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Laurent Brehelin



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Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes

Christophe Menichelli , Vincent Guitard , Rafael Miyazawa Martins , Sophie Lèbre , José Juan Lopez-Rubio et al.
PLoS Computational Biology, 2021, 17 (4), pp.e1008909. ⟨10.1371/journal.pcbi.1008909⟩
Journal articles hal-03253460v1
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Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers

Fabienne Bejjani , Claire Tolza , Mathias Boulanger , Damien Downes , Raphaël Romero et al.
Nucleic Acids Research, 2021, 49 (5), pp.2488-2508. ⟨10.1093/nar/gkab053⟩
Journal articles hal-03253453v1
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Mathys Grapotte , Manu Saraswat , Chloé Bessière , Christophe Menichelli , Jordan A. Ramilowski et al.
Nature Communications, 2021, 12, pp.1-18/3297. ⟨10.1038/s41467-021-23143-7⟩
Journal articles hal-03255754v1
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Accounting for ambiguity in ancestral sequence reconstruction

Adrien Oliva , Sylvain Pulicani , Vincent Lefort , Laurent Brehelin , Olivier Gascuel et al.
Bioinformatics, 2019, 35 (21), pp.4290-4297. ⟨10.1093/bioinformatics/btz249⟩
Journal articles pasteur-02404399v1
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Probing transcription factor combinatorics in different promoter classes and in enhancers

Jimmy Vandel , Océane Cassan , Sophie Lèbre , Charles-Henri Lecellier , Laurent Brehelin et al.
BMC Genomics, 2019, 20 (103), ⟨10.1186/s12864-018-5408-0⟩
Journal articles hal-02070201v1
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Improving pairwise comparison of protein sequences with domain co-occurrence

Christophe Menichelli , Olivier Gascuel , Laurent Brehelin
PLoS Computational Biology, 2018, 14 (1), pp.e1005889. ⟨10.1371/journal.pcbi.1005889⟩
Journal articles lirmm-01744475v1
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Probing instructions for expression regulation in gene nucleotide compositions

Chloé Bessière , May Taha , Florent Petitprez , Jimmy Vandel , Jean-Michel Marin et al.
PLoS Computational Biology, 2018, 14 (1), pp.e1005921. ⟨10.1371/journal.pcbi.1005921⟩
Journal articles lirmm-01744469v1
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Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection

Amel Ghouila , Isabelle Florent , Fatma Zahra Guerfali , Nicolas Terrapon , Dhafer Laouini et al.
PLoS ONE, 2014, 9 (6), pp.e95275. ⟨10.1371/journal.pone.0095275⟩
Journal articles pasteur-01060276v1
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Computational discovery of regulatory elements in a continuous expression space

Mathieu Lajoie , Olivier Gascuel , Vincent Lefort , Laurent Brehelin
Genome Biology, 2012, 13 (11), pp.41. ⟨10.1186/gb-2012-13-11-r109⟩
Journal articles lirmm-00796453v1

Galvestine-1, a novel chemical probe for the study of the glycerolipid homeostasis system in plant cells.

Laurence Boudière , Cyrille y Botté , Nadia Saidani , Mathieu Lajoie , Jessica Marion et al.
Molecular BioSystems, 2012, 8 (8), pp.2023-35. ⟨10.1039/c2mb25067e⟩
Journal articles hal-00720135v1
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Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum.

Nicolas Terrapon , Olivier Gascuel , Eric Marechal , Laurent Brehelin
BMC Bioinformatics, 2012, 13 (1), pp.67. ⟨10.1186/1471-2105-13-67⟩
Journal articles hal-00701611v1

Chemical inhibitors of monogalactosyldiacylglycerol synthases in Arabidopsis thaliana.

