Laurent Brehelin

Documents

Publications

	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 Nature Communications, 2021, 12, pp.1-18/3297. ⟨10.1038/s41467-021-23143-7⟩ Article dans une revue hal-03255754v1
	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 Nucleic Acids Research, 2021, 49 (5), pp.2488-2508. ⟨10.1093/nar/gkab053⟩ Article dans une revue hal-03253453v1
	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 PLoS Computational Biology, 2021, 17 (4), pp.e1008909. ⟨10.1371/journal.pcbi.1008909⟩ Article dans une revue hal-03253460v1
	Probing transcription factor combinatorics in different promoter classes and in enhancers Jimmy Vandel , Océane Cassan , Sophie Lèbre , Charles-Henri Lecellier , Laurent Brehelin BMC Genomics, 2019, 20 (103), ⟨10.1186/s12864-018-5408-0⟩ Article dans une revue hal-02070201v1
	Accounting for ambiguity in ancestral sequence reconstruction Adrien Oliva , Sylvain Pulicani , Vincent Lefort , Laurent Brehelin , Olivier Gascuel Bioinformatics, 2019, 35 (21), pp.4290-4297. ⟨10.1093/bioinformatics/btz249⟩ Article dans une revue pasteur-02404399v1
	Probing instructions for expression regulation in gene nucleotide compositions Chloé Bessière , May Taha , Florent Petitprez , Jimmy Vandel , Jean-Michel Marin PLoS Computational Biology, 2018, 14 (1), pp.e1005921. ⟨10.1371/journal.pcbi.1005921⟩ Article dans une revue lirmm-01744469v1
	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⟩ Article dans une revue lirmm-01744475v1
	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 PLoS ONE, 2014, 9 (6), pp.e95275. ⟨10.1371/journal.pone.0095275⟩ Article dans une revue pasteur-01060276v1
	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⟩ Article dans une revue hal-00701611v1
	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 Molecular BioSystems, 2012, 8 (8), pp.2023-35. ⟨10.1039/c2mb25067e⟩ Article dans une revue hal-00720135v1
	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⟩ Article dans une revue lirmm-00796453v1
	EuPathDomains: The Divergent Domain Database for Eukaryotic Pathogens Amel Ghouila , Nicolas Terrapon , Olivier Gascuel , Fatma Guerfali , Dhafer Laouini Infection, Genetics and Evolution, 2011, 11 (4), pp.698-707. ⟨10.1016/j.meegid.2010.09.008⟩ Article dans une revue lirmm-00540932v1
	Chemical inhibitors of monogalactosyldiacylglycerol synthases in Arabidopsis thaliana. Cyrille y Botté , Michael Deligny , Aymeric Roccia , Anne-Laure Bonneau , Nadia Saïdani Nature Chemical Biology, 2011, 7 (11), pp.834-842. ⟨10.1038/nchembio.658⟩ Article dans une revue hal-00636525v1
	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⟩ Article dans une revue lirmm-00540866v1
	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⟩ Article dans une revue hal-02659756v1
	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 BMC Genomics, 2009, 10, pp.235-252. ⟨10.1186/1471-2164-10-235⟩ Article dans une revue lirmm-00395282v1
	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⟩ Article dans une revue lirmm-00431171v1
	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 Nucleic Acids Research, 2009, 37 (15 e104), pp.11. ⟨10.1093/nar/gkp492⟩ Article dans une revue lirmm-00415899v1
	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 Cellular Oncology, 2009, 31 (2), pp.145-146 Article dans une revue lirmm-00416012v1
	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⟩ Article dans une revue lirmm-00327273v2
	Using repeated measurements to validate hierarchical gene clusters Laurent Brehelin , Olivier Gascuel , Olivier Martin Bioinformatics, 2008, 24 (5), pp.682-688. ⟨10.1093/bioinformatics/btn017⟩ Article dans une revue hal-04235625v1
	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⟩ Article dans une revue lirmm-00272116v1
	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 Article dans une revue 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 JOBIM 2021 - 21èmes Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2021, Paris, France Communication dans un congrès hal-03385869v1
	Modélisation de l'expression des gènes à partir de données de séquence ADN May Taha , Chloé Bessière , Florent Petitprez , Jimmy Vandel , Jean-Michel Marin JdS 2017, 49èmes Journées de Statistique de la SFdS, May 2017, Avignon, France Communication dans un congrès 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 Communication dans un congrès lirmm-01397412v1
	Recherche de motifs de régulation à l'aide de donner d'expression Laurent Brehelin SeqBio, Nov 2014, Montpellier, France Communication dans un congrès lirmm-01397396v1
	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 Communication dans un congrès lirmm-00725490v1
	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 Communication dans un congrès lirmm-00725501v1
	Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction Assays Nicolas Philippe , Anthony Boureux , Laurent Brehelin , Jorma Tarhio , Thérèse Commes SMPGD'09: Statistical Methods for Post-genomic Data Workshop, Jan 2009, Paris, France. pp.3 Communication dans un congrès lirmm-00375005v1
	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 Communication dans un congrès lirmm-00414954v1
	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 Communication dans un congrès lirmm-00195262v1
	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 Communication dans un congrès lirmm-00195493v1
	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 Communication dans un congrès lirmm-00195264v1
	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 Communication dans un congrès lirmm-00113353v1
	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 Communication dans un congrès lirmm-00120171v1
	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⟩ Communication dans un congrès lirmm-00327792v1
	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 Communication dans un congrès lirmm-00106135v1
	Une Approche Bayésienne pour la Classification de Cinétiques d'Expression de Gènes Laurent Brehelin JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jun 2004, Montreal, Canada Communication dans un congrès lirmm-00108938v1
	Outlier Detection in Gene Expression Data Improves Classification Accuracy Laurent Brehelin , F. Major IRIS Machine Learning Workshop, 2004 Communication dans un congrès lirmm-00108666v1

