Extracting brain regions from rest fMRI with total-variation constrained dictionary learning, International Conference on Medical Image Computing and Computer-Assisted Intervention, pp.607-615, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00853242
A method and server for predicting damaging missense mutations, Nature methods, vol.7, p.248, 2010. ,
Differential expression analysis for sequence count data, Genome Biol, vol.11, p.106, 2010. ,
Building the foundation for genomics in precision medicine, Nature, vol.526, pp.336-342, 2015. ,
Theory of reproducing kernels, Transactions of the American mathematical society, vol.68, pp.337-404, 1950. ,
Genetic Interactions in Cancer Progression and Treatment, In: Cell, vol.145, pp.30-38, 2011. ,
Integrating node embeddings and biological annotations for genes to predict disease-gene associations, BMC Systems Biology, vol.12, 2018. ,
Approximate residual balancing: debiased inference of average treatment effects in high dimensions, Journal of the Royal Statistical Society: Series B (Statistical Methodology), 2018. ,
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines, Nature, vol.465, pp.627-631, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00468440
Machine learning and genomics: precision medicine vs. patient privacy, Philosophical Transactions of the Royal Society A, vol.376, p.2128, 2018. ,
Efficient network-guided multi-locus association mapping with graph cuts, Proceedings of the 21st Annual International Conference on Intelligent Systems for Molecular Biology, vol.29, pp.171-179, 2013. ,
One-to four-dimensional kernels for virtual screening and the prediction of physical, chemical and biological properties, Journal of Chemical Information and Modeling, vol.47, pp.965-974, 2007. ,
The inconvenience of data of convenience: computational research beyond post-mortem analyses, Nature methods, vol.14, p.937, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01679028
Structured sparsity-inducing norms through submodular functions, NIPS, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00511310
Multi-Net: A Scalable Multiplex Network Embedding Framework, International Conference on Complex Networks and their Applications, pp.119-131, 2018. ,
Network medicine: a network-based approach to human disease, Nature Reviews Genetics, vol.12, pp.56-68, 2011. ,
Network biology: understanding the cell's functional organization, Nature Reviews Genetics, vol.5, pp.101-113, 2004. ,
Pathway and network-based analysis of genome-wide association studies in multiple sclerosis, Hum Mol Genet, vol.18, pp.2078-2090, 2009. ,
The p-filter: multilayer false discovery rate control for grouped hypotheses, J. R. Stat. Soc. B, vol.79, pp.1247-1268, 2017. ,
Mapping Patient Trajectories using Longitudinal Extraction and Deep Learning in the MIMIC-III Critical Care Database, pp.123-132, 2017. ,
Hit-and-Run Algorithms for Generating Multivariate Distributions, Mathematics of Operations Research, vol.18, pp.255-266, 1993. ,
Multitask feature selection with task descriptors, Pacific Symposium on Biocomputing, vol.21, pp.261-272, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01246697
Hit-and-run algorithms for the identification of nonredundant linear inequalities, Mathematical Programming, vol.37, pp.184-207, 1987. ,
Supervised prediction of drug-target interactions using bipartite local models, Bioinformatics, vol.25, pp.2397-2403, 2009. ,
Multi-task Gaussian process prediction, NIPS 20, pp.153-160, 2007. ,
An experimental comparison of mincut/max-flow algorithms for energy minimization in vision, IEEE Trans. Pattern Anal. Mach. Intell, vol.26, pp.1124-1137, 2004. ,
An Expanded View of Complex Traits: From Polygenic to Omnigenic, Cell 169, vol.7, pp.1177-1186, 2017. ,
Linkage and association mapping of Arabidopsis thaliana flowering time in nature, PLoS genetics, vol.6, p.1000940, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00468455
Federated learning of predictive models from federated Electronic Health Records, In: International journal of medical informatics, vol.112, pp.59-67, 2018. ,
Disease gene prioritization, PLoS computational biology, vol.9, p.1002902, 2013. ,
Spectral networks and locally connected networks on graphs, 2013. ,
Controlling the Rate of GWAS False Discoveries, Genetics 205, vol.1, pp.61-75, 2017. ,
Chapter 11: Genome-Wide Association Studies, PLoS Comput Biol, vol.8, p.1002822, 2012. ,
