GECO Génomique Computationnelle et Evolutive

Jacob Laurent

Chargé de recherche

CNRS

Adresse : 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

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

Affichage des publications 1 à 30 sur 43 au total

CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS

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

DOI: 10.1101/2021.11.05.467462

2021

Pré-publication

voir la publication

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

2021

Pré-publication

voir la publication

SLIT2/ROBO signaling in tumor-associated microglia and macrophages drives glioblastoma immunosuppression and vascular dysmorphia

Luiz Geraldo, yunling Xu, Laurent Jacob, Laurence Pibouin-Fragner, Rohit Rao, Nawal Maissa...

The Journal of clinical investigation . 131 ( 16 )

DOI: 10.1172/JCI141083

2021

Article dans une revue

voir la publication

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

2020

Article dans une revue

voir la publication

Three-Dimensional Imaging of the Vertebral Lymphatic Vasculature and Drainage using iDISCO⁺ and Light Sheet Fluorescence Microscopy

Laurent Jacob, Jose Brito, Jean-Leon Thomas

Journal of visualized experiments : JoVE . ( 159 ) : e61099 |

DOI: 10.3791/61099

2020

Article dans une revue

voir la publication

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

2020

Article dans une revue

voir la publication

Convolutional Kernel Networks for Graph-Structured Data

Dexiong Chen, Laurent Jacob, Julien Mairal

ICML 2020 - 37th International Conference on Machine Learning . 119 : 1576-1586

2020

Acte de congrès

voir la publication

Recurrent Kernel Networks

Dexiong Chen, Laurent Jacob, Julien Mairal

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

2019

Acte de congrès

voir la publication

Biological Sequence Modeling with Convolutional Kernel Networks

Dexiong Chen, Laurent Jacob, Julien Mairal

Bioinformatics . 35 ( 18 ) : 3294–3302

DOI: 10.1093/bioinformatics/btz094

2019

Article dans une revue

voir la publication

An IgG-induced neutrophil activation pathway contributes to human drug-induced anaphylaxis

Friederike Jönsson, Luc de Chaisemartin, Vanessa Granger, Aurélie Gouel-Chéron, Caitlin Gillis, Qianqian Zhu...

Science Translational Medicine . 11 ( 500 ) : eaat1479

DOI: 10.1126/scitranslmed.aat1479

2019

Article dans une revue

voir la publication

RNA Profiling of the Human and Mouse Spinal Cord Stem Cell Niches Reveals an Embryonic-like Regionalization with MSX1+ Roof-Plate-Derived Cells

Hussein Ghazale, Chantal Ripoll, Nicolas Leventoux, Laurent Jacob, Safa Azar, Daria Mamaeva...

Current Stem Cell Reports . 12 ( 5 ) : 1159-1177

DOI: 10.1016/j.stemcr.2019.04.001

2019

Article dans une revue

voir la publication

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

2019

Acte de congrès

voir la publication

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

2019

Article dans une revue

voir la publication

Anatomy and function of the vertebral column lymphatic network in mice

Laurent Jacob, Ligia Simoes Braga Boisserand, Luiz Henrique Medeiros Geraldo, Jose de Brito Neto, Thomas Mathivet, Salli Antila...

Nature Communications . 10 : 4594

DOI: 10.1038/s41467-019-12568-w

2019

Article dans une revue

voir la publication

RNA Profiling of the Human and Mouse Spinal Cord Stem Cell Niches Reveals an Embryonic-like Regionalization with MSX1+ Roof-Plate-Derived Cells

Hussein Ghazale, Chantal Ripoll, Nicolas Leventoux, Laurent Jacob, Safa Azar, Daria Mamaeva...

Stem Cell Reports . 12 ( 5 ) : 1159-1177

DOI: 10.1016/j.stemcr.2019.04.001

2019

Article dans une revue

voir la publication

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

2018

Article dans une revue

voir la publication

Thoracic Epidural Analgesia and Mortality in Acute Pancreatitis A Multicenter Propensity Analysis

Matthieu Jabaudon, Nouria Belhadj-Tahar, Thomas Rimmelé, Olivier Joannes-Boyau, Stéphanie Bulyez, Jean-yves Lefrant...

