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, n^o 1, p. 31-36.
3E. Bon, A. Delaherche, E. Bilhère, A. De Daruvar, A. Lonvaud-Funel, C. Le Marrec.

Oenococcus oeni genome plasticity is associated with fitness, in: Applied and Environmental Microbiology, 2009, vol. 75, n^o 7, p. 2079-90.

http://hal.inria.fr/inria-00392015/en/
4J. 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, n^o 7, p. 650-3. [ DOI : 10.1038/nbt0710-650 ]

http://hal.inria.fr/inria-00544750/en
5A. 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, n^o 9, 145 p. [ DOI : 10.1038/ncomms1150 ]

http://hal.inria.fr/inria-00562005/en/
6B. 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, n^o 6995, p. 35-44. [ DOI : 10.1038/nature02579 ]

http://hal.archives-ouvertes.fr/hal-00104411/en/
7P. 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, e1000200 p. [ DOI : 10.1371/journal.pcbi.1000200 ]

http://hal.inria.fr/inria-00341569/en/
8A. 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, p. 315-322.

http://hal.archives-ouvertes.fr/hal-00341672/en/
9M. Nikolski, D. J. Sherman.

Family relationships: should consensus reign?- consensus clustering for protein families, in: Bioinformatics, 2007, vol. 23, p. e71–e76. [ DOI : 10.1093/bioinformatics/btl314 ]

http://hal.inria.fr/inria-00202434/en/
10D. 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, p. D550-D554. [ DOI : 10.1093/nar/gkn859 ]

http://hal.inria.fr/inria-00341578/en/
11J.-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, p. 1696-1709.

http://hal.inria.fr/inria-00407511/en/

Publications of the year

Doctoral Dissertations and Habilitation Theses

12N. Loira.

Scaffold-based Reconstruction Method for Genome-Scale Metabolic Models, Université Sciences et Technologies - Bordeaux I, January 2012.

http://hal.inria.fr/tel-00678991

Articles in International Peer-Reviewed Journals

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, n^o 1-3, p. 63-72. [ DOI : 10.1016/j.biosystems.2012.01.008 ]

http://hal.inria.fr/hal-00681022
14F. El Gharniti, M. Dols-Lafargue, E. Bon, O. Claisse, C. Miot-Sertier, A. Lonvaud-Funel, C. Le Marrec.

IS30 elements are mediators of genetic diversity in Oenococcus oeni., in: International Journal of Food Microbiology, August 2012, vol. 158, n^o 1, p. 14-22. [ DOI : 10.1016/j.ijfoodmicro.2012.06.009 ]

http://hal.inria.fr/hal-00722965
15V. Leh Louis, L. Despons, A. Friedrich, T. Martin, P. Durrens, S. Casaregola, C. Neuvéglise, C. Fairhead, C. Marck, J. A. Cruz, M.-L. Straub, V. Kugler, C. Sacerdot, Z. Uzunov, A. Thierry, S. Weiss, C. Bleykasten, J. De Montigny, N. Jacques, P. Jung, M. Lemaire, S. Mallet, G. Morel, G.-F. Richard, A. Sarkar, G. Savel, J. Schacherer, M.-L. Seret, E. Talla, G. Samson, C. Jubin, J. Poulain, B. Vacherie, V. Barbe, E. Pelletier, D. J. Sherman, E. Westhof, J. Weissenbach, P. Baret, P. Wincker, C. Gaillardin, B. Dujon, J.-L. Souciet.

Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization, in: Genes|Genomes|Genetics, February 2012, vol. 2, n^o 2, p. 299-311, the Consortium National de Recherche en Génomique (CNRG) to Génoscope, CNRS (GDR 2354, Génolevures), The computer framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program "Génotypage et Génomique Comparée," and the ACI IMPBIO "Génolevures En Ligne.". [ DOI : 10.1534/g3.111.000745 ]

http://hal.inria.fr/hal-00674198
16N. Loira, T. Dulermo, J.-M. Nicaud, D. J. Sherman.

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica., in: BMC Systems Biology, May 2012, vol. 6, n^o 1, 35 p. [ DOI : 10.1186/1752-0509-6-35 ]

http://hal.inria.fr/hal-00724286

Invited Conferences

17T. Martin.