Performance of epistasis detection methods in semi-simulated, GWAS". In: BMC Bioinformatics, vol.19, p.1, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01832976
The BioGRID interaction database: 2015 update, Nucleic Acids Res, vol.43, pp.470-478, 2015. ,
Approximating the minimum spanning tree weight in sublinear time, In: SIAM J. Comput, vol.34, pp.1370-1379, 2005. ,
Discovering epistasis in large scale genetic association studies by exploiting graphics cards, Frontiers in Genetics, vol.4, 2013. ,
Insights into Colon Cancer Etiology via a Regularized Approach to Gene Set Analysis of GWAS Data, Am J Hum Genet, vol.86, pp.860-871, 2010. ,
A two-graph guided multi-task Lasso approach for eQTL mapping, 2012. ,
Identification of novel susceptibility loci for inflammatory bowel disease on chromosomes 1p, 3q, and 4q: Evidence for epistasis between 1p and IBD1, Proceedings of the National Academy of Sciences 95, vol.13, pp.7502-7507, 1998. ,
Networkbased classification of breast cancer metastasis, Mol Syst Biol, vol.3, p.140, 2007. ,
Assessing binary classifiers using only positive and unlabeled data, 2015. ,
The properties of high-dimensional data spaces: implications for exploring gene and protein expression data, Nature Reviews Cancer, vol.8, pp.37-49, 2008. ,
, GWAS incorporating networks in R. 2017
Block HSIC Lasso: model-free biomarker detection for ultra-high dimensional data, Bioinformatics, vol.35, 2019. ,
R package for networkguided Genome-Wide Association Studies, 25th Conference on Intelligent Systems for Molecular Biology (poster), 2017. ,
Judging genetic loci by the company they keep: Comparing network-based methods for biomarker discovery in familial breast cancer, 68th Annual Meeting of the American Society of Human Genetics (poster), 2018. ,
Epistasis in sporadic Alzheimer's disease, Neurobiology of Aging, vol.30, pp.1333-1349, 2009. ,
So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests, Am. J. Hum. Genet, vol.81, pp.1158-1168, 2007. ,
Detecting gene-gene interactions that underlie human diseases, Nature Reviews Genetics, vol.10, pp.392-404, 2009. ,
Multilocus Linkage Tests Based on Affected Relative Pairs, The American Journal of Human Genetics, vol.66, pp.1273-1286, 2000. ,
Elements of Information Theory. 2nd, 2006. ,
Network propagation: a universal amplifier of genetic associations, Nature Reviews Genetics, vol.18, pp.551-562, 2017. ,
Loci on chromosomes 2 ( NIDDM1 ) and 15 interact to increase susceptibility to diabetes in Mexican Americans, Nature Genetics, vol.21, pp.213-215, 1999. ,
Convolutional neural networks on graphs with fast localized spectral filtering, Advances in neural information processing systems, pp.3844-3852, 2016. ,
Analysis of feature selection stability on high dimension and small sample data, Computational Statistics & Data Analysis, vol.71, pp.681-693, 2014. ,
Minimum Redundancy Feature Selection from Microarray Gene Expression Data, Journal of Bioinformatics and Computational Biology, pp.185-205, 2005. ,
Interpretable genotype-to-phenotype classifiers with performance guarantees, Scientific Reports, vol.9, p.4071, 2019. ,
Reoptimization of MDL Keys for Use in Drug Discovery, Journal of Chemical Information and Computer Sciences, vol.42, issue.6, pp.1273-1280, 2002. ,
Improving efficiency in epistasis detection with a gene-based analysis using functional filters". 28th International Genetic Epidemiology Society meeting (poster), 2019. ,
Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia, Genome Med, vol.7, issue.1, p.8, 2015. ,
Opportunities and limitations in the prediction of population responses to toxic compounds assessed through a collaborative competition, Nature Biotechnology, vol.33, pp.933-940, 2015. ,
Least angle regression, The Annals of statistics, vol.32, pp.407-499, 2004. ,
Outcome signature genes in breast cancer: is there a unique set?, In: Bioinformatics, vol.21, pp.171-178, 2005. ,
Collaborative filtering on a family of biological targets, Journal of chemical information and modeling, vol.46, issue.2, pp.626-635, 2006. ,
Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks, Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, vol.18, pp.1561-1574, 2011. ,
Learning multiple tasks with kernel methods, J Mach Learn Res, pp.615-637, 2005. ,
