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44

List of publications - Laurent Bréhélin


Journal articles22 documents

  • Christophe Menichelli, Vincent Guitard, Rafael Miyazawa Martins, Sophie Lèbre, José Juan Lopez-Rubio, et al.. Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes. PLoS Computational Biology, Public Library of Science, 2021, 17 (4), pp.e1008909. ⟨10.1371/journal.pcbi.1008909⟩. ⟨hal-03253460⟩
  • Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A. Ramilowski, et al.. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, Nature Publishing Group, 2021, 12, pp.1-18. ⟨10.1038/s41467-021-23143-7⟩. ⟨hal-03255754⟩
  • Fabienne Bejjani, Claire Tolza, Mathias Boulanger, Damien Downes, Raphaël Romero, et al.. Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers. Nucleic Acids Research, Oxford University Press, 2021, 49 (5), pp.2488-2508. ⟨10.1093/nar/gkab053⟩. ⟨hal-03253453⟩
  • Jimmy Vandel, Océane Cassan, Sophie Lèbre, Charles-Henri Lecellier, Laurent Brehelin. Probing transcription factor combinatorics in different promoter classes and in enhancers. BMC Genomics, BioMed Central, 2019, 20 (103), ⟨10.1186/s12864-018-5408-0⟩. ⟨hal-02070201⟩
  • Adrien Oliva, Sylvain Pulicani, Vincent Lefort, Laurent Brehelin, Olivier Gascuel, et al.. Accounting for ambiguity in ancestral sequence reconstruction. Bioinformatics, Oxford University Press (OUP), 2019, 35 (21), pp.4290-4297. ⟨10.1093/bioinformatics/btz249⟩. ⟨pasteur-02404399⟩
  • Christophe Menichelli, Olivier Gascuel, Laurent Brehelin. Improving pairwise comparison of protein sequences with domain co-occurrence. PLoS Computational Biology, Public Library of Science, 2018, 14 (1), pp.e1005889. ⟨10.1371/journal.pcbi.1005889⟩. ⟨lirmm-01744475⟩
  • Chloé Bessière, May Taha, Florent Petitprez, Jimmy Vandel, Jean-Michel Marin, et al.. Probing instructions for expression regulation in gene nucleotide compositions. PLoS Computational Biology, Public Library of Science, 2018, 14 (1), pp.e1005921. ⟨10.1371/journal.pcbi.1005921⟩. ⟨lirmm-01744469⟩
  • Amel Ghouila, Isabelle Florent, Fatma Zahra Guerfali, Nicolas Terrapon, Dhafer Laouini, et al.. Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection. PLoS ONE, Public Library of Science, 2014, 9 (6), pp.e95275. ⟨10.1371/journal.pone.0095275⟩. ⟨pasteur-01060276⟩
  • Mathieu Lajoie, Olivier Gascuel, Vincent Lefort, Laurent Brehelin. Computational discovery of regulatory elements in a continuous expression space. Genome Biology, BioMed Central, 2012, 13 (11), pp.41. ⟨lirmm-00796453⟩
  • Nicolas Terrapon, Olivier Gascuel, Eric Marechal, Laurent Brehelin. Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum.. BMC Bioinformatics, BioMed Central, 2012, 13 (1), pp.67. ⟨10.1186/1471-2105-13-67⟩. ⟨hal-00701611⟩
  • Laurence Boudière, Cyrille y Botté, Nadia Saidani, Mathieu Lajoie, Jessica Marion, et al.. Galvestine-1, a novel chemical probe for the study of the glycerolipid homeostasis system in plant cells.. Molecular BioSystems, Royal Society of Chemistry, 2012, 8 (8), pp.2023-35. ⟨10.1039/c2mb25067e⟩. ⟨hal-00720135⟩
