Jean-Philippe Vert

发表

Reconstruction of Biological Networks by Supervised Machine Learning Approaches

Jean-Philippe Vert, Jean-Philippe Vert, 2008 .

Consistency of one-class SVM and related algorithms

Jean-Philippe Vert, Régis Vert, Régis Vert, 2005, NIPS.

Differentiable Deep Clustering with Cluster Size Constraints pdf

Jean-Philippe Vert, Aude Genevay, Gabriel Dulac-Arnold, 2019, ArXiv.

Supervised Quantile Normalization for Low-rank Matrix Approximation pdf

Jean-Philippe Vert, Marco Cuturi, Olivier Teboul, 2020, ArXiv.

Supervised Quantile Normalization for Low Rank Matrix Factorization

Jean-Philippe Vert, Marco Cuturi, Olivier Teboul, 2020, ICML 2020.

Gene Expression Analysis: Joint Feature Selection and Classifier Design

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

High-level feature extraction using SVM with walk-based graph kernel

Shin'ichi Satoh, Tomoko Matsui, Jean-Philippe Vert, 2009, 2009 IEEE International Conference on Acoustics, Speech and Signal Processing.

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

William Stafford Noble, Jean-Philippe Vert, Jian Qiu, 2007, BMC Bioinformatics.

A Kernel for Time Series Based on Global Alignments

Tomoko Matsui, Jean-Philippe Vert, Marco Cuturi, 2006, 2007 IEEE International Conference on Acoustics, Speech and Signal Processing - ICASSP '07.

QSAR and Virtual Screening with Support Vector Machines

Jean-Philippe Vert, Jean-Philippe Vert, 2006 .

Learning with Differentiable Perturbed Optimizers pdf

Francis Bach, Jean-Philippe Vert, Marco Cuturi, 2020, ArXiv.

Group lasso with overlap and graph lasso

Jean-Philippe Vert, Guillaume Obozinski, Laurent Jacob, 2009, ICML '09.

Virtual screening with support vector machines and structure kernels

Jean-Philippe Vert, Pierre Mahé, Jean-Philippe Vert, 2007, Combinatorial chemistry & high throughput screening.

Gradient-based musical feature extraction based on scale-invariant feature transform

Masataka Goto, Tomoko Matsui, Jean-Philippe Vert, 2011, 2011 19th European Signal Processing Conference.

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel

Tatsuya Akutsu, Jean-Philippe Vert, Morihiro Hayashida, 2018, BMC Bioinformatics.

The Pharmacophore Kernel for Virtual Screening with Support Vector Machines

Jean-Philippe Vert, Véronique Stoven, Liva Ralaivola, 2006, J. Chem. Inf. Model..

An accurate and interpretable model for siRNA efficacy prediction

Jean-Philippe Vert, Christian Lajaunie, Nicolas Foveau, 2006, BMC Bioinformatics.

Supervised Quantile Normalisation pdf

Jean-Philippe Vert, Marine Le Morvan, Jean-Philippe Vert, 2017, ArXiv.

Kernel methods for in silico chemogenomics

Jean-Philippe Vert, Laurent Jacob, Jean-Philippe Vert, 2007, 0709.3931.

A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

Jean-Philippe Vert, Véronique Stoven, Brice Hoffmann, 2010, BMC Bioinformatics.

On Learning Matrices with Orthogonal Columns or Disjoint Supports

Alexandre d'Aspremont, Jean-Philippe Vert, Kevin Vervier, 2014, ECML/PKDD.

Relating Leverage Scores and Density using Regularized Christoffel Functions

Jean-Philippe Vert, Edouard Pauwels, Francis Bach, 2018, NeurIPS.

Text Categorization Using Adaptive Context Trees

Jean-Philippe Vert, 2001, CICLing.

SegAnnDB: interactive Web-based genomic segmentation

Francis R. Bach, Jean-Philippe Vert, Gudrun Schleiermacher, 2014, Bioinform..

Glycan classification with tree kernels

Yoshihiro Yamanishi, Francis R. Bach, Jean-Philippe Vert, 2007, Bioinform..

Clusterpath: an Algorithm for Clustering using Convex Fusion Penalties

Francis R. Bach, Jean-Philippe Vert, Armand Joulin, 2011, ICML.

Differentiable Sorting using Optimal Transport: The Sinkhorn CDF and Quantile Operator pdf

Jean-Philippe Vert, Marco Cuturi, Olivier Teboul, 2019, NeurIPS 2019.

