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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⟩
Article dans une revue hal-00803134v3
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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⟩
Article dans une revue hal-01076146v1
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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⟩
Article dans une revue inserm-00690001v1
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SegAnnDB: interactive web-based genomic segmentation

Toby D. Hocking , Valentina Boeva , Guillem Rigaill , Gudrun Schleiermacher , Isabelle Janoueix-Lerosey , et al.
Bioinformatics, 2014, 30 (11), pp.1539-1546. ⟨10.1093/bioinformatics/btu072⟩
Article dans une revue hal-01101868v1
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Graph kernels based on tree patterns for molecules

Pierre Mahé , Jean-Philippe Vert
2006
Pré-publication, Document de travail hal-00095488v1
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Kernel Multitask Regression for Toxicogenetics

Elsa Bernard , Yunlong Jiao , Erwan Scornet , Véronique Stoven , Thomas Walter , et al.
Molecular Informatics, 2017, 36 (10), ⟨10.1002/minf.201700053⟩
Article dans une revue hal-01679030v1
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Reconstruction of biological networks by supervised machine learning approaches

Jean-Philippe Vert
2008
Pré-publication, Document de travail hal-00283945v2

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
Article dans une revue hal-00433569v1
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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⟩
Article dans une revue hal-01123141v3

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⟩
Article dans une revue hal-01246676v1
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Clustered Multi-Task Learning: A Convex Formulation

Laurent Jacob , Francis Bach , Jean-Philippe Vert
2008
Pré-publication, Document de travail hal-00320573v1
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The group fused Lasso for multiple change-point detection

Kevin Bleakley , Jean-Philippe Vert
2011
Pré-publication, Document de travail hal-00602121v1

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⟩
Article dans une revue hal-00433567v1
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Many-to-Many Graph Matching: a Continuous Relaxation Approach

Mikhail Zaslavskiy , Francis Bach , Jean-Philippe Vert
2009
Pré-publication, Document de travail hal-00465916v1
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A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction.

Brice Hoffmann , Mikhail Zaslavskiy , Jean-Philippe Vert , Véronique Stoven
BMC Bioinformatics, 2010, 11 (1), pp.99. ⟨10.1186/1471-2105-11-99⟩
Article dans une revue inserm-00663528v1

A general and flexible method for signal extraction from single-cell RNA-seq data

Davide Risso , Fanny Perraudeau , Svetlana Gribkova , Sandrine Dudoit , Jean-Philippe Vert
Nature Communications, 2018, 9 (1)
Article dans une revue hal-01985432v1

The Kendall and Mallows Kernels for Permutations

Yunlong Jiao , Jean-Philippe Vert
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2018, 40 (7), pp.1755-1769. ⟨10.1109/TPAMI.2017.2719680⟩
Article dans une revue hal-01679012v1

An accurate and interpretable model for siRNA efficacy prediction.

Jean-Philippe Vert , Nicolas Foveau , Christian Lajaunie , Yves Vandenbrouck
BMC Bioinformatics, 2006, 7, pp.520. ⟨10.1186/1471-2105-7-520⟩
Article dans une revue hal-00433579v1
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Classification of arrayCGH data using fused SVM.

Franck Rapaport , Emmanuel Barillot , Jean-Philippe Vert
Bioinformatics, 2008, 24 (13), pp.i375-82. ⟨10.1093/bioinformatics/btn188⟩
Article dans une revue inserm-00293893v1
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CloneSig can jointly infer intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data

Judith Abécassis , Fabien Reyal , Jean-Philippe Vert
Nature Communications, 2021, 12 (1), pp.5352. ⟨10.1038/s41467-021-24992-y⟩
Article dans une revue hal-03510272v1

A new pairwise kernel for biological network inference with support vector machines.

Jean-Philippe Vert , Jian Qiu , William S Noble
BMC Bioinformatics, 2007, 8 Suppl 10, pp.S8. ⟨10.1186/1471-2105-8-S10-S8⟩
Article dans une revue hal-00433573v1

Classification of microarray data using gene networks.

Franck Rapaport , Andrei Zinovyev , Marie Dutreix , Emmanuel Barillot , Jean-Philippe Vert
BMC Bioinformatics, 2007, 8, pp.35. ⟨10.1186/1471-2105-8-35⟩
Article dans une revue hal-00433577v1

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

Ferhat Ay , Evelien M. Bunnik , Nelle Varoquaux , Sebastiaan M. Bol , Jacques Prudhomme , et al.
Genome Research, 2014, 24, pp.974-988. ⟨10.1101/gr.169417.113⟩
Article dans une revue hal-01101873v1
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Metric learning pairwise kernel for graph inference

Jean-Philippe Vert , Jian Qiu , William Noble
2006
Pré-publication, Document de travail hal-00108477v1

Large-scale machine learning for metagenomics sequence classification

Kevin Vervier , Pierre Mahé , Maud Tourmoud , Jean-Baptiste Veyrieras , Jean-Philippe Vert
Bioinformatics, 2016, 32 (7), pp.1023-32
Article dans une revue hal-01420829v1
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kernelPSI: a Post-Selection Inference Framework for Nonlinear Variable Selection

Lotfi Slim , Clement Chatelain , Chloé-Agathe Azencott , Jean-Philippe Vert
36th International Conference on Machine Learning (ICML 2019), Jun 2019, Long Beach, CA, United States
Communication dans un congrès hal-02441304v1
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Spectral analysis of gene expression profiles using gene networks

Franck Rapaport , Andrei Zinovyev , Marie Dutreix , Emmanuel Barillot , Jean-Philippe Vert
2006
Pré-publication, Document de travail hal-00021785v1

Supervised reconstruction of biological networks with local models.

Kevin Bleakley , Gérard Biau , Jean-Philippe Vert
Bioinformatics, 2007, 23 (13), pp.i57-65. ⟨10.1093/bioinformatics/btm204⟩
Article dans une revue hal-00433575v1
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Tight convex relaxations for sparse matrix factorization

Emile Richard , Guillaume Obozinski , Jean-Philippe Vert
2014
Pré-publication, Document de travail hal-01025959v3
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ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

Fantine Mordelet , Jean-Philippe Vert
2011
Pré-publication, Document de travail hal-00594774v1