Cyrille y Botté , Michael Deligny , Aymeric Roccia , Anne-Laure Bonneau , Nadia Saïdani et al.
Nature Chemical Biology, 2011, 7 (11), pp.834-842. ⟨10.1038/nchembio.658⟩
Journal articles hal-00636525v1
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EuPathDomains: The Divergent Domain Database for Eukaryotic Pathogens

Amel Ghouila , Nicolas Terrapon , Olivier Gascuel , Fatma Guerfali , Dhafer Laouini et al.
Infection, Genetics and Evolution, 2011, 11 (4), pp.698-707. ⟨10.1016/j.meegid.2010.09.008⟩
Journal articles lirmm-00540932v1
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Bioinformatic strategies to provide functional clues to the unknown genes in Plasmodium falciparum genome

Isabelle Florent , Eric Maréchal , Olivier Gascuel , Laurent Brehelin
Parasite, 2010, 17 (4), pp.273-283. ⟨10.1051/parasite/2010174273⟩
Journal articles hal-02659756v1
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Assessing Functional Annotation Transfers with Inter-Species Conserved Coexpression: Application to Plasmodium Falciparum

Laurent Brehelin , Isabelle Florent , Olivier Gascuel , Eric Maréchal
BMC Genomics, 2010, 11 (35), pp.1471-2164. ⟨10.1186/1471-2164-11-35⟩
Journal articles lirmm-00540866v1
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A Plasmodium Falciparum FcB1-Schizont-EST Collection Providing Clues to Schizont Specific Gene Structure and Polymorphism

Isabelle Florent , Betina M Porcel , Elodie Guillaume , Corinne da Silva , François Artiguenave et al.
BMC Genomics, 2009, 10, pp.235-252. ⟨10.1186/1471-2164-10-235⟩
Journal articles lirmm-00395282v1

Estimation of sequence errors and capacity of genomic annotation in transcriptomic and DNA-protein interaction assays based on next generation sequencers

Nicolas Philippe , Anthony Boureux , Laurent Brehelin , Jorma Tarhio , Thérèse Commes et al.
Cellular Oncology, 2009, 31 (2), pp.145-146
Journal articles lirmm-00416012v1
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Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

Nicolas Philippe , Anthony Boureux , Laurent Brehelin , Jorma Tarhio , Thérèse Commes et al.
Nucleic Acids Research, 2009, 37 (15 e104), pp.11. ⟨10.1093/nar/gkp492⟩
Journal articles lirmm-00415899v1
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Detection of new protein domains using co-occurrence: application to Plasmodium falciparum

Nicolas Terrapon , Olivier Gascuel , Eric Maréchal , Laurent Brehelin
Bioinformatics, 2009, 25, pp.3077-83. ⟨10.1093/bioinformatics/btp560⟩
Journal articles lirmm-00431171v1
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Using Repeated Measurements to Validate Hierarchical Gene Clusters

Laurent Brehelin , Olivier Gascuel , Olivier C. Martin
Bioinformatics, 2008, 24 (5), pp.682-688. ⟨10.1093/bioinformatics/btn017⟩
Journal articles lirmm-00272116v1
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PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data

Laurent Brehelin , Jean-François Dufayard , Olivier Gascuel
BMC Bioinformatics, 2008, 9, pp.9:440. ⟨10.1186/1471-2105-9-440⟩
Journal articles lirmm-00327273v2

A Bayesian Approach for the Clustering of Short Time Series

Laurent Brehelin
Revue des Sciences et Technologies de l'Information - Série RIA : Revue d'Intelligence Artificielle, 2006, 20, pp.697-716
Journal articles lirmm-00113350v1

A systematic analysis of the genomic features involved in specificities of transcription factor binding

Raphaël Romero , Jean-Michel Marin , Sophie Lèbre , Charles-Henri Lecellier , Laurent Brehelin et al.
JOBIM 2021 - 21èmes Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2021, Paris, France
Conference papers hal-03385869v1
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Modélisation de l'expression des gènes à partir de données de séquence ADN

May Taha , Chloé Bessière , Florent Petitprez , Jimmy Vandel , Jean-Michel Marin et al.
JdS 2017, 49èmes Journées de Statistique de la SFdS, May 2017, Avignon, France
Conference papers hal-02068289v1

