Friends and neighbors on the web, Social Networks, vol.25, issue.3, pp.211-230, 2003. ,
Link prediction using supervised learning, Proceedings of SDM 06 workshop on Link Analysis, Counterterrorism and Security, 2006. ,
The relationship between variable selection and data augmentation and a method for prediction, Technometrics, vol.16, issue.1, pp.125-127, 1974. ,
Interrogating protein interaction networks through structural biology, Proceedings of the National Academy of Sciences, vol.99, issue.9, pp.5896-5901, 2002. ,
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
Kernels for vector-valued functions : a review, 2011. ,
Processing of cftr : Traversing the cellular maze -how much cftr needs to go through to avoid cystic fibrosis, Pediatric Pulmonology, vol.39, pp.479-491, 2005. ,
When is there a representer theorem ? Vector vs matrix regularizers, Journal of Machine Learning Research, vol.10, pp.2507-2529, 2009. ,
Theory of reproducing kernels, Transactions of the American Mathematical Society, vol.68, issue.3, pp.337-404, 1950. ,
Gene ontology : tool for the unification of biology, Nature Genetics, vol.25, issue.1, pp.25-29, 2000. ,
Bind : the biomolecular interaction network database, Nucleic Acids Research, vol.31, issue.1, pp.248-250, 2003. ,
The enzyme database in 2000, Nucleic Acids Research, vol.28, issue.1, pp.304-305, 2000. ,
Multi-output learning via spectral filtering, Machine Learning, vol.87, pp.259-301, 2012. ,
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles, Bioinformatics, vol.22, issue.7, pp.815-822, 2006. ,
Network biology : understanding the cell's functional organization, Nature Review Genetics, vol.5, pp.101-113, 2004. ,
Evolution of the social network of scientific collaborations, Physica A : Statistical Mechanics and its Applications, vol.311, issue.3-4, pp.590-614, 2002. ,
Unifying collaborative and content-based filtering, Proceedings of the 21st International Conference on Machine Learning (ICML), 2004. ,
Using manifold structure for partially labeled classification, Advances in Neural Information Processing Systems, vol.15, 2003. ,
Semi-supervised learning on riemannian manifolds. Machine Learning, vol.56, pp.209-239, 2004. ,
Towards a theoritical foundation for laplacian-based manifold methods, Proceedings of the 18th Annual Conference on Learning Theory, pp.486-500, 2005. ,
Manifold regularization : A geometric framework for learning from labeled and unlabeled examples, Journal of Machine Learning Research, vol.7, pp.2399-2434, 2006. ,
Kernel methods for predicting protein-protein interactions, Bioinformatics, vol.21, issue.1, pp.38-46, 2005. ,
The protein data bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000. ,
Machine learning for pairwise data : applications for preference learning and supervised network inference, 2011. ,
Combining protein and network topology information for predicting protein-protein interactions : a bayesian approach, 2012. ,
Supervised prediction of drug-target interactions using bipartite local models, Bioinformatics, vol.25, issue.18, pp.2397-2403, 2009. ,
Supervised reconstruction of biological networks with local models, Bioinformatics, vol.23, issue.13, pp.57-65, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00433575
Predicting protein-protein interactions from primary structure, Bioinformatics, vol.17, issue.5, pp.455-460, 2001. ,
A training algorithm for optimal margin classifiers, Proceedings of the 5th Annual ACM Workshop on Computational Learning Theory, pp.144-152, 1992. ,
The anatomy of a large-scale hypertextual web search engine. Computer Networks and ISDN Systems, vol.30, pp.107-117, 1998. ,
Semi-supervised penalized output kernel regression for link prediction, Proceedings of the 28th International Conference on Machine Learning, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00654123
Learning a markov logic network for supervised gene regulatory network inference, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00868767
Discovering functional relationships between rna expression and chemotherapeutic susceptibility using relevance networks, Proceedings of the National Academy of Sciences, vol.97, issue.22, pp.12182-12186, 2000. ,
Universal multitask kernels, Journal of Machine Learning Research, vol.9, pp.1615-1646, 2008. ,
LIBSVM : A library for support vector machines, ACM Transactions on Intelligent Systems and Technology, vol.2, 2011. ,
Semi-supervised classification by low density separation, Proceedings of the Tenth International Workshop on Artificial Intelligence and Statistics, 2005. ,
Semi-Supervised Learning, 2006. ,
Increasing confidence of protein interactomes using network topological metrics, Bioinformatics, vol.22, issue.16, 1998. ,
Function of cftr protein : ion transport, Cystic Fibrosis in the 21st Century, pp.38-44, 2006. ,
