David Simoncini

David Simoncini
country
country

AgreenSkills session, year: 2nd session, 2013

Receiving laboratory: MIAT Applied Mathematics and Informatics Toulouse, France

Country of origin : Japan

E-Mail:

 

 

Mobility project

Computational design of proteins using a fragment-based approach and cost function network model

I obtained my ph.D. in Computer Science from the University of Nice Sophia Antipolis. I was studying evolutionary algorithms, which are some population-based search methods: my objective was to find new methods to control the search dynamics of spatially structured evolutionary algorithms.  After I passed my ph.D. I wanted to apply my methods on some specific problems, so I went to RIKEN in Tokyo in order to study protein structure prediction. I stayed there as a postdoc fellow for almost 3 years and developed a software for protein structure prediction (Edafold). I came back to France in september 2013 as an ATER at the i3s laboratory of Sophia Antipolis. I am interested by interdisciplinary work. I like to tackle problems in collaboration with researchers from various fields, each of them bringing their competences. My research interests focus on protein structure prediction and computational protein design.

Biography & research interests

I obtained my ph.D. in Computer Science from the University of Nice Sophia Antipolis. I was studying evolutionary algorithms, which are some population-based search methods: my objective was to find new methods to control the search dynamics of spatially structured evolutionary algorithms.  After I passed my ph.D. I wanted to apply my methods on some specific problems, so I went to RIKEN in Tokyo in order to study protein structure prediction. I stayed there as a postdoc fellow for almost 3 years and developed a software for protein structure prediction (Edafold). I came back to France in september 2013 as an ATER at the i3s laboratory of Sophia Antipolis. I am interested by interdisciplinary work. I like to tackle problems in collaboration with researchers from various fields, each of them bringing their competences. My research interests focus on protein structure prediction and computational protein design.

Selected publications
  1. Simoncini, D., Zhang, K. Y. J. (2013)
    Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm.
    PLoS ONE, 8(7): e68954, 1-10. doi:10.1371/journal.pone.0068954
  2. Shrestha, R., Simoncini, D., Zhang, K. Y. J. (2012)
    Error estimation guided rebuilding of de novo models increases the success rate for ab initio phasing.
    Acta Cryst., D68, 1522-1534.
  3. Simoncini, D., Berenger, F., Shrestha, R., Zhang, K. Y. J. (2012)
    A probabilistic fragment-based protein structure prediction algorithm.
    PLoS ONE 7(7): e38799, 1-11, doi: 10.1371/journal.pone.0038799.
  4. Berenger, F., Shrestha, R., Zhou, Y., Simoncini, D., Zhang, K. Y. J. (2011)
    Durandal: fast exact clustering of protein decoys.
    J. Comp. Chem., 33, 471-474.
  5. David Simoncini, Philippe Collard, Sebastien Verel, and Manuel Clergue.
    Centric selection: a Way to Tune the Exploration/Exploitation Trade-off.
    In Genetic and Evolutionary Computation – GECCO-2009, pages 891–898, July 2009.
  6. David Simoncini, Philippe Collard, Sebastien Verel, and Manuel Clergue.
    On the Influence of Selection Operators on Performances in Cellular Genetic Algorithms.
    In Proceedings of the IEEE Congress on Evolutionary Computation CEC 2007, pages 4706-4713, September 2007.
  7. David Simoncini, Sebastien Verel, Philippe Collard, and Manuel Clergue.
    Anisotropic selection in cellular genetic algorithms.
    In Genetic and Evolutionary Computation – GECCO-2006, pages 559–566, Seatle, 8-12 July 2006. ACM.
    Nomination for the “Best Paper Award”.
  8. David Simoncini, Philippe Collard, Sebastien Verel, and Manuel Clergue.
    From Cells to Islands: An unified Model of Cellular Parallel Genetic Algorithms.
    In ACRI 2006, 7th International Conference, LNCS 4173, pages 248-257, Perpignan, France, sept 2006.
  9. David Simoncini, Michael Defoin Platel.
    Spatial anisotropy encourages parapatric speciation in Evolutionary Algorithms.
    In the 18th colloquium of the Spatial Information Research Center – SIRC-2006
  10. David Simoncini, Sebastien Verel, Philippe Collard, and Manuel Clergue.
    A preliminary investigation of anisotropic selection in celullar genetic algorithms.
    In Poster at Evolution Artificielle, 7th International Conference, Lille, France, 2005.

Contact:

E-Mail:

Website(s): http://carlit.toulouse.inra.fr/UBIAT

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