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Jean-Philippe Vert · SciRah

Researcher profile · Semantic Scholar

Jean-Philippe Vert

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Jean-Philippe Vert — researcher profile on SciRah

h-index: 71
Works: 249
Citations: 23K

Most-cited papers

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
N. Servant, Nelle Varoquaux, B. Lajoie, E. Viara +5 more
2015Genome Biology2,278 citations Open access
Semantic Scholar
A general and flexible method for signal extraction from single-cell RNA-seq data
D. Risso, Fanny Perraudeau, S. Gribkova, S. Dudoit +1 more
2017Nature Communications634 citations Open access
Semantic Scholar
Efficient and Modular Implicit Differentiation
M. Blondel, Quentin Berthet, Marco Cuturi, Roy Frostig +4 more
2021Neural Information Processing Systems393 citations
Semantic Scholar
Causal Inference Methods for Combining Randomized Trials and Observational Studies: A Review
B. Colnet, Imke Mayer, Guan-Hua Chen, Awa Dieng +5 more
2020Statistical Science235 citations Open access
Semantic Scholar
Differentiable Ranks and Sorting using Optimal Transport
Marco Cuturi, Olivier Teboul, Jean-Philippe Vert
2019196 citations
Semantic Scholar
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
K. Van den Berge, Fanny Perraudeau, C. Soneson, M. Love +5 more
2018Genome Biology193 citations Open access
Semantic Scholar
Learning with Differentiable Pertubed Optimizers
Quentin Berthet, M. Blondel, Olivier Teboul, Marco Cuturi +2 more
2020Neural Information Processing Systems182 citations
Semantic Scholar
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer
Gunjan Baid, Daniel E. Cook, Kishwar Shafin, Taedong Yun +15 more
2022Nature Biotechnology161 citations
Semantic Scholar
Learning with Differentiable Perturbed Optimizers
Quentin Berthet, M. Blondel, Olivier Teboul, Marco Cuturi +2 more
2020arXiv.org154 citations
Semantic Scholar
Changes in correlation between promoter methylation and gene expression in cancer
Matahi Moarii, V. Boeva, Jean-Philippe Vert, F. Reyal
2015BMC Genomics152 citations Open access
Semantic Scholar
On Mixup Regularization
Luigi Carratino, M. Cissé, Rodolphe Jenatton, Jean-Philippe Vert
2020Journal of machine learning research139 citations
Semantic Scholar
Jointly Embedding Multiple Single-Cell Omics Measurements
Jie Liu, Yuan-Hao Huang, Ritambhara Singh, Jean-Philippe Vert +1 more
2019bioRxiv126 citations Open access
Semantic Scholar
Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference
Pierre-Cyril Aubin-Frankowski, Jean-Philippe Vert
2018bioRxiv114 citations Open access
Semantic Scholar
Prediction of human population responses to toxic compounds by a collaborative competition
F. Eduati, L. Mangravite, Tao Wang, Hao Tang +120 more
2015Nature Biotechnology112 citations Open access
Semantic Scholar
Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages
E. Bunnik, Kate B. Cook, Nelle Varoquaux, G. Batugedara +14 more
2018Nature Communications107 citations Open access
Semantic Scholar
Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution.
M. Aynaud, O. Mirabeau, N. Gruel, S. Grossetête +18 more
2020Cell Reports94 citations Open access
Semantic Scholar
AI-based mobile application to fight antibiotic resistance
M. Pascucci, G. Royer, Jakub Adamek, Mai Al Asmar +17 more
2021Nature Communications88 citations Open access
Semantic Scholar
Large-scale machine learning for metagenomics sequence classification
K. Vervier, P. Mahé, M. Tournoud, Jean-Baptiste Veyrieras +1 more
2015Bioinform.82 citations Open access
Semantic Scholar
How will generative AI disrupt data science in drug discovery?
Jean-Philippe Vert
2023Nature Biotechnology72 citations
Semantic Scholar
The Kendall and Mallows Kernels for Permutations
Yunlong Jiao, Jean-Philippe Vert
2015IEEE Transactions on Pattern Analysis and Machine Intelligence68 citations Open access
Semantic Scholar
Accurate identification of centromere locations in yeast genomes using Hi-C
Nelle Varoquaux, I. Liachko, F. Ay, J. Burton +4 more
2015Nucleic Acids Research67 citations Open access
Semantic Scholar
Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C
Ferhat Ay, T. Vu, Michael J. Zeitz, Nelle Varoquaux +4 more
2015BMC Genomics63 citations Open access
Semantic Scholar
Differentiable Divergences Between Time Series
M. Blondel, Arthur Mensch, Jean-Philippe Vert
2020International Conference on Artificial Intelligence and Statistics62 citations
Semantic Scholar
Deep multi-class learning from label proportions
Gabriel Dulac-Arnold, Neil Zeghidour, Marco Cuturi, Lucas Beyer +1 more
2019arXiv.org61 citations
Semantic Scholar
Deep embedding and alignment of protein sequences
Felipe Llinares-López, Quentin Berthet, M. Blondel, Olivier Teboul +1 more
