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

Judith Abécassis , Fabien Reyal , Jean-Philippe Vert
Nature Communications, 2021, 12 (1), pp.5352. ⟨10.1038/s41467-021-24992-y⟩
Journal articles hal-03510272v1

Endoscopic management of 345 small rectal neuroendocrine tumours: A national study from the French group of endocrine tumours (GTE)

Caroline Fine , Guillaume Roquin , Eric Terrebonne , Thierry Lecomte , Romain Coriat et al.
United European Gastroenterology Journal, 2019, 7 (8), pp.1102-1112. ⟨10.1177/2050640619861883⟩
Journal articles hal-02549178v1
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Risk-reducing salpingo-oophorectomy, natural menopause, and breast cancer risk: an international prospective cohort of BRCA1 and BRCA2 mutation carriers

Nasim Mavaddat , Antonis C. Antoniou , Thea Mooij , Maartje Hooning , Bernadette Heemskerk-Gerritsen et al.
Breast Cancer Research, 2020, 22 (1), pp.8. ⟨10.1186/s13058-020-1247-4⟩
Journal articles inserm-02445596v1

Autoimmunity affecting the biliary tract fuels the immunosurveillance of cholangiocarcinoma

Juliette Paillet , Céleste Plantureux , Sarah Lévesque , Julie Le Naour , Gautier Stoll et al.
Journal of Experimental Medicine, 2021, 218 (10), pp.1-33. ⟨10.1084/jem.20200853⟩
Journal articles hal-03378827v1

Contribution of epigenetic landscapes and transcription factors to X-chromosome reactivation in the inner cell mass

Maud Borensztein , Ikuhiro Okamoto , Laurène Syx , Guillaume Guilbaud , Christel Picard et al.
Nature Communications, 2017, 8 (1), ⟨10.1038/s41467-017-01415-5⟩
Journal articles hal-03437406v1

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

Jean-Philippe Vert , Jian Qiu , William S Noble
BMC Bioinformatics, 2007, 8 Suppl 10, pp.S8. ⟨10.1186/1471-2105-8-S10-S8⟩
Journal articles hal-00433573v1
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Metric learning pairwise kernel for graph inference

Jean-Philippe Vert , Jian Qiu , William Noble
2006
Preprints, Working Papers, ... hal-00108477v1
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A new hybrid record linkage process to make epidemiological databases interoperable: application to the GEMO and GENEPSO studies involving BRCA1 and BRCA2 mutation carriers

Yue Jiao , Fabienne Lesueur , Chloé-Agathe Azencott , Maïté Laurent , Noura Mebirouk et al.
BMC Medical Research Methodology, 2021, 21 (1), pp.155. ⟨10.1186/s12874-021-01299-6⟩
Journal articles inserm-03313811v1
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A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport

Adham Safieddine , Emeline Coleno , Soha Salloum , Arthur Imbert , Abdel-Meneem Traboulsi et al.
Nature Communications, 2021, 12 (1), pp.1352. ⟨10.1038/s41467-021-21585-7⟩
Journal articles hal-03014936v2

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Anna Niarakis , Dagmar Waltemath , James Glazier , Falk Schreiber , Sarah Keating et al.
Briefings in Bioinformatics, 2022, 23 (4), pp.1-11. ⟨10.1093/bib/bbac212⟩
Journal articles hal-03690604v1
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A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction.

Brice Hoffmann , Mikhail Zaslavskiy , Jean-Philippe Vert , Véronique Stoven
BMC Bioinformatics, 2010, 11 (1), pp.99. ⟨10.1186/1471-2105-11-99⟩
Journal articles inserm-00663528v1
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Determining the optimal number of independent components for reproducible transcriptomic data analysis

Ulykbek Kairov , Laura Cantini , Alessandro Greco , Askhat Molkenov , Urszula Czerwinska et al.
BMC Genomics, 2017, 18 (1), pp.712. ⟨10.1186/s12864-017-4112-9⟩
Journal articles inserm-02064099v1
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Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction

Daniel Gamermann , Arnau Montagud , J Alberto Conejero , Pedro Fernández de Córdoba , Javier F Urchueguía et al.
PLoS ONE, 2019, 14 (9), pp.e0221631. ⟨10.1371/journal.pone.0221631⟩
Journal articles inserm-02317883v1
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Validation de biomarqueurs prédictifs de la réponse au traitement : extension des courbes de prédictivités à un critère de jugement censuré

Bassirou Mboup
Statistiques [math.ST]. Université Paris-Saclay, 2020. Français. ⟨NNT : 2020UPASR011⟩
Theses tel-03176621v1
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Genetic markers and phosphoprotein forms of beta-catenin pβ-Cat552 and pβ-Cat675 are prognostic biomarkers of cervical cancer

