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37

List of publications - Laurent Bréhélin


Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier   

Journal articles20 documents

  • Jimmy Vandel, Océane Cassan, Sophie Lebre, 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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, pp.35. ⟨10.1186/1471-2164-11-35⟩. ⟨hal-00468687⟩
  • 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, pp.273-283. ⟨lirmm-00544139⟩
  • 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⟩
  • 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 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⟩
  • N. Philippe, A. Boureux, Laurent Brehelin, J. Tarhio, T. 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), pp.e104. ⟨hal-00452377⟩
  • 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, 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. ⟨http://www.biomedcentral.com/1471-2105/9/440⟩. ⟨10.1186/1471-2105-9-440⟩. ⟨lirmm-00327273v2⟩
  • Laurent Brehelin, Olivier Gascuel, Olivier Martin. Using Repeated Measurements to Validate Hierarchical Gene Clusters. Bioinformatics, Oxford University Press (OUP), 2008, 24, pp.682-688. ⟨lirmm-00272116⟩
  • 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 papers15 documents

  • 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⟩
  • 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⟩
  • 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⟩
  • 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 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⟩
  • 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 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. Annual Workshop on Statistical Methods for Post Genomic Data, ⟨https://smpgd2019.sciencesconf.org/⟩. ⟨hal-02068254⟩

Preprints, Working Papers, ...1 document

  • Jimmy Vandel, Océane Cassan, Sophie Lèbre, Charles-Henri Lecellier, Laurent Brehelin. Modeling transcription factor combinatorics in promoters and enhancers. 2018. ⟨hal-01821485⟩