Machine Learning in Bioinformatics

Gunnar Rätsch, Cheng Soon Ong, Alexander Zien, 2009, Encyclopedia of Database Systems.

Advanced Application of Support Vector Machines

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

Graph kernels based on tree patterns for molecules

Jean-Philippe Vert, Pierre Mahé, Jean-Philippe Vert, 2006, Machine Learning.

Large-scale prediction of protein-protein interactions from structures

William Stafford Noble, Jean-Philippe Vert, Michael Riffle, 2010, BMC Bioinformatics.

A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples

Julien Mairal, Jean-Philippe Vert, Laurent Jacob, 2015, BMC Bioinformatics.

ASNI: Adaptive Structured Noise Injection for shallow and deep neural networks pdf

Jean-Philippe Vert, Beyrem Khalfaoui, Joseph Boyd, 2019, ArXiv.

Classification of microarray data using gene networks

Emmanuel Barillot, Jean-Philippe Vert, Andrei Yu. Zinovyev, 2007, BMC Bioinformatics.

Adaptive context trees and text clustering

Jean-Philippe Vert, Jean-Philippe Vert, 2001, IEEE Trans. Inf. Theory.

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

Jean-Philippe Vert, Paola Vera-Licona, Fantine Mordelet, 2012, BMC Systems Biology.

A Primer on KernelMethods

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

Efficient peptide-MHC-I binding prediction for alleles with few known binders

Jean-Philippe Vert, Laurent Jacob, Jean-Philippe Vert, 2008, Bioinform..

Supervised reconstruction of biological networks with local models

Jean-Philippe Vert, Gérard Biau, Kevin Bleakley, 2007, ISMB/ECCB.

Jointly Embedding Multiple Single-Cell Omics Measurements

William Stafford Noble, Jean-Philippe Vert, Jie Liu, 2019, bioRxiv.

Group Lasso with Overlaps: the Latent Group Lasso approach pdf

Jean-Philippe Vert, Guillaume Obozinski, Laurent Jacob, 2011, ArXiv.

The importance and difficulty to tune parameters of methods for single-cell RNA-seq dimensionality reduction

Jean-Philippe Vert, Felix Raimundo, Céline Vallot, 2020 .

Some new methods for robust high-dimensional classification

Jean-Philippe Vert, 2015 .

A New Approach to Collaborative Filtering: Operator Estimation with Spectral Regularization pdf

Francis R. Bach, Jean-Philippe Vert, Jacob D. Abernethy, 2008, J. Mach. Learn. Res..

WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models pdf

Jean-Philippe Vert, Marine Le Morvan, Jean-Philippe Vert, 2018, ICML.

Inferring diploid 3D chromatin structures from Hi-C data

William Stafford Noble, Jean-Philippe Vert, Nelle Varoquaux, 2019, bioRxiv.

Jointly Embedding Multiple Single-Cell Omics Measurements

William Stafford Noble, Jean-Philippe Vert, Jie Liu, 2019, bioRxiv.

Comparison of SVM-Based Methods for Remote Homology Detection

Tatsuya Akutsu, Jean-Philippe Vert, Hiroto Saigo, 2002 .

The optimal assignment kernel is not positive definite pdf

Jean-Philippe Vert, Jean-Philippe Vert, 2008, ArXiv.

Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis

Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa, 2003, ISMB.

NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis

Jean-Philippe Vert, Andrei Yu. Zinovyev, Marine Le Morvan, 2017, PLoS Comput. Biol..

Deep multi-class learning from label proportions pdf

Lucas Beyer, Jean-Philippe Vert, Marco Cuturi, 2019, ArXiv.

Causal inference methods for combining randomized trials and observational studies: a review

Shu Yang, Jean-Philippe Vert, Julie Josse, 2020, 2011.08047.

FlipFlop: Fast Lasso-based Isoform Prediction as a Flow Problem

Julien Mairal, Jean-Philippe Vert, Laurent Jacob, 2013 .

LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes

Jean-Philippe Vert, Véronique Stoven, Olivier Collier, 2018, bioRxiv.

Graph-Driven Feature Extraction From Microarray Data Using Diffusion Kernels and Kernel CCA

Jean-Philippe Vert, Minoru Kanehisa, M. Kanehisa, 2002, NIPS.

The Kendall and Mallows Kernels for Permutations

Jean-Philippe Vert, Yunlong Jiao, Jean-Philippe Vert, 2015, IEEE Transactions on Pattern Analysis and Machine Intelligence.