Suzy M Scholl , Jonas Beal , Leanne de Koning , Elodie Girard , Marina Popovic et al.
EBioMedicine, 2020, 61, pp.103049. ⟨10.1016/j.ebiom.2020.103049⟩
Journal articles hal-03492821v1
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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⟩
Journal articles hal-01741718v1
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Tight convex relaxations for sparse matrix factorization

Emile Richard , Guillaume Obozinski , Jean-Philippe Vert
2014
Preprints, Working Papers, ... hal-01025959v3
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Rôle de la phosphatase PRL-3 et de CRMP2 dans la migration et l'invasion du mélanome uvéal

Laura Duciel
Cancer. Université Paris Saclay (COmUE), 2018. Français. ⟨NNT : 2018SACLS233⟩
Theses tel-02304146v1
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An autocrine ActivinB mechanism drives TGF β/Activin signaling in Group 3 medulloblastoma

Morgane Morabito , Magalie Larcher , Florence M G Cavalli , Chloé Foray , Antoine Forget et al.
EMBO Molecular Medicine, 2019, 6, pp.e9830. ⟨10.15252/emmm.201809830⟩
Journal articles hal-02347105v1

A community effort to assess and improve drug sensitivity prediction algorithms

James C Costello , Laura M Heiser , Elisabeth Georgii , Mehmet Gönen , Michael P Menden et al.
Nature Biotechnology, 2014, 32, pp.1202-1212. ⟨10.1038/nbt.2877⟩
Journal articles hal-01101874v1

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

Alice Schoenauer Sebag , Sandra Plancade , Céline Raulet-Tomkiewicz , Robert Barouki , Jean-Philippe Vert et al.
Bioinformatics, 2015, 31 (12), pp.i320-i328. ⟨10.1093/bioinformatics/btv225⟩
Journal articles hal-01246689v1
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SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

Bruno Zeitouni , Valentina Boeva , Isabelle Janoueix-Lerosey , Sophie Loeillet , Patricia Legoix-Né et al.
Bioinformatics Application note, 2010, 26 (15), pp.1895-1896. ⟨10.1093/bioinformatics/btq293⟩
Journal articles inserm-00508372v1

Interest of Colchicine for the Treatment of Cystic Fibrosis Patients. Preliminary Report

I. Sermet-Gaudelus , Véronique Stoven , J. Annereau , V. Witko-Sarsat , P. Reinert et al.
Mediators of Inflammation, 1999, 8 (1), pp.13-15. ⟨10.1080/09629359990667⟩
Journal articles hal-03116923v1
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CinéBreast-factors influencing the time to first metastatic recurrence in breast cancer: Analysis of real-life data from the French ESME MBC database

P. Gougis , M. Carton , C. Tchokothe , M. Campone , F. Dalenc et al.
The Breast, 2020, 49, pp.17-24. ⟨10.1016/j.breast.2019.10.004⟩
Journal articles hal-02888468v1
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BRCAness, SLFN11, and RB1 loss predict response to topoisomerase I inhibitors in triple-negative breast cancers

Florence Coussy , Rania El-Botty , Sophie Château-Joubert , Ahmed Dahmani , Elodie Montaudon et al.
Science Translational Medicine, 2020, 12 (531), pp.eaax2625. ⟨10.1126/scitranslmed.aax2625⟩
Journal articles hal-02508765v1

Prognosis and chemosensitivity of non-V600E BRAF mutations in metastatic colorectal carcinoma (mCRC): An AGEO French multicenter retrospective cohort.

Aline Derosiere , Vincent Nicolai , David Malka , Astrid Pozet , Julien Lazartigues et al.
Journal of Clinical Oncology, 2019, 37 (15, S), ⟨10.1200/JCO.2019.37.15\_suppl.3575⟩
Journal articles hal-03606012v1

Supervised reconstruction of biological networks with local models.

Kevin Bleakley , Gérard Biau , Jean-Philippe Vert
Bioinformatics, 2007, 23 (13), pp.i57-65. ⟨10.1093/bioinformatics/btm204⟩
Journal articles hal-00433575v1

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

Ferhat Ay , Evelien M. Bunnik , Nelle Varoquaux , Sebastiaan M. Bol , Jacques Prudhomme et al.
Genome Research, 2014, 24, pp.974-988. ⟨10.1101/gr.169417.113⟩
Journal articles hal-01101873v1

Large-scale machine learning for metagenomics sequence classification

Kevin Vervier , Pierre Mahé , Maud Tourmoud , Jean-Baptiste Veyrieras , Jean-Philippe Vert et al.
Bioinformatics, 2016, 32 (7), pp.1023-32
Journal articles hal-01420829v1

Telomere length, ATM mutation status and cancer risk in Ataxia-Telangiectasia families

Anne Laure Renault , Noura Mebirouk , Eve Cavaciuti , Dorothée Le Gal , J. Lecarpentier et al.
Carcinogenesis, 2017, 38 (10), pp.994-1003. ⟨10.1093/carcin/bgx074⟩
Journal articles hal-01658591v1