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Bibliography

Major publications by the team in recent years
  • 1R. Barriot, D. J. Sherman, I. Dutour.

    How to decide which are the most pertinent overly-represented features during gene set enrichment analysis, in: BMC Bioinformatics, 2007, vol. 8. [ DOI : 10.1186/1471-2105-8-332 ]

    http://hal.inria.fr/inria-00202721/en/
  • 2G. Blandin, P. Durrens, F. Tekaia, M. Aigle, M. Bolotin-Fukuhara, E. Bon, S. Casaregola, J. de Montigny, C. Gaillardin, A. Lépingle, B. Llorente, A. Malpertuy, C. Neuvéglise, O. Ozier-Kalogeropoulos, A. Perrin, S. Potier, J.-L. Souciet, E. Talla, C. Toffano-Nioche, M. Wésolowski-Louvel, C. Marck, B. Dujon.

    Genomic Exploration of the Hemiascomycetous Yeasts: 4. The genome of Saccharomyces cerevisiae revisited, in: FEBS Letters, December 2000, vol. 487, no 1, pp. 31-36.
  • 3J. Bourbeillon, S. Orchard, I. Benhar, C. Borrebaeck, A. De Daruvar, S. Dübel, R. Frank, F. Gibson, D. Gloriam, N. Haslam, T. Hiltker, I. Humphrey-Smith, M. Hust, D. Juncker, M. Koegl, Z. Konthur, B. Korn, S. Krobitsch, S. Muyldermans, P.-A. Nygren, S. Palcy, B. Polic, H. Rodriguez, A. Sawyer, M. Schlapshy, M. Snyder, O. Stoevesandt, M. J. Taussig, M. Templin, M. Uhlen, S. Van Der Maarel, C. Wingren, H. Hermjakob, D. J. Sherman.

    Minimum information about a protein affinity reagent (MIAPAR), in: Nature Biotechnology, 07 2010, vol. 28, no 7, pp. 650-3. [ DOI : 10.1038/nbt0710-650 ]
  • 4A. 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 yeast strains, in: Nature Communications, 12 2010, vol. 1, no 9, Article number : 145. [ DOI : 10.1038/ncomms1150 ]

    http://hal.inria.fr/inria-00562005/en/
  • 5B. Dujon, D. J. Sherman, G. Fischer, P. Durrens, S. Casaregola, I. Lafontaine, J. De Montigny, C. Marck, C. Neuvéglise, E. Talla, N. Goffard, L. Frangeul, M. Aigle, V. Anthouard, A. Babour, V. Barbe, S. Barnay, S. Blanchin, J.-M. Beckerich, E. Beyne, C. Bleykasten, A. Boisramé, J. Boyer, L. Cattolico, F. Confanioleri, A. De Daruvar, L. Despons, E. Fabre, C. Fairhead, H. Ferry-Dumazet, A. Groppi, F. Hantraye, C. Hennequin, N. Jauniaux, P. Joyet, R. Kachouri-Lafond, A. Kerrest, R. Koszul, M. Lemaire, I. Lesur, L. Ma, H. Muller, J.-M. Nicaud, M. Nikolski, S. Oztas, O. Ozier-Kalogeropoulos, S. Pellenz, S. Potier, G.-F. Richard, M.-L. Straub, A. Suleau, D. Swennen, F. Tekaia, M. Wésolowski-Louvel, E. Westhof, B. Wirth, M. Zeniou-Meyer, I. Zivanovic, M. Bolotin-Fukuhara, A. Thierry, C. Bouchier, B. Caudron, C. Scarpelli, C. Gaillardin, J. Weissenbach, P. Wincker, J.-L. Souciet.

    Genome evolution in yeasts, in: Nature, 07 2004, vol. 430, no 6995, pp. 35-44. [ DOI : 10.1038/nature02579 ]

    http://hal.archives-ouvertes.fr/hal-00104411/en/
  • 6P. Durrens, M. Nikolski, D. J. Sherman.

    Fusion and fission of genes define a metric between fungal genomes, in: PLoS Computational Biology, 10 2008, vol. 4. [ DOI : 10.1371/journal.pcbi.1000200 ]

    http://hal.inria.fr/inria-00341569/en/
  • 7A. Goëffon, M. Nikolski, D. J. Sherman.

    An Efficient Probabilistic Population-Based Descent for the Median Genome Problem, in: Proceedings of the 10th annual ACM SIGEVO conference on Genetic and evolutionary computation (GECCO 2008), Atlanta United States, ACM, 2008, pp. 315-322.

    http://hal.archives-ouvertes.fr/hal-00341672/en/
  • 8M. Nikolski, D. J. Sherman.