Modeling gene expression with differential equations, Pacific Symposium on Biocomputing, pp.29-40, 1999. ,
Introduction to Modern Information Retrieval, 2010. ,
Support vector networks, Machine Learning, vol.20, pp.273-297, 1995. ,
A general regression technique for learning transductions, Proceedings of the 22nd International Conference on Machine Learning, pp.153-160, 2005. ,
Conservation of gene order : a fingerprint of proteins that physically interact, Trends in biochemical sciences, vol.23, issue.9, pp.324-328, 1998. ,
The relationship between precision-recall and roc curves, Proceedings of the 23rd International Conference on Machine Learning, pp.233-240, 2006. ,
Protein-protein interactions essentials : key concepts to building and analyzing interactive networks, PLOS Computational Biology, vol.6, issue.6, p.1000807, 2010. ,
Protein interactions : two methods for assessment of the reliability of high throughput observations, Molecular & Cellular Proteomics, vol.1, issue.5, pp.349-356, 2002. ,
Inferring domain-domain interactions from protein-protein interactions, Genome Research, vol.12, issue.10, pp.1540-1548, 2002. ,
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks, Nature Biotechnology, vol.23, pp.377-383, 2005. ,
Learning output kernels with block coordinate descent, Proceedings of the 28th International Conference on Machine Learning, 2011. ,
Cluster analysis and display of genome-wide expression patterns, Proceedings of the National Academy of Sciences, vol.95, issue.25, pp.14863-14868, 1998. ,
Protein interaction maps for complete genomes based on gene fusion events, Nature, vol.402, pp.86-90, 1999. ,
On random graphs, Publicationes Mathematicae, vol.6, pp.290-297, 1959. ,
Learning multiple tasks with kernel methods, Journal of Machine Learning Research, vol.6, pp.615-637, 2005. ,
Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles, PLoS Biology, vol.5, issue.1, p.8, 2007. ,
An introduction to roc analysis, Pattern Recognition Letters, vol.27, pp.861-874, 2005. ,
Learning probabilistic relational models, Proceedings of the 16th international joint conference on artificial intelligence, IJCAI'99, 1999. ,
Using bayesian networks to analyse expression data, Journal of Computational Biology, vol.7, 2004. ,
Inferring genetic networks and identifying compound mode of action via expression profiling, Science, vol.301, pp.102-105, 2003. ,
, , vol.415, pp.141-147, 2002.
Correlation between transcriptome and interactome mapping data from saccharomyces cerevisiae, Nature Genetics, vol.29, issue.4, pp.482-486, 2001. ,
Link mining : a survey, SIGKDD Explorations Newsletters, vol.7, issue.2, pp.3-12, 2005. ,
Introduction to statistical relational learning, 2007. ,
Learning probabilistic models of link structure, Journal of Machine Learning Research, vol.3, pp.679-707, 2002. ,
Kernelizing the output of tree-based methods, Proceedings of the 23th International Conference on Machine learning, pp.345-352, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00341946
Inferring biological networks with output kernel trees, BMC Bioinformatics (PMSB06 special issue), vol.8, issue.2, p.4, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00341942
A protein interaction map of drosophila melanogaster, Science, vol.302, issue.5651, pp.1727-1736, 2003. ,
Euclidean embedding of co-occurrence data, Journal of Machine Learning Research, vol.8, pp.2265-2295, 2007. ,
Assessing experimentally derived interactions in a small world, Proceedings of the National Academy of Sciences, vol.100, issue.8, pp.4372-4376, 2003. ,
Generalized cross-validation as a method for choosing a good ridge parameter, Technometrics, vol.21, pp.215-223, 1979. ,
Measuring statistical dependence with hilbert-schmidt norms, Algorithmic Learning Theory, vol.3734, pp.63-77, 2005. ,
Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences, Nucleic Acids Research, vol.36, issue.9, pp.3025-3030, 2008. ,
Confirmation of human protein interaction data by human expression data, BMC Bioinformatics, vol.6, issue.1, p.112, 2005. ,
A domain combination based probabilistic framework for protein-protein interaction prediction, Genome Informatics, vol.14, pp.250-259, 2003. ,
The elements of statistical learning, 2008. ,
Trustful inference of gene regulation using stability selection, BMC Systems Biology, vol.6, issue.1, p.145, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00694218
Systematic identification of protein complexes in saccharomyces cerevisiae by mass spectrometry, Nature, vol.415, issue.6868, pp.180-183, 2002. ,
Ridge regression : biases estimation for nonorthogonal problems, Technometrics, vol.12, issue.1, pp.55-67, 1970. ,
Multiplicative latent factor models for description and prediction of social networks. Computational and Mathematical Organization Theory, 2008. ,
Latent space approaches to social network analysis, Journal of the American Statistical Association, vol.97, pp.1090-1098, 2002. ,
