computer environment for sequence annotation and analysis, Bioinformatics, vol.15, issue.1, pp.2-15, 1999. ,
DOI : 10.1093/bioinformatics/15.1.2
Comparison of expression systems in the yeasts Saccharomyces cerevisiae, Hansenula polymorpha, Klyveromyces lactis, Schizosaccharomyces pombe and Yarrowia lipolytica. cloning of two novel promoters from Yarrowia lipolytica, Yeast, vol.14, issue.14, pp.141267-1283, 1998. ,
DOI : 10.1002/(SICI)1097-0061(1998100)14:14<1267::AID-YEA327>3.3.CO;2-U
Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications., Proceedings of the National Academy of Sciences, vol.93, issue.13, pp.936470-6475, 1996. ,
DOI : 10.1073/pnas.93.13.6470
The Yeasts, a Taxonomic Study, 1998. ,
Protein expression and secretion in the yeast Yarrowia lipolytica, FEMS Yeast Research, vol.2, pp.371-379, 2002. ,
Family relationships: should consensus reign?--consensus clustering for protein families, Bioinformatics, vol.23, issue.2, pp.71-76, 2007. ,
DOI : 10.1093/bioinformatics/btl314
URL : https://hal.archives-ouvertes.fr/inria-00202434
NEW EMBO MEMBER'S REVIEW: Diversity of protein-protein interactions, The EMBO Journal, vol.22, issue.14, pp.3486-3492, 2003. ,
DOI : 10.1093/emboj/cdg359
T-coffee: a novel method for fast and accurate multiple sequence alignment, Journal of Molecular Biology, vol.302, issue.1, pp.205-217, 2000. ,
DOI : 10.1006/jmbi.2000.4042
A relationship between GC content and coding-sequence length, Journal of Molecular Evolution, vol.36, issue.3, pp.216-239, 1996. ,
DOI : 10.1007/BF02338829
The complete DNA sequence of yeast chromosome III, Nature, vol.85, issue.6373, pp.38-46, 1992. ,
DOI : 10.1016/S0076-6879(80)65059-9
The minimum information required for reporting a molecular interaction experiment (MIMIx), Nature Biotechnology, vol.165, issue.8, p.6, 2006. ,
DOI : 10.1038/nbt1324
Gene Density and Human Nucleotide Polymorphism, Molecular Biology and Evolution, vol.19, issue.3, pp.336-340, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004086
URL : http://mbe.oxfordjournals.org/cgi/content/short/19/3/336
Improved tools for biological sequence comparison., Proceedings of the National Academy of Sciences, vol.85, issue.8, pp.2444-2448, 1988. ,
DOI : 10.1073/pnas.85.8.2444
Sequence arrangement of the rDNA of Drosophila melanogaster, Cell, vol.10, issue.2, pp.213-224, 1977. ,
DOI : 10.1016/0092-8674(77)90215-X
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles, Proceedings of the National Academy of Sciences, vol.96, issue.8, pp.964285-4288, 1999. ,
DOI : 10.1073/pnas.96.8.4285
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16324
Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae, Journal of Molecular Biology, vol.268, issue.2, pp.322-330, 1997. ,
DOI : 10.1006/jmbi.1997.0942
Funky, not junky, Genome Biology, vol.4, issue.2, p.104, 2003. ,
DOI : 10.1186/gb-2003-4-2-104
Characterization of an Extracellular Lipase Encoded by LIP2 in Yarrowia lipolytica, Journal of Bacteriology, vol.182, issue.10, pp.1822802-2810, 2000. ,
DOI : 10.1128/JB.182.10.2802-2810.2000
The Tandem Affinity Purification (TAP) Method: A General Procedure of Protein Complex Purification, Methods, vol.24, issue.3, pp.218-247, 2001. ,
DOI : 10.1006/meth.2001.1183
C4.5 : Programs for Machine Learning, 1993. ,
A generic protein purification method for protein complex characterization and proteome exploration, Nature Biotechnology, vol.17, issue.10, pp.1030-1032, 1999. ,
DOI : 10.1038/13732
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents, Molecular and Cellular Proteomics, vol.3, issue.12, pp.1154-1169, 2004. ,
In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists, Bioinformatics, vol.23, issue.4, pp.414-420, 2007. ,
DOI : 10.1093/bioinformatics/btl639
