Major publications by the team in recent years
  • 1P. Almeida, C. Gonçalves, S. Teixeira, D. Libkind, M. Bontrager, I. Masneuf-Pomarede, 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

  • 4W. Albertin, M. Chernova, P. Durrens, E. Guichoux, D. J. Sherman, I. Masneuf-Pomarede, P. Marullo.

    Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human-related fermentations, in: Yeast, January 2018, vol. 35, no 1, pp. 141-156. [ DOI : 10.1002/yea.3248 ]

  • 5F. Keck, A. A. Franc, M. Kahlert.

    Disentangling the processes driving the biogeography of freshwater diatoms: A multiscale approach, in: Journal of Biogeography, July 2018, vol. 45, no 7, pp. 1582-1592.


Scientific Books (or Scientific Book chapters)

  • 6F. Leese, A. Bouchez, K. Abarenkov, F. Altermatt, A. Borja, K. Bruce, T. Ekrem, F. Čiampor, Z. Čiampor, F. Costa, S. Duarte, V. Elbrecht, D. Fontaneto, A. A. Franc, M. Geiger, D. Hering, M. Kahlert, B. Kalamujić Stroil, M. Kelly, E. Keskin, I. Liska, P. Mergen, K. Meissner, J. Pawlowski, L. Penev, Y. Reyjol, A. Rotter, D. Steinke, B. van der Wal, S. S. Vitecek, J. Zimmermann, A. Weigand.

    Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action, in: Next Generation Biomonitoring: Part 1, Elsevier, 2018, vol. 58, pp. 63-99.


Internal Reports

Other Publications

  • 10T. Lang, P. P. Abadie, V. Léger, T. Decourcelle, J.-M. Frigerio, C. Burban, C. Bodenes, E. Guichoux, G. G. Le Provost, C. Robin, N. Tani, P. P. Léger, C. Lepoittevin, V. A. El Mujtar, F. Hubert, J. Tibbits, J. Paiva, A. A. Franc, F. Raspail, S. Mariette, M.-P. M. Reviron, C. Plomion, A. Kremer, M.-L. Desprez-Loustau, P. Garnier-Gere.

    High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraeaandQ. robur), August 2018, working paper or preprint. [ DOI : 10.1101/388447 ]

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 ]

  • 14R. 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.

  • 15R. 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 ]

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    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.
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  • 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.
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    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.

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  • 30J. Wang.

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