Preimage problem in kernel-based machine learning, IEEE Signal Processing Magazine, vol.28, issue.2, pp.77-88, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01965582
A unified recommendation framework based on probabilistic relational models, 14th annual Workshop on Information Technologies and Systems (WITS), pp.8-13, 2004. ,
Large-scale prediction of proteinprotein interactions from structures, BMC Bioinformatics, vol.11, issue.1, p.144, 2010. ,
URL : https://hal.archives-ouvertes.fr/inserm-00663765
Global analysis of protein localization in budding yeast, Nature, vol.425, pp.686-691, 2003. ,
Toward a protein-protein interaction map of the budding yeast : A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins, Proceedings of the National Academy of Sciences, vol.97, issue.3, pp.1143-1147, 2000. ,
Protein-ligand interaction prediction : an improved chemogenomics approach, Bioinformatics, vol.24, issue.19, pp.2149-2156, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00433572
Clustered multi-task learning : A convex formulation, Advances in Neural Information Processing Systems, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00320573
Towards an integrated protein-protein interaction network : a relational markov network approach, Journal of Computational Biology, vol.13, pp.145-164, 2006. ,
An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology, BMC Bioinformatics, vol.11, issue.1, p.562, 2010. ,
Relating whole-genome expression data with protein-protein interactions, Genome Research, vol.12, pp.37-46, 2002. ,
A bayesian networks approach for predicting protein-protein interactions from genomic data, Science, vol.302, issue.5644, pp.449-453, 2003. ,
Simrank : a measure of structural-context similarity, Proceedings of the eighth ACM SIGKDD international conference on Knowledge discovery and data mining, KDD '02, pp.538-543, 2002. ,
Lethality and centrality in protein networks, Nature, vol.411, issue.6833, pp.41-42, 2001. ,
Transductive inference for text classification using support vector machines, Proceedings of the International Conference on Machine Learning, 1999. ,
Nonlinear functional regression : a functional rkhs approach, JMLR Proceedings of International Conference on Artificial Intelligence and Statistics, vol.9, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00510411
Functional regularized least squares classification with operator-valued kernels, Proceedings of the 28th International Conference on Machine Learning, 2011. ,
Multiple operator-valued kernel learning, Advances in Neural Information Processing Systems, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00677012
A parameterized probabilistic model of network evolution for supervised link prediction, Sixth International Conference on Data Mining (ICDM), pp.340-349, 2006. ,
Link propagation : A fast semi-supervised learning algorithm for link prediction, Proceedings of the 9th SIAM International Conference on Data Mining, pp.1099-1110, 2009. ,
Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information, Bioinformatics, vol.25, issue.22, pp.2962-2968, 2009. ,
Selective integration of multiple biological data for supervised network inference, Bioinformatics, vol.21, issue.10, pp.2488-2495, 2005. ,
A new status index derived from sociometric analysis, Psycometrika, vol.18, issue.1, pp.39-43, 1953. ,
The intact molecular interaction database in 2012, Nucleic Acids Research, vol.40, issue.D1, pp.841-846, 2012. ,
Principles of protein-protein interactions : what are the preferred ways for proteins to interact ?, Chemical Reviews, vol.108, pp.1225-1244, 2008. ,
Large scale statistical prediction of proteinprotein interaction by potentially interacting domain (pid) pair, Genome Informatics, vol.13, pp.42-50, 2002. ,
Journal of mathematical analysis and applications, vol.33, pp.82-95, 1971. ,
Diffusion kernels on graphs and other discrete input spaces, Proceedings of the 19th International Conference on Machine Learning, pp.315-322, 2002. ,
Learning the kernel matrix with semidefinite programming, Journal of Machine Learning Research, vol.5, pp.27-72, 2004. ,
nextprot : a knowledge platform for human proteins, Nucleic Acids Research, vol.40, issue.D1, pp.76-83, 2012. ,
Machine learning in bioinformatics, Briefings in Bioinformatics, vol.7, issue.1, pp.86-112, 2006. ,
An integrated approach to the prediction of domain-domain interactions, BMC Bioinformatics, vol.7, issue.1, p.269, 2006. ,
Introduction to protein science, 2010. ,
The spectrum kernel : a string kernel for svm protein classification, Proceedings of the Pacific Symposium on Biocomputing, pp.564-575, 2002. ,
RCV1 : A new benchmark collection for text categorization research, Journal of Machine Learning Research, vol.5, pp.361-397, 2004. ,
, , vol.303, pp.540-543, 2004.
