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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

  • 1H. Campbell-Sills, M. El Khoury, M. Favier, A. Romano, F. Biasioli, G. Spano, D. J. Sherman, O. Bouchez, E. Coton, M. Coton, S. Okada, N. Tanaka, M. Dols-Lafargue, P. M. Lucas.

    Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines, in: Genome Biology and Evolution, May 2015, vol. 7, no 6, pp. 1506-18. [ DOI : 10.1093/gbe/evv084 ]

    https://hal.inria.fr/hal-01202801
  • 2N. Loira, A. Zhukova, D. J. Sherman.

    Pantograph: A template-based method for genome-scale metabolic model reconstruction, in: Journal of Bioinformatics and Computational Biology, January 2015, vol. 10, 1550006 p. [ DOI : 10.1142/S0219720015500067 ]

    https://hal.inria.fr/hal-01123733
  • 3S. Mariette, F. Wong Jun Tai, G. Roch, A. Barré, A. Chague, S. Decroocq, A. Groppi, Y. Laizet, P. Lambert, D. Tricon, M. Nikolski, J.-M. Audergon, A. G. Abbott, V. Decroocq.

    Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca), in: New Phytologist, September 2015, DOI: 10.1111/nph.13627 p. [ DOI : 10.1111/nph.13627 ]

    https://hal.archives-ouvertes.fr/hal-01198840
  • 4S. Poque, G. Pagny, L. Ouibrahim, A. Chague, J.-P. Eyquard, M. Caballero, T. Candresse, C. Caranta, S. Mariette, V. Decroocq.

    Allelic variation at the rpv1 locus controls partial resistance to Plum pox virus infection in Arabidopsis thaliana, in: BMC Plant Biology, June 2015, vol. 15, 159 p.

    https://hal.inria.fr/hal-01262384
  • 5A. Zhukova, D. J. Sherman.

    Mimoza: web-based semantic zooming and navigation in metabolic networks, in: BMC Systems Biology, February 2015, vol. 9, 10 p. [ DOI : 10.1186/s12918-015-0151-5 ]

    https://hal.inria.fr/hal-01123715

Invited Conferences

  • 6D. J. Sherman.

    Diversity and Domestication in Oenological Yeasts, in: Moscow Conference on Computational and Molecular Biology (MCCMB'15), Moscow, Russia, July 2015.

    https://hal.inria.fr/hal-01212044

Conferences without Proceedings

  • 7M. Daydé, B. Depardon, A. Franc, J.-F. Gibrat, R. Guillier, Y. Karami, C. Pérez, F. Suter, M. Chabbert, B. Taddese, S. Thérond.

    E-Biothon: an experimental platform for BioInformatics, in: International Conference on Computer Science and Information Technologies, Yerevan, Armenia, September 2015.

    https://hal.inria.fr/hal-01207320
  • 8W. Dyrka, P. Durrens, M. Paoletti, S. J. Saupe, D. J. Sherman.

    Deciphering the language of fungal pathogen recognition receptors, in: 8th Symposium of the Polish Bioinformatics Society, Lublin, Poland, Polish Bioinformatics Society, September 2015.

    https://hal.inria.fr/hal-01203357

Other Publications

References in notes
  • 11R. Alur.

    SIGPLAN Notices, in: Generating Embedded Software from Hierarchical Hybrid Models, 2003, vol. 38, no 7, pp. 171–82.
  • 12B. Arnold, R. Corbett-Detig, D. Hartl, K. Bomblies.

    RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling, in: Mol. Ecol., 2013, vol. 22, no 11, pp. 3179–90.
  • 13R. Assar, A. V. Leisewitz, A. Garcia, N. C. Inestrosa, M. A. Montecino, D. J. Sherman.

    Reusing and composing models of cell fate regulation of human bone precursor cells., in: BioSystems, April 2012, vol. 108, no 1-3, pp. 63-72. [ DOI : 10.1016/j.biosystems.2012.01.008 ]

    https://hal.inria.fr/hal-00681022
  • 14R. Assar, M. A. Montecino, A. Maass, D. J. Sherman.

    Modeling acclimatization by hybrid systems: Condition changes alter biological system behavior models, in: BioSystems, June 2014, vol. 121, pp. 43-53. [ DOI : 10.1016/j.biosystems.2014.05.007 ]

    https://hal.inria.fr/hal-01002987
  • 15R. Assar, D. J. Sherman.

    Implementing biological hybrid systems: Allowing composition and avoiding stiffness, in: Applied Mathematics and Computation, August 2013, vol. 223, pp. 167–79.

    https://hal.inria.fr/hal-00853997
  • 16R. Assar, F. Vargas, D. J. Sherman.

    Reconciling competing models: a case study of wine fermentation kinetics, in: Algebraic and Numeric Biology 2010, Hagenberg, Austria, K. Horimoto, M. Nakatsui, N. Popov (editors), Springer, July 2010, vol. 6479, pp. 68–83. [ DOI : 10.1007/978-3-642-28067-2_6 ]

    https://hal.inria.fr/inria-00541215
  • 17C. Combes.

    Parasitism: The Ecology and Evolution of Intimate Interactions, University of Chicago Press, 2001.
  • 18P. Gayral, J. Melo-Ferreira, S. Glemin.

    Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap, in: PLoS Genetic, 2013, vol. 9, no 4, e1003457.
  • 19R. Issa.

    symbolic analysis and inference of metabolic models, Université de Bordeaux, July 2015.

    https://tel.archives-ouvertes.fr/tel-01216599
  • 20M. Lynch.

    Estimation of Nucleotide Diversity, Disequilibrium Coefficients, and Mutation Rates from High-Coverage Genome-Sequencing Projects, in: Mol. Biol. Evol., 2008, vol. 25, no 11, pp. 2409–19.
  • 21R. E. Ricklefs.

    A comprehensive framework for global patterns in biodiversity, in: Ecology Letters, 2004, vol. 7, no 1, pp. 1–15.

    http://dx.doi.org/10.1046/j.1461-0248.2003.00554.x
  • 22S. T. Roweis, Z. Ghahramani.

    A unifying review of linear Gaussian Models, in: Neural Computation, 1999, vol. 11, no 2, pp. 305–45.
  • 23L. K. Saul, S. T. Roweis.

    Think globally, fit locally: unsupervised learning of low dimensional manifolds, in: Journal of Machine Learning Research, 2003, vol. 4, pp. 119–55.
  • 24D. J. Sherman, T. Martin, M. Nikolski, C. Cayla, J.-L. Souciet, P. Durrens.

    Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes, in: Nucleic Acids Research (NAR), 2009, pp. D550-4. [ DOI : 10.1093/nar/gkn859 ]

    http://hal.inria.fr/inria-00341578/en/
  • 25D. W. Thompson.

    On Growth and Form, Cambridge University Press, 1917.
  • 26A. Zhukova, D. J. Sherman.

    Knowledge-based generalization of metabolic models, in: Journal of Computational Biology, 2014, vol. 21, no 7, pp. 534-47. [ DOI : 10.1089/cmb.2013.0143 ]

    https://hal.inria.fr/hal-00925881


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