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

Laurent Jacob , Jean-Philippe Vert
Bioinformatics, 2008, 24 (3), pp.358-66. ⟨10.1093/bioinformatics/btm611⟩
Journal articles hal-00433574v1

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

Pierre Mahé , Nobuhisa Ueda , Tatsuya Akutsu , Jean-Luc Perret , Jean-Philippe Vert et al.
Journal of Chemical Information and Modeling, 2005, 45 (4), pp.939-51. ⟨10.1021/ci050039t⟩
Journal articles hal-00433584v1

A structural alignment kernel for protein structures.

Jian Qiu , Martial Hue , Asa Ben-Hur , Jean-Philippe Vert , William Stafford Noble et al.
Bioinformatics, 2007, 23 (9), pp.1090-8. ⟨10.1093/bioinformatics/btl642⟩
Journal articles hal-00433578v1
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Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

Nicolas Levy , Aurélien Naldi , Céline Hernandez , Gautier Stoll , Denis Thieffry et al.
Frontiers in Physiology, 2018, 9, pp.787. ⟨10.1101/319780⟩
Journal articles hal-01809081v1

The pharmacophore kernel for virtual screening with support vector machines.

Pierre Mahé , Liva Ralaivola , Véronique Stoven , Jean-Philippe Vert
Journal of Chemical Information and Modeling, 2006, 46 (5), pp.2003-14. ⟨10.1021/ci060138m⟩
Journal articles hal-00433580v1
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Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

Anna Niarakis , Martin Kuiper , Marek Ostaszewski , Rahuman Malik Sheriff , Cristina Casals-Casas et al.
Briefings in Bioinformatics, 2021, 22 (2), pp.1848--1859. ⟨10.1093/bib/bbaa046⟩
Journal articles hal-02549796v1
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Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision

Stéphanie Chevalier , Vincent Noël , Laurence Calzone , Andrei Zinovyev , Loïc Paulevé et al.
18th International Conference on Computational Methods in Systems Biology (CMSB), 2020, Online, Germany. pp.193--209, ⟨10.1007/978-3-030-60327-4_11⟩
Conference papers hal-02898849v2

Extracting active pathways from gene expression data.

Jean-Philippe Vert , Minoru Kanehisa
Bioinformatics, 2003, 19 Suppl 2, pp.ii238-44
Journal articles hal-00433588v1

Protein homology detection using string alignment kernels.

Hiroto Saigo , Jean-Philippe Vert , Nobuhisa Ueda , Tatsuya Akutsu
Bioinformatics, 2004, 20 (11), pp.1682-9. ⟨10.1093/bioinformatics/bth141⟩
Journal articles hal-00433587v1

Where Do We Stand in Regularization for Life Science Studies?

Veronica Tozzo , Chloé-Agathe Azencott , Samuele Fiorini , Emanuele Fava , Andrea Trucco et al.
Journal of Computational Biology, 2021, ⟨10.1089/cmb.2019.0371⟩
Journal articles hal-03367708v1

A systematic analysis of gene-gene interaction in multiple sclerosis

Lotfi Slim , Clément Chatelain , Hélène de Foucauld , Chloé-Agathe Azencott
BMC Medical Genomics, 2022, 15 (1), pp.100. ⟨10.1186/s12920-022-01247-3⟩
Journal articles hal-03122122v1

Nonlinear post-selection inference for genome-wide association studies

Lotfi Slim , Clément Chatelain , Chloé-Agathe Azencott
Pacific Symposium on Biocomputing, Jan 2022, Kohala Coast, Hawaii, United States. ⟨10.1101/2020.09.30.320515⟩
Conference papers hal-03122125v1
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Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm.

Gautier Stoll , Eric Viara , Emmanuel Barillot , Laurence Calzone
BMC Systems Biology, 2012, 6 (1), pp.116. ⟨10.1186/1752-0509-6-116⟩
Journal articles inserm-00762304v1
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Études d'association génome entier guidées par des réseaux

Héctor Climente González
Bio-informatique [q-bio.QM]. Université Paris sciences et lettres, 2020. Français. ⟨NNT : 2020UPSLM001⟩
Theses tel-03270879v1
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Machine learning approaches for drug virtual screening

Benoit Playe
Bioinformatics [q-bio.QM]. Université Paris sciences et lettres, 2019. English. ⟨NNT : 2019PSLEM010⟩
Theses tel-02186833v1
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Increasing stability and interpretability of gene expression signatures

Anne-Claire Haury , Laurent Jacob , Jean-Philippe Vert
Preprints, Working Papers, ... hal-00448395v1
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ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples.