2021bioRxiv59 citations Open access
Semantic Scholar
Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum
F. Ay, E. Bunnik, Nelle Varoquaux, Jean-Philippe Vert +2 more
2014Bioessays57 citations Open access
Semantic Scholar
A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates
J. Plouhinec, Sofía Medina-Ruíz, Caroline Borday, E. Bernard +4 more
2017PLoS Biology55 citations Open access
Semantic Scholar
Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution
M. Aynaud, O. Mirabeau, N. Gruel, S. Grossetête +17 more
2019bioRxiv52 citations Open access
Semantic Scholar
LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes
O. Collier, V. Stoven, Jean-Philippe Vert
2018bioRxiv52 citations Open access
Semantic Scholar
Regression as Classification: Influence of Task Formulation on Neural Network Features
Lawrence Stewart, F. Bach, Quentin Berthet, Jean-Philippe Vert
2022International Conference on Artificial Intelligence and Statistics43 citations Open access
Semantic Scholar
Differentiable Deep Clustering with Cluster Size Constraints
A. Genevay, Gabriel Dulac-Arnold, Jean-Philippe Vert
2019arXiv.org43 citations
Semantic Scholar
Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics
Romain Menegaux, Jean-Philippe Vert
2018bioRxiv41 citations Open access
Semantic Scholar
Framing RNN as a kernel method: A neural ODE approach
Adeline Fermanian, P. Marion, Jean-Philippe Vert, G. Biau
2021Neural Information Processing Systems34 citations
Semantic Scholar
Effective normalization for copy number variation in Hi-C data
N. Servant, Nelle Varoquaux, E. Heard, E. Barillot +1 more
2017BMC Bioinformatics33 citations Open access
Semantic Scholar
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis
Marine Le Morvan, A. Zinovyev, Jean-Philippe Vert
2017PLoS Comput. Biol.30 citations Open access
Semantic Scholar
Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
Félix Raimundo, C. Vallot, Jean-Philippe Vert
2020Genome Biology29 citations Open access
Semantic Scholar
Machine learning for single cell genomics data analysis
Félix Raimundo, Laetitia Papaxanthos, C. Vallot, Jean-Philippe Vert
2021bioRxiv26 citations Open access
Semantic Scholar
Scaling ResNets in the Large-depth Regime
P. Marion, Adeline Fermanian, G. Biau, Jean-Philippe Vert
2022Journal of machine learning research24 citations Open access
Semantic Scholar
Semi-supervised single-cell cross-modality translation using Polarbear
Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble
2021bioRxiv24 citations Open access
Semantic Scholar
Computational Systems Biology of Cancer
E. Barillot, L. Calzone, P. Hupé, Jean-Philippe Vert +1 more
202024 citations
Semantic Scholar
Relating Leverage Scores and Density using Regularized Christoffel Functions
Edouard Pauwels, F. Bach, Jean-Philippe Vert
2018Neural Information Processing Systems23 citations
Semantic Scholar
A generic methodological framework for studying single cell motility in high-throughput time-lapse data
Alice Schoenauer-Sebag, S. Plancade, Céline Raulet-Tomkiewicz, R. Barouki +2 more
2015Bioinform.23 citations Open access
Semantic Scholar
Noisy Adaptive Group Testing using Bayesian Sequential Experimental Design
Marco Cuturi, Olivier Teboul, Jean-Philippe Vert
2020arXiv.org22 citations
Semantic Scholar
Novel methods for epistasis detection in genome-wide association studies
Lotfi Slim, Clément Chatelain, Chloé-Agathe Azencott, Jean-Philippe Vert
2018bioRxiv21 citations Open access
Semantic Scholar
Measuring significant changes in chromatin conformation with ACCOST
Kate B. Cook, B. Hristov, K. L. Le Roch, Jean-Philippe Vert +1 more
2019bioRxiv20 citations Open access
Semantic Scholar
Reverse-Complement Equivariant Networks for DNA Sequences
Vincent Mallet, Jean-Philippe Vert
2021bioRxiv19 citations Open access
Semantic Scholar
Integrative DNA methylation and gene expression analysis to assess the universality of the CpG island methylator phenotype
Matahi Moarii, F. Reyal, Jean-Philippe Vert
2015Human Genomics19 citations Open access
Semantic Scholar
CloneSig can jointly infer intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data
J. Abécassis, F. Reyal, Jean-Philippe Vert
2021Nature Communications18 citations Open access
Semantic Scholar
Faculty Opinions recommendation of Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming.
Jean-Philippe Vert
2019Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature18 citations Open access
Semantic Scholar
Assessing reliability of intra-tumor heterogeneity estimates from single sample whole exome sequencing data
J. Abécassis, A. Hamy, C. Laurent, Benjamin Sadacca +3 more
2018bioRxiv18 citations Open access
Semantic Scholar

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