Major publications by the team in recent years
  • 1P. Almeida, C. Gonçalves, S. Teixeira, D. Libkind, M. Bontrager, I. Masneu-Pomarède, W. Albertin, P. Durrens, D. J. Sherman, P. Marullo, C. Todd Hittinger, P. Gonçalves, J. P. Sampaio.

    A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum., in: Nature Communications, 2014, vol. 5, 4044 p. [ DOI : 10.1038/ncomms5044 ]

  • 2R. 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 ]

  • 3D. 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, 2009, vol. 37, pp. D550-D554. [ DOI : 10.1093/nar/gkn859 ]

Publications of the year

Articles in International Peer-Reviewed Journals

  • 4B. Bailet, A. Bouchez, A. A. Franc, J.-M. Frigerio, F. Keck, S.-M. Karjalainen, F. Rimet, S. Schneider, M. Kahlert.

    Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status, in: Metabarcoding and Metagenomics, June 2019, vol. 3. [ DOI : 10.3897/mbmg.3.34002 ]

  • 5H. Caron, J. Molino, D. Sabatier, P. P. Léger, P. Chaumeil, C. Scotti-Saintagne, J.-M. Frigerio, I. Scotti, A. A. Franc, R. J. Petit.

    Chloroplast DNA variation in a hyperdiverse tropical tree community, in: Ecology and Evolution, March 2019, vol. 9, no 8, pp. 4897-4905. [ DOI : 10.1002/ece3.5096 ]

  • 6A. A. Franc, P. Blanchard, O. Coulaud.

    Nonlinear mapping and distance geometry, in: Optimization Letters, May 2019. [ DOI : 10.1007/s11590-019-01431-y ]

  • 7P. Marullo, P. Durrens, E. Peltier, M. Bernard, C. Mansour, D. Dubourdieu.

    Natural allelic variations of Saccharomyces cerevisiae impact stuck fermentation due to the combined effect of ethanol and temperature; a QTL-mapping study, in: BMC Genomics, December 2019, vol. 20, no 1. [ DOI : 10.1186/s12864-019-5959-8 ]

  • 8N. D. P. Peyrard, S. De Givry, A. A. Franc, S. Robin, R. R. Sabbadin, T. Schiex, M. Vignes.

    Exact or approximate inference in graphical models: why the choice is dictated by the treewidth, and how variable elimination can be exploited, in: Australian and New Zealand Journal of Statistics, June 2019, vol. 61, no 2, pp. 89-133. [ DOI : 10.1111/anzs.12257 ]


Internal Reports

  • 9S. Kanchan.

    In silico comparative function prediction of enzymes, applied to fatty acid metabolism in microalgae : Final Report, Inria Bordeaux Sud-Ouest, December 2019.

References in notes
  • 10R. Alur.

    SIGPLAN Notices, in: Generating Embedded Software from Hierarchical Hybrid Models, 2003, vol. 38, no 7, pp. 171–82.
  • 11B. 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.
  • 12R. 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 ]

  • 13R. 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.

  • 14R. 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 ]

  • 15M. Bakonyi, C. R. Johnson.

    The Euclidean Distance Matrix Completion Problem, in: SIAM J. Matrix Anal. App., 1995, vol. 16, no 2, pp. 646-654.
  • 16P. Blanchard, P. Chaumeil, J.-M. Frigerio, F. RIMET, F. Salin, S. Thérond, O. Coulaud, A. Franc.

    A geometric view of Biodiversity: scaling to metagenomics, Inria ; INRA, January 2018, no RR-9144, pp. 1-16, https://arxiv.org/abs/1803.02272.

  • 17E. J. Candès, B. Recht.

    Exact Matrix Completion via Convex Optimization, in: Found. Comput. Math., 2009, vol. 9, pp. 717-772.
  • 18A. Carlsson, J. Yilmaz, A. Green, S. Stymne, P. Hofvander.

    Replacing fossil oil with fresh oil - with what and for what?, in: Eur J Lipid Sci Technol, 2011, vol. 113, no 7, pp. 812-831.
  • 19C. Combes.

    Parasitism: The Ecology and Evolution of Intimate Interactions, University of Chicago Press, 2001.
  • 20P. 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.
  • 21M. Hasimoto, S. Hossain, A. Al Mamun, K. Matsuzaki, H. Arai.

    Docosahexaenoic acid: one molecule diverse functions, in: Crit Rev Biotechnol., Aug 2017, vol. 37, no 5, pp. 579-597.

  • 22L. Liberti, C. Lavor, N. Maculan, A. Mucherino.

    Euclidean Distance Geometry and Applications, in: SIAM review, 2014, vol. 56(1), pp. 3-69.
  • 23M. 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.
  • 24F. Morcillo, D. Cros, N. Billotte, G. Ngando-Ebongue, H. Domonhédo, M. Pizot, T. Cuéllar, S. Espéout, R. Dhouib, F. Bourgis, S. Claverol, T. Tranbarger, B. Nouy, V. Arondel.

    Improving palm oil quality through identification and mapping of the lipase gene causing oil deterioration, in: Nat Commun, 2013, vol. 4, 2160 p.

  • 25R. E. Ricklefs.

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

  • 26F. Rimet, P. Chaumeil, F. Keck, L. Kermarrec, V. Vasselon, M. Kahlert, A. Franc, A. Bouchez.

    R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring, in: Database - The journal of Biological Databases and Curation, February 2016, vol. 2016. [ DOI : 10.1093/database/baw016 ]

  • 27S. T. Roweis, Z. Ghahramani.

    A unifying review of linear Gaussian Models, in: Neural Computation, 1999, vol. 11, no 2, pp. 305–45.
  • 28L. 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.
  • 29D. W. Thompson.

    On Growth and Form, Cambridge University Press, 1917.
  • 30J. Wang.

    Geometric structure of high-dimensional data and dimensionality reduction, Springer & Higher Education Press, 2012.