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Etienne Birmelé


Journal articles23 documents

  • Margot Correa, Emmanuelle Lerat, Etienne E. Birmelé, Franck Samson, Bérengère Bouillon, et al.. The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2021, 13 (5), ⟨10.1093/gbe/evab062⟩. ⟨hal-03367114⟩
  • Juliana Alves Pegoraro, Sophie Lavault, Nicolas Wattiez, Thomas Similowski, Jésus Gonzalez-Bermejo, et al.. Machine-learning based feature selection for a non-invasive breathing change detection. BioData Mining, BioMed Central, 2021, 14 (1), ⟨10.1186/s13040-021-00265-8⟩. ⟨hal-03292741⟩
  • Magali Champion, Julien Chiquet, Pierre Neuvial, Mohamed Elati, François Radvanyi, et al.. Identification of Deregulated Mechanisms Specific to Bladder Cancer Subtypes. Journal of Bioinformatics and Computational Biology, World Scientific Publishing, 2021, 19 (1), ⟨10.1142/S0219720021400035⟩. ⟨hal-03079966⟩
  • Einar Holsbø, Vittorio Perduca, Lars Ailo Ailo Bongo, Eiliv Lund, Etienne Birmele. Predicting breast cancer metastasis from whole-blood transcriptomic measurements. BMC Research Notes, BioMed Central, 2020, 13 (1), ⟨10.1186/s13104-020-05088-0⟩. ⟨hal-02872374⟩
  • Etienne Birmele, Fabien de Montgolfier, Léo Planche. On the Minimum Eccentricity Isometric Cycle Problem. Electronic Notes in Theoretical Computer Science, Elsevier, 2019, 346, pp.159-169. ⟨10.1016/j.entcs.2019.08.015⟩. ⟨hal-02430756⟩
  • Thomas Picchetti, Julien Chiquet, Mohamed Elati, Pierre Neuvial, Rémy Nicolle, et al.. A model for gene deregulation detection using expression data. BMC Systems Biology, BioMed Central, 2015, 9, ⟨10.1186/1752-0509-9-S6-S6⟩. ⟨hal-01154154v2⟩
  • Paulo Vieira Milreu, Cecilia Coimbra Klein, Ludovic Cottret, Vicente Acuña, Etienne E. Birmelé, et al.. Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. Bioinformatics, Oxford University Press (OUP), 2014, 30 (1), pp.61-70. ⟨10.1093/bioinformatics/btt597⟩. ⟨hal-00922567⟩
  • Pierre Latouche, Etienne E. Birmelé, Christophe Ambroise. Model Selection in Overlapping Stochastic Block Models. Electronic Journal of Statistics , Shaker Heights, OH : Institute of Mathematical Statistics, 2014, 8, pp.762-794. ⟨10.1214/14-EJS903⟩. ⟨hal-00990277⟩
  • Pierre Latouche, Etienne E. Birmelé, Christophe Ambroise. Variational Bayesian Inference and Complexity Control for Stochastic Block Models. Statistical Modelling, SAGE Publications, 2012, 12 (1), pp.93-115. ⟨10.1177/1471082X1001200105⟩. ⟨hal-00624536⟩
  • Vicente Acuña, Etienne Birmelé, Ludovic Cottret, Pierluigi Crescenzi, Fabien Jourdan, et al.. Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets. Theoretical Computer Science, Elsevier, 2012, 457, pp.1--9. ⟨10.1016/j.tcs.2012.07.023⟩. ⟨hal-00764025⟩
  • Etienne Birmele. Detecting local network motifs. Electronic Journal of Statistics , Shaker Heights, OH : Institute of Mathematical Statistics, 2012, 6, pp.908-933. ⟨10.1214/12-EJS698⟩. ⟨hal-00726215⟩
  • Etienne Birmele, François Delbot, Christian Laforest. Analyse du nombre de perturbations lors du maintien d'un arbre de connexion de faible diamètre. Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, Lavoisier, 2011, 30 (7), pp.781--808. ⟨10.3166/tsi.30.781-808⟩. ⟨hal-00730900⟩
  • Pierre Latouche, Etienne Birmelé, Christophe Ambroise. OVERLAPPING STOCHASTIC BLOCK MODELS WITH APPLICATION TO THE FRENCH POLITICAL BLOGOSPHERE. Annals of Applied Statistics, Institute of Mathematical Statistics, 2011, 5 (1), pp.309 - 336. ⟨10.1214/10-AOAS382⟩. ⟨hal-02652556⟩
  • Etienne Birmele. A scale-free graph model based on bipartite graphs. Discrete Applied Mathematics, Elsevier, 2009, 157 (10), pp.2267-2284. ⟨10.1016/j.dam.2008.06.052⟩. ⟨hal-00730793⟩
  • Etienne Birmele, Adrian Bondy, Bruce Reed. Tree-width of graphs without a 3 by 3 graph minor. Discrete Applied Mathematics, Elsevier, 2009, 157 (12), pp.2577-2596. ⟨hal-00730791⟩
  • Etienne Birmele, François Delbot, Christian Laforest. Mean analysis of an online algorithm for the vertex cover problem. Information Processing Letters, Elsevier, 2009, 109 (9), pp.436--439. ⟨10.1016/j.ipl.2008.12.021⟩. ⟨hal-00730897⟩
  • Etienne Birmele. Every longest circuit of a $3$-connected, $K_ {3,3}$-minor free graph has a chord. Journal of Graph Theory, Wiley, 2008, pp.293-298. ⟨hal-00730767⟩
  • Etienne Birmele, Mohamed Elati, Céline Rouveirol, Christophe Ambroise. Identification of functional modules based on transcriptional regulation structure. BMC Proceedings, BioMed Central, 2008, 2 (4), pp.S4. ⟨hal-00730904⟩
  • Etienne Birmele, Adrian Bondy, Bruce Reed. The Erdos-Posa property for long circuits. Combinatorica, Springer Verlag, 2007, pp.135-145. ⟨hal-00730773⟩
  • C. Matias, Sophie S. Schbath, Etienne Birmelé, Jean-Jacques J.-J. Daudin, Stephane S. Robin. Network motifs : mean and variance for the count. REVSTAT - Statistical Journal, Instituto Nacional de Estatistica, 2006, 4 (1), pp.31-51. ⟨hal-02655236⟩
  • Catherine Matias, Sophie Schbath, Etienne E. Birmelé, Jj Daudin, Stéphane Robin. Networks motifs: mean and variance for the count. REVSTAT - Statistical Journal, Instituto Nacional de Estatistica, 2006, 4 (1), pp.31-51. ⟨hal-00730901⟩
  • Stéphane Bessy, Etienne E. Birmelé, Frédéric Havet. Arc-chromatic number of digraphs in which every vertex has bounded outdegree or bounded indegree. Journal of Graph Theory, Wiley, 2006, 53 (4), pp.315-332. ⟨10.1002/jgt.20189⟩. ⟨lirmm-00153978⟩
  • Etienne Birmele. Tree-width and circumference of graphs. Journal of Graph Theory, Wiley, 2003, pp.24-25. ⟨hal-00730764⟩