  • Cyrille y Botté, Michael Deligny, Aymeric Roccia, Anne-Laure Bonneau, Nadia Saïdani, et al.. Chemical inhibitors of monogalactosyldiacylglycerol synthases in Arabidopsis thaliana.. Nature Chemical Biology, Nature Publishing Group, 2011, 7 (11), pp.834-842. ⟨10.1038/nchembio.658⟩. ⟨hal-00636525⟩
  • Amel Ghouila, Nicolas Terrapon, Olivier Gascuel, Fatma Guerfali, Dhafer Laouini, et al.. EuPathDomains: The Divergent Domain Database for Eukaryotic Pathogens. Infection, Genetics and Evolution, Elsevier, 2011, 11 (4), pp.698-707. ⟨10.1016/j.meegid.2010.09.008⟩. ⟨lirmm-00540932⟩
  • Laurent Brehelin, Isabelle Florent, Olivier Gascuel, Eric Maréchal. Assessing Functional Annotation Transfers with Inter-Species Conserved Coexpression: Application to Plasmodium Falciparum. BMC Genomics, BioMed Central, 2010, 11 (35), pp.1471-2164. ⟨10.1186/1471-2164-11-35⟩. ⟨lirmm-00540866⟩
  • Isabelle Florent, Eric Maréchal, Olivier Gascuel, Laurent Brehelin. Bioinformatic strategies to provide functional clues to the unknown genes in Plasmodium falciparum genome. Parasite, EDP Sciences, 2010, 17 (4), pp.273-283. ⟨10.1051/parasite/2010174273⟩. ⟨hal-02659756⟩
  • Isabelle Florent, Betina M Porcel, Elodie Guillaume, Corinne da Silva, François Artiguenave, et al.. A Plasmodium Falciparum FcB1-Schizont-EST Collection Providing Clues to Schizont Specific Gene Structure and Polymorphism. BMC Genomics, BioMed Central, 2009, 10, pp.235-252. ⟨10.1186/1471-2164-10-235⟩. ⟨lirmm-00395282⟩
  • Nicolas Philippe, Anthony Boureux, Laurent Brehelin, Jorma Tarhio, Thérèse Commes, et al.. Estimation of sequence errors and capacity of genomic annotation in transcriptomic and DNA-protein interaction assays based on next generation sequencers. Cellular Oncology, IOS Press, 2009, 31 (2), pp.145-146. ⟨lirmm-00416012⟩
  • Nicolas Terrapon, Olivier Gascuel, Eric Maréchal, Laurent Brehelin. Detection of new protein domains using co-occurrence: application to Plasmodium falciparum. Bioinformatics, Oxford University Press (OUP), 2009, 25, pp.3077-83. ⟨10.1093/bioinformatics/btp560⟩. ⟨lirmm-00431171⟩
  • Nicolas Philippe, Anthony Boureux, Laurent Brehelin, Jorma Tarhio, Thérèse Commes, et al.. Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Research, Oxford University Press, 2009, 37 (15 e104), pp.11. ⟨10.1093/nar/gkp492⟩. ⟨lirmm-00415899⟩
  • Laurent Brehelin, Olivier Gascuel, Olivier C. Martin. Using Repeated Measurements to Validate Hierarchical Gene Clusters. Bioinformatics, Oxford University Press (OUP), 2008, 24 (5), pp.682-688. ⟨lirmm-00272116⟩
  • Laurent Brehelin, Jean-François Dufayard, Olivier Gascuel. PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data. BMC Bioinformatics, BioMed Central, 2008, 9, pp.9:440. ⟨10.1186/1471-2105-9-440⟩. ⟨lirmm-00327273v2⟩
  • Laurent Brehelin. A Bayesian Approach for the Clustering of Short Time Series. Revue des Sciences et Technologies de l'Information - Série RIA : Revue d'Intelligence Artificielle, Lavoisier, 2006, 20, pp.697-716. ⟨lirmm-00113350⟩