The l1-l2 regularization framework unmasks the hypoxia signature hidden in the transcriptome of a set of heterogeneous neuroblastoma cell lines, BMC Genomics, vol.10, p.474, 2009. ,
Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor, Bioinformatics, vol.24, pp.225-233, 2008. ,
Structured feature selection and task relationship inference for multi-task learning, Knowledge and Information Systems, vol.35, pp.345-364, 2013. ,
Primary immunodeficiencies suggest redundancy within the human immune system, Science immunology, vol.1, issue.6, p.5861, 2016. ,
XV.-The Correlation between Relatives on the Supposition of Mendelian Inheritance, Transactions of the Royal Society of Edinburgh, vol.52, pp.399-433, 1919. ,
Human diseases through the lens of network biology, Trends in Genetics, vol.29, pp.150-159, 2013. ,
A fast parametric maximum flow algorithm and applications, SIAM Journal on Computing, vol.18, pp.30-55, 1989. ,
MR-based in vivo hippocampal volumetrics: 1. Review of methodologies currently employed, Molecular Psychiatry, vol.10, pp.147-159, 2005. ,
Guilt by association" is the exception rather than the rule in gene networks, PLoS computational biology, vol.8, issue.3, p.1002444, 2012. ,
Integrative methods for analyzing big data in precision medicine, Proteomics, vol.16, pp.741-758, 2016. ,
The human disease network, Proceedings of the National Academy of Sciences, vol.104, pp.8685-8690, 2007. ,
Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization, Bioinformatics, vol.28, pp.2304-2310, 2012. ,
GWIS -model-free, fast and exhaustive search for epistatic interactions in case-control GWAS, BMC Genomics, vol.14, p.10, 2013. ,
Exact maximum a posteriori estimation for binary images, J. R. Stat. Soc, vol.51, issue.2, 1989. ,
Measuring statistical dependence with Hilbert-Schmidt norms, 2005. ,
A Kernel Statistical Test of Independence, Advances in Neural Information Processing Systems 20, pp.585-592, 2008. ,
Kernel Constrained Covariance for Dependence Measurement, Proceedings of the Tenth International Workshop on Artificial Intelligence and Statistics, pp.1-8, 2005. ,
The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity, Human Mutation, vol.36, issue.5, pp.513-523, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01246688
, Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining -KDD '16, pp.855-864, 2016.
A large-scale benchmark of gene prioritization methods, Scientific reports, vol.7, p.46598, 2017. ,
Many sequence variants affecting diversity of adult human height, Nature Genetics, vol.40, pp.609-615, 2008. ,
Methods and Tools in Genome-wide Association Studies, Computational Cell Biology, pp.93-136, 2018. ,
An introduction to variable and feature selection, J. Mach. Learn. Res, vol.3, pp.1157-1182, 2003. ,
Inductive representation learning on large graphs, Advances in Neural Information Processing Systems, pp.1024-1034, 2017. ,
Representation Learning on Graphs: Methods and Applications, 2017. ,
The entire regularization path for the support vector machine, Journal of Machine Learning Research, vol.5, pp.1391-1415, 2005. ,
Statistical Learning with Sparsity: The Lasso and Generalizations, 2015. ,
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection, BMC Systems Biology, vol.6, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00694218
The Influence of Feature Selection Methods on Accuracy, Stability and Interpretability of Molecular Signatures, PLoS ONE 6, vol.12, p.28210, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00559580
Leveraging information across HLA alleles/supertypes improves epitope prediction, J Comput Biol, vol.14, pp.736-746, 2007. ,
Linear versus logistic regression when the dependent variable is a dichotomy, Quality & Quantity, vol.43, pp.59-74, 2009. ,
EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards, Bioinformatics, vol.27, pp.1462-1465, 2011. ,
Differential variability analysis of gene expression and its application to human diseases, Bioinformatics, vol.24, pp.390-398, 2008. ,
Model-specific tests on variance heterogeneity for detection of potentially interacting genetic loci, BMC Genet, vol.13, p.59, 2012. ,
SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk genetic epistasis in bipolar disorder, Cell Research, vol.20, pp.854-857, 2010. ,
Learning with structured sparsity, J. Mach. Learn. Res, vol.12, pp.3371-3412, 2011. ,
Discovering regulatory and signalling circuits in molecular interaction networks, Bioinformatics 18.suppl, pp.233-240, 2002. ,
