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Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries

Valentina Boeva , Caroline Louis-Brennetot , Agathe Peltier , Simon Durand , Cecile Pierre-Eugene , et al.
Nature Genetics, 2017, 49 (9), pp.1408-1413. ⟨10.1038/ng.3921⟩
Article dans une revue hal-01741718v1

The Kendall and Mallows Kernels for Permutations

Yunlong Jiao , Jean-Philippe Vert
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2018, 40 (7), pp.1755-1769. ⟨10.1109/TPAMI.2017.2719680⟩
Article dans une revue hal-01679012v1
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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Aurélien Naldi , Céline Hernandez , Nicolas Levy , Gautier Stoll , Pedro Monteiro , et al.
Frontiers in Physiology, 2018, 9, pp.n°680:1-13. ⟨10.3389/fphys.2018.00680⟩
Article dans une revue hal-01794294v2
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Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis

Michel Adam Wassef , Verónica Rodilla , Aurélie Teissandier , Bruno Zeitouni , Nadège Gruel , et al.
Genes and Development, 2015, 29 (24), pp.2547-2562. ⟨10.1101/gad.269522.115⟩
Article dans une revue hal-02559123v1

Classification of gene signatures for their information value and functional redundancy

Laura Cantini , Laurence Calzone , Loredana Martignetti , Mattias Rydenfelt , Nils Blüthgen , et al.
npj Systems Biology and Applications, 2018, 4 (1), ⟨10.1038/s41540-017-0038-8⟩
Article dans une revue hal-02129604v1

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

Davide Risso , Fanny Perraudeau , Svetlana Gribkova , Sandrine Dudoit , Jean-Philippe Vert
Nature Communications, 2018, 9 (1)
Article dans une revue hal-01985432v1

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

Evelien Bunnik , Kate Cook , Nelle Varoquaux , Gayani Batugedara , Jacques Prudhomme , et al.
Nature Communications, 2018, 9 (1)
Article dans une revue hal-01985437v1
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The French Early Breast Cancer Cohort (FRESH): A Resource for Breast Cancer Research and Evaluations of Oncology Practices Based on the French National Healthcare System Database (SNDS)

Elise Dumas , Lucie Laot , Florence Coussy , Beatriz Grandal Rejo , Eric Daoud , et al.
Cancers, 2022, 14 (11), pp.2671. ⟨10.3390/cancers14112671⟩
Article dans une revue hal-03901737v1

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

Guillem Rigaill , Toby Dylan Hocking , Francis Bach , Jean-Philippe Vert
ICML 2013 - 30 th International Conference on Machine Learning, Supported by the International Machine Learning Society (IMLS), Jun 2013, Atlanta, United States
Communication dans un congrès hal-00824075v1
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Supervised Quantile Normalisation

Marine Le Morvan , Jean-Philippe Vert
2017
Pré-publication, Document de travail hal-01525306v1

On learning matrices with orthogonal columns or disjoint supports

Kevin Vervier , Pierre Mahé , Alexandre d'Aspremont , Jean-Baptiste Veyrieras , Jean-Philippe Vert
European Conference, ECML PKDD 2014, Sep 2014, Nancy, France. pp.274-289, ⟨10.1007/978-3-662-44845-8_18⟩
Communication dans un congrès hal-01101875v1
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Global alignment of protein-protein interaction networks by graph matching methods.

Mikhail Zaslavskiy , Francis Bach , Jean-Philippe Vert
Bioinformatics, 2009, 25 (12), pp.i259-67. ⟨10.1093/bioinformatics/btp196⟩
Article dans une revue hal-00382501v1
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Learning smoothing models of copy number profiles using breakpoint annotations

Toby Dylan Hocking , Gudrun Schleiermacher , Isabelle Janoueix-Lerosey , Olivier Delattre , Francis Bach , et al.
2012
Pré-publication, Document de travail hal-00663790v1
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Intersecting singularities for multi-structured estimation

Emile Richard , Francis Bach , Jean-Philippe Vert
ICML 2013 - 30th International Conference on Machine Learning, Jun 2013, Atlanta, United States
Communication dans un congrès hal-00918253v1

