Andrei Zinovyev

Summary

Affiliation: Institut Curie
Country: France

Publications

  1. ncbi request reprint Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences
    Alexander N Gorban
    Institute of Computational Modeling, Russian Academy of Science, Russia
    In Silico Biol 5:265-82. 2005
  2. pmc Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps
    Andrei Zinovyev
    Institut Curie, Paris, France
    PLoS Comput Biol 9:e1003016. 2013
  3. pmc NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
    Inna Kuperstein
    Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 5, France
    BMC Syst Biol 7:100. 2013
  4. pmc Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways
    Elena Kutumova
    Institute of Systems Biology, Ltd, 15 Detskiy proezd, Novosibirsk 630090, Russia
    BMC Syst Biol 7:13. 2013
  5. doi request reprint Mathematical modeling of microRNA-mediated mechanisms of translation repression
    Andrei Zinovyev
    Institut Curie, Paris, France
    Adv Exp Med Biol 774:189-224. 2013
  6. doi request reprint Blind source separation methods for deconvolution of complex signals in cancer biology
    Andrei Zinovyev
    Institute Curie, Paris, France
    Biochem Biophys Res Commun 430:1182-7. 2013
  7. pmc Robust simplifications of multiscale biochemical networks
    Ovidiu Radulescu
    IRMAR CNRS UMR 6025, Universite de Rennes 1, Rennes, France
    BMC Syst Biol 2:86. 2008
  8. pmc Dynamical modeling of microRNA action on the protein translation process
    Andrei Zinovyev
    Institut Curie, Bioinformatics and Computational Systems Biology of Cancer, Paris, France
    BMC Syst Biol 4:13. 2010
  9. doi request reprint Cell death and life in cancer: mathematical modeling of cell fate decisions
    Andrei Zinovyev
    U900 INSERM Institut Curie Ecole de Mines, Institut Curie, 26 Rue d Ulm, Paris 75005, France
    Adv Exp Med Biol 736:261-74. 2012
  10. ncbi request reprint BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
    Andrei Zinovyev
    Institut Curie, Service de Bioinformatique, 26 Rue d Ulm, F 75248 Paris Cedex 05, France
    Bioinformatics 24:876-7. 2008