	Using positional information for predicting transcription factor binding sites Raphaël Romero , Christophe Menichelli , Jean-Michel Marin , Sophie Lèbre , Charles-Henri Lecellier SMPGD: Statistical Methods for Post Genomic Data, Jan 2019, Barcelone, Spain. Poster de conférence hal-02068254v1

	Optimizing data integration improves Gene Regulatory Network inference in Arabidopsis thaliana Océane Cassan , Charles Henri Lecellier , Antoine Martin , Laurent Brehelin , Sophie Lèbre 2023 Pré-publication, Document de travail hal-04228523v1
	Advancing regulatory genomics with machine learning Laurent Brehelin 2023 Pré-publication, Document de travail lirmm-04271442v1
	The Hippo pathway terminal effector TAZ/WWTR1 mediates oxaliplatin sensitivity in colon cancer cells Věra Slaninová , Lisa Heron-Milhavet , Mathilde Robin , Laura Jeanson , Diala Kantar 2023 Pré-publication, Document de travail lirmm-04299945v1
	Systematic analysis of the genomic features involved in the binding preferences of transcription factors Raphaël Romero , Christophe Menichelli , Jean-Michel Marin , Sophie Lèbre , Charles-Henri Lecellier 2022 Pré-publication, Document de travail hal-03796420v1
	Evidence of transcription at polyT short tandem repeats Chloé Bessiere , Manu Saraswat , Mathys Grapotte , Christophe Menichelli , Jordan A. Ramilowski 2021 Pré-publication, Document de travail hal-02404809v1
	Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes Christophe Menichelli , Vincent Guitard , Rafael Martins , Sophie Lèbre , José‑juan Lopez‑rubio 2020 Pré-publication, Document de travail hal-03024898v1
	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 2020 Pré-publication, Document de travail hal-03024896v1
	Modeling transcription factor combinatorics in promoters and enhancers Jimmy Vandel , Océane Cassan , Sophie Lèbre , Charles-Henri Lecellier , Laurent Brehelin 2018 Pré-publication, Document de travail hal-01821485v1

Laurent Brehelin

Publications

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers

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

Probing transcription factor combinatorics in different promoter classes and in enhancers

Accounting for ambiguity in ancestral sequence reconstruction

Probing instructions for expression regulation in gene nucleotide compositions

Improving pairwise comparison of protein sequences with domain co-occurrence

Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection

Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum.

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

Computational discovery of regulatory elements in a continuous expression space

EuPathDomains: The Divergent Domain Database for Eukaryotic Pathogens

Chemical inhibitors of monogalactosyldiacylglycerol synthases in Arabidopsis thaliana.

Assessing Functional Annotation Transfers with Inter-Species Conserved Coexpression: Application to Plasmodium Falciparum

Bioinformatic strategies to provide functional clues to the unknown genes in Plasmodium falciparum genome

A Plasmodium Falciparum FcB1-Schizont-EST Collection Providing Clues to Schizont Specific Gene Structure and Polymorphism

Detection of new protein domains using co-occurrence: application to Plasmodium falciparum

Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

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

PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data

Using repeated measurements to validate hierarchical gene clusters

Using Repeated Measurements to Validate Hierarchical Gene Clusters

A Bayesian Approach for the Clustering of Short Time Series

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

Modélisation de l'expression des gènes à partir de données de séquence ADN

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

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

Identification of Regulatory Elements from Gene Expression Data without Clustering

Fitting Hidden Markov Models of Protein Domains to a Target Species

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

Détection de nouveaux domaines protéiques par co-occurence : Application à P. falciparum

Bias and Benefit Induced by Intra-Species Paralogy in Guilt by Association Methods to Predict Protein Function

A new type of Hidden Markov Models to predict complex domain architecture in protein sequences

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

Bias and benefit induced by intra-species homologies in guilt by association methods to predict protein function

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

Clustering Gene Expression Series with Prior Knowledge

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

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

Outlier Detection in Gene Expression Data Improves Classification Accuracy

Using positional information for predicting transcription factor binding sites

Optimizing data integration improves Gene Regulatory Network inference in Arabidopsis thaliana

Advancing regulatory genomics with machine learning

The Hippo pathway terminal effector TAZ/WWTR1 mediates oxaliplatin sensitivity in colon cancer cells

Systematic analysis of the genomic features involved in the binding preferences of transcription factors

Evidence of transcription at polyT short tandem repeats

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

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Modeling transcription factor combinatorics in promoters and enhancers