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Combining calls from multiple somatic mutation-callers

 S. Y. Kim , Laurent Jacob , T. P. Speed
BMC Bioinformatics, 2014, 15, pp.154. ⟨10.1186/1471-2105-15-154⟩
Article dans une revue hal-02046830v1
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Increasing stability and interpretability of gene expression signatures

 Anne-Claire Haury , Laurent Jacob , Jean-Philippe Vert
2010
Pré-publication, Document de travail hal-00448395v1

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⟩
Article dans une revue hal-00433574v1
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The healthy ageing gene expression signature for Alzheimer’s disease diagnosis: a random sampling perspective

 Laurent Jacob , Terence Paul Speed
Genome Biology, 2018, 19 (1), ⟨10.1186/s13059-018-1481-6⟩
Article dans une revue hal-02388728v1
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CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS

 Hector Roux de Bézieux , Leandro Lima , Fanny Perraudeau , Arnaud Mary , Sandrine Dudoit , et al.
Bioinformatics, 2022, ⟨10.1093/bioinformatics/btac238⟩
Article dans une revue hal-03433563v1
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Convolutional Kernel Networks for Graph-Structured Data

 Dexiong Chen , Laurent Jacob , Julien Mairal
ICML 2020 - 37th International Conference on Machine Learning, Jul 2020, Vienna, Austria. pp.1576-1586
Communication dans un congrès hal-02504965v2

Protein-ligand interaction prediction: an improved chemogenomics approach.

 Laurent Jacob , Jean-Philippe Vert
Bioinformatics, 2008, 24 (19), pp.2149-56. ⟨10.1093/bioinformatics/btn409⟩
Article dans une revue hal-00433572v1

Statistical methods for handling unwanted variation in metabolomics data

 Alysha M. de Liyera , Marko Sysi Aho , Laurent Jacob , Johann A. Gagnon Bartsch , Sandra Castillo , et al.
Analytical Chemistry, 2015, 87 (7), pp.3606-3615. ⟨10.1021/ac502439y⟩
Article dans une revue hal-02639505v1

Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed

 Laurent Jacob , J. A. Gagnon-Bartsch , T. P. Speed
Biostatistics, 2016, 17, pp.16-28. ⟨10.1093/biostatistics/kxv026⟩
Article dans une revue hal-02012377v1

Machine learning for in silico virtual screening and chemical genomics: new strategies.

 Jean-Philippe Vert , Laurent Jacob
Combinatorial Chemistry and High Throughput Screening, 2008, 11 (8), pp.677-85
Article dans une revue hal-00433569v1
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Clustered Multi-Task Learning: A Convex Formulation

 Laurent Jacob , Francis Bach , Jean-Philippe Vert
2008
Pré-publication, Document de travail hal-00320573v1

The cost of growing large: costs of post-weaning growth on body mass senescence in a wild mammal

 Frédéric Douhard , J.M. Gaillard , M. Pellerin , Laurent Jacob , Jean-François Lemaître
Oikos, 2017, 126 (9), pp.1329-1338. ⟨10.1111/oik.04421⟩
Article dans une revue hal-02049674v1
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Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows

 Elsa Bernard , Laurent Jacob , Julien Mairal , Jean-Philippe Vert
Bioinformatics, 2014, 30 (17), pp.2447-2455. ⟨10.1093/bioinformatics/btu317⟩
Article dans une revue hal-00803134v3
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A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples

 Elsa Bernard , Laurent Jacob , Julien Mairal , Eric Viara , Jean-Philippe Vert
BMC Bioinformatics, 2015, 16 (1), pp.262:1-10. ⟨10.1186/s12859-015-0695-9⟩
Article dans une revue hal-01123141v3
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Biological Sequence Modeling with Convolutional Kernel Networks

 Dexiong Chen , Laurent Jacob , Julien Mairal
Bioinformatics, 2019, 35 (18), pp.3294-3302. ⟨10.1093/bioinformatics/btz094⟩
Article dans une revue hal-01632912v3
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Virtual screening of GPCRs: An in silico chemogenomics approach

