Jean-Philippe Vert

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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..

Large-Scale Machine Learning

Jean-Philippe Vert, 2020, Mining of Massive Datasets.

The group fused Lasso for multiple change-point detection

Jean-Philippe Vert, K. Bleakley, 2011, 1106.4199.

Local Alignment Kernels for Biological Sequences

Jean-Philippe Vert, Hiroto Saigo, T. Akutsu, 2004 .

Consistency of Random Forests

Jean-Philippe Vert, Erwan Scornet, G. Biau, 2014, 1405.2881.

A covariance kernel for proteins

Marco Cuturi, Jean-Philippe Vert, 2003, q-bio/0310022.

A tree kernel to analyze phylog enetic profi les

Jean-Philippe Vert, 2002 .

The Influence of Feature Selection Methods on Accuracy, Stability and Interpretability of Molecular Signatures

Jean-Philippe Vert, Anne-Claire Haury, P. Gestraud, 2011, PloS one.

Clusterpath: an Algorithm for Clustering using Convex Fusion Penalties

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

Low-rank matrix factorization with attributes pdf

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

Heterogeneous Data Comparison and Gene Selection with Kernel Canonical Correlation Analysis

B. Schölkopf, Jean-Philippe Vert, K. Tsuda, 2004 .

Graph-driven features extraction from microarray data

M. Kanehisa, Jean-Philippe Vert, 2002, physics/0206055.

Group lasso with overlap and graph lasso

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

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

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

Accurate Splice Site Detection for Caenorhabditis elegans

B. Schölkopf, Jean-Philippe Vert, K. Tsuda, 2004 .

Clustered Multi-Task Learning: A Convex Formulation

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

Kernel Methods in Computational Biology

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

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

S. Dudoit, Jean-Philippe Vert, D. Risso, 2018, Nature Communications.

Group Lasso with Overlaps: the Latent Group Lasso approach pdf

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

Kernel Methods in Genomics and Computational Biology

Jean-Philippe Vert, 2005, q-bio/0510032.

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

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

Semigroup Kernels on Measures

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

A mutual information kernel for sequences

Marco Cuturi, Jean-Philippe Vert, 2004, 2004 IEEE International Joint Conference on Neural Networks (IEEE Cat. No.04CH37541).

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.

Support Vector Machine Applications in Computational Biology

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

Supervised Graph Inference

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

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

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

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

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

Kernels for gene regulatory regions

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

Inferring diploid 3D chromatin structures from Hi-C data

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

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

William Stafford Noble, Kate B. Cook, Jean-Philippe Vert, 2018, Nature Communications.

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

William Stafford Noble, Jean-Philippe Vert, E. Bunnik, 2014, Genome research.

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

William Stafford Noble, Michael J. Zeitz, Jean-Philippe Vert, 2015, BMC Genomics.

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.

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

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

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Jean-Philippe Vert, J. Dekker, E. Barillot, 2015, Genome Biology.

Jointly Embedding Multiple Single-Cell Omics Measurements

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

White Functionals for Anomaly Detection in Dynamical Systems

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

The context-tree kernel for strings

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

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.

Signaling Pathway Activities Improve Prognosis for Breast Cancer

Marta R. Hidalgo, Jean-Philippe Vert, J. Dopazo, 2017, bioRxiv.

A novel representation of protein sequences for prediction of subcellular location using support vector machines

Jean-Philippe Vert, Hiroto Saigo, T. Akutsu, 2005, Protein science : a publication of the Protein Society.

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.

DeepConsensus: Gap-Aware Sequence Transformers for Sequence Correction

Waleed Ammar, Jean-Philippe Vert, Quentin Berthet, 2021, bioRxiv.

Φ-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays

Laurent Guyon, Christian Lajaunie, Jean-Philippe Vert, 2015, Scientific Reports.

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Matti Pirinen, Jukka Corander, Krister Wennerberg, 2016, Nature Communications.

Kernel matrix regression

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

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.

Accurate identification of centromere locations in yeast genomes using Hi-C

William Stafford Noble, Maitreya J. Dunham, J. Shendure, 2015, Nucleic acids research.

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.

An Optimization Framework for the Adaptive Design of Robust Choice Questionnaires

Jacob D. Abernethy, J. Abernethy, T. Evgeniou, 2005 .

Analysis of the impact degree distribution in metabolic networks using branching process approximation

Jean-Philippe Vert, T. Akutsu, W. Ching, 2011, 1108.2588.

CONSISTENCY OF RANDOM FORESTS 1

Jean-Philippe Vert, Erwan Scornet, G. Biau, 2015 .

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

William Stafford Noble, Jean-Philippe Vert, E. Bunnik, 2014 .