    Family relationships: should consensus reign?- consensus clustering for protein families, in: Bioinformatics, 2007, vol. 23. [ DOI : 10.1093/bioinformatics/btl314 ]

    http://hal.inria.fr/inria-00202434/en/
  • 9D. 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/
  • 10J.-L. Souciet, B. Dujon, C. Gaillardin, M. Johnston, P. 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 Louis, M. Lemaire, J. De Montigny, C. Neuvéglise, A. Thierry, I. Blanc-Lenfle, C. Bleykasten, J. Diffels, E. Fritsch, L. Frangeul, A. Goëffon, 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.

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

Articles in International Peer-Reviewed Journals

  • 11P. Almeida, C. Gonçalves, S. Teixeira, D. Libkind, M. Bontrager, I. Masneuf-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, Article number: 4044. [ DOI : 10.1038/ncomms5044 ]

    https://hal.inria.fr/hal-01002466
  • 12R. Assar, M. A. Montecino, A. Maass, D. J. Sherman.

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

    https://hal.inria.fr/hal-01002987
  • 13W. Dyrka, M. Lamacchia, P. Durrens, B. Kobe, A. Daskalov, M. Paoletti, D. J. Sherman, S. J. Saupe.

    Diversity and variability of NOD-like receptors in fungi, in: Genome Biology and Evolution, November 2014, forthcoming. [ DOI : 10.1093/gbe/evu251 ]

    https://hal.inria.fr/hal-01083450
  • 14G. Kunze, C. Gaillardin, M. Czernicka, P. Durrens, T. Martin, E. Böer, T. Gabaldón, J. Cruz, E. Talla, C. Marck, A. Goffeau, V. Barbe, P. Baret, K. Baronian, S. Beier, C. Bleykasten, R. Bode, S. Casaregola, L. Despons, C. Fairhead, M. Giersberg, P. P. Gierski, U. Hähnel, A. Hartmann, D. Jankowska, C. Jubin, P. Jung, I. Lafontaine, V. Leh-Louis, M. Lemaire, M. Marcet-Houben, M. Mascher, G. Morel, G.-F. Richard, J. Riechen, C. Sacerdot, A. Sarkar, G. Savel, J. Schacherer, D. Sherman, N. Stein, M.-L. Straub, A. Thierry, A. Trautwein-Schult, B. Vacherie, E. Westhof, S. Worch, B. Dujon, J.-L. Souciet, P. Wincker, U. Scholz, C. Neuvéglise.

    The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest, in: Biotechnology for Biofuels, 2014, vol. 7, no 1, 66 p. [ DOI : 10.1186/1754-6834-7-66 ]

    https://hal-pasteur.archives-ouvertes.fr/pasteur-00988609
  • 15A. 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
  • 16A. Zhukova, D. J. Sherman.

    Knowledge-based generalization of metabolic networks: a practical study, in: Journal of Bioinformatics and Computational Biology, 2014, vol. 12(2), no 1441001. [ DOI : 10.1142/S0219720014410017 ]

    https://hal.inria.fr/hal-00906911
  • 17A. 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. [ DOI : 10.1371/journal.pone.0086298 ]

    https://hal.inria.fr/hal-00986680

Scientific Popularization

Other Publications

  • 19W. Dyrka, P. Durrens, M. Paoletti, S. J. Saupe, D. J. Sherman.

    Deciphering the language of fungal pathogen recognition receptors, October 2014.

    https://hal.inria.fr/hal-01083421
References in notes
  • 20R. Assar, F. Vargas, D. J. Sherman.

    Reconciling competing models: a case study of wine fermentation kinetics, in: Algebraic and Numeric Biology 2010, Austria Hagenberg, K. Horimoto, M. Nakatsui, N. Popov (editors), Research Institute for Symbolic Computation, Johannes Kepler University of Linz, 08 2010, pp. 68–83.
  • 21R. Barriot, J. Poix, A. Groppi, A. Barre, N. Goffard, D. J. Sherman, I. Dutour, A. De Daruvar.

    New strategy for the representation and the integration of biomolecular knowledge at a cellular scale, in: Nucleic Acids Research (NAR), 2004, vol. 32, pp. 3581-9. [ DOI : 10.1093/nar/gkh681 ]

    http://hal.inria.fr/inria-00202722/en/
  • 22L. Bourgeade, T. Martin, E. Bon.

    PSEUDOE: A computational method to detect Psi-genes and explore PSEUDome dynamics in wine bacteria from the Oenococcus genus, in: JOBIM2012- 13ème Journées Ouvertes en Biologie, Informatique et Mathématiques, Rennes, France, D. T. François Cost (editor), SFBI, Inria, July 2012, pp. 435-436.

    http://hal.inria.fr/hal-00722968
  • 23W. Dyrka, J.-C. Nebel, M. Kotulska.

    Probabilistic grammatical model for helix-helix contact site classification, in: Algorithms for Molecular Biology, 2013, vol. 8, 31 p. [ DOI : 10.1186/1748-7188-8-31 ]

    http://hal.inria.fr/hal-00923291
  • 24A. Garcia, D. J. Sherman.

