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Bibliography

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 ]

    https://hal.inria.fr/hal-01002466
  • 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 ]

    https://hal.inria.fr/hal-01002987
  • 3A. B. Canelas, N. Harrison, A. Fazio, J. Zhang, J.-P. Pitkänen, J. Van Den Brink, B. M. Bakker, L. Bogner, J. Bouwman, J. I. Castrillo, A. Cankorur, P. Chumnanpuen, P. Daran-Lapujade, D. Dikicioglu, K. Van Eunen, J. C. Ewald, J. J. Heijnen, B. Kirdar, I. Mattila, F. I. C. Mensonides, A. Niebel, M. Penttilä, J. T. Pronk, M. Reuss, L. Salusjärvi, U. Sauer, D. J. Sherman, M. Siemann-Herzberg, H. Westerhoff, J. De Winde, D. Petranovic, S. G. Oliver, C. T. Workman, N. Zamboni, J. Nielsen.

    Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference y east strains., in: Nature Communications, December 2010, vol. 1, no 9, 145 p. [ DOI : 10.1038/ncomms1150 ]

    https://hal.inria.fr/inria-00562005
  • 4L. Kermarrec, A. Franc, F. Rimet, P. Chaumeil, J.-M. Frigerio, J.-F. Humbert, A. Bouchez.

    A next-generation sequencing approach to river biomonitoring using benthic diatoms, in: Freshwater Science, 2014, vol. 33, no 1, pp. 349-363.

    http://www.jstor.org/stable/10.1086/675079
  • 5D. 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 ]

    https://hal.inria.fr/inria-00341578
  • 6J.-L. Souciet, B. Dujon, C. Gaillardin, M. Johnston, P. V. Baret, P. Cliften, D. J. Sherman, J. Weissenbach, E. Westhof, P. Wincker, C. Jubin, J. Poulain, V. Barbe, B. Ségurens, F. Artiguenave, V. Anthouard, B. Vacherie, M.-E. Val, R. S. Fulton, P. Minx, R. Wilson, P. Durrens, G. Jean, C. Marck, T. Martin, M. Nikolski, T. Rolland, M.-L. Seret, S. Casaregola, L. Despons, C. Fairhead, G. Fischer, I. Lafontaine, V. Leh, M. Lemaire, J. De Montigny, C. Neuveglise, A. Thierry, I. Blanc-Lenfle, C. Bleykasten, J. Diffels, E. Fritsch, L. Frangeul, A. Goeffon, N. Jauniaux, R. Kachouri-Lafond, C. Payen, S. Potier, L. Pribylova, C. Ozanne, G.-F. Richard, C. Sacerdot, M.-L. Straub, E. Talla.

    Comparative genomics of protoploid Saccharomycetaceae., in: Genome Research, 2009, vol. 19, pp. 1696-1709. [ DOI : 10.1101/gr.091546.109 ]

    https://hal.inria.fr/inria-00407511
Publications of the year

Articles in International Peer-Reviewed Journals

  • 7F. Keck, A. Bouchez, A. Franc, F. Rimet.

    Linking phylogenetic similarity and pollution sensitivity to develop ecological assessment methods: a test with river diatoms, in: Journal of Applied Ecology, March 2016, vol. 53, no 3, pp. 856 - 864. [ DOI : 10.1111/1365-2664.12624 ]

    https://hal.inria.fr/hal-01426853
  • 8F. Keck, F. Rimet, A. Bouchez, A. Franc.

    phylosignal: an R package to measure, test, and explore the phylogenetic signal, in: Ecology and Evolution, March 2016, vol. 6, no 9, pp. 2774 - 2780. [ DOI : 10.1002/ece3.2051 ]

    https://hal.inria.fr/hal-01426773
  • 9F. Keck, F. Rimet, A. Franc, A. Bouchez.

    Phylogenetic signal in diatom ecology: perspectives for aquatic ecosystems biomonitoring, in: Ecological Applications, April 2016, vol. 26, no 3, pp. 861 - 872. [ DOI : 10.1890/14-1966 ]

    https://hal.inria.fr/hal-01426854
  • 10F. 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 ]

    https://hal.inria.fr/hal-01426772
  • 11M. C. Simeone, G. W. Grimm, A. Papini, F. Vessella, S. Cardoni, E. Tordoni, R. Piredda, A. Franc, T. Denk.