Measuring significant changes in chromatin conformation with ACCOST

William Stafford Noble, Borislav H. Hristov, Kate B. Cook, 2019, bioRxiv.

Fast Kernels for String and Tree Matching

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

Advanced Application of Support Vector Machines

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

Kernel-Based Integration of Genomic Data Using Semidefinite Programming

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

A Primer on KernelMethods

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

Kernels for Biological Data

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

A Primer on Kernel Methods

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

Kernel multitask regression for toxicogenetics

Jean-Philippe Vert, Erwan Scornet, Yunlong Jiao, 2017, bioRxiv.

The first AI-based mobile application for antibiotic resistance testing

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

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

Jean-Philippe Vert, F. Reyal, C. Laurent, 2018, bioRxiv.

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

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

Title Analysis of the impact degree distribution in metabolicnetworks using branching process approximation

Jean-Philippe Vert, T. Akutsu, W. Ching, 2019 .

Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis

Jean-Philippe Vert, C. Vallot, Félix Raimundo, 2020, bioRxiv.

Scaling ResNets in the Large-depth Regime

Jean-Philippe Vert, G. Biau, Adeline Fermanian, 2022, ArXiv.

Efficient and Modular Implicit Differentiation

Marco Cuturi, Roy Frostig, Fabian Pedregosa, 2021, ArXiv.

Kernel Methods in Genomics and Computational Biology

Jean-Philippe Vert, 2005, q-bio/0510032.

Deep embedding and alignment of protein sequences

Mathieu Blondel, Jean-Philippe Vert, Quentin Berthet, 2021, bioRxiv.

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

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

Jointly Embedding Multiple Single-Cell Omics Measurements

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

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.

CloneSig can jointly infer intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data

Jean-Philippe Vert, F. Reyal, J. Abécassis, 2019, Nature Communications.

Scaling ResNets in the Large-depth Regime

Jean-Philippe Vert, G. Biau, Adeline Fermanian, 2022, ArXiv.

DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer

Waleed Ammar, Jean-Philippe Vert, Quentin Berthet, 2022, Nature Biotechnology.

Best practices for single-cell histone modification analysis

Jean-Philippe Vert, C. Vallot, Pacôme Prompsy, 2022, bioRxiv.

Efficient and Modular Implicit Differentiation

Marco Cuturi, Roy Frostig, Fabian Pedregosa, 2021, NeurIPS.

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.

Regression as Classification: Influence of Task Formulation on Neural Network Features

F. Bach, Jean-Philippe Vert, Quentin Berthet, 2022, ArXiv.

Learning with Differentiable Pertubed Optimizers

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

Supervised Quantile Normalization for Low Rank Matrix Factorization

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

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

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

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

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

Eliciting Consumer Preferences Using Robust Adaptive Choice Questionnaires

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

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

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

Consistency of one-class SVM and related algorithms

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

Protein homology detection using string alignment kernels

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

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

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

Learning with Differentiable Perturbed Optimizers pdf

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

Large-scale prediction of protein-protein interactions from structures

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

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

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

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

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

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

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

1 A primer on kernel methods

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

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

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

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

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

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

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

Classification of microarray data using gene networks

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

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..

Semi-supervised single-cell cross-modality translation using Polarbear

William Stafford Noble, Jean-Philippe Vert, Laetitia Meng-Papaxanthos, 2021, bioRxiv.

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates

M. Eisen, Jean-Philippe Vert, J. Plouhinec, 2017, PLoS biology.

Changes in correlation between promoter methylation and gene expression in cancer

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

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

S. Dudoit, Jean-Philippe Vert, M. Robinson, 2018, bioRxiv.

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

S. Dudoit, Jean-Philippe Vert, D. Risso, 2018, Nature Communications.

Machine learning for single cell genomics data analysis

Jean-Philippe Vert, C. Vallot, Laetitia Papaxanthos, 2021, bioRxiv.

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.

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.

SIRENE: supervised inference of regulatory networks

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

Differentiable Deep Clustering with Cluster Size Constraints pdf

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

Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis

Felix Raimundo, Celine Vallot, Jean Philippe Vert, 2020, Genome Biology.

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

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

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

Jean-Philippe Vert, M. Moarii, F. Reyal, 2015, Human Genomics.

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.

Classification of arrayCGH data using fused SVM

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

SegAnnDB: interactive Web-based genomic segmentation

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

Tight convex relaxations for sparse matrix factorization

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

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..

Epigenomic Alterations in Breast Carcinoma from Primary Tumor to Locoregional Recurrences

Jean-Philippe Vert, M. Moarii, F. Reyal, 2014, PloS one.

Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution

E Barillot, Jean-Philippe Vert, E. Barillot, 2019, bioRxiv.

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Jean-Philippe Vert, J. Dekker, E. Barillot, 2015, Genome Biology.

Prediction of human population responses to toxic compounds by a collaborative competition

Ana L. Teixeira, Eleni G. Christodoulou, Jeffrey T. Chang, 2015, Nature Biotechnology.

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

G. Varoquaux, Jean-Philippe Vert, Shu Yang, 2020, 2011.08047.

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

William Stafford Noble, Jean-Philippe Vert, E. Bunnik, 2014 .

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.

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.

Large-scale machine learning for metagenomics sequence classification

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

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

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

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.

Protein network inference from multiple genomic data: a supervised approach

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

A tree kernel to analyse phylogenetic profiles

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

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

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

Epitope prediction improved by multitask support vector machines

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

Continuous embeddings of DNA sequencing reads, and application to metagenomics

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

Protein-ligand interaction prediction: an improved chemogenomics approach

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

Kernel methods for in silico chemogenomics

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

The Pharmacophore Kernel for Virtual Screening with Support Vector Machines

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

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

William Stafford Noble, Jean-Philippe Vert, N. Varoquaux, 2021, bioRxiv.

A bagging SVM to learn from positive and unlabeled examples

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

AI-based mobile application to fight antibiotic resistance

Jean-Philippe Vert, Gabriel Dulac-Arnold, C. Ambroise, 2021, Nature Communications.

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

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

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

Jean-Philippe Vert, M. Moarii, F. Reyal, 2015, Human Genomics.

Differentiable Divergences Between Time Series

Mathieu Blondel, Jean-Philippe Vert, A. Mensch, 2020, AISTATS.

Extensions of marginalized graph kernels

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

Reconstruction of Biological Networks by Supervised Machine Learning Approaches

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

Supervised reconstruction of biological networks with local models

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

On Learning Matrices with Orthogonal Columns or Disjoint Supports

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

A Simple Explanation of Partial Least Squares Kee Siong

Jean-Philippe Vert, 2013 .

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.

On Mixup Regularization pdf

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

Joint segmentation of many aCGH profiles using fast group LARS

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

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

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

A Path Following Algorithm for the Graph Matching Problem

M. Zaslavskiy, F. Bach, J.-P. Vert, 2008, IEEE Transactions on Pattern Analysis and Machine Intelligence.

Virtual screening of GPCRs: An in silico chemogenomics approach

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

Noisy Adaptive Group Testing using Bayesian Sequential Experimental Design

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

On learning with kernels for unordered pairs

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

Novel methods for epistasis detection in genome-wide association studies

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

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

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

A Path Following Algorithm for Graph Matching

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

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.

Virtual screening with support vector machines and structure kernels

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

Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons

Jean-Philippe Vert, L. Mesrob, C. Tourette, 2012, BMC Genomics.

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

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

How will generative AI disrupt data science in drug discovery?

Jean-Philippe Vert, 2023, Nature Biotechnology.

Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning

William Stafford Noble, Jean-Philippe Vert, Laetitia Meng-Papaxanthos, 2022, J. Comput. Biol..

ISM TRECVID2009 High-level Feature Extraction

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

Differentiable Ranking and Sorting using Optimal Transport

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

ISMB 2014 Proceedings Papers Committee

William Stafford Noble, Noah M. Daniels, D. Heckerman, 2014, Bioinformatics.

Computational Systems Biology of Cancer

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

Graph kernels based on tree patterns for molecules

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

The optimal assignment kernel is not positive definite pdf

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

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

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

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

Jean-Philippe Vert, M. Zaslavskiy, V. Stoven, 2010, BMC bioinformatics.

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..

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.

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

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

Semigroup Kernels on Finite Sets

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

A Kernel for Protein Secondary Structure Prediction

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

Effective normalization for copy number variation in Hi-C data

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

Measuring significant changes in chromatin conformation with ACCOST

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

Robust Seriation and Applications to Cancer Genomics

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

The Weighted Kendall and High-order Kernels for Permutations

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

Large-Scale Machine Learning

Jean-Philippe Vert, Sanjiv Kumar, 2020, Mining of Massive Datasets.

Embedding the de Bruijn graph, and applications to metagenomics

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

Deep multi-class learning from label proportions pdf

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

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

S. Dudoit, Jean-Philippe Vert, D. Risso, 2017, Nature Communications.

Reverse-Complement Equivariant Networks for DNA Sequences

Jean-Philippe Vert, Vincent Mallet, 2021, bioRxiv.