Group lasso with overlap and graph lasso, Proceedings of the 26th Annual International Conference on Machine Learning, pp.433-440, 2009. ,
Protein-ligand interaction prediction: an improved chemogenomics approach, Bioinformatics, vol.24, pp.2149-2156, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00433572
Recovering True Classifier Performance in Positive-Unlabeled Learning, 2017. ,
Biological function through network topology: a survey of the human diseasome, Briefings in functional genomics, vol.11, issue.6, pp.522-532, 2012. ,
Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia, PLoS Comput Biol, vol.8, issue.7, p.1002587, 2012. ,
Hierarchical clustering schemes, Psychometrika, vol.32, pp.241-254, 1967. ,
Statistical challenges of highdimensional data, In: Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, vol.367, pp.4237-53, 1906. ,
Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs, Bioinformatics, vol.27, pp.214-221, 2011. ,
EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units, European Journal of Human Genetics, vol.19, pp.465-471, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00598939
GLIDE: GPU-based linear regression for the detection of epistasis, Human Heredity, vol.73, pp.220-236, 2012. ,
Learning to predict chemical reactions, Journal of Chemical Information and Modeling, vol.51, pp.2209-2222, 2011. ,
A multivariate regression approach to association analysis of a quantitative trait network, Bioinformatics, vol.25, p.12, 2009. ,
A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease Association, Journal of Computational Biology, vol.12, pp.1243-1260, 2005. ,
Semi-Supervised Classification with Graph Convolutional Networks, 2016. ,
A general framework for estimating the relative pathogenicity of human genetic variants, Nature genetics, vol.46, p.310, 2014. ,
Walking the Interactome for Prioritization of Candidate Disease Genes, The American Journal of Human Genetics, vol.82, pp.949-958, 2008. ,
The Neuronal Transporter Gene SLC6A15 Confers Risk to Major Depression, Neuron, vol.70, pp.252-265, 2011. ,
What energy functions can be minimized via graph cuts, IEEE Trans. Pattern Anal. Mach. Intell, vol.26, pp.147-159, 2004. ,
Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets, Journal of chemical information and modeling, vol.50, pp.1961-1969, 2010. ,
Profile-based string kernels for remote homology detection and motif extraction, Journal of bioinformatics and computational biology, vol.3, pp.527-550, 2005. ,
A Stability Index for Feature Selection, Proceedings of the 25th Conference on Proceedings of the 25th IASTED International Multi-Conference: Artificial Intelligence and Applications, pp.390-395, 2007. ,
Evaluation of feature ranking ensembles for high-dimensional biomedical data, ICDM Workshops, pp.49-56, 2012. ,
Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps ,
A Powerful and Flexible Multilocus Association Test for Quantitative Traits, The American Journal of Human Genetics, vol.82, pp.386-397, 2008. ,
Predicting drug-target interactions for new drug compounds using a weighted nearest neighbor profile, PloS one, vol.8, issue.6, p.66952, 2013. ,
Gaussian interaction profile kernels for predicting drug-target interaction, Bioinformatics, vol.27, pp.3036-3043, 2011. ,
DrugBank 4.0: shedding new light on drug metabolism, Nucleic acids research, vol.42, pp.1091-1097, 2013. ,
Incidence of adverse drug reactions in hospitalized patients: a meta-analysis of prospective studies, Jama, vol.279, pp.1200-1205, 1998. ,
WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models, Proceedings of the 35th International Conference on Machine Learning. Ed. by Jennifer Dy and Andreas Krause, vol.80, pp.3635-3644, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01711018
Exact post-selection inference, with application to the lasso, The Annals of Statistics, vol.44, pp.907-927, 2016. ,
Rare-Variant Association Analysis: Study Designs and Statistical Tests, Am J Hum Genet, vol.95, pp.5-23, 2014. ,
Leveraging input and output structures for joint mapping of epistatic and marginal eQTLs, Bioinformatics, vol.28, pp.137-146, 2012. ,
Network-constrained regularization and variable selection for analysis of genomic data, Bioinformatics, vol.24, pp.1175-1182, 2008. ,
