GECO Evolutionary and Computational Genomics

Baobab Group

Jacob Laurent

Chargé de recherche

CNRS

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 04 72 44 85 98

Email

Twitter

I am generally interested in developing statistical and machine learning methods to solve problems in molecular biology.

In particular, I have ongoing projects on :

  • GWAS for bacterial genomes and metagenomes, with collaborators at Pendulum and UC Berkeley.
  • Improving the inference of phylogenetic trees, with local collaborators at LBBE.
  • Predicting phenotypes from sequences using sparse learning and convolutional networks, with collaborators at Inria.

Publications

Display of 1 to 30 publications on 34 in total

Neural Networks beyond explainability: Selective inference for sequence motifs

Antoine Villié, Philippe Veber, Yohann de Castro, Laurent Jacob

Preprint

see the publication

Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity

Charlotte Genestet, Guislaine Refrégier, Elisabeth Hodille, Rima Zein-Eddine, Adrien Le Meur, Fiona Hak...

International Journal of Infectious Diseases . 125 : 74-83

DOI: 10.1016/j.ijid.2022.10.026

Journal article

see the publication

CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS

Hector Roux de Bézieux, Leandro Lima, Fanny Perraudeau, Arnaud Mary, Sandrine Dudoit, Laurent Jacob

Bioinformatics .

DOI: 10.1093/bioinformatics/btac238

Journal article

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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, Emilie Westeel...

DOI: 10.1101/2021.04.07.438754

Preprint

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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, Jeroen van den Akker...

Communications Biology . 3

DOI: 10.1038/s42003-020-1111-1

Journal article

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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, Patricia Martins-Simoes...

Nature Microbiology . 5 ( 5 ) : 735-745

DOI: 10.1038/s41564-020-0676-2

Journal article

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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 . 119 : 1576-1586

Conference paper

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Recurrent Kernel Networks

Dexiong Chen, Laurent Jacob, Julien Mairal

NeurIPS 2019 - Thirty-third Conference on Neural Information Processing Systems .

Conference paper

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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 . 11467 : 292-293

DOI: 10.1007/978-3-030-17083-7

Conference paper

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Hormonal pleiotropy and the evolution of allocation trade‐offs

Salomé Bourg, Laurent Jacob, Frédéric Menu, Etienne Rajon

Evolution - International Journal of Organic Evolution . 73 ( 4 ) : 661-674

DOI: 10.1111/evo.13693

Journal article

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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, Vincent Lacroix...

PLoS Genetics . 14 ( 11 ) : 1-28

DOI: 10.1371/journal.pgen.1007758

Journal article

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PEPA test: fast and powerful differential analysis from relative quantitative proteomics data using shared peptides

Laurent Jacob, Florence Combes, Thomas Burger

Biostatistics .

DOI: 10.1093/biostatistics/kxy021

Journal article

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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 . 19 ( 1 )

DOI: 10.1186/s13059-018-1481-6

Journal article

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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, Gilles Bourgoin, Hubert Ferté...

Scientific Reports . 7 ( 1 )

DOI: 10.1038/s41598-017-13686-5

Journal article

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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 . 126 ( 9 ) : 1329-1338

DOI: 10.1111/oik.04421

Journal article

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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 . 17 : 16-28

DOI: 10.1093/biostatistics/kxv026

Journal article

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Statistical methods for handling unwanted variation in metabolomics data

Alysha M. de Liyera, Marko Sysi Aho, Laurent Jacob, Johann A. Gagnon Bartsch, Sandra Castillo, Julie A. Simpson...

Analytical Chemistry . 87 ( 7 ) : 3606-3615

DOI: 10.1021/ac502439y

Journal article

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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 . 16 ( 1 ) : 262:1-10

DOI: 10.1186/s12859-015-0695-9

Journal article

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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 . 30 ( 17 ) : 2447-2455

DOI: 10.1093/bioinformatics/btu317

Journal article

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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 . 6 ( 2 ) : 561-600

DOI: 10.1214/11-AOAS528

Journal article

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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, Laurent Jacob...

Clinical Cancer Research . 18 ( 6 ) : 1704-15

DOI: 10.1158/1078-0432.CCR-11-1954

Journal article

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Group Lasso with Overlaps: the Latent Group Lasso approach

Guillaume Obozinski, Laurent Jacob, Jean-Philippe Vert

: 60

Report

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Increasing stability and interpretability of gene expression signatures

Anne-Claire Haury, Laurent Jacob, Jean-Philippe Vert

Preprint

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Structured priors for supervised learning in computational biology

Laurent Jacob

Thesis

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

Jean-Philippe Vert, Laurent Jacob

Combinatorial Chemistry and High Throughput Screening . 11 ( 8 ) : 677-85

Journal article

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