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Metric learning pairwise kernel for graph inference

Jean-Philippe Vert , Jian Qiu , William Noble
Preprints, Working Papers, ... hal-00108477v1
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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
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Joseph Boyd , Zelia Gouveia , Franck Perez , Thomas Walter
2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), Apr 2020, Iowa City, United States. pp.886-890, ⟨10.1109/ISBI45749.2020.9098696⟩
Conference papers hal-02976141v1
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National recommendations of the French Genetics and Cancer Group - Unicancer on the modalities of multi-genes panel analyses in hereditary predispositions to tumors of the digestive tract

Marion Dhooge , Stéphanie Baert-Desurmont , Carole Corsini , Olivier Caron , Nadine Andrieu , et al.
European Journal of Medical Genetics, 2020, 63 (12), pp.104080. ⟨10.1016/j.ejmg.2020.104080⟩
Journal articles inserm-03182974v1
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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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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

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

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

Classification of microarray data using gene networks.

Franck Rapaport , Andrei Zinovyev , Marie Dutreix , Emmanuel Barillot , Jean-Philippe Vert
BMC Bioinformatics, 2007, 8, pp.35. ⟨10.1186/1471-2105-8-35⟩
Journal articles hal-00433577v1

An accurate and interpretable model for siRNA efficacy prediction.

Jean-Philippe Vert , Nicolas Foveau , Christian Lajaunie , Yves Vandenbrouck
BMC Bioinformatics, 2006, 7, pp.520. ⟨10.1186/1471-2105-7-520⟩
Journal articles hal-00433579v1
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Toxicity assays in nanodrops combining bioassay and morphometric endpoints.

Frédéric Lemaire , Céline A Mandon , Julien Reboud , Alexandre Papine , Jesus Angulo , et al.
PLoS ONE, 2007, 2 (1), pp.e163. ⟨10.1371/journal.pone.0000163⟩
Journal articles hal-00193387v1
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Spectral analysis of gene expression profiles using gene networks

Franck Rapaport , Andrei Zinovyev , Marie Dutreix , Emmanuel Barillot , Jean-Philippe Vert
Preprints, Working Papers, ... hal-00021785v1
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Classification of arrayCGH data using fused SVM.

Franck Rapaport , Emmanuel Barillot , Jean-Philippe Vert
Bioinformatics, 2008, 24 (13), pp.i375-82. ⟨10.1093/bioinformatics/btn188⟩
Journal articles inserm-00293893v1
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ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

Fantine Mordelet , Jean-Philippe Vert
Preprints, Working Papers, ... hal-00594774v1

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
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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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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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Evaluation of least significant changes of pulse contour analysis-derived parameters

Hugues de Courson , Loic Ferrer , Grégoire Cane , Eric Verchère , Musa Sesay , et al.
Annals of Intensive Care, 2019, 9 (1), pp.116. ⟨10.1186/s13613-019-0590-z⟩
Journal articles inserm-02467629v1

Large-scale machine learning for metagenomics sequence classification

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

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
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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

Dimeric G-quadruplex motifs determine a large fraction of strong replication origins in vertebrates

Jérémy Poulet-Benedetti , Caroline Tonnerre-Doncarli , Anne-Laure Valton , Marc Laurent , Marie Gérard , et al.
Journal articles hal-03932439v1

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

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

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⟩
Journal articles hal-01679012v1

Nuclei segmentation in histopathology images using deep neural networks

Peter Naylor , Marik Laé , Fabien Reyal , Thomas Walter
2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), 2017, Melbourne, Australia
Conference papers hal-01683969v1
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Exome sequencing reveals aberrant signalling pathways as hallmark of treatment-naive anal squamous cell carcinoma

W. Cacheux , V. Dangles-Marie , E. Rouleau , J. Lazartigues , E. Girard , et al.
Oncotarget, 2018, 9 (1), pp.464-476. ⟨10.18632/oncotarget.23066⟩
Journal articles hal-01717339v1
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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

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

Molecular profiling of non-small-cell lung cancer patients with or without brain metastases included in the randomized SAFIR02-LUNG trial and association with intracranial outcome

Alice Mogenet , Fabrice Barlesi , Benjamin Besse , Stefan Michiels , Maryam Karimi , et al.
Lung Cancer, 2022, 169, pp.31-39. ⟨10.1016/j.lungcan.2022.05.004⟩
Journal articles hal-03925563v1