Variable selection and regression analysis for graphstructured covariates with an application to genomics, Ann. Appl. Stat, vol.4, issue.3, pp.1498-1516, 2010. ,
Personalized medicine -the promised land: are we there yet?, In: Clinical Genetics, vol.79, pp.403-412, 2011. ,
DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes, Bioinformatics, 2018. ,
Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data, BMC Genomics, vol.13, p.27, 2012. ,
Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models, BMC bioinformatics, vol.9, p.292, 2008. ,
Semiparametric regression of multidimensional genetic pathway data: Least-squares kernel machines and linear mixed models, Biometrics, vol.63, pp.1079-1088, 2007. ,
A Versatile Gene-Based Test for Genome-wide Association Studies, Am J Hum Genet, vol.87, pp.139-145, 2010. ,
Accounting for linkage disequilibrium in genome-wide association studies: A penalized regression method, Statistics and Its Interface, vol.6, pp.99-115, 2013. ,
Principled Multilayer Network Embedding, 2017. ,
Neighborhood regularized logistic matrix factorization for drug-target interaction prediction, PLoS computational biology, vol.12, p.1004760, 2016. ,
Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio, Genetics, vol.208, pp.1397-1408, 2018. ,
Selective inference in regression models with groups of variables, 2015. ,
Random Walks on Graphs: A Survey, Combinatorics, vol.2, pp.1-46, 1993. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol. 15, vol.12, p.550, 2014. ,
Stratification and weighting via the propensity score in estimation of causal treatment effects: A comparative study, Statistics in Medicine, vol.23, pp.2937-2960, 2004. ,
Graph kernels for molecular structure-activity relationship analysis with support vector machines, Journal of chemical information and modeling, vol.45, pp.939-951, 2005. ,
Precision medicine -A promising, yet challenging road lies ahead, Current Opinion in Systems Biology, vol.7, pp.1-7, 2018. ,
Finding the missing heritability of complex diseases, Nature, vol.461, pp.747-753, 2009. ,
Variance of gene expression identifies altered network constraints in neurological disease, PLoS Genet. 7, vol.8, p.1002207, 2011. ,
Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases, Nature methods, vol.13, p.366, 2016. ,
Celer: a Fast Solver for the Lasso with Dual Extrapolation, ICML 2018 -35th International Conference on Machine Learning, vol.80, pp.3321-3330, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01833398
Systematic localization of common disease-associated variation in regulatory DNA, Science, vol.337, pp.1190-1195, 2012. ,
Drugtarget interaction prediction by learning from local information and neighbors, Bioinformatics, vol.29, pp.238-245, 2013. ,
Stability selection, J. R. Stat. Soc, vol.72, pp.417-473, 2010. ,
Laplacian matrices of graphs: a survey, Linear Algebra Appl, vol.197, pp.143-176, 1994. ,
Regularizers for structured sparsity, Adv. Comput. Math, vol.38, pp.455-489, 2013. ,
Total variation regularization for fMRI-based prediction of behavior, IEEE transactions on medical imaging, vol.30, pp.1328-1340, 2011. ,
Efficient Estimation of Word Representations in Vector Space, 2013. ,
Integrative approaches for finding modular structure in biological networks, Nat Rev Genet, vol.14, pp.719-732, 2013. ,
A global view of epistasis, Nature Genetics, vol.37, pp.13-14, 2005. ,
Bioinformatics challenges for genome-wide association studies, Bioinformatics, p.713, 2010. ,
A bagging SVM to learn from positive and unlabeled examples, Pattern Recognition Letters, vol.37, pp.201-209, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01101852
ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples, BMC Bioinformatics, vol.12, p.389, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00594774
Explainable Prediction of Medical Codes from Clinical Text, pp.1101-1111, 2018. ,
VariBench: a benchmark database for variations, Human mutation, vol.34, pp.42-49, 2013. ,
A farewell to Bonferroni: the problems of low statistical power and publication bias, Behavioral Ecology, vol.15, pp.1044-1045, 2004. ,
Drug repositioning: a machine-learning approach through data integration, In: J. Cheminformatics, vol.5, p.30, 2013. ,
Gap safe screening rules for sparsity enforcing penalties, The Journal of Machine Learning Research, vol.18, pp.4671-4703, 2017. ,
, Introductory Lectures on Convex Optimization, vol.87, 2004.