Fantine Mordelet , Jean-Philippe Vert
BMC Bioinformatics, 2011, 12 (1), pp.389. ⟨10.1186/1471-2105-12-389⟩
Journal articles inserm-00641298v1
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Virtual screening with support vector machines and structure kernels.

Pierre Mahé , Jean-Philippe Vert
Combinatorial Chemistry and High Throughput Screening, 2009, 12 (4), pp.409-23
Journal articles hal-00166188v1
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Predicting drug side-effect profiles: a chemical fragment-based approach.

Edouard Pauwels , Véronique Stoven , Yoshihiro Yamanishi
BMC Bioinformatics, 2011, 12 (1), pp.169. ⟨10.1186/1471-2105-12-169⟩
Journal articles inserm-00663945v1
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EMA - A R package for Easy Microarray data analysis.

Nicolas Servant , Eleonore Gravier , Pierre Gestraud , Cecile Laurent , Caroline Paccard et al.
BMC Research Notes, 2010, 3 (1), pp.277. ⟨10.1186/1756-0500-3-277⟩
Journal articles inserm-00984710v1

The Weighted Kendall and High-order Kernels for Permutations

Yunlong Jiao , Jean-Philippe Vert
35th International Conference on Machine Learning, Jul 2018, Stockholm, Sweden. pp.2314--2322
Conference papers hal-01717385v1

Learning with minimal effort: leveraging in silico labeling for cell and nucleus segmentation

Thomas Bonte , Maxence Philbert , Emeline Coleno , Edouard Bertrand , Arthur Imbert et al.
ECCV 2022 proceedings (Bio-image computing workshop), 2023
Proceedings hal-03935104v1
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Mathematical modelling of cell-fate decision in response to death receptor engagement.

Laurence Calzone , Laurent Tournier , Simon Fourquet , Denis Thieffry , Boris Zhivotovsky et al.
PLoS Computational Biology, 2010, 6 (3), pp.e1000702. ⟨10.1371/journal.pcbi.1000702⟩
Journal articles inserm-00704979v1

martini: an R package for genome-wide association studies using SNP networks

Chloé-Agathe Azencott , Héctor Climente-González
Preprints, Working Papers, ... hal-03122108v1

pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods

Abdelkader Behdenna , Julien Haziza , Chloé-Agathe Azencott , Akpéli Nordor
Preprints, Working Papers, ... hal-03114226v1
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Novel Methods for Epistasis Detection in Genome-Wide Association Studies

Lotfi Slim , Clement Chatelain , Jean-Philippe Vert , Chloé-Agathe Azencott
PLoS ONE, 2020, 15 (11), pp.e0242927. ⟨10.1371/journal.pone.0242927⟩
Journal articles hal-01984919v2
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Biological networks and GWAS: comparing and combining network methods to understand the genetics of familial breast cancer susceptibility in the GENESIS study

Héctor Climente-González , Christine Lonjou , Fabienne Lesueur , Dominique Stoppa-Lyonnet , Nadine Andrieu et al.
PLoS Computational Biology, 2021, ⟨10.1101/2020.05.04.076661⟩
Journal articles hal-03114234v1
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Meta-Analysis of Esophageal Cancer Transcriptomes Using Independent Component Analysis

Ainur Seisenova , Asset Daniyarov , Askhat Molkenov , Aigul Sharip , Andrei Zinovyev et al.
Frontiers in Genetics, 2021, 12, ⟨10.3389/fgene.2021.683632⟩
Journal articles hal-03447487v1
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Waterpixels: Superpixels based on the watershed transformation

Vaïa Machairas , Etienne Decencière , Thomas Walter
IEEE International Conference On Image Processing, Oct 2014, Paris, France. ⟨10.1109/ICIP.2014.7025882⟩
Conference papers hal-01139797v1
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Les applications industrielles de la bio-informatique

Jean-Philippe Vert
Réalités industrielles. Annales des mines, 2013, Février 2013, pp.17-23
Journal articles hal-00796732v1