Microbial gene identification using interpolated Markov models, Nucleic Acids Research, vol.26, issue.2, pp.544-548, 1998. ,
DOI : 10.1093/nar/26.2.544
URL : http://doi.org/10.1093/nar/26.2.544
Molecular Cloning : a molecular manual, 2001. ,
Electrophoretic separation of multiprotein complexes from blood platelets and cell lines: Technique for the analysis of diseases with defects in oxidative phosphorylation, Electrophoresis, vol.268, issue.4, pp.709-714, 1996. ,
DOI : 10.1002/elps.1150170415
Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa, Analytical Biochemistry, vol.166, issue.2, pp.368-379, 1987. ,
DOI : 10.1016/0003-2697(87)90587-2
Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form, Analytical Biochemistry, vol.199, issue.2, pp.223-231, 1991. ,
DOI : 10.1016/0003-2697(91)90094-A
Two-hybrid system and false positives. Approaches to detection and elimination, Methods in Molecular Biology, vol.177, pp.123-134, 2001. ,
Genolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts, Nucleic Acids Research, vol.32, issue.90001, pp.32315-318, 2004. ,
DOI : 10.1093/nar/gkh091
URL : https://hal.archives-ouvertes.fr/inria-00407519
Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts, Nucleic Acids Research, vol.34, issue.90001, pp.34-432, 2006. ,
DOI : 10.1093/nar/gkj160
URL : https://hal.archives-ouvertes.fr/hal-00118142
PROSITE: A documented database using patterns and profiles as motif descriptors, Briefings in Bioinformatics, vol.3, issue.3, pp.265-274, 2002. ,
DOI : 10.1093/bib/3.3.265
In search of the minimal Escherichia coli genome, Trends in Microbiology, vol.11, issue.1, pp.6-8, 2003. ,
DOI : 10.1016/S0966-842X(02)00008-2
Identification of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, pp.195-197, 1981. ,
DOI : 10.1016/0022-2836(81)90087-5
Pfam: A comprehensive database of protein domain families based on seed alignments, Proteins: Structure, Function, and Genetics, vol.183, issue.3, pp.405-420, 1997. ,
DOI : 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L
Sequence comparison among subunits of multicatalytic proteinase, Biomed Biochim Acta, vol.50, pp.459-564, 1991. ,
Génolevures : Genomic exploration of the hemiascomycetous yeasts, FEBS Letters Special Issue, vol.487, issue.1, 2000. ,
How Reliable are Experimental Protein???Protein Interaction Data?, Journal of Molecular Biology, vol.327, issue.5, pp.919-923, 2003. ,
DOI : 10.1016/S0022-2836(03)00239-0
Gene Prediction with a Hidden Markov Model, 2003. ,
BioGRID: a general repository for interaction datasets, Nucleic Acids Research, vol.34, issue.90001, pp.535-53, 2006. ,
DOI : 10.1093/nar/gkj109
An Overview of <i>C. elegans</i> Biology, Methods Mol Biol, vol.351, pp.1-12, 2006. ,
DOI : 10.1385/1-59745-151-7:1
Refined phylogenetic profiles method for predicting protein-protein interactions, Bioinformatics, vol.21, issue.16, pp.3409-3415, 2005. ,
DOI : 10.1093/bioinformatics/bti532
The COG database : an updated version includes eukaryotes, BMC Bioinformatics, vol.4, issue.1, p.41, 2003. ,
DOI : 10.1186/1471-2105-4-41
The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Research, vol.28, issue.1, pp.33-36, 2000. ,
DOI : 10.1093/nar/28.1.33
A Genomic Perspective on Protein Families, Science, vol.278, issue.5338, pp.278631-637, 1997. ,
DOI : 10.1126/science.278.5338.631
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae, Nature, issue.6770, pp.403623-627, 2000. ,
Computational methods for the prediction of protein interactions, Current Opinion in Structural Biology, vol.12, issue.3, pp.368-373, 2002. ,
DOI : 10.1016/S0959-440X(02)00333-0
MaGe: a microbial genome annotation system supported by synteny results, Nucleic Acids Research, vol.34, issue.1, pp.53-65, 2006. ,
DOI : 10.1093/nar/gkj406