    Mixed-formalism hierarchical modeling and simulation with BioRica, in: 11th International Conference on Systems Biology (ICSB 2010), United Kingdom Edimbourg, 10 2010, Poster.
  • 25D. Gloriam, S. Orchard, D. Bertinetti, E. Björling, E. Bongcam-Rudloff, C. Borrebaeck, J. Bourbeillon, A. R. M. Bradbury, A. De Daruvar, S. Dübel, R. Frank, T. J. Gibson, L. Gold, N. Haslam, F. W. Herberg, T. Hiltker, J. D. Hoheisel, S. Kerrien, M. Koegl, Z. Konthur, B. Korn, U. Landegren, L. Montecchi-Palazzi, S. Palcy, H. Rodriguez, S. Schweinsberg, V. Sievert, O. Stoevesandt, M. J. Taussig, M. Ueffing, M. Uhlén, S. Van Der Maarel, C. Wingren, P. Woollard, D. J. Sherman, H. Hermjakob.

    A community standard format for the representation of protein affinity reagents, in: Mol Cell Proteomics, 01 2010, vol. 9, no 1, pp. 1-10. [ DOI : 10.1074/mcp.M900185-MCP200 ]
  • 26A. Goulielmakis, J. Bridier, A. Barré, O. Claisse, David James. Sherman, P. Durrens, A. Lonvaud-Funel, E. Bon.

    How does Oenococcus oeni adapt to its environment? A pangenomic oligonucleotide microarray for analysis O. oeni gene expression under wine shock, in: OENO2011- 9th International Symposium of Oenology, Bordeaux, France, P. Darriet, L. Geny, P. Lucas, A. Lonvaud, G. de Revel, P. Teissedre (editors), Dunod, Paris, April 2012, pp. 358-363.

    http://hal.inria.fr/hal-00646867
  • 27H. Hermjakob, L. Montecchi-Palazzi, G. Bader, J. Wojcik, L. Salwinski, A. Ceol, S. Moore, S. Orchard, U. Sarkans, C. von Mering, B. Roechert, S. Poux, E. Jung, H. Mersch, P. Kersey, M. Lappe, Y. Li, R. Zeng, D. Rana, M. Nikolski, H. Husi, C. Brun, K. Shanker, S. Grant, C. Sander, P. Bork, W. Zhu, A. Pandey, A. Brazma, B. Jacq, M. Vidal, D. J. Sherman, P. Legrain, G. Cesareni, I. Xenarios, D. Eisenberg, B. Steipe, C. Hogue, R. Apweiler.

    The HUPO PSI's molecular interaction format–a community standard for the representation of protein interaction data, in: Nat. Biotechnol., Feb. 2004, vol. 22, no 2, pp. 177-83.
  • 28G. Jean, D. J. Sherman, M. Nikolski.

    Mining the semantics of genome super-blocks to infer ancestral architectures, in: Journal of Computational Biology, 2009.

    http://hal.inria.fr/inria-00414692/en/
  • 29N. Loira, T. Dulermo, M. Nikolski, J.-M. Nicaud, D. J. Sherman.

    Genome-scale Metabolic Reconstruction of the Eukaryote Cell Factory Yarrowia Lipolytica, in: 11th International Conference on Systems Biology (ICSB 2010), United Kingdom Edimbourg, 10 2010, Poster.
  • 30N. Loira, D. J. Sherman, P. Durrens.

    Reconstruction and Validation of the genome-scale metabolic model of Yarrowia lipolytica iNL705, in: Journée Ouvertes Biologie Informatique Mathématiques, JOBIM 2010, France Montpellier, 09 2010.

    http://www.jobim2010.fr/?q=fr/node/55
  • 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, e00097-12. [ DOI : 10.1128/genomeA.00097-12 ]

    http://hal.inria.fr/hal-00863284
  • 32D. J. Sherman, P. Durrens, E. Beyne, M. Nikolski, J.-L. Souciet.

    Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts, in: Nucleic Acids Research (NAR), 2004, vol. 32, GDR CNRS 2354 “Génolevures”. [ DOI : 10.1093/nar/gkh091 ]

    http://hal.inria.fr/inria-00407519/en/
  • 33D. J. Sherman, P. Durrens, F. Iragne, E. Beyne, M. Nikolski, J.-L. Souciet.

    Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts, in: Nucleic Acids Res, 01 2006, vol. 34. [ DOI : 10.1093/nar/gkj160 ]

    http://hal.archives-ouvertes.fr/hal-00118142/en/
  • 34N. Vyahhi, A. Goëffon, D. J. Sherman, M. Nikolski.

    Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement Scenarios, in: ACM SIGEVO Conference on Genetic and evolutionary computation, F. Rothlauf (editor), ACM, 2009.

    http://hal.inria.fr/inria-00407508/en/


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