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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

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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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
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Reconstruction of biological networks by supervised machine learning approaches

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

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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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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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

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

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⟩
Article dans une revue hal-01246674v1
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WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models.

Marine Le Morvan , Jean-Philippe Vert
35th International Conference on Machine Learning, Jul 2018, Stockholm, Sweden. pp.3635--3644
Communication dans un congrès hal-01711018v1

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

Nelle Varoquaux , William Noble , Jean-Philippe Vert
2021
Pré-publication, Document de travail hal-03375900v1

Reverse-Complement Equivariant Networks for DNA Sequences

Vincent Mallet , Jean-Philippe Vert
2022
Pré-publication, Document de travail hal-03510326v1

Tight convex relaxations for sparse matrix factorization

Emile Richard , Guillaume Obozinski , Jean-Philippe Vert
Neural Information Processing Systems, Dec 2014, Montreal, Canada. pp.3284-3292
Communication dans un congrès hal-01101878v1
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The Kendall and Mallows Kernels for Permutations

Yunlong Jiao , Jean-Philippe Vert
2016
Pré-publication, Document de travail hal-01279273v2
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Joint segmentation of many aCGH profiles using fast group LARS

Kevin Bleakley , Jean-Philippe Vert
2009
Pré-publication, Document de travail hal-00422430v1

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⟩
Article dans une revue hal-01246696v1
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Epitope prediction improved by multitask support vector machines

Laurent Jacob , Jean-Philippe Vert
2007
Autre publication scientifique hal-00129062v1
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The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures

Anne-Claire Haury , Pierre Gestraud , Jean-Philippe Vert
PLoS ONE, 2011, pp.6(12): e28210. ⟨10.1371/journal.pone.0028210⟩
Article dans une revue hal-00559580v2

Glycan classification with tree kernels.

Yoshihiro Yamanishi , Francis Bach , Jean-Philippe Vert
Bioinformatics, 2007, 23 (10), pp.1211-6. ⟨10.1093/bioinformatics/btm090⟩
Article dans une revue hal-00433576v1
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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⟩
Article dans une revue hal-01246683v1
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Relating Leverage Scores and Density using Regularized Christoffel Functions

Edouard Pauwels , Francis Bach , Jean-Philippe Vert
32nd Conference on Neural Information Processing Systems (NIPS 2018), Dec 2018, Montréal, Canada. pp.1-21
Communication dans un congrès hal-01796591v2

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)
Article dans une revue hal-01985437v1
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A community effort to assess and improve drug sensitivity prediction algorithms

James C Costello , Laura M Heiser , Elisabeth Georgii , Mehmet Gönen , Michael P Menden , et al.
Nature Biotechnology, 2014, 32, pp.1202-1212. ⟨10.1038/nbt.2877⟩
Article dans une revue hal-01101874v1

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⟩
Article dans une revue hal-02444747v1