SIFT: Predicting amino acid changes that affect protein function, Nucleic acids research, vol.31, pp.3812-3814, 2003. ,
A survey about methods dedicated to epistasis detection, Bioinformatics and Computational Biology, p.285, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01205577
Consistent Feature Selection for Pattern Recognition in Polynomial Time, Journal of Machine Learning Research, vol.8, pp.589-612, 2007. ,
Measuring the stability of feature selection, Machine Learning and Knowledge Discovery in Databases, vol.9852, pp.442-457, 2016. ,
Multi-task feature selection, 2006. ,
Post-marketing withdrawal of 462 medicinal products because of adverse drug reactions: a systematic review of the world literature, BMC medicine, vol.14, p.10, 2016. ,
A faster strongly polynomial time algorithm for submodular function minimization, Math. Program, vol.118, pp.237-251, 2009. ,
Predicting disease genes using protein-protein interactions, Journal of medical genetics, vol.43, issue.8, pp.691-698, 2006. ,
Adjusted sequence kernel association test for rare variants controlling for cryptic and family relatedness, Genet. Epidemiol, vol.37, pp.366-376, 2013. ,
Toward more realistic drug-target interaction predictions, Briefings in bioinformatics, p.10, 2014. ,
Choice of population structure informative principal components for adjustment in a case-control study, BMC genetics, vol.12, p.64, 2011. ,
Feature Selection Based on Mutual Information: Criteria of Max-Dependency, Max-Relevance, and Min-Redundancy, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.27, pp.1226-1237, 2005. ,
Genetic influences on human brain structure: A review of brain imaging studies in twins, Human Brain Mapping, vol.28, pp.464-473, 2007. ,
DeepWalk: Online Learning of Social Representations, Proceedings of the 20th ACM SIGKDD international conference on Knowledge discovery and data mining -KDD '14, pp.701-710, 2014. ,
A community resource benchmarking predictions of peptide binding to MHC-I molecules, PLoS Comput Biol, vol.2, issue.6, p.65, 2006. ,
Machine learning approaches for drug virtual screening, 2019. ,
Efficient multitask chemogenomics for drug specificity prediction, PLoS ONE, vol.13, p.204999, 2018. ,
New approaches to population stratification in genome-wide association studies, Nature Reviews Genetics, vol.11, issue.7, p.459, 2010. ,
Large-scale RNAseq datasets enable the detection of genes with a differential expression dispersion in cancer, Computer Science and Mathematics (poster), 2019. ,
Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr, In: Bioinformatics, 2018. ,
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses, The American Journal of Human Genetics, vol.81, pp.559-575, 2007. ,
Linear score tests for variance components in linear mixed models and applications to genetic association studies, Biometrics, vol.69, pp.883-892, 2013. ,
Graph kernels for chemical informatics, Neural Networks, vol.18, pp.1093-1110, 2005. ,
Gene expression variability and the analysis of largescale RNA-seq studies with the MDSeq, Nucleic Acids Res, vol.45, p.127, 2017. ,
A Hidden Markov Technique for Haplotype Reconstruction, Lecture Notes in Computer Science, pp.140-151, 2005. ,
A General Framework for Estimation and Inference From Clusters of Features, Journal of the American Statistical Association, vol.113, pp.280-293, 2017. ,
The search for gene-gene interactions in genome-wide association studies: challenges in abundance of methods, practical considerations, and biological interpretation, Annals of translational medicine, vol.6, 2018. ,
Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer, The American Journal of Human Genetics, vol.69, pp.138-147, 2001. ,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, pp.139-140, 2010. ,
Extended-connectivity fingerprints, Journal of chemical information and modeling, vol.50, pp.742-754, 2010. ,
Estimating causal effects of treatments in randomized and nonrandomized studies, In: Journal of Educational Psychology, vol.66, pp.688-701, 1974. ,
Co-expression networks reveal the tissue-specific regulation of transcription and splicing, Genome research, vol.27, pp.1843-1858, 2017. ,
Protein homology detection using string alignment kernels, Bioinformatics, vol.20, pp.1682-1689, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00433587
Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks, Cell Rep, vol.2, issue.5, pp.1207-1219, 2012. ,
A fast and flexible statistical model for largescale population genotype data: applications to inferring missing genotypes and haplotypic phase, In: American journal of human genetics, vol.78, issue.4, pp.629-673, 2006. ,
Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis, Journal of chemical information and modeling, vol.49, pp.308-317, 2009. ,
Modeling Relational Data with Graph Convolutional Networks, 2017. ,
Learning with Kernels, 2002. ,
Personalized medicine: Time for one-person trials, Nature News, vol.520, p.609, 2015. ,
FastEpistasis: a high performance computing solution for quantitative trait epistasis, Bioinformatics, vol.26, pp.1468-1469, 2010. ,
Variable selection with error control: another look at stability selection, Journal of the Royal Statistical Society, vol.75, pp.55-80, 2013. ,
Pitfalls of Graph Neural Network Evaluation, 2018. ,
gat2vec: representation learning for attributed graphs, In: Computing, pp.1-23, 2018. ,
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis, Nature Communications, vol.7, p.12460, 2016. ,
Heritability of adult body height: a comparative study of twin cohorts in eight countries, Twin Research and Human Genetics, vol.6, pp.399-408, 2003. ,
Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps, Stat Appl Genet Mol Biol, vol.11, issue.1, p.7, 2012. ,
kernelPSI: Post-Selection Inference for Nonlinear Variable Selection, 2010. ,
, epiGWAS: Robust Methods for Epistasis Detection, 2018.