Characterization of the Yeast Transcriptome, Cell, vol.88, issue.2, pp.243-251, 1997. ,
DOI : 10.1016/S0092-8674(00)81845-0
The sequence of the human genome, Science, issue.5507, pp.2911304-1351, 2001. ,
URL : https://hal.archives-ouvertes.fr/hal-00465088
A tree kernel to analyse phylogenetic profiles, Bioinformatics, vol.18, issue.Suppl 1, pp.276-284, 2002. ,
DOI : 10.1093/bioinformatics/18.suppl_1.S276
URL : https://hal.archives-ouvertes.fr/hal-00433591
The ZNF75 Zinc Finger Gene Subfamily: Isolation and Mapping of the Four Members in Humans and Great Apes, Genomics, vol.35, issue.2, pp.312-320, 1996. ,
DOI : 10.1006/geno.1996.0362
Comparative assessment of large-scale data sets of protein-protein interactions, Nature, issue.6887, pp.417399-403, 2002. ,
A Brief Review of Computational Gene Prediction Methods, Genomics, Proteomics & Bioinformatics, vol.2, issue.4, pp.216-221, 2004. ,
DOI : 10.1016/S1672-0229(04)02028-5
Two's company, three's a crowd: the yeast two hybrid system for mapping molecular interactions, Structure, vol.5, issue.1, pp.13-17, 1997. ,
DOI : 10.1016/S0969-2126(97)00162-7
Functional analysis of three adjacent open reading frames from the right arm of yeast chromosome XVI, Yeast, vol.1, issue.11, pp.1027-1039, 1998. ,
DOI : 10.1002/(SICI)1097-0061(199808)14:11<1027::AID-YEA295>3.0.CO;2-S
Initial sequencing and comparative analysis of the mouse genome, Nature, issue.6915, pp.420520-562, 2002. ,
Genetical implications of the structure of desoxyribonucleic acid, Nature, issue.4361, pp.171964-967, 1953. ,
MOLECULAR STRUCTURE OF NUCLEIC ACIDS, JAMA, vol.269, issue.15, pp.171737-738, 1953. ,
DOI : 10.1001/jama.1993.03500150078030
The structural organization of ribosomal DNA in drosophila melanogaster, Cell, vol.10, issue.2, pp.193-212, 1977. ,
DOI : 10.1016/0092-8674(77)90214-8
Filtering erroneous protein annotation, Bioinformatics, vol.20, issue.Suppl 1, pp.342-347, 2004. ,
DOI : 10.1093/bioinformatics/bth938
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/20/suppl_1/i342
Blue native PAGE, Nature Protocols, vol.13, issue.1, pp.418-428, 2006. ,
DOI : 10.1038/nprot.2006.62
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya., Proceedings of the National Academy of Sciences, vol.87, issue.12, pp.4576-4579, 1990. ,
DOI : 10.1073/pnas.87.12.4576
Archaebacteria, Journal of Molecular Evolution, vol.113, issue.3, pp.245-252, 1978. ,
DOI : 10.1007/BF01734485
Automatic annotation of organellar genomes with DOGMA, Bioinformatics, vol.20, issue.17, pp.3252-3255, 2004. ,
DOI : 10.1093/bioinformatics/bth352
Variation in sequence and organization of splicing regulatory elements in vertebrate genes, Proceedings of the National Academy of Sciences, vol.101, issue.44, pp.15700-15705, 2004. ,
DOI : 10.1073/pnas.0404901101
DEG: a database of essential genes, Nucleic Acids Research, vol.32, issue.90001, pp.271-272, 2004. ,
DOI : 10.1093/nar/gkh024
A computational approach for identifying pseudogenes in the ENCODE regions, Genome Biology, vol.7, issue.Suppl 1, p.13, 2006. ,
DOI : 10.1186/gb-2006-7-s1-s13
Junk DNA and sectorial gene repression, Gene, vol.205, issue.1-2, pp.323-343, 1997. ,
DOI : 10.1016/S0378-1119(97)00543-X
A complexomic study of Escherichia coli using two dimensional Blue Native / SDS Polyacrylamide Gel Electrophoresis, Liste des publications, pp.16-3306, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00306561
Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts, Database issue), pp.432-437, 2006. ,
DOI : 10.1093/nar/gkj160
URL : https://hal.archives-ouvertes.fr/hal-00118142
Genolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts, Database issue), pp.315-323, 2004. ,
DOI : 10.1093/nar/gkh091
URL : https://hal.archives-ouvertes.fr/inria-00407519
Novel transporters from hemoascomycete yeasts, 2003. ,