Méthodes bioinformatiques pour la prédiction de la fonction des gènes : identification des domaines protéiques dans les génomes de pathogènes

Laurent Brehelin
JFMPM: Journées Franco-Maghrébines de Parasitologie-Mycologie, Oct 2015, Tunis, Tunisie
Conference papers lirmm-01397412v1

Recherche de motifs de régulation à l'aide de donner d'expression

Laurent Brehelin
SeqBio, Nov 2014, Montpellier, France
Conference papers lirmm-01397396v1

Fitting Hidden Markov Models of Protein Domains to a Target Species

Nicolas Terrapon , Olivier Gascuel , Laurent Brehelin
JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jun 2011, Paris, France. pp.193-194
Conference papers lirmm-00725501v1

Identification of Regulatory Elements from Gene Expression Data without Clustering

Mathieu Lajoie , Olivier Gascuel , Laurent Brehelin
JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jun 2011, Paris, France. pp.89-90
Conference papers lirmm-00725490v1
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Détection de nouveaux domaines protéiques par co-occurence : Application à P. falciparum

Nicolas Terrapon , Olivier Gascuel , Laurent Brehelin
JOBIM'09 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.43-48
Conference papers lirmm-00414954v1

Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction Assays

Nicolas Philippe , Anthony Boureux , Laurent Brehelin , Jorma Tarhio , Thérèse Commes et al.
SMPGD'09: Statistical Methods for Post-genomic Data Workshop, Jan 2009, Paris, France. pp.3
Conference papers lirmm-00375005v1

GONNA: a Gene Ontology Nearest Neighbor Approach for the Functional Prediction of P.falciparum Orphan Genes

Laurent Brehelin , Olivier Gascuel
International Conference on the Bioinformatics of African Pathogens and Disease Vectors, May 2007, Nairobi, Kenya
Conference papers lirmm-00195264v1
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A new type of Hidden Markov Models to predict complex domain architecture in protein sequences

Raluca Uricaru , Laurent Brehelin , Eric Rivals
JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2007, Marseille, France. pp.97-102
Conference papers lirmm-00195493v1
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Bias and Benefit Induced by Intra-Species Paralogy in Guilt by Association Methods to Predict Protein Function

Laurent Brehelin , Olivier Gascuel
SMPGD'07: Statistical Methods for Post-Genomic Data, Jan 2007, Paris, France
Conference papers lirmm-00195262v1

A new type of Hidden Markov Models to predict complex motif organization in protein sequences

Raluca Uricaru , Laurent Brehelin , Eric Rivals
Integrative Post-Genomics, 2006, Lyon, pp.43
Conference papers lirmm-00120171v1
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Bias and benefit induced by intra-species homologies in guilt by association methods to predict protein function

Laurent Brehelin , Olivier Gascuel
JOBIM'06 : Journées ouvertes de Biologie, Informatique, Mathématiques, Jul 2006, pp.59-66
Conference papers lirmm-00113353v1

Evaluation des Classes d'une Hiérarchie par la Prise en Compte des Répétitions Expérimentales

Laurent Brehelin , Olivier C. Martin
JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2005, Lyon, France. pp.125-134
Conference papers lirmm-00106135v1
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Clustering Gene Expression Series with Prior Knowledge

Laurent Brehelin
WABI'05: 5th International Workshop on Algorithms in Bioinformatics, Oct 2005, Mallorca, Spain. pp.27-38, ⟨10.1007/11557067_3⟩
Conference papers lirmm-00327792v1

Une Approche Bayésienne pour la Classification de Cinétiques d'Expression de Gènes

Laurent Brehelin
JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jun 2004, Montreal, Canada
Conference papers lirmm-00108938v1

Outlier Detection in Gene Expression Data Improves Classification Accuracy

Laurent Brehelin , F. Major
IRIS Machine Learning Workshop, 2004
Conference papers lirmm-00108666v1