Conference papers13 documents

  • Magali Champion, Julien Chiquet, Pierre Neuvial, Mohamed Elati, François Radvanyi, et al.. Identification of deregulated transcription factors involved in subtypes of cancers. Proceedings of the 12th International Conference on Bioinformatics and Computational Biology, Mar 2020, SAN FRANCISCO, United States. pp.1--10, ⟨10.29007/v7qj⟩. ⟨hal-01516892v2⟩
  • Etienne E. Birmelé, Fabien de Montgolfier, Léo Planche, Laurent Viennot. Decomposing a Graph into Shortest Paths with Bounded Eccentricity. 28th International Symposium on Algorithms and Computation (ISAAC 2017), Dec 2017, Phuket, Thailand. ⟨10.4230/LIPIcs.ISAAC.2017.15⟩. ⟨hal-01671718⟩
  • Etienne E. Birmelé, Fabien de Montgolfier, Léo Planche. Minimum Eccentricity Shortest Path Problem: An Approximation Algorithm and Relation with the k-Laminarity Problem. COCOA 2016, Combinatorial Optimization and Applications - 10th International Conference, Dec 2016, Hong Kong, China. pp.216 - 229, ⟨10.1007/978-3-319-48749-6_16⟩. ⟨hal-01424469⟩
  • Ricardo Andrade, Etienne E. Birmelé, Arnaud Mary, Thomas Picchetti, Marie-France Sagot. Incremental complexity of a bi-objective hypergraph transversal problem. Fundamentals of Computation Theory (FCT2015), Aug 2015, Gdansk, Poland. pp.202-213, ⟨10.1007/978-3-319-22177-9_16⟩. ⟨hal-01149392⟩
  • Etienne E. Birmelé, Rui Ferreira, Roberto Grossi, Andrea Marino, Nadia Pisanti, et al.. Optimal Listing of Cycles and st-Paths in Undirected Graphs. 24th Annual ACM-SIAM Symposium on Discrete Algorithms, Jan 2013, New Orleans, United States. ⟨hal-00751345⟩
  • Etienne E. Birmelé, Pierluigi Crescenzi, Rui Ferreira, Roberto Grossi, Vincent Lacroix, et al.. Efficient Bubble Enumeration in Directed Graphs. String Processing and Information Retrieval (SPIRE), Oct 2012, Cartagena, Colombia. pp.118-129, ⟨10.1007/978-3-642-34109-0_13⟩. ⟨hal-00738927⟩
  • Michel M. Koskas, Gilles G. Grasseau, Etienne E. Birmelé, Sophie S. Schbath, Stephane S. Robin. NeMo: Fast Count and Statistical Significance of Network Motifs. MARAMI 2011 : 2. Conférence sur les Modèles et l'Analyse des Réseaux : Approches Mathématiques et Informatique, Oct 2011, Grenoble, France. n.p. ⟨hal-00999907⟩
  • Michel M. Koskas, Gilles G. Grasseau, Etienne E. Birmelé, Sophie S. Schbath, Stephane S. Robin. NeMo: Fast Count of Network Motifs. Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), Jun 2011, Paris, France. pp.53-60. ⟨hal-01000038⟩
  • Vicente Acuña, Etienne Birmele, Ludovic Cottret, Pierluigi Crescenzi, Fabien Jourdan, et al.. Telling Stories. ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA), 2011, Zurich, Switzerland. ⟨10.1016/j.tcs.2012.07.023⟩. ⟨hal-00748788⟩
  • Paulo Vieira Milreu, Vicente Acuña, Etienne E. Birmelé, Pierluigi Crescenzi, Alberto Marchetti-Spaccamela, et al.. Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms. Workshop on Algorithms in Bioinformatics (WABI), Sep 2010, Liverpool, United Kingdom. pp.226-237, ⟨10.1007/978-3-642-15294-8_19⟩. ⟨hal-00751339⟩
  • Pierre Latouche, Etienne E. Birmelé, Christophe Ambroise. Modèles de graphe aléatoire à classes chevauchantes pour l'analyse des réseaux. 42èmes Journées de Statistique, 2010, Marseille, France, France. ⟨inria-00494820⟩
  • Pierre Latouche, Etienne E. Birmelé, Christophe Ambroise. A latent logistic model to uncover overlapping clusters in networks. Atelier AGS (Apprentissage et Graphes pour les Systèmes complexes), May 2009, Hammamet, Tunisia. pp.3-8. ⟨hal-00629310⟩
  • Pierre Latouche, Etienne E. Birmelé, Christophe Ambroise. Uncovering overlapping clusters in biological networks. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jun 2009, Nantes, France. pp.28. ⟨hal-00629321⟩