The link-prediction problem for social networks, Journal of the American Society for Information Science and Technology, vol.58, issue.7, pp.1019-1031, 2007. ,
Mint, the molecular interaction database : 2012 update, Nucleic Acids Research, vol.40, issue.D1, pp.857-861, 2012. ,
New perspectives and methods in link prediction, Proceedings of the 16th ACM SIGKDD international conference on Knowledge discovery and data mining, pp.243-252, 2010. ,
Information assessment on predicting protein-protein interactions, BMC Bioinformatics, vol.5, issue.1, p.154, 2004. ,
A kernel method for unsupervised structured network inference, Proceedings of the 12th International Conference on Artificial Intelligence and Statistics (AISTATS), pp.368-375, 2009. ,
Multimeric threading-based prediction of protein-protein interactions on a genomic scale : application to the saccharomyces cerevisiae proteome, Genome Research, vol.13, pp.1146-1154, 2003. ,
Assessing the limits of genomic data integration for predicting protein networks, Genome Research, vol.15, issue.7, pp.945-953, 2005. ,
Detecting protein function and protein-protein interactions from genome sequences, Science, vol.285, issue.5428, pp.751-753, 1999. ,
Predicting protein-protein interactions using signature products, Bioinformatics, vol.21, pp.218-226, 2005. ,
Identification of potential interaction networks using sequencebased searches for conserved protein-protein interactions of 'interologs', Genome Research, vol.11, issue.12, pp.2120-2126, 2001. ,
Mips : analysis and annotation of proteins from whole genomes, Nucleic Acids Research, vol.32, pp.41-45, 2004. ,
Kernels for multi-task learning, Advances in Neural Information Processing Systems, vol.17, pp.921-928, 2004. ,
On learning vector-valued functions, Neural Computation, vol.17, pp.177-204, 2005. ,
Interoporc : automated inference of highly conserved protein interaction networks, Bioinformatics, vol.24, issue.14, pp.1625-1631, 2008. ,
Nonparametric latent feature models for link prediction, Advances in Neural Information Processing Systems, vol.22, pp.1276-1284, 2009. ,
Sirene : supervised inference of regulatory networks, Bioinformatics, vol.24, issue.16, pp.76-82, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00259119
Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data, Bioinformatics, vol.23, issue.15, 2004. ,
Clustering and preferential attachment in growing networks, Physical Review E, vol.64, p.25102, 2001. ,
Integrative approach for computationally inferring protein domain interactions, Bioinformatics, vol.19, issue.8, pp.923-929, 2003. ,
Integrating information for protein function prediction, Bioinformatics-From Genomes to Therapies, 2007. ,
Diversity of protein-protein interactions, EMBO Journal, vol.22, issue.14, pp.3486-3492, 2003. ,
Inparanoid : a comprehensive database of eukaryotic orthologs, Nucleic Acids Research, vol.33, issue.1, pp.476-480, 2005. ,
Cystic fibrosis enters the proteomics scene : New answers to old questions, Proteomics, vol.6, issue.14, pp.4084-4099, 2006. ,
The use of gene clusters to infer functional coupling, Proceedings of the National Academy of Sciences, vol.96, issue.6, pp.2896-2901, 1999. ,
Similarity of phylogenetic trees as indicator of proteinprotein interaction, Protein Engineering, vol.14, issue.9, pp.609-614, 2001. ,
Assigning protein functions by comparative genome analysis : Protein phylogenetic profiles, Proceedings of the National Academy of Sciences, vol.96, issue.8, pp.4285-4288, 1999. ,
A generalized inverse for matrices, Mathematical Proceedings of the Cambridge Philosophical Society, vol.51, pp.406-413, 1955. ,
Transient protein-protein interactions : structural, functional, and network properties, Structure, vol.18, issue.10, pp.1233-1243, 2010. ,
Statistical relational learning for link prediction, Proceedings of the workshop on learning statistical models from relational data at IJCAI, 2003. ,
Human protein reference database -2009 update, Nucleic Acids Research, vol.37, pp.767-772, 2009. ,
The pfam protein families database, Nucleic Acids Research, vol.40, pp.290-301, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01294685
Protein interaction networks : protein domain interaction and protein function prediction, pp.427-459, 2011. ,
Random forest similarity for protein-protein interaction prediction from multiple sources, Proceedings of the Pacific Symposium on Biocomputing, vol.10, pp.531-542, 2005. ,
Evaluation of different biological data and computational classification methods for use in protein interaction prediction, Proteins, vol.63, pp.490-500, 2006. ,
The protein-protein interaction map of helicobacter pylori, Nature, vol.409, pp.211-215, 2001. ,
, Journal of Machine Learning Research, vol.9, pp.2491-2521, 2008.