Learning Sparse Penalties for Change-point Detection using Max Margin Interval Regression

Francis R. Bach, Jean-Philippe Vert, Toby Hocking, 2013, ICML.

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

Jean-Philippe Vert, Pierre-Cyril Aubin-Frankowski, Jean-Philippe Vert, 2020, Bioinformatics.

Semigroup Kernels on Measures

Kenji Fukumizu, Jean-Philippe Vert, Marco Cuturi, 2005, J. Mach. Learn. Res..

Graph kernels and applications in chemoinformatics

Jean-Philippe Vert, 2007 .

Supervised Graph Inference

Yoshihiro Yamanishi, Jean-Philippe Vert, Jean-Philippe Vert, 2004, NIPS.

Classification of Biological Sequences with Kernel Methods

Jean-Philippe Vert, Jean-Philippe Vert, 2006, ICGI.

Supervised inference of gene regulatory networks from positive and unlabeled examples.

Jean-Philippe Vert, Fantine Mordelet, 2013, Methods in molecular biology.

Global alignment of protein–protein interaction networks by graph matching methods

Francis Bach, Jean-Philippe Vert, Mikhail Zaslavskiy, 2009, Bioinform..

ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

Jean-Philippe Vert, Fantine Mordelet, Jean-Philippe Vert, 2011, BMC Bioinformatics.

Tight convex relaxations for sparse matrix factorization

Jean-Philippe Vert, Guillaume Obozinski, Emile Richard, 2014, NIPS.

A new protein binding pocket similarity measure based on comparison of 3D atom clouds: application to ligand prediction

Jean-Philippe Vert, Brice Hoffmann, Mikhail Zaslavskiy, 2009 .

Noisy Adaptive Group Testing using Bayesian Sequential Experimental Design pdf

Jean-Philippe Vert, Marco Cuturi, Olivier Teboul, 2020, ArXiv.

A Kernel for Protein Secondary Structure Prediction

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

Graph Kernels for Molecular Structure-Activity Relationship Analysis with Support Vector Machines

Tatsuya Akutsu, Jean-Philippe Vert, Pierre Mahé, 2005, J. Chem. Inf. Model..

Classification of arrayCGH data using fused SVM

Emmanuel Barillot, Jean-Philippe Vert, Franck Rapaport, 2008, ISMB.

Many-to-Many Graph Matching: a Continuous Relaxation Approach pdf

Francis R. Bach, Jean-Philippe Vert, Mikhail Zaslavskiy, 2010, ECML/PKDD.

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

Emmanuel Barillot, Jean-Philippe Vert, Andrei Yu. Zinovyev, 2010, Bioinform..

Intersecting singularities for multi-structured estimation

Francis R. Bach, Jean-Philippe Vert, Emile Richard, 2013, ICML.

Effective normalization for copy number variation in Hi-C data

Emmanuel Barillot, Jean-Philippe Vert, Nicolas Servant, 2017, BMC Bioinformatics.

Kernel Multitask Regression for Toxicogenetics

Jean-Philippe Vert, Erwan Scornet, Thomas Walter, 2017, Molecular informatics.

Kernel Methods in Computational Biology

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2005 .

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

Jean-Philippe Vert, Sandrine Dudoit, Davide Risso, 2019, Nature Communications.

Fast Kernels for String and Tree Matching

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

Kernels for gene regulatory regions

William Stafford Noble, Jean-Philippe Vert, Robert E. Thurman, 2005, NIPS.

Support Vector Machine Prediction of Signal Peptide Cleavage Site Using a New Class of Kernels for Strings

Jean-Philippe Vert, Jean-Philippe Vert, 2001, Pacific Symposium on Biocomputing.

An introduction to DNA microarrays and some mathematical challenges behind them

Jean-Philippe Vert, 達也阿久津, Jean-Philippe Vert, 2003 .

Support Vector Machine Applications in Computational Biology

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

Continuous embeddings of DNA sequencing reads, and application to metagenomics

Jean-Philippe Vert, Romain Menegaux, Jean-Philippe Vert, 2018, bioRxiv.

The Weighted Kendall and High-order Kernels for Permutations

Jean-Philippe Vert, Yunlong Jiao, Jean-Philippe Vert, 2018, ICML.

Novel methods for epistasis detection in genome-wide association studies

Jean-Philippe Vert, Chloé-Agathe Azencott, Clément Chatelain, 2018, bioRxiv.

MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification.

Jean-Philippe Vert, Pierre Mahé, Kévin Vervier, 2018, Methods in molecular biology.

Differentiable Ranking and Sorting using Optimal Transport

Jean-Philippe Vert, Marco Cuturi, Olivier Teboul, 2019, NeurIPS.

Epitope prediction improved by multitask support vector machines

Jean-Philippe Vert, Laurent Jacob, Jean-Philippe Vert, 2007, q-bio/0702008.

Kernel Methods in Genomics and Computational Biology

Jean-Philippe Vert, 2005 .

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

Jean-Philippe Vert, Pierre-Cyril Aubin-Frankowski, Jean-Philippe Vert, 2018, bioRxiv.

A tree kernel to analyse phylogenetic profiles

Jean-Philippe Vert, Jean-Philippe Vert, 2002, ISMB.

CloneSig: Joint inference of intra-tumor heterogeneity and signature deconvolution in tumor bulk sequencing data

Jean-Philippe Vert, Fabien Reyal, Judith Abécassis, 2019, bioRxiv.

Clustered Multi-Task Learning: A Convex Formulation

Jean-Philippe Vert, Francis Bach, Laurent Jacob, 2008, NIPS.

Machine learning for personalized genomics Jean-Philippe Vert

Jean-Philippe Vert, 2014 .

MissDeepCausal: Causal Inference from Incomplete Data Using Deep Latent Variable Models pdf

Jean-Philippe Vert, Julie Josse, Imke Mayer, 2020, ArXiv.

Supervised enzyme network inference from the integration of genomic data and chemical information

Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa, 2005, ISMB.

Differentiable Divergences Between Time Series pdf

Arthur Mensch, Jean-Philippe Vert, Mathieu Blondel, 2020, ArXiv.

Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data pdf

Jean-Philippe Vert, Pierre Mahé, Kevin Vervier, 2015, ArXiv.

On Mixup Regularization pdf

Luigi Carratino, Jean-Philippe Vert, Rodolphe Jenatton, 2020, J. Mach. Learn. Res..

ASNI: Adaptive Structured Noise Injection for shallow and deep neural networks

Jean-Philippe Vert, Joseph Boyd, Beyrem Khalfaoui, 2019, ArXiv.

Kernels for Biological Data

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

Faculty Opinions recommendation of Iterative random forests to discover predictive and stable high-order interactions.

Jean-Philippe Vert, Jean-Philippe Vert, 2018, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

A structural alignment kernel for protein structures

William Stafford Noble, Jean-Philippe Vert, Asa Ben-Hur, 2007, Bioinform..

Inexact Matching String Kernels for Protein Classification

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

SIRENE: supervised inference of regulatory networks

Jean-Philippe Vert, Fantine Mordelet, Jean-Philippe Vert, 2008, ECCB.

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

Jean-Philippe Vert, Sandrine Dudoit, Davide Risso, 2017, bioRxiv.

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

William Stafford Noble, Jean-Philippe Vert, Ferhat Ay, 2014 .

Extracting active pathways from gene expression data

Jean-Philippe Vert, Minoru Kanehisa, M. Kanehisa, 2003, ECCB.

A generic methodological framework for studying single cell motility in high-throughput time-lapse data

Jean-Philippe Vert, Thomas Walter, Robert Barouki, 2015, Bioinform..

Efficient RNA isoform identification and quantification from RNA-Seq data with network flows

Julien Mairal, Jean-Philippe Vert, Laurent Jacob, 2014, Bioinform..

Low-rank matrix factorization with attributes pdf

Francis R. Bach, Theodoros Evgeniou, Jean-Philippe Vert, 2006, ArXiv.

Large-scale machine learning for metagenomics sequence classification

Jean-Philippe Vert, Pierre Mahé, Jean-Baptiste Veyrieras, 2015, Bioinform..

Embedding the de Bruijn graph, and applications to metagenomics

Jean-Philippe Vert, Romain Menegaux, Jean-Philippe Vert, 2020, bioRxiv.

Machine Learning for In Silico Virtual Screening and Chemical Genomics: New Strategies

Jean-Philippe Vert, Laurent Jacob, Jean-Philippe Vert, 2008, Combinatorial chemistry & high throughput screening.

Semigroup Kernels on Finite Sets

Jean-Philippe Vert, Marco Cuturi, Marco Cuturi, 2004, NIPS.