 Laurent Jacob , Brice Hoffmann , Véronique Stoven , Jean-Philippe Vert
BMC Bioinformatics, 2008, 9, pp.363. ⟨10.1186/1471-2105-9-363⟩
Article dans une revue hal-00220396v2
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Phyloformer: towards fast and accurate phylogeny estimation with self-attention networks

 Luca Nesterenko , Bastien Boussau , Laurent Jacob
2022
Pré-publication, Document de travail hal-03756990v1
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Epitope prediction improved by multitask support vector machines

 Laurent Jacob , Jean-Philippe Vert
2007
Autre publication scientifique hal-00129062v1

Hormonal pleiotropy and the evolution of allocation trade‐offs

 Salomé Bourg , Laurent Jacob , Frédéric Menu , Etienne Rajon
Evolution - International Journal of Organic Evolution, 2019, 73 (4), pp.661-674. ⟨10.1111/evo.13693⟩
Article dans une revue hal-02307231v1

Within-host genetic micro-diversity of Mycobacterium tuberculosis and the link with tuberculosis disease features

 Charlotte Genestet , Elisabeth Hodille , François Massol , Guislaine Refrégier , Alexia Barbry , et al.
2021
Pré-publication, Document de travail hal-03433572v1
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Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial

 Laurent Jacob , Anke Witteveen , Inès Beumer , Leonie Delahaye , Diederik Wehkamp , et al.
Communications Biology, 2020, 3, ⟨10.1038/s42003-020-1111-1⟩
Article dans une revue hal-02990043v1
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Recurrent Kernel Networks

 Dexiong Chen , Laurent Jacob , Julien Mairal
NeurIPS 2019 - Thirty-third Conference on Neural Information Processing Systems, Dec 2019, Vancouver, Canada
Communication dans un congrès hal-02151135v2
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Biological Sequence Modeling with Convolutional Kernel Networks

 Dexiong Chen , Laurent Jacob , Julien Mairal
RECOMB 2019 - 23rd Annual International Conference Research in Computational Molecular Biology, May 2019, Washington DC, United States. pp.292-293, ⟨10.1007/978-3-030-17083-7⟩
Communication dans un congrès hal-02388776v1
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Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity

 Charlotte Genestet , Guislaine Refrégier , Elisabeth Hodille , Rima Zein-Eddine , Adrien Le Meur , et al.
International Journal of Infectious Diseases, 2022, 125, pp.74-83. ⟨10.1016/j.ijid.2022.10.026⟩
Article dans une revue hal-03836738v1
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A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

 Magali Jaillard , Leandro Lima , Maud Tournoud , Pierre Mahé , Alex van Belkum , et al.
PLoS Genetics, 2018, 14 (11), pp.1-28. ⟨10.1371/journal.pgen.1007758⟩
Article dans une revue hal-01920359v1
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Search for a gene expression signature of breast cancer local recurrence in young women.

 Nicolas Servant , Marc Bollet , Hans Halfwerk , Kevin Bleakley , Bas Kreike , et al.
Clinical Cancer Research, 2012, 18 (6), pp.1704-15. ⟨10.1158/1078-0432.CCR-11-1954⟩
Article dans une revue hal-00756723v1
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More power via graph-structured tests for differential expression of gene networks

 Laurent Jacob , Pierre Neuvial , Sandrine Dudoit
Annals of Applied Statistics, 2012, 6 (2), pp.561-600. ⟨10.1214/11-AOAS528⟩
Article dans une revue hal-00521097v2
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Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis

 Thierry Wirth , Marine Bergot , Jean-Philippe Rasigade , Bruno Pichon , Maxime Barbier , et al.
Nature Microbiology, 2020, 5 (5), pp.735-745. ⟨10.1038/s41564-020-0676-2⟩
Article dans une revue hal-03056509v1
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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
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Immunosenescence patterns differ between populations but not between sexes in a long-lived mammal

 Louise Cheynel , Jean-François Lemaître , Jean-Michel Gaillard , Benjamin Rey , G. Bourgoin , et al.
Scientific Reports, 2017, 7 (1), ⟨10.1038/s41598-017-13686-5⟩
Article dans une revue hal-03225790v1
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