Book sections3 documents

  • Pierre Latouche, Etienne E. Birmelé, Christophe Ambroise. Overlapping clustering methods for networks. Edoardo M. Airoldi, David Blei, Elena A. Erosheva, Stephen E. Fienberg. Chapman and Hall/CRC. Handbook of Mixed Membership Models and Their Applications, Chapman and Hall/CRC, in press, 2014. ⟨hal-00984395⟩
  • Pierre Latouche, Etienne E. Birmelé, Christophe Ambroise. Bayesian methods for graph clustering. Andreas Fink, Berthold Lausen, Wilfried Seidel and Alfred Ultsch. Advances in Data Analysis, Data Handling and Business Intelligence, Springer, pp.229-239, 2009, Studies in Classification, Data Analysis, and Knowledge Organization, 978-3-642-01043-9. ⟨10.1007/978-3-642-01044-6⟩. ⟨hal-00629294⟩
  • Etienne Birmele, Adrian Bondy, Bruce Reed. Brambles, prisms and grids. Graph Theory in Paris - Proceedings of a Conference in Memory of Claude Berge, Birkhauser, pp.37-44, 2007. ⟨hal-00730790⟩

Directions of work or proceedings1 document

  • Etienne E. Birmelé, Mohamed Elati, Blaise Hanczar, Lydia Boudjeloud-Assala. Atelier Grands Graphes et Bioinformatique. 16e Journées des Connaissances (EGC 2016), Jan 2016, Reims, France. pp.40, 2016. ⟨hal-03122986⟩

Preprints, Working Papers, ...5 documents

  • Jennifer Wong, Thomas Pichetti, François Radvanyi, Etienne E. Birmelé. ENUMERATING SETS OF GENOMIC ALTERATIONS CHARACTERIZING A USER-DEFINED SUBGROUP. 2021. ⟨hal-03174404⟩
  • Allan Jerolon, Laura Baglietto, Etienne Birmele, Vittorio Perduca, Flora Alarcon. Causal mediation analysis in presence of multiple mediators uncausally related. 2018. ⟨hal-01879552⟩
  • Etienne E. Birmelé, Fabien de Montgolfier, Léo Planche, Laurent Viennot. Decomposing a Graph into Shortest Paths with Bounded Eccentricity. 2017. ⟨hal-01511357v2⟩
  • Etienne E. Birmelé, Fabien de Montgolfier, Léo Planche. Minimum Eccentricity Shortest Path Problem: an Approximation Algorithm and Relation with the k-Laminarity Problem. 2016. ⟨hal-01366782⟩
  • Etienne Birmele. Choose Outsiders First: a mean 2-approximation random algorithm for covering problems.. 2012. ⟨hal-00726287⟩

Reports1 document

  • Stéphane Bessy, Etienne E. Birmelé, Frédéric Havet. Arc-chromatic number of digraphs in which each vertex has bounded outdegree or bounded indegree. [Research Report] RR-5364, INRIA. 2004, pp.20. ⟨inria-00070639⟩

Habilitation à diriger des recherches1 document

  • Etienne Birmele. Etude structurelle des réseaux : modèles aléatoires, motifs et cycles.. Bio-informatique [q-bio.QM]. Université d'Evry-Val d'Essonne, 2011. ⟨tel-00750375⟩