A Bayesian active learning strategy for sequential experimental design in systems biology

Jean-Philippe Vert, Edouard Pauwels, Christian Lajaunie, 2014, BMC Systems Biology.

Kernel-Based Integration of Genomic Data Using Semidefinite Programming

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

Deriving kernels from probabilistic models on discrete objects

Jean-Philippe Vert, 2001 .

Learning with Differentiable Pertubed Optimizers

Francis R. Bach, Jean-Philippe Vert, Marco Cuturi, 2020, NeurIPS.

Statistical Learning with Graph Kernels

Jean-Philippe Vert, Jean-Philippe Vert, 2007 .

DropLasso: A robust variant of Lasso for single cell RNA-seq data pdf

Jean-Philippe Vert, Beyrem Khalfaoui, Jean-Philippe Vert, 2018, ArXiv.

Protein-ligand interaction prediction: an improved chemogenomics approach

Jean-Philippe Vert, Laurent Jacob, Jean-Philippe Vert, 2008, Bioinform..

Metric learning pairwise kernel for graph inference pdf

William Stafford Noble, Jean-Philippe Vert, Jian Qiu, 2006, ArXiv.

A bagging SVM to learn from positive and unlabeled examples

Jean-Philippe Vert, Fantine Mordelet, Jean-Philippe Vert, 2010, Pattern Recognit. Lett..

Protein homology detection using string alignment kernels

Tatsuya Akutsu, Jean-Philippe Vert, Hiroto Saigo, 2004, Bioinform..

Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications

Mark D. Robinson, Charlotte Soneson, Jean-Philippe Vert, 2018 .

Inferring Diploid 3D Chromatin Structures from Hi-C Data

William Stafford Noble, Jean-Philippe Vert, Nelle Varoquaux, 2019, WABI.

Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks

Tatsuya Akutsu, Takeyuki Tamura, Yang Zhao, 2013, Bioinform..

A Path Following Algorithm for Graph Matching

Francis R. Bach, Jean-Philippe Vert, Mikhail Zaslavskiy, 2008, ICISP.

The context-tree kernel for strings

Jean-Philippe Vert, Marco Cuturi, Marco Cuturi, 2005, Neural Networks.

Fast detection of multiple change-points shared by many signals using group LARS

Jean-Philippe Vert, Kevin Bleakley, Jean-Philippe Vert, 2010, NIPS.

Robust Seriation and Applications to Cancer Genomics

Alexandre d'Aspremont, Jean-Philippe Vert, Antoine Recanati, 2018, 1806.00664.

The first AI-based mobile application for antibiotic resistance testing

Christophe Ambroise, Jean-Philippe Vert, Gabriel Dulac-Arnold, 2020, bioRxiv.

Kernel Methods for QSAR and Virtual Screening

Jean-Philippe Vert, Jean-Philippe Vert, 2008 .

Extensions of marginalized graph kernels

Tatsuya Akutsu, Jean-Philippe Vert, Pierre Mahé, 2004, ICML.

A statistical approach for inferring the 3D structure of the genome

William Stafford Noble, Jean-Philippe Vert, Ferhat Ay, 2014, Bioinform..

Infering an ontology of single cell motions from high-throughput microscopy data

Jean-Philippe Vert, Thomas Walter, Robert Barouki, 2015, 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI).

LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes

Jean-Philippe Vert, Olivier Collier, Véronique Stoven, 2019, PLoS computational biology.

Data Fusion with Kernel Methods

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

Protein network inference from multiple genomic data: a supervised approach

Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa, 2004, ISMB/ECCB.

Novel methods for epistasis detection in genome-wide association studies

Jean-Philippe Vert, Chloé-Agathe Azencott, Clément Chatelain, 2020, PloS one.

On learning with kernels for unordered pairs

Jean-Philippe Vert, Martial Hue, Jean-Philippe Vert, 2010, ICML.

White Functionals for Anomaly Detection in Dynamical Systems

Alexandre d'Aspremont, Jean-Philippe Vert, Marco Cuturi, 2009, NIPS.

Continuous embeddings of DNA sequencing reads, and application to metagenomics

Jean-Philippe Vert, Romain Menegaux, Jean-Philippe Vert, 2018, bioRxiv.

Learning smoothing models of copy number profiles using breakpoint annotations

Francis R. Bach, Jean-Philippe Vert, Gudrun Schleiermacher, 2013, BMC Bioinformatics.

Eliciting Consumer Preferences Using Robust Adaptive Choice Questionnaires

Olivier Toubia, Theodoros Evgeniou, Jean-Philippe Vert, 2008, IEEE Transactions on Knowledge and Data Engineering.