    Plastome data reveal multiple geographic origins of Quercus Group Ilex, in: PeerJ, April 2016, vol. 4, e1897. [ DOI : 10.7717/peerj.1897 ]

    https://hal.inria.fr/hal-01426766

Other Publications

  • 12P. BLANCHARD, O. Coulaud, E. Darve, A. Franc.

    FMR: Fast randomized algorithms for covariance matrix computations, June 2016, Platform for Advanced Scientific Computing (PASC), Poster.

    https://hal.archives-ouvertes.fr/hal-01334747
  • 13J.-M. Frigerio, F. Rimet, A. Bouchez, E. Chancerel, P. Chaumeil, F. Salin, S. Thérond, M. Kahlert, A. Franc.

    diagno-syst: a tool for accurate inventories in metabarcoding, November 2016, working paper or preprint.

    https://hal.inria.fr/hal-01426764
References in notes
  • 14R. Alur.

    SIGPLAN Notices, in: Generating Embedded Software from Hierarchical Hybrid Models, 2003, vol. 38, no 7, pp. 171–82.
  • 15B. 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.
  • 16R. 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
  • 17R. 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
  • 18R. 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
  • 19A. Bankevich.

    SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, in: Journal of Computational Biology, 2012, vol. 19, pp. 455-477.
  • 20B. Chevreux.

    Genome sequence assembly using trace signals and additional sequence information, in: Proceedings of the German Conference on Bioinformatics (GCB), 1999.
  • 21R. Chikhi, G. Rizk.

    Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter, in: Proceedings of the 12th Workshop on Algorithms in Bioinformatics (WABI), 2012.
  • 22C. Combes.

    Parasitism: The Ecology and Evolution of Intimate Interactions, University of Chicago Press, 2001.
  • 23R. Corley, P. Tinker.

    The Oil Palm, 4th ed, Blackwell, 2003, 562 p.
  • 24A. Favel.

    Colony Morphology Switching of Candida Lusitaniae and Acquisition of Multidrug Resistance During Treatment of a Renal Infection in a Newborn: Case Report and Review of the Literature, in: Diagn. Microbiol. Infect. Dis., 2003, vol. 47, pp. 331-339.
  • 25P. 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.
  • 26M. Grabherr.

    Full-length transcriptome assembly from RNA-Seq data without a reference genome, in: Nat Biotechnol., 2011, vol. 29, pp. 644-652.
  • 27M. Lachance.

    The D1/D2 domain of the large-subunit rDNA of the yeast species Clavispora lusitaniae is unusually polymorphic, in: FEMS Yeast Res., 2003, vol. 4, pp. 253–258.
  • 28M. 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.
  • 29D. Pappagianis.

    Development of resistance to amphotericin B in Candida lusitaniae infecting a human, in: Antimicrob Agents Chemother., 1979, vol. 16, pp. 123-126.
  • 30R. 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
  • 31A. Romano, H. Trip, H. Campbell-Sills, O. Bouchez, D. Sherman, J. S. Lolkema, P. M. Lucas.

    Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines, in: Genome Announcements, January 2013, vol. 1, no 1, pp. e00097-12. [ DOI : 10.1128/genomeA.00097-12 ]

    https://hal.inria.fr/hal-00863284
  • 32S. T. Roweis, Z. Ghahramani.

    A unifying review of linear Gaussian Models, in: Neural Computation, 1999, vol. 11, no 2, pp. 305–45.
  • 33L. 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.
  • 34H. Teh.

    Differential metabolite profiles during fruit development in high-yielding oil palm mesocarp, in: PLoS One., 2013, vol. 8, no 4, e61344 p.
  • 35D. W. Thompson.

    On Growth and Form, Cambridge University Press, 1917.
  • 36A. Zimmer, C. Durand, N. Loira, P. Durrens, D. J. Sherman, P. Marullo.

    QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite, in: PLoS ONE, 2014, vol. 9, no 1, e86298 p. [ DOI : 10.1371/journal.pone.0086298 ]

    https://hal.inria.fr/hal-00986680
  • 37R. de Miranda.

    Clavispora, a new yeast genus of the Saccharomycetales, in: Antonie van Leeuwenhoek., 1979, vol. 45, pp. 479-483.


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