Novel methods for epistasis detection in genome-wide association studies, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01984919
kernelPSI: a post-selection inference framework for nonlinear variable selection, Proceedings of the Thirty-Sixth International Conference on Machine Learning (ICML), vol.97, pp.5857-5865, 2019. ,
Kernels and regularization on graphs, Learning Theory and Kernel Machines, vol.2777, pp.144-158, 2003. ,
Pathway-Based Genomics Prediction using Generalized Elastic Net, PLoS Comput Biol, vol.12, p.1004790, 2016. ,
Supervised feature selection via dependence estimation, Proceedings of the 24th international conference on Machine learning -ICML '07, 2007. ,
Feature selection via dependence maximization, JMLR 13, pp.1393-1434, 2012. ,
Population structure in genetic studies: Confounding factors and mixed models, PLoS genetics 14, vol.12, p.1007309, 2018. ,
Haplotype inference using a Bayesian Hidden Markov model, Genetic Epidemiology, vol.31, pp.937-948, 2007. ,
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval, Bioinformatics, vol.26, pp.1348-1356, 2010. ,
The Influence Relevance Voter: an accurate and interpretable virtual high throughput screening method, Journal of Chemical Information and Modeling, vol.49, pp.756-766, 2009. ,
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity, Bioinformatics 21.suppl, pp.359-368, 2005. ,
Multi-level Lasso for Sparse Multitask Regression, Proceedings of the 29th International Conference on Machine Learning (ICML-12, pp.361-368, 2012. ,
STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Research, vol.43, pp.447-452, 2015. ,
Epistasis between catechol-O-methyltransferase and type II metabotropic glutamate receptor 3 genes on working memory brain function, Proceedings of the National Academy of Sciences, vol.104, pp.12536-12541, 2007. ,
Selecting causal genes from genome-wide association studies via functionally coherent subnetworks, Nat Methods, vol.12, pp.154-159, 2015. ,
On multi-marker tests for association in case-control studies, In: Front. Genet, vol.4, p.252, 2013. ,
, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls, Nature, vol.447, pp.661-678, 2007.
Statistical Methods for Genome-Wide and Sequencing Association Studies of Complex Traits in Related Samples, Curr Protoc Hum Genet, vol.84, 2015. ,
A Simple Method for Estimating Interactions Between a Treatment and a Large Number of Covariates, Journal of the American Statistical Association, vol.109, pp.1517-1532, 2014. ,
Regression shrinkage and selection via the Lasso, J. R. Stat. Soc, vol.58, pp.267-288, 1994. ,
Sparsity and smoothness via the fused lasso, J Roy Stat Soc B, vol.67, pp.91-108, 2005. ,
Handbook of molecular descriptors, vol.11, 2008. ,
Mapping eQTL Networks with mixed Graphical Markov Models, Genetics, vol.198, pp.1377-1393, 2014. ,
Random walk with restart on multiplex and heterogeneous biological networks, Bioinformatics, vol.35, pp.497-505, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-01946427
Clinical analysis and interpretation of cancer genome data, J. Clin. Oncol. 31, vol.15, pp.1825-1833, 2013. ,
Associating genes and protein complexes with disease via network propagation, PLoS computational biology, vol.6, p.1000641, 2010. ,
Machine learning for in silico virtual screening and chemical genomics: new strategies, Combinatorial chemistry & high throughput screening, vol.11, pp.677-685, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00433569
10 years of GWAS discovery: biology, function, and translation, The American Journal of Human Genetics, vol.101, issue.1, pp.5-22, 2017. ,
Estimation of Mutual Information: A Survey, Rough Sets and Knowledge Technology, pp.389-396, 2009. ,
BOOST: A Fast Approach to Detecting Gene-Gene Interactions in Genome-wide Case-Control Studies, The American Journal of Human Genetics, vol.87, pp.325-340, 2010. ,
Similarity network fusion for aggregating data types on a genomic scale, Nature Methods, vol.11, issue.3, pp.333-337, 2014. ,