ISM TRECVID2009 High-level Feature Extraction

Shin'ichi Satoh, Tomoko Matsui, Jean-Philippe Vert, 2008, TRECVID.

A Primer on Kernel Methods

Bernhard Schölkopf, Jean-Philippe Vert, Koji Tsuda, 2004 .

3D Ligand-Based Virtual Screening with Support Vector Machines

Jean-Philippe Vert, Jean-Philippe Vert, 2011 .

Optimizing amino acid substitution matrices with a local alignment kernel

Tatsuya Akutsu, Jean-Philippe Vert, Hiroto Saigo, 2006, BMC Bioinformatics.

kernelPSI: a Post-Selection Inference Framework for Nonlinear Variable Selection

Jean-Philippe Vert, Chloé-Agathe Azencott, Clément Chatelain, 2019, ICML.

Virtual screening of GPCRs: An in silico chemogenomics approach

Jean-Philippe Vert, Véronique Stoven, Brice Hoffmann, 2008, BMC Bioinformatics.

Consistency and Convergence Rates of One-Class SVMs and Related Algorithms

Jean-Philippe Vert, Régis Vert, Régis Vert, 2006, J. Mach. Learn. Res..

Efficient and Modular Implicit Differentiation pdf

Stephan Hoyer, Jean-Philippe Vert, Marco Cuturi, 2021, ArXiv.

Framing RNN as a kernel method: A neural ODE approach pdf

Pierre Marion, Jean-Philippe Vert, Adeline Fermanian, 2021, NeurIPS.

Machine learning for single-cell genomics data analysis

Jean-Philippe Vert, Laetitia Meng-Papaxanthos, Félix Raimundo, 2021 .

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

William Stafford Noble, Jean-Philippe Vert, Nelle Varoquaux, 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

Measuring significant changes in chromatin conformation with ACCOST

William Stafford Noble, Jean-Philippe Vert, Karine G. Le Roch, 2019, bioRxiv.

Changes in correlation between promoter methylation and gene expression in cancer

Jean-Philippe Vert, Valentina Boeva, Fabien Reyal, 2015, BMC Genomics.

Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers.

Jean-Philippe Vert, Jean-Philippe Vert, J. Plouhinec, 2014, Developmental biology.

The Wnt Receptor Ryk Reduces Neuronal and Cell Survival Capacity by Repressing FOXO Activity During the Early Phases of Mutant Huntingtin Pathogenicity

Jean-Philippe Vert, Wange Lu, Christian Neri, 2014, PLoS biology.

RNA Isoform Identication and Quantication from RNA-Seq Data with Network Flows

Julien Mairal, Jean-Philippe Vert, Laurent Jacob, 2014 .

Joint segmentation of many aCGH profiles using fast group LARS

Jean-Philippe Vert, Kevin Bleakley, Jean-Philippe Vert, 2009, 0910.1167.

On Mixup Regularization pdf

Luigi Carratino, Jean-Philippe Vert, Rodolphe Jenatton, 2020, ArXiv.

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

Charlotte Soneson, Jean-Philippe Vert, Sandrine Dudoit, 2018, Genome Biology.

Kernel matrix regression

Yoshihiro Yamanishi, Jean-Philippe Vert, Jean-Philippe Vert, 2007, q-bio/0702054.

Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution.

Andrei Zinovyev, Emmanuel Barillot, Jean-Philippe Vert, 2020, Cell reports.

Genome informatics for data-driven biology

Kenta Nakai, Jean-Philippe Vert, 2002, Genome Biology.

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

Jean-Philippe Vert, Christian Lajaunie, Nicolas Foveau, 2012, PloS one.

Computational Systems Biology of Cancer

Andrei Zinovyev, Emmanuel Barillot, Jean-Philippe Vert, 2020 .

Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants

Jean-Philippe Vert, Etienne Rouleau, Sophie Krieger, 2012, Human mutation.

Increasing stability and interpretability of gene expression signatures

Jean-Philippe Vert, Laurent Jacob, Anne-Claire Haury, 2010, 1001.3109.

Assessing reliability of intra-tumor heterogeneity estimates from single sample whole exome sequencing data

Jean-Philippe Vert, Fabien Reyal, Judith Abécassis, 2018, bioRxiv.

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

William Stafford Noble, Jean-Philippe Vert, David A. Fidock, 2018, bioRxiv.