Regression as Classification: Influence of Task Formulation on Neural Network Features

F. Bach, Jean-Philippe Vert, Quentin Berthet, 2022, International Conference on Artificial Intelligence and Statistics.

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

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

Transcription

William Stafford Noble, C. M. Sperberg-McQueen, Claus Huitfeldt, 2005, Chemistry and Biology of Non‐Canonical Nucleic Acids.

Increasing stability and interpretability of gene expression signatures

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

Metric learning pairwise kernel for graph inference pdf

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

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Suleiman A. Khan, Michael A. Goren, Donna E. Dillenberger, 2016, Nature Communications.

Phi-score : A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays

Jean-Philippe Vert, X. Gidrol, C. Lajaunie, 2018 .

Supervised Quantile Normalization for Low-rank Matrix Approximation

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

Extracting active pathways from gene expression data

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

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 .

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.

LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis

William Stafford Noble, Marco Cuturi, Jean-Philippe Vert, 2022, bioRxiv.

A benchmark of computational pipelines for single-cell histone modification data

Jean-Philippe Vert, C. Vallot, Pacôme Prompsy, 2023, Genome Biology.

Intersecting singularities for multi-structured estimation

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

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

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

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

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

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

Jean-Philippe Vert, M. Zaslavskiy, V. Stoven, 2009 .

Adaptive context trees and text clustering

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

Bioinformatics Applications Note Genome Analysis Control-free Calling of Copy Number Alterations in Deep-sequencing Data Using Gc-content Normalization

Jean-Philippe Vert, K. Bleakley, E. Barillot, 2022 .

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

William Stafford Noble, Jean-Philippe Vert, N. Varoquaux, 2023, Bioinform..

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

William Stafford Noble, Michael J. Zeitz, Jean-Philippe Vert, 2015, BMC Genomics.

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

Jean-Philippe Vert, K. Bleakley, E. Barillot, 2010, Bioinform..

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

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

The Kendall and Mallows Kernels for Permutations

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

Classification of microarray data using gene networks

Jean-Philippe Vert, E. Barillot, A. Zinovyev, 2007, BMC Bioinformatics.

Classification of Biological Sequences with Kernel Methods

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

The Pharmacophore Kernel for Virtual Screening with Support Vector Machines

Jean-Philippe Vert, L. Ralaivola, V. Stoven, 2006, Journal of Chemical Information and Modeling.

Increasing stability and interpretability of gene expression signatures

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

3D Ligand-Based Virtual Screening with Support Vector Machines

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

Kernel Methods for QSAR and Virtual Screening

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

QSAR and Virtual Screening with Support Vector Machines

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

Semigroup Kernels on Measures Kenji Fukumizu Jean-philippe Vert

K. Fukumizu, Marco Cuturi, Jean-Philippe Vert, 2022 .

Supervised reconstruction of biological networks with local models

Jean-Philippe Vert, K. Bleakley, G. Biau, 2007, ISMB/ECCB.

Optimizing amino acid substitution matrices with a local alignment kernel

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

Protein Homology Detection Using String Alignment Kernels

Jean-Philippe Vert, Hiroto Saigo, Nobuhisa Ueda, 2022 .

1 A primer on kernel methods

Jean-Philippe Vert, Koji Tsuda, B. Scholkopf, 2004 .

Statistical Learning with Graph Kernels

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

Learning smoothing models of copy number profiles using breakpoint annotations

F. Bach, Jean-Philippe Vert, T. Hocking, 2013, BMC Bioinformatics.

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

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

Clusterpath: an Algorithm for Clustering using Convex Fusion Penalties

F. Bach, Jean-Philippe Vert, Armand Joulin, 2011, ICML.

Large-scale machine learning for metagenomics sequence classification

Jean-Philippe Vert, P. Mahé, K. Vervier, 2015, Bioinform..

Tight convex relaxations for sparse matrix factorization

G. Obozinski, Jean-Philippe Vert, E. Richard, 2014, NIPS.

A bagging SVM to learn from positive and unlabeled

Jean-Philippe Vert, F. Mordelet, 2013 .

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Jean-Philippe Vert, J. Dekker, E. Barillot, 2015, Genome Biology.

Causal Inference Methods for Combining Randomized Trials and Observational Studies: A Review

G. Varoquaux, Jean-Philippe Vert, Shu Yang, 2020, Statistical Science.

Relating Leverage Scores and Density using Regularized Christoffel Functions

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

An introduction to DNA microarrays and some mathematical challenges behind them

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

Multi-condition and multi-modal temporal profile inference during mouse embryonic development

Jean-Philippe Vert, Xinxian Deng, Chengxiang Qiu, 2024, bioRxiv.