Probabilistic model of the human protein-protein interaction network, Nature Biotechnology, vol.23, pp.951-959, 2005. ,
Markov logic : a unifying framework for statistical relational learning, Proceedings of the ICML-2004 Workshop on Statistical Relational Learning and its Connections to Other Fields, pp.49-54, 2004. ,
Markov logic networks, Machine Learning, vol.62, pp.107-136, 2006. ,
Notes on regularized least-squares, 2007. ,
Inferring protein domain interactions from databases of interacting proteins, Genome Biology, vol.6, issue.10, p.89, 2005. ,
Identification of the cystic fibrosis gene : cloning and characterization of complementary dna, Science, vol.245, pp.1066-1073, 1989. ,
Identification of the cystic fibrosis gene : chromosome walking and jumping, Science, vol.245, pp.1059-1065, 1989. ,
, Nature, vol.437, issue.7062, pp.1173-1178, 2005.
A structural perspective on protein-protein interactions, Current Opinion in Structural Biology, vol.14, issue.3, pp.313-324, 2004. ,
Interaction generality, a measurement to assess the reliability of a protein-protein interaction, Nucleic Acids Research, vol.30, issue.5, pp.1163-1168, 2002. ,
The database of interacting proteins : 2004 update, Nucleic Acids Research, vol.32, pp.449-451, 2004. ,
Link prediction and path analysis using markov chains, Computer Networks, vol.33, pp.377-386, 2000. ,
Learning with kernels, 2002. ,
Probabilistic prediction and ranking of human proteinprotein interactions, BMC Bioinformatics, vol.8, issue.1, p.239, 2007. ,
Hilbert spaces of operator-valued functions, Lithuanian Mathematical Journal, vol.13, issue.4, pp.665-670, 1973. ,
Cytoscape : A software environment for integrated models of biomolecular interaction networks, Genome Research, vol.13, issue.11, pp.2498-2504, 2003. ,
Network-based prediction of protein function, Molecular Systems Biology, issue.3, 2007. ,
Graphical multi-task learning, 2008. ,
Predicting protein-protein interactions based only on sequences information, Proceedings of the National Academy of Sciences, vol.104, issue.11, pp.4337-4341, 2007. ,
Deciphering protein-protein interactions. part i. experimental techniques and databases, PLoS Computational Biology, vol.3, issue.3, p.42, 2007. ,
Deciphering protein-protein interactions. part ii. computational methods to predict protein and domain interaction partners, PLoS Computational Biology, vol.3, issue.4, p.43, 2007. ,
Defects in processing and trafficking of the cystic fibrosis transmembrane conductance regulator, Kidney International, vol.57, pp.825-831, 2000. ,
Prediction of protein-protein interactions by docking methods, Current Opinion in Structural Biology, vol.12, issue.1, pp.28-35, 2002. ,
Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization, Molecular Biology of the Cell, vol.9, issue.12, pp.3273-3297, 1998. ,
Correlated sequence-signatures as markers of proteinprotein interaction, Journal of Molecular Biology, vol.311, issue.4, pp.681-692, 2001. ,
The biogrid interaction database : 2011 update, Nucleic Acids Research, 2010. ,
Dynamic interactions of proteins in complex networks : a more structured view, FEBS Journal, vol.276, issue.19, pp.5390-5405, 2009. ,
A human protein-protein interaction network : a resource for annotating the proteome, Cell, vol.122, issue.6, pp.957-968, 2005. ,
Cross-validatory choice and assessment of statistical predictions, Journal of the Royal Statistical Society, vol.36, issue.2, pp.111-147, 1974. ,
A gene atlas of the mouse and human protein-encoding transcriptomes, Proceedings of the National Academy of Sciences, vol.101, issue.16, pp.6062-6067, 2004. ,
Learning via linear operators : Maximum margin regression, 2005. ,
The string database in 2011 : functional interaction networks of proteins, globally integrated and scored, Nucleic Acids Research, vol.39, pp.561-568, 2011. ,
