List of works - Jean-Philippe Vert

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

scientific article

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

scientific article published on 19 August 2015

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

scientific article published on 18 January 2018

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

scientific article

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

scientific article published on 19 October 2017

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 4 May 2015

An accurate and interpretable model for siRNA efficacy prediction

scientific article

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

article

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

scientific article published on 07 November 2019

Changes in correlation between promoter methylation and gene expression in cancer

scientific article published on 28 October 2015

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

scientific article

Classification of arrayCGH data using fused SVM.

scientific article

Classification of microarray data using gene networks

scientific article

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

scientific article

DSIR: assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes ⬇️

scientific article

Effective normalization for copy number variation in Hi-C data

scientific article published on 06 September 2018

Effective normalization for copy number variation in Hi-C data

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

scientific article

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

scientific article published on 14 December 2007

Epigenomic alterations in breast carcinoma from primary tumor to locoregional recurrences.

scientific article

Glycan classification with tree kernels

scientific article published on 7 March 2007

Graph kernels based on tree patterns for molecules

scientific article (publication date: 4 October 2008)

Graph kernels for molecular structure-activity relationship analysis with support vector machines

scientific article published in July 2005

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Kernel Multitask Regression for Toxicogenetics.

scientific article published on 26 September 2017

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

scientific article published on 30 September 2019

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

scientific article

Large-scale prediction of protein-protein interactions from structures

scientific article

Learning smoothing models of copy number profiles using breakpoint annotations

scientific article

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

scientific article (publication date: September 2008)

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum

scientific article

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

scientific article

Novel Methods for Epistasis Detection in Genome-Wide Association Studies

Novel methods for epistasis detection in genome-wide association studies

scientific article published on 30 November 2020

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

scholarly article published 18 January 2018

Optimizing amino acid substitution matrices with a local alignment kernel

scientific article published on 5 May 2006

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

scientific article published on 17 December 2013

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

scientific article

Protein homology detection using string alignment kernels

scientific article published on 26 February 2004

Protein-ligand interaction prediction: an improved chemogenomics approach.

scientific article published on August 2008

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

scientific article published in Nature Communications

SIRENE: supervised inference of regulatory networks

scientific article

SegAnnDB: interactive Web-based genomic segmentation

scientific article

Signaling Pathway Activities Improve Prognosis for Breast Cancer

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

scientific article published in June 2005

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

scientific article published in January 2013

Supervised reconstruction of biological networks with local models

scientific article published in July 2007

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection.

scientific article

The Kendall and Mallows Kernels for Permutations

scientific article

The Pharmacophore Kernel for Virtual Screening with Support Vector Machines

scientific article (publication date: September 2006)

The Wnt receptor Ryk reduces neuronal and cell survival capacity by repressing FOXO activity during the early phases of mutant huntingtin pathogenicity

scientific article

The context-tree kernel for strings

scientific article published on 27 September 2005

The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures

scientific article

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

scientific article

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

scientific article published on 24 August 2020

Virtual screening of GPCRs: an in silico chemogenomics approach

scientific article

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

scholarly article published 6 April 2017

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

scientific article published on 18 September 2015

List of works by Jean-Philippe Vert

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

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

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

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

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

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

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

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

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

An accurate and interpretable model for siRNA efficacy prediction

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

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

Changes in correlation between promoter methylation and gene expression in cancer

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

Classification of arrayCGH data using fused SVM.

Classification of microarray data using gene networks

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

DSIR: assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes ⬇️

Effective normalization for copy number variation in Hi-C data

Effective normalization for copy number variation in Hi-C data

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

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

Epigenomic alterations in breast carcinoma from primary tumor to locoregional recurrences.

Glycan classification with tree kernels

Graph kernels based on tree patterns for molecules

Graph kernels for molecular structure-activity relationship analysis with support vector machines

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

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

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

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

Kernel Multitask Regression for Toxicogenetics.

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

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

Large-scale prediction of protein-protein interactions from structures

Learning smoothing models of copy number profiles using breakpoint annotations

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

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum

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

Novel Methods for Epistasis Detection in Genome-Wide Association Studies

Novel methods for epistasis detection in genome-wide association studies

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

Optimizing amino acid substitution matrices with a local alignment kernel

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

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

Protein homology detection using string alignment kernels

Protein-ligand interaction prediction: an improved chemogenomics approach.

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

SIRENE: supervised inference of regulatory networks

SegAnnDB: interactive Web-based genomic segmentation

Signaling Pathway Activities Improve Prognosis for Breast Cancer

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

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

Supervised reconstruction of biological networks with local models

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection.

The Kendall and Mallows Kernels for Permutations

The Pharmacophore Kernel for Virtual Screening with Support Vector Machines

The Wnt receptor Ryk reduces neuronal and cell survival capacity by repressing FOXO activity during the early phases of mutant huntingtin pathogenicity

The context-tree kernel for strings

The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures

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

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

Virtual screening of GPCRs: an in silico chemogenomics approach

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

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