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Protein-ligand interaction prediction: an improved chemogenomics approach.

Laurent Jacob , Jean-Philippe Vert
Bioinformatics, 2008, 24 (19), pp.2149-56. ⟨10.1093/bioinformatics/btn409⟩
Journal articles hal-00433572v1
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The optimal assignment kernel is not positive definite

Jean-Philippe Vert
Preprints, Working Papers, ... hal-00218278v1
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SIRENE: Supervised Inference of Regulatory Networks

Fantine Mordelet , Jean-Philippe Vert
Bioinformatics, 2008, 24 (16), pp.i76-82. ⟨10.1093/bioinformatics/btn273⟩
Journal articles hal-00259119v1
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Epigenomic Alterations in Breast Carcinoma from Primary Tumor to Locoregional Recurrences

Matahi Moarii , Alice Pinheiro , Brigitte Sigal-Zafrani , Alain Fourquet , Martial Caly , et al.
PLoS ONE, 2014, 9 (8), pp.e103986. ⟨10.1371/journal.pone.0103986⟩
Journal articles hal-01064211v1

A statistical approach for inferring the three-dimensional structure of the genome

Nelle Varoquaux , Ferhat Ay , William Stafford Noble , Jean-Philippe Vert
Bioinformatics, 2014, 30 (12), pp.i26-i33. ⟨10.1093/bioinformatics/btu268⟩
Journal articles hal-01101869v1

Protein network inference from multiple genomic data: a supervised approach.

Y. Yamanishi , Jean-Philippe Vert , M. Kanehisa
Bioinformatics, 2004, 20 Suppl 1, pp.i363-70. ⟨10.1093/bioinformatics/bth910⟩
Journal articles hal-00433586v1
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NetNorM: capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis

Marine Le Morvan , Andrei Zinovyev , Jean-Philippe Vert
Preprints, Working Papers, ... hal-01341856v2

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages

Evelien Bunnik , Kate Cook , Nelle Varoquaux , Gayani Batugedara , Jacques Prudhomme , et al.
Nature Communications, 2018, 9 (1)
Journal articles hal-01985437v1

Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics

Romain Menegaux , Jean-Philippe Vert
Journal of Computational Biology, 2019, 26 (6), pp.509-518. ⟨10.1089/cmb.2018.0174⟩
Journal articles hal-02444747v1

Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference

Pierre-Cyril Aubin-Frankowski , Jean-Philippe Vert
Bioinformatics, 2020, ⟨10.1101/464479⟩
Journal articles hal-03114385v1

DSIR: Assessing the Design of Highly Potent siRNA by Testing a Set of Cancer-Relevant Target Genes

Odile Filhol , Delphine Ciais , Christian Lajaunie , Peggy Charbonnier , Nicolas Foveau , et al.
PLoS ONE, 2012, 7 (10), pp.e48057. ⟨10.1371/journal.pone.0048057⟩
Journal articles hal-02084719v1
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Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

S Sieberts , Fan Zhu , Javier García-García , Eli Stahl , Abhishek Pratap , et al.
Nature Communications, 2016, 7, pp.12460. ⟨10.1038/ncomms12460⟩
Journal articles hal-01420921v1
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Graph kernels based on tree patterns for molecules

Pierre Mahé , Jean-Philippe Vert
Preprints, Working Papers, ... hal-00095488v1
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Reconstruction of biological networks by supervised machine learning approaches

Jean-Philippe Vert
Preprints, Working Papers, ... hal-00283945v2
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The Wnt Receptor Ryk Reduces Neuronal and Cell Survival Capacity by Repressing FOXO Activity During the Early Phases of Mutant Huntingtin Pathogenicity

Cendrine Tourette , Francesca Farina , Rafael P. Vasquez-Manrique , Anne-Marie Orfila , Jessica Voisin , et al.
PLoS Biology, 2014, 12 (6), pp.e1001895. ⟨10.1371/journal.pbio.1001895⟩
Journal articles hal-01076146v1

A path following algorithm for the graph matching problem.

Mikhail Zaslavskiy , Francis Bach , Jean-Philippe Vert
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2009, 31 (12), pp.2227-42. ⟨10.1109/TPAMI.2008.245⟩
Journal articles hal-00433567v1
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The group fused Lasso for multiple change-point detection

Kevin Bleakley , Jean-Philippe Vert
Preprints, Working Papers, ... hal-00602121v1
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Many-to-Many Graph Matching: a Continuous Relaxation Approach

Mikhail Zaslavskiy , Francis Bach , Jean-Philippe Vert
Preprints, Working Papers, ... hal-00465916v1

Integrative DNA methylation and gene expression analysis to assess the universality of the CpG island methylator phenotype

Matahi Moarii , Fabien Reyal , Jean-Philippe Vert
Human Genomics, 2015, 9 (26), ⟨10.1186/s40246-015-0048-9⟩
Journal articles hal-01246676v1
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Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons.

François-Xavier Lejeune , Lilia Mesrob , Frédéric Parmentier , Cedric Bicep , Rafael Vazquez-Manrique , et al.
BMC Genomics, 2012, 13 (1), pp.91. ⟨10.1186/1471-2164-13-91⟩
Journal articles inserm-00690001v1
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A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples

Elsa Bernard , Laurent Jacob , Julien Mairal , Eric Viara , Jean-Philippe Vert
BMC Bioinformatics, 2015, 16 (1), pp.262:1-10. ⟨10.1186/s12859-015-0695-9⟩
Journal articles hal-01123141v3
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Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows

Elsa Bernard , Laurent Jacob , Julien Mairal , Jean-Philippe Vert
Bioinformatics, 2014, 30 (17), pp.2447-2455. ⟨10.1093/bioinformatics/btu317⟩
Journal articles hal-00803134v3

Machine learning for in silico virtual screening and chemical genomics: new strategies.

Jean-Philippe Vert , Laurent Jacob
Combinatorial Chemistry and High Throughput Screening, 2008, 11 (8), pp.677-85
Journal articles hal-00433569v1
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Clustered Multi-Task Learning: A Convex Formulation

Laurent Jacob , Francis Bach , Jean-Philippe Vert
Preprints, Working Papers, ... hal-00320573v1

Reverse-Complement Equivariant Networks for DNA Sequences

Vincent Mallet , Jean-Philippe Vert
Preprints, Working Papers, ... hal-03510326v1
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Phi-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays

Laurent Guyon , Christian Lajaunie , Frédéric Fer , Ricky Bhajun , Eric Sulpice , et al.
Scientific Reports, 2015, 5 (14221), ⟨10.1038/srep14221⟩
Journal articles hal-01246683v1
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The Kendall and Mallows Kernels for Permutations

Yunlong Jiao , Jean-Philippe Vert
Preprints, Working Papers, ... hal-01279273v2

Inference of genome 3D architecture by modeling overdispersion of Hi-C data

Nelle Varoquaux , William Noble , Jean-Philippe Vert
Preprints, Working Papers, ... hal-03375900v1

Changes in gene expression control by DNA methylation in cancer

Matahi Moarii , Valentina Boeva , Jean-Philippe Vert , Fabien Reyal
BMC Genomics, 2015, 16 (873), ⟨10.1186/s12864-015-1994-2⟩
Journal articles hal-01246674v1

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum

Ferhat Ay , Evelien M. Bunnik , Nelle Varoquaux , Jean-Philippe Vert , William Stafford Noble , et al.
BioEssays, 2015, 37 (2), pp.182-194. ⟨10.1002/bies.201400145⟩
Journal articles hal-01246696v1