IntegrativeBioChile is an Associate Team between INRIA project-team "Symbiose" and the "Laboratory of Bioinformatics and Mathematics of the Genome" hosted at CMM at University of Chile. The Associated team is funded from 2011 to 2013.

News




Interview in Emergence: link

September 2011: a ph-D student (S. Videla) joins the team in Rennes (ANR support)

November 2011: a post-doc (S. Thiele) joins the team (INRIA post-doc support)

General description



We aim at combining automatic reasoning on biological sequences and networks with probabilistic approaches to manage, explore and integrate large sets of heterogeneous omics data into networks of interactions allowing to produce biomarkers of their behavior. We shall focus on the identification of a relevant set of biological components required to describe the complexity of a biological phenomenon. Starting from observations at several levels (genomics, transcriptomics, metabolomics) we shall select with products are relevant to the observed phenomena and complement this list with their regulators and those components that share the same metabolic and signalling pathways. Our long-term goal is to exhibit from the network obtained at the previous stage biomarkers for the different biological phenomena observed for an organism. Applications are mainly focused on biomining, based on the experience acquired at CMM in analysing several sets of data on biomining bacteria. Methods combine a fine tuning of sequence analysis, efficient constraint base programming and asymptotic study of Markov models properties.

Members



In Rennes

Anne Siegel (DR CNRS), Jacques Nicolas (DR Inria), François Coste (CR Inria), Dominique Lavenier (DR CNRS), Sylvain Prigent (ph-D student), Santiago Videla (ph-D student), Sven Thiele (post-doc)

In Nantes

Jérémie Bourdon (Associate professor), Damien Eveillard (Associate professor)

In Santiago de Chile

Alejandro Masss (Professor, group leader), Mauricio Gonzalez (Associate Professor), Tomas Pérez (Researcher), Andrès Aravena (Ph-D student), Mauricio Latorre (Ph-D student), Marko Budinich (biotechnology engineer), Marìa Paz Cortès (biotechnology engineer), Luis Zapata (biotechnology engineer), Alex Di Genova (bioinformatics engineer), Dante Travisany (bioinformatics engineer)

Program



2011: identification of relevant genomic actors

Reconstruction of a transcriptomic network by combining optimization (probabilist) approaches and constraint-based programming; confrontation to transcriptome observations

Identification of operons by aligning genome, metabolic and transcriptome maps

Detection of structural variations in genomes

2012: validation & software development. Robustness and reduction issues

Transcriptomic network : experimental validation. Correction and robustness issues. Software development

Identification of operons: validation. Extension to the detection of modules in metabolic networks : reduction issues.

Detection of structural variations in genomes. Validation.

Visits



February 2012. Three weeks visit from A. Maass in Rennes

February to July 2012. Five month visit from A. Aravena in Rennes (co-funded by Universite Europeenne de Bretagne and Conicyt). Methods for the construction of transcriptional biological networks

May 2012. One month visit of Marko Budinich (engineer) in Rennes. Reconstruction and study of metabolic network with reduction methods.

June 2012. One month visit of Alex Di Genova (engineer) in Rennes. Detection of structural variations in genomes.

July 2012. Two weeks visit of Damien Eveillard (assistant professor) in Santiago. Co-funded by conycit. Reduction methods for the analysis of metabolic networks.

October 2012. Two weeks visit of François Coste (researcher) in Santiago. Co-funded by conycit.

October 2012. Two weeks visit of Jérémie Bourdon (assistant professor) in Santiago

November 2012. 10 days visit of Anne Siegel (researcher) in Santiago

November-December 2012. One month visit of Sylvain Prigent (ph-D student) in Santiago. Co-funded by conycit.

PhD thesis



Andres Aravena is undergoing a co-advised Phd within CMM and the Symbiose project team.

Santiago Videla will undergo a ph-D thesis in the Symbiose team on the associated team scientific project (ANR support)

Publications



Automatic reasoning over biological sequences and networks

  • T. Baumuratova, D. Surdez, B. Delyon, G. Stoll, O. Delattre, O. Radulescu, A. Siegel, Localizing potentially active post-transcriptional regulations in the Ewing’s sarcoma gene regulatory network BMC Systems Biology 4 (1), 2010, p. 144.
  • C. Guziolowski, S. Blachon, T. Baumuratova, G. Stoll, O. Radulescu, A. Siegel, Designing logical rules to model the response of biomolecular networks with complex interactions : an application to cancer modeling. Transactions on Computational Biology and bioinformatics, 2010
  • Philippe Bordron, Damien Eveillard & Irena Rusu. Integrated analysis of the gene neighboring impact on bacterial metabolic networks. IET Systems Biology. In press
  • M. Gebser, C. Guziolowski, M. Ivanchev, T. Schaub, A. Siegel, P. Veber and S. Thiele Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming KR'2010 - International Conference on the Principles of Knowledge Representation and Reasoning, Toronto, 2010
  • G. Risk, D. Lavenier, GASSST: Global Alignment Short Sequence Search Tool, Bioinformatics, vol 26, no 20, 2010
  • P. Perterlongo, J. Nicolas, D. Lavenier, R. Vorc h, J. Querellou, c-GAMMA: comparative genome analysis of molecular markers, 4th IAPR International Conference on Pattern Recognition in Bioinformatics, LNCS 5780 , Sheffield, UK, 2009
  • C. Guziolowski, A. Bourdé, F. Moreews and A. Siegel, BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks, BMC genomics, 2009, 10:244
  • P Veber, C Guziolowski, M Le Borgne, O Radulescu, and A Siegel, Inferring the role of transcription factors in regulatory networks, BMC BioInformatics 9, 2008:228

Probabilistic methods for the design of biomarkers

  • N. Ehrenfeld, A. Aravena, A. Reyes-Jara, N. Barreto, R. Assar, A. Maass, P. Parada, Design and use of oligonucleotide microarrays for identification of Biomining microorganisms. Advanced Materials Research 71-73 (2009) 155-158.
  • G. Levicán, J. A. Ugalde, N. Ehrenfeld, A. Maass, P. Parada, Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC-Genomics 9 (2008) 581.
  • E. Pécou, A. Maass, D. Remenik, J. Briche, M Gonzàlez, A mathematical model for copper homeostasis in Enterococcus hirae , Mathematical Biosciences 203, 2, 222-239, 2006
  • Hart, S. Martínez, L. Videla, A simple maximization model inspired by algorithms for the organization of genetic candidates in bacterial DNA, Advances in Applied Probability 38, 4, 1071-1097, 2006. Presented as invited lecture at International Workshop on Applied Probability, Connecticut, May 2006.

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