Retour d'expérience : assemblage, in: Ecole NGS 2012 : De la production à l'analyse des données " Next Generation Sequencing ", Lyon, France, January 2012.

http://hal.inria.fr/hal-00734501

International Conferences with Proceedings

18R. Assar, M. A. Montecino, D. J. Sherman.

Stochastic Modeling of Complex Systems and Systems Biology: From Stochastic Transition Systems to Hybrid Systems, in: XII Latin American Congress of Probability and Mathematical Statistics, Viña del Mar, Chile, March 2012.

http://hal.inria.fr/hal-00686072
19R. 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), Lecture Notes in Computer Science, Springer, 2012, vol. 6479, p. 68–83. [ DOI : 10.1007/978-3-642-28067-2_6 ]

http://hal.inria.fr/inria-00541215
20L. 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, F. Cost, D. Tagu (editors), SFBI, Inria, July 2012, p. 435-436.

http://hal.inria.fr/hal-00722968
21A. 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-Funel, G. de Revel, P. Teissedre (editors), Dunod, Paris, April 2012, p. 358-363.

http://hal.inria.fr/hal-00646867
22T. Martin, P. Durrens.

Feedback in the management of genomic data in the GDR Génolevures, in: ICY2012 13th International Congress on Yeasts, Madison, United States, August 2012.

http://hal.inria.fr/hal-00734502

National Conferences with Proceeding

23L. Bourgeade, T. Martin, A. Goulielmakis, A. Lonvaud-Funel, P. Lucas, E. Bon.

Cracking the Pseudome Code: Inside the "silent" Psi-genes language to reconstruct Oenococcus oeni evolutionary adaptation to wine, in: 18th CBL-Club des Bactéries Lactiques Meeting, Clermont-Ferrand, France, UR CALITYSS - VetAgroSup (editor), May 2012, page 82 p.

http://hal.inria.fr/hal-00722971
24T. Martin, P. Durrens.

Génolevures : Politique d'annotation automatique des génomes de levures (YAGA), in: 10e rencontre Levures Modèles & Outils, Toulouse, France, Jean-Luc PARROU, April 2012.

http://hal.inria.fr/hal-00734500
25T. Martin.

Retour d'expérience dans la gestion des données génomiques au sein du GDR Génolevures., in: 10e rencontre Levures Modèles & Outils, Toulouse, France, Jean-Luc PARROU, April 2012.

http://hal.inria.fr/hal-00734499

References in notes

26R. Assar, A. Garcia, D. J. Sherman.

Modeling Stochastic Switched Systems with BioRica, in: Journées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2011, Paris, France, Institut Pasteur, July 2011, p. 297–304.

http://hal.inria.fr/inria-00617419/en
27R. 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, p. 68–83.

http://hal.inria.fr/inria-00541215/en
28A. Athane, E. Bilhère, E. Bon, P. Lucas, G. Morel, A. Lonvaud-Funel, C. Le Hénaff-Le Marrec.

Characterization of an acquired-dps-containing gene island in the lactic acid bacterium Oenococcus oeni, in: Journal of Applied Microbiology, 2008, Received 22 October 2007, revised 8 April 2008 & Accepted 8 May 2008 (In press).

http://hal.inria.fr/inria-00340058/en/
29R. 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, p. 3581-9. [ DOI : 10.1093/nar/gkh681 ]

http://hal.inria.fr/inria-00202722/en/
30G. 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, n^o 1, p. 31-36.
31E. Bon, S. Casaregola, G. Blandin, B. Llorente, C. Neuvéglise, M. Munsterkotter, U. Guldener, H.-W. Mewes, J. Van Helden, B. Dujon, C. Gaillardin.

Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns., in: Nucleic Acids Research, February 2003, vol. 31, n^o 4, p. 1121-35.

http://hal.inria.fr/inria-00339881/en/
32E. Bon, C. Granvalet, F. Remize, D. Dimova, P. Lucas, D. Jacob, A. Groppi, S. Penaud, C. Aulard, A. De Daruvar, A. Lonvaud-Funel, J. Guzzo.

Insights into genome plasticity of the wine-making bacterium Oenococcus oeni strain ATCC BAA-1163 by decryption of its whole genome., in: 9th Symposium on Lactic Acid Bacteria, Egmond aan Zee Netherlands, 2008.

http://hal.inria