SegAnnDB: interactive web-based genomic segmentation

Toby D. Hocking , Valentina Boeva , Guillem Rigaill , Gudrun Schleiermacher , Isabelle Janoueix-Lerosey , et al.
Bioinformatics, 2014, 30 (11), pp.1539-1546. ⟨10.1093/bioinformatics/btu072⟩
Article dans une revue hal-01101868v1
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Clusterpath An Algorithm for Clustering using Convex Fusion Penalties

Toby Dylan Hocking , Armand Joulin , Francis Bach , Jean-Philippe Vert
28th international conference on machine learning, Jun 2011, United States. pp.1
Communication dans un congrès hal-00591630v1
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A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting

Racha Chouaib , Adham Safieddine , Xavier Pichon , Arthur Imbert , Oh Sung Kwon , et al.
Developmental Cell, 2020, 54 (6), pp.773 - 791.e5. ⟨10.1016/j.devcel.2020.07.010⟩
Article dans une revue pasteur-02925687v1
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Group Lasso with Overlaps: the Latent Group Lasso approach

Guillaume Obozinski , Laurent Jacob , Jean-Philippe Vert
[Research Report] 2011, pp.60
Rapport inria-00628498v1

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
Communication dans un congrès hal-01717385v1
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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⟩
Article dans une revue hal-02549796v1
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Dynamical Boolean Modeling of Immunogenic Cell Death

Andrea Checcoli , Jonathan Pol , Aurelien Naldi , Vincent Noël , Emmanuel Barillot , et al.
Frontiers in Physiology, 2020, 11, pp.590479. ⟨10.3389/fphys.2020.590479⟩
Article dans une revue hal-03050475v1
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Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision

Luca Grieco , Laurence Calzone , Isabelle Bernard-Pierrot , François Radvanyi , Brigitte Kahn-Perlès , et al.
PLoS Computational Biology, 2013, 9 (10), pp.e1003286. ⟨10.1371/journal.pcbi.1003286⟩
Article dans une revue inserm-02152259v1

Robust Seriation and Applications to Cancer Genomics

Antoine Recanati , Nicolas Servant , Jean-Philippe Vert , Alexandre d'Aspremont
2018
Pré-publication, Document de travail hal-01851960v1
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On learning matrices with orthogonal columns or disjoint supports

Kevin Vervier , Pierre Mahé , Alexandre d'Aspremont , Jean-Baptiste Veyrieras , Jean-Philippe Vert
2014
Pré-publication, Document de travail hal-00985654v2
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The intestinal microbiota interferes with the microRNA response upon oral Listeria infection.

Cristel Archambaud , Odile Sismeiro , Joern Toedling , Guillaume Soubigou , Christophe Bécavin , et al.
mBio, 2012, 4 (6), pp.e00707-13. ⟨10.1128/mBio.00707-13⟩
Article dans une revue hal-01350904v1
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Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation.

Constance Ciaudo , Nicolas Servant , Valérie Cognat , Alexis Sarazin , Emmanuelle Kieffer , et al.
PLoS Genetics, 2009, 5 (8), pp.e1000620. ⟨10.1371/journal.pgen.1000620⟩
Article dans une revue inserm-00438642v1
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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⟩
Article dans une revue hal-01809081v1
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SegAnnot: an R package for fast segmentation of annotated piecewise constant signals

Toby Dylan Hocking , Guillem Rigaill
2012
Pré-publication, Document de travail hal-00759129v1
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Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses

Mélanie Durand , Thomas Walter , Tiphène Pirnay , Thomas Naessens , Paul Guéguen , et al.
Journal of Experimental Medicine, 2019, 216 (7), pp.1561-1581. ⟨10.1084/jem.20181994⟩
Article dans une revue hal-02440608v1

A path following algorithm for the graph matching problem.

Mikhail Zaslavskiy , Francis Bach , Jean-Philippe Vert
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2009, 31 (12), pp.2227-42. ⟨10.1109/TPAMI.2008.245⟩
Article dans une revue hal-00433567v1