Conference papers17 documents

  • Raphaël Romero, Jean-Michel Marin, Sophie Lèbre, Charles-Henri Lecellier, Laurent Brehelin. A systematic analysis of the genomic features involved in specificities of transcription factor binding. JOBIM 2021 - 21èmes Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2021, Paris, France. ⟨hal-03385869⟩
  • May Taha, Chloé Bessière, Florent Petitprez, Jimmy Vandel, Jean-Michel Marin, et al.. Modélisation de l'expression des gènes à partir de données de séquence ADN. JdS 2017, 49èmes Journées de Statistique de la SFdS, May 2017, Avignon, France. ⟨hal-02068289⟩
  • Laurent Brehelin. Méthodes bioinformatiques pour la prédiction de la fonction des gènes : identification des domaines protéiques dans les génomes de pathogènes. JFMPM: Journées Franco-Maghrébines de Parasitologie-Mycologie, Oct 2015, Tunis, Tunisie. ⟨lirmm-01397412⟩
  • Laurent Brehelin. Recherche de motifs de régulation à l'aide de donner d'expression. SeqBio, Nov 2014, Montpellier, France. ⟨lirmm-01397396⟩
  • Nicolas Terrapon, Olivier Gascuel, Laurent Brehelin. Fitting Hidden Markov Models of Protein Domains to a Target Species. JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jun 2011, Paris, France. pp.193-194. ⟨lirmm-00725501⟩
  • Mathieu Lajoie, Olivier Gascuel, Laurent Brehelin. Identification of Regulatory Elements from Gene Expression Data without Clustering. JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jun 2011, Paris, France. pp.89-90. ⟨lirmm-00725490⟩
  • Nicolas Terrapon, Olivier Gascuel, Laurent Brehelin. Détection de nouveaux domaines protéiques par co-occurence : Application à P. falciparum. JOBIM'09 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.43-48. ⟨lirmm-00414954⟩
  • Nicolas Philippe, Anthony Boureux, Laurent Brehelin, Jorma Tarhio, Thérèse Commes, et al.. Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction Assays. SMPGD'09: Statistical Methods for Post-genomic Data Workshop, Jan 2009, Paris, France. pp.3. ⟨lirmm-00375005⟩
  • Laurent Brehelin, Olivier Gascuel. GONNA: a Gene Ontology Nearest Neighbor Approach for the Functional Prediction of P.falciparum Orphan Genes. International Conference on the Bioinformatics of African Pathogens and Disease Vectors, May 2007, Nairobi, Kenya. ⟨lirmm-00195264⟩
  • Laurent Brehelin, Olivier Gascuel. Bias and Benefit Induced by Intra-Species Paralogy in Guilt by Association Methods to Predict Protein Function. SMPGD'07: Statistical Methods for Post-Genomic Data, Jan 2007, Paris, France. ⟨lirmm-00195262⟩
  • Raluca Uricaru, Laurent Brehelin, Eric Rivals. A new type of Hidden Markov Models to predict complex domain architecture in protein sequences. JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2007, Marseille, France. pp.97-102. ⟨lirmm-00195493⟩
  • Raluca Uricaru, Laurent Brehelin, Eric Rivals. A new type of Hidden Markov Models to predict complex motif organization in protein sequences. Integrative Post-Genomics, 2006, Lyon, pp.43. ⟨lirmm-00120171⟩
  • Laurent Brehelin, Olivier Gascuel. Bias and benefit induced by intra-species homologies in guilt by association methods to predict protein function. JOBIM'06 : Journées ouvertes de Biologie, Informatique, Mathématiques, Jul 2006, pp.59-66. ⟨lirmm-00113353⟩
  • Laurent Brehelin, Olivier C. Martin. Evaluation des Classes d'une Hiérarchie par la Prise en Compte des Répétitions Expérimentales. JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2005, Lyon, France. pp.125-134. ⟨lirmm-00106135⟩
  • Laurent Brehelin. Clustering Gene Expression Series with Prior Knowledge. WABI'05: 5th International Workshop on Algorithms in Bioinformatics, Oct 2005, Mallorca, Spain. pp.27-38, ⟨10.1007/11557067_3⟩. ⟨lirmm-00327792⟩
  • Laurent Brehelin, F. Major. Outlier Detection in Gene Expression Data Improves Classification Accuracy. IRIS Machine Learning Workshop, 2004. ⟨lirmm-00108666⟩
  • Laurent Brehelin. Une Approche Bayésienne pour la Classification de Cinétiques d'Expression de Gènes. JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jun 2004, Montreal, Canada. ⟨lirmm-00108938⟩

Poster communications1 document

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

Preprints, Working Papers, ...4 documents

  • Chloé Bessiere, Manu Saraswat, Mathys Grapotte, Christophe Menichelli, Jordan A. Ramilowski, et al.. Evidence of transcription at polyT short tandem repeats. 2021. ⟨hal-02404809⟩
  • Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A. Ramilowski, et al.. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. 2020. ⟨hal-03024896⟩
  • Christophe Menichelli, Vincent Guitard, Rafael Martins, Sophie Lèbre, José‑juan Lopez‑rubio, et al.. Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes. 2020. ⟨hal-03024898⟩
  • Jimmy Vandel, Océane Cassan, Sophie Lèbre, Charles-Henri Lecellier, Laurent Brehelin. Modeling transcription factor combinatorics in promoters and enhancers. 2018. ⟨hal-01821485⟩