Deep learning for sensor-based activity recognition: A survey, Pattern Recognition Letters. Deep Learning for Pattern Recognition, vol.119, pp.3-11, 2019. ,
PINBPA: Cytoscape app for network analysis of GWAS data, Bioinformatics, vol.31, pp.262-264, 2015. ,
Comparative Evaluation of 11 Scoring Functions for Molecular Docking, Journal of Medicinal Chemistry, vol.46, pp.2287-2303, 2003. ,
A general model for multilocus epistatic interactions in case-control studies, PLoS ONE, vol.5, p.11384, 2010. ,
The Graph-Guided Group Lasso for Genome-Wide Association Studies, Regularization, Optimization, Kernels, and Support Vector Machines, pp.131-157, 2014. ,
Functional mapping and annotation of genetic associations with FUMA, Nature communications, vol.8, issue.1, p.1826, 2017. ,
Further improvements to linear mixed models for genomewide association studies, Scientific reports, vol.4, p.6874, 2014. ,
Multilocus Analysis of Hypertension: A Hierarchical Approach, Hum Hered, vol.57, pp.28-38, 2004. ,
Fast embedding of multilayer networks: An algorithm and application to group fMRI, 2018. ,
Rare-variant association testing for sequencing data with the Sequence Kernel Association Test, Am. J. Hum. Genet, vol.89, pp.82-93, 2011. ,
Genome-wide association analysis by lasso penalized logistic regression, Bioinformatics, vol.25, pp.714-721, 2009. ,
, A comprehensive survey on graph neural networks". In: arXiv preprint, 2019.
Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces, BMC systems biology 4.Suppl, p.6, 2010. ,
Efficient Generalized Fused Lasso and its Application to the Diagnosis of Alzheimer's Disease, Twenty-Eighth AAAI Conference on Artificial Intelligence, 2014. ,
High-Dimensional Feature Selection by Feature-Wise Kernelized Lasso, Neural computation, vol.26, pp.185-207, 2014. ,
Post Selection Inference with Kernels, Proceedings of the Twenty-First International Conference on Artificial Intelligence and Statistics, vol.84, pp.152-160, 2018. ,
Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data, IEEE Transactions on Knowledge and Data Engineering, vol.30, pp.1352-1365, 2018. ,
Prediction of drug-target interaction networks from the integration of chemical and genomic spaces, Bioinformatics, vol.24, pp.232-240, 2008. ,
Selective inference for group-sparse linear models, Advances in Neural Information Processing Systems, pp.2469-2477, 2016. ,
Common SNPs explain a large proportion of the heritability for human height, Nature genetics, vol.42, p.565, 2010. ,
Feature grouping and selection over an undirected graph, Proceedings of the 18th ACM SIGKDD international conference on knowledge discovery and data mining, pp.922-930, 2012. ,
GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies, Bioinformatics, vol.27, pp.1309-1310, 2011. ,
Increased Variability of Genomic Transcription in Schizophrenia, In: Sci Rep, vol.5, p.17995, 2015. ,
A fast multilocus test with adaptive SNP selection for largescale genetic-association studies, Eur. J. Hum. Genet, vol.22, pp.696-702, 2014. ,
Large-scale kernel methods for independence testing, Statistics and Computing, vol.28, pp.113-130, 2018. ,
Probabilistic multi-task feature selection, NIPS. 2010, pp.2559-2567 ,
Pathway-based analysis using reduced gene subsets in genome-wide association studies, BMC Bioinformatics, vol.12, p.17, 2011. ,
Collaborative matrix factorization with multiple similarities for predicting drug-target interactions, Proceedings of the 19th ACM SIGKDD international conference on Knowledge discovery and data mining, pp.1025-1033, 2013. ,
Exclusive Lasso for multi-task feature selection, J. Mach. Learn. Res, vol.9, pp.989-995, 2010. ,
Predicting multicellular function through multi-layer tissue networks, Bioinformatics, vol.33, pp.190-198, 2017. ,
Regularization and variable selection via the elastic net, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol.67, pp.301-320, 2005. ,
The mystery of missing heritability: Genetic interactions create phantom heritability, Proceedings of the National Academy of Sciences of the United States of America, vol.109, pp.1193-1201, 2012. ,