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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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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
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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
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In Silico screening on the three-dimensional model of the Plasmodium vivax SUB1 protease leads to the validation of a novel anti-parasite compound.

Anthony Bouillon , David Giganti , Christophe Benedet , Olivier Gorgette , Stéphane Pêtres , et al.
Journal of Biological Chemistry, 2013, 288, pp.18561-73. ⟨10.1074/jbc.M113.456764⟩
Journal articles pasteur-01457905v1
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Tight convex relaxations for sparse matrix factorization

Emile Richard , Guillaume Obozinski , Jean-Philippe Vert
Preprints, Working Papers, ... hal-01025959v3
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Vector quantization and clustering in presence of censoring

Svetlana Gribkova
Preprints, Working Papers, ... hal-01075676v1
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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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A new scoring system in cancer genetics: application to criteria for BRCA1 and BRCA2 mutation screening.

Bernard Bonaïti , Flora Alarcon , Nadine Andrieu , Valérie Bonadona , Marie-Gabrielle Dondon , et al.
Journal of Medical Genetics, 2013, 51 (2), epub ahead of print. ⟨10.1136/jmedgenet-2013-101674⟩
Journal articles hal-00923931v1
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Variation in breast cancer risk associated with factors related to pregnancies according to truncating mutation location, in the French National BRCA1/2 carrier cohort (GENEPSO).

Julie Lecarpentier , Catherine Noguès , Emmanuelle Mouret-Fourme , Marion Gauthier-Villars , Christine Lasset , et al.
Breast Cancer Research, 2012, 14 (4), pp.R99. ⟨10.1186/bcr3218⟩
Journal articles inserm-00724092v1
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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⟩
Journal articles hal-02559123v1
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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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Variation in breast cancer risk with mutation position smoking alcohol and chest X-ray history in the French National BRCA1/2 carrier cohort (GENEPSO)

Julie Lecarpentier , Catherine Noguès , Emmanuelle Mouret-Fourme , Dominique Stoppa-Lyonnet , Christine Lasset , et al.
Breast Cancer Research and Treatment, 2011, 130 (3), pp.927-938. ⟨10.1007/s10549-011-1655-3⟩
Journal articles hal-00698006v1
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[Cancer genetics: estimation of the needs of the population in France for the next ten years]

Catherine Bonaïti-Pellié , Nadine Andrieu , Patrick Arveux , Valérie Bonadona , Bruno Buecher , et al.
Bulletin du Cancer, 2009, 96 (9), pp.875-900. ⟨10.1684/bdc.2009.0943⟩
Journal articles inserm-00419527v1
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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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Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis

Gautier Stoll , Didier Surdez , Franck Tirode , Karine Laud , Emmanuel Barillot , et al.
Nucleic Acids Research, 2013, 41 (19), pp.8853-8871. ⟨10.1093/nar/gkt678⟩
Journal articles inserm-02438745v1
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Mechanical induction of the tumorigenic b-catenin pathway by tumour growth pressure

Maria Elena Fernandez-Sanchez , Sandrine Barbier , Joanne Whitehead , Gaelle Bealle , Aude Michel , et al.
Nature, 2015, 523 (7558), pp.92-95. ⟨10.1038/nature14329⟩
Journal articles inserm-02441063v1
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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
Preprints, Working Papers, ... 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⟩
Journal articles hal-01350904v1
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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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Supervised Reconstruction of Biological Networks with Local Models

Kevin Bleakley , Gérard Biau , Jean-Philippe Vert
Preprints, Working Papers, ... hal-00130277v1
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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⟩
Journal articles inserm-00438642v1
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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
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Genomic instability : a stronger prognostic marker than proliferation for early stage luminal breast carcinomas

Anne Vincent-Salomon , Vanessa Benhamo , Eleonore Gravier , Guillem Rigaill , Nadège Gruel , et al.
PLoS ONE, 2013, 8 (10), ⟨10.1371/journal.pone.0076496⟩
Journal articles hal-01219550v1
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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
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Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

Ferhat Ay , Thanh H. Vu , Michael J. Zeitz , Nelle Varoquaux , Jan E. Carette , et al.
BMC Genomics, 2015, 16, pp.121. ⟨10.1186/s12864-015-1236-7⟩
Journal articles hal-01152400v1
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Transcriptome analysis of Wnt3a-treated triple-negative breast cancer cells

Sylvie Maubant , Bruno Tesson , Virginie Maire , Mengliang Ye , Guillem Rigaill , et al.
PLoS ONE, 2015, 10 (4), 26 p. ⟨10.1371/journal.pone.0122333⟩
Journal articles hal-02639667v1