Critical Care Medicine . 46 ( 3 ) : e198-e205

DOI: 10.1097/CCM.0000000000002874

2018

Article dans une revue

voir la publication

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

2018

Article dans une revue

voir la publication

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

2018

Article dans une revue

voir la publication

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

2017

Article dans une revue

voir la publication

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

2017

Article dans une revue

voir la publication

Acute kidney injury in the perioperative period and in intensive care units (excluding renal replacement therapies)

Carole Ichai, Christophe Vinsonneau, Bertrand Souweine, Fabien Armando, Emmanuel Canet, Christophe Clec’h...

Anaesthesia Critical Care & Pain Medicine . 35 ( 2 ) : 151-165

DOI: 10.1016/j.accpm.2016.03.004

2016

Article dans une revue

voir la publication

Inhibition of PlexA1-mediated brain tumor growth and tumor-associated angiogenesis using a transmembrane domain targeting peptide

Laurent Jacob, Paul Sawma, Norbert Garnier, Lionel A.T. Meyer, Justine Fritz, Thomas Hussenet...

Oncotarget .

DOI: 10.18632/oncotarget.11072

2016

Article dans une revue

voir la publication

Inhibition of primary breast tumor growth and metastasis using a neuropilin-1 transmembrane domain interfering peptide

Alexia Arpel, Coralie Gamper, Caroline Spenlé, Aurore Fernandez, Laurent Jacob, Nadège Baumlin...

Oncotarget . 7 ( 34 )

DOI: 10.18632/oncotarget.10101

2016

Article dans une revue

voir la publication

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

2016

Article dans une revue

voir la publication

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

2015

Article dans une revue

voir la publication

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

2015

Article dans une revue

voir la publication

Transmembrane Recognition of the Semaphorin Co-Receptors Neuropilin 1 and Plexin A1 : Coarse-Grained Simulations

Samia Aci-Sèche, Paul Sawma, Pierre Hubert, James N. Sturgis, Dominique Bagnard, Laurent Jacob...

PLoS ONE . 9 ( 5 ) : e97779

DOI: 10.1371/journal.pone.0097779

2014

Article dans une revue

voir la publication

Combining calls from multiple somatic mutation-callers

S. y. Kim, Laurent Jacob, T. P. Speed

BMC Bioinformatics . 15 : 154

DOI: 10.1186/1471-2105-15-154

2014

Article dans une revue

voir la publication

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

2014

Article dans une revue

voir la publication

Publications

CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS

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

SLIT2/ROBO signaling in tumor-associated microglia and macrophages drives glioblastoma immunosuppression and vascular dysmorphia

Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial

Three-Dimensional Imaging of the Vertebral Lymphatic Vasculature and Drainage using iDISCO+ and Light Sheet Fluorescence Microscopy

Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis

Convolutional Kernel Networks for Graph-Structured Data

Recurrent Kernel Networks

Biological Sequence Modeling with Convolutional Kernel Networks

An IgG-induced neutrophil activation pathway contributes to human drug-induced anaphylaxis

RNA Profiling of the Human and Mouse Spinal Cord Stem Cell Niches Reveals an Embryonic-like Regionalization with MSX1+ Roof-Plate-Derived Cells

Biological Sequence Modeling with Convolutional Kernel Networks

Hormonal pleiotropy and the evolution of allocation trade‐offs

Anatomy and function of the vertebral column lymphatic network in mice

RNA Profiling of the Human and Mouse Spinal Cord Stem Cell Niches Reveals an Embryonic-like Regionalization with MSX1+ Roof-Plate-Derived Cells

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

Thoracic Epidural Analgesia and Mortality in Acute Pancreatitis A Multicenter Propensity Analysis

The healthy ageing gene expression signature for Alzheimer’s disease diagnosis: a random sampling perspective

A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

Immunosenescence patterns differ between populations but not between sexes in a long-lived mammal

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

Acute kidney injury in the perioperative period and in intensive care units (excluding renal replacement therapies)

Inhibition of PlexA1-mediated brain tumor growth and tumor-associated angiogenesis using a transmembrane domain targeting peptide

Inhibition of primary breast tumor growth and metastasis using a neuropilin-1 transmembrane domain interfering peptide

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

Statistical methods for handling unwanted variation in metabolomics data

A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples

Transmembrane Recognition of the Semaphorin Co-Receptors Neuropilin 1 and Plexin A1 : Coarse-Grained Simulations

Combining calls from multiple somatic mutation-callers

Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows

Three-Dimensional Imaging of the Vertebral Lymphatic Vasculature and Drainage using iDISCO⁺ and Light Sheet Fluorescence Microscopy