Collaborators

Detail Information

Publications23

  1. ncbi request reprint Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences
    Alexander N Gorban
    Institute of Computational Modeling, Russian Academy of Science, Russia
    In Silico Biol 5:265-82. 2005
    ..ihes.fr/~zinovyev/7clusters). The findings can be readily introduced into software for gene prediction, sequence alignment or microbial genomes classification...
  2. pmc Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps
    Andrei Zinovyev
    Institut Curie, Paris, France
    PLoS Comput Biol 9:e1003016. 2013
    ..These observations extend the canonical interpretation of synthetic-lethal or synthetic-sick interactions with direct implications to reconstruct molecular pathways and improve therapeutic approaches to diseases such as cancer...
  3. pmc NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
    Inna Kuperstein
    Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 5, France
    BMC Syst Biol 7:100. 2013
    ..It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them...
  4. pmc Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways
    Elena Kutumova
    Institute of Systems Biology, Ltd, 15 Detskiy proezd, Novosibirsk 630090, Russia
    BMC Syst Biol 7:13. 2013
    ..Thus, it is necessary to reduce existing models to identify key elements determining their dynamics, and it is also required to design the methods allowing us to combine them...
  5. doi request reprint Mathematical modeling of microRNA-mediated mechanisms of translation repression
    Andrei Zinovyev
    Institut Curie, Paris, France
    Adv Exp Med Biol 774:189-224. 2013
    ..The limiting place can vary from one experimental setting to another. This model explains the majority of existing controversies reported...
  6. doi request reprint Blind source separation methods for deconvolution of complex signals in cancer biology
    Andrei Zinovyev
    Institute Curie, Paris, France
    Biochem Biophys Res Commun 430:1182-7. 2013
    ..We focus more specifically on the analysis of gene expression in cancer. The review is finalized by listing available software implementations for the methods described...
  7. pmc Robust simplifications of multiscale biochemical networks
    Ovidiu Radulescu
    IRMAR CNRS UMR 6025, Universite de Rennes 1, Rennes, France
    BMC Syst Biol 2:86. 2008
    ..In systems biology we also need to compare models or to couple them as parts of larger models. In these situations reduction to a common level of complexity is needed...
  8. pmc Dynamical modeling of microRNA action on the protein translation process
    Andrei Zinovyev
    Institut Curie, Bioinformatics and Computational Systems Biology of Cancer, Paris, France
    BMC Syst Biol 4:13. 2010
    ..For their analysis they used two simple kinetic models of protein translation...
  9. doi request reprint Cell death and life in cancer: mathematical modeling of cell fate decisions
    Andrei Zinovyev
    U900 INSERM Institut Curie Ecole de Mines, Institut Curie, 26 Rue d Ulm, Paris 75005, France
    Adv Exp Med Biol 736:261-74. 2012
    ..Using an original parameter sensitivity analysis developed for discrete dynamic systems, we determine variables that appear to be critical in the cellular fate decision and discuss how they are exploited by existing cancer therapies...
  10. ncbi request reprint BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
    Andrei Zinovyev
    Institut Curie, Service de Bioinformatique, 26 Rue d Ulm, F 75248 Paris Cedex 05, France
    Bioinformatics 24:876-7. 2008
    ..BiNoM comes as a library and as a Cytoscape plugin which adds a rich set of operations to Cytoscape such as path and cycle analysis, clustering sub-networks, decomposition of network into modules, clipboard operations and others...
  11. doi request reprint Practical use of BiNoM: a biological network manager software
    Eric Bonnet
    Institut Curie, Paris, France
    Methods Mol Biol 1021:127-46. 2013
    ..In this tutorial, we present a detailed and practical case study of how to use BiNoM to analyze biological networks...
  12. doi request reprint From a biological hypothesis to the construction of a mathematical model
    David Cohen
    Institut Curie, Paris, France
    Methods Mol Biol 1021:107-25. 2013
    ..This chapter aims at introducing modeling to experts in molecular biology that would like to convert their hypotheses into mathematical models...
  13. pmc A comprehensive modular map of molecular interactions in RB/E2F pathway
    Laurence Calzone
    Institut Curie, Service Blolnforrnatique, Paris, France
    Mol Syst Biol 4:173. 2008
    ..The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway...
  14. pmc BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats
    Eric Bonnet
    Institut Curie, 26 Rue d Ulm, Paris, F 75248, France
    BMC Syst Biol 7:18. 2013
    ..However, large-scale molecular maps are not always easy to mine and interpret...
  15. pmc Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis
    Gautier Stoll
    Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 05, France, INSERM U900, Bioinformatique, biostatistique et épidémiologie d un système complexe, Paris, France, Mines ParisTech, Fontainebleau, France, INSERM U830, Unité de Génétique et Biologie des Cancers, Paris, France and Institut Curie, Unité de Génétique Somatique, Paris, France
    Nucleic Acids Res 41:8853-71. 2013
    ..Altogether, using an original methodology of data integration, we provide the first version of EWS-FLI1 network model of cell cycle and apoptosis regulation. ..
  16. doi request reprint [Systems biology of cancer]
    Emmanuel Barillot
    Institut Curie, 26, rue d Ulm, F 75248 Paris Cedex 05, INSERM, U900, F 75248 Paris, France
    Med Sci (Paris) 25:601-7. 2009
    ..These characteristics emphasize the important role of Systems Biology of Cancer in the future of biomedical research...
  17. pmc Antagonism pattern detection between microRNA and target expression in Ewing's sarcoma
    Loredana Martignetti
    Institut Curie, Paris, France
    PLoS ONE 7:e41770. 2012
    ..The procedure allows us to infer crucial miRNA regulators and their potential targets in Ewing's sarcoma disease. It can be considered as a valid statistical approach to discover new insights in the miRNA regulatory mechanisms...
  18. pmc Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
    Valentina Boeva
    Institut Curie, INSERM, U900, Paris, France
    Bioinformatics 27:268-9. 2011
    ..We demonstrate that for Illumina single-end, mate-pair or paired-end sequencing, GC-contentr normalization provides smooth profiles that can be further segmented and analyzed in order to predict CNAs...
  19. pmc Mathematical modelling of cell-fate decision in response to death receptor engagement
    Laurence Calzone
    Institut Curie, Paris, France
    PLoS Comput Biol 6:e1000702. 2010
    ..Moreover, our current model can be used to assess contradictory or controversial data from the literature. Ultimately, it constitutes a valuable reasoning tool to delineate novel experiments...
  20. doi request reprint OCSANA: optimal combinations of interventions from network analysis
    Paola Vera-Licona
    Institut Curie, Paris F 75248, France, INSERM, U900, Paris F 75248, France
    Bioinformatics 29:1571-3. 2013
    ..With the crucial ability to cope with very large networks, OCSANA includes an exact solution and a novel selective enumeration approach for the combinatorial interventions' problem...
  21. pmc Classification of microarray data using gene networks
    Franck Rapaport
    lnstitut Curie, Service de Bioinformatique, 26 Rue d Ulm, F 75248 Paris Cedex 05, France
    BMC Bioinformatics 8:35. 2007
    ..However, integrating a priori knowledge of the gene networks could help in the statistical analysis of gene expression data and in their biological interpretation...
  22. doi request reprint Identification of shortened 3' untranslated regions from expression arrays
    Loredana Martignetti
    Institut Curie, 26 Rue d Ulm, Paris, F 75248, France
    J Bioinform Comput Biol 10:1241001. 2012
    ..Selected gene sets are significantly enriched for annotated splice variant genes as well as genes involved in estrogen dependent cancer mechanisms, confirming the validity of the proposed procedure...
  23. doi request reprint How much non-coding DNA do eukaryotes require?
    Sebastian E Ahnert
    Institut Curie, Bioinformatics, 26 Rue d Ulm, Paris 75248, France
    J Theor Biol 252:587-92. 2008
    ..Thus, our findings confirm that eukaryotic life depends on a substantial fraction of ncDNA and also make a prediction of the size of this fraction, which matches the data closely...