Partially labeled classification with markov random walks, Advances in Neural Information Processing Systems, vol.14, 2002. ,
Link prediction in relational data, Advances in Neural Information Processing Systems 15, 2003. ,
Prediction of interactions between hiv-1 and human proteins by information integration, Pacific Symposium on Biocomputing (PSB, vol.14, pp.516-527, 2009. ,
The yeastract database : a tool for the analysis of transcription regulatory associations in saccharomyces cerevisiae, Nucleic Acids Research, vol.34, issue.1, pp.446-451, 2005. ,
Solutions of ill posed problems, 1977. ,
The em algorithm for kernel matrix completion with auxiliary data, Journal of Machine Learning Research, vol.4, pp.67-81, 2003. ,
A comprehensive analysis of protein-protein interactions in saccharomyces cerevisiae, Nature, vol.403, pp.623-627, 2000. ,
Towards a knowledge-based human protein atlas, Nature Biotechnology, vol.28, pp.1248-50, 2010. ,
The nature of statistical learning theory, 1995. ,
Statistical learning theory, 1998. ,
Ordered risk minimization (i and ii), vol.34, pp.1226-1235, 1974. ,
Supervised graph inference, Advances in Neural Information Processing Systems, pp.1433-1440, 2005. ,
A new pairwise kernel for biological network inference with support vector machines, BMC Bioinformatics, vol.8, issue.10, p.8, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00433573
Comparative assessment of large-scale data sets of protein-protein interactions, Nature, vol.417, pp.399-403, 2002. ,
Protein interaction mapping in c. elegans using proteins involved in vulval development, Science, vol.287, issue.5450, pp.116-122, 2000. ,
Local probabilistic models for link prediction, Proceedings of the 7th IEEE ICDM, pp.322-331, 2007. ,
Hsp90 cochaperone aha1 downregulation rescues misfolding cftr in cystic fibrosis, Cell, vol.127, issue.4, pp.803-815, 2006. ,
Collective dynamics of /'small-world/' networks, Nature, vol.393, pp.440-442, 1998. ,
Kernel dependency estimation, Advances in Neural Information Processing Systems 15, 2003. ,
Prediction of yeast proteinprotein interaction network : insights from the gene ontology and annotations, Nucleic Acids Research, vol.34, issue.7, pp.2137-2150, 2006. ,
Intnetdb v1.0 : an integrated protein-protein interaction network database generated by a probabilistic model, BMC Bioinformatics, vol.7, issue.1, p.508, 2006. ,
Phylopro : a web-based tool for the generation and visualization of phylogenetic profiles across eukarya, Bioinformatics, vol.27, issue.6, pp.877-878, 2011. ,
Kernel matrix regression, Proceedings of the 12th International Conference on Applied Stochastic Models and Data Analysis (ASMDA), 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00133355
Protein network inference from multiple genomic data : a supervised approach, Bioinformatics, vol.20, pp.363-370, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00433586
Prediction of drug-target interaction networks from the integration of chemical and genomic spaces, Bioinformatics, vol.24, issue.13, pp.232-240, 2008. ,
A comprehensive collection of known and predicted domain-domain interactions, Nucleic Acids Research, vol.39, pp.730-735, 2011. ,
Training set expansion : an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions, Bioinformatics, vol.25, issue.2, pp.243-250, 2009. ,
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins, BMC Bioinformatics, vol.11, issue.1, p.167, 2010. ,
Predicting co-complexed protein pairs using genomic and proteomic data integration, BMC Bioinformatics, vol.5, pp.38-53, 2004. ,
Learning with local and global consistency, Advances in Neural Information Processing Systems, vol.16, 2004. ,
Learning from labeled and unlabeled data with label propagation, 2002. ,
Semi-supervised learning using gaussian fields and harmonic functions, Proceedings of the 20th International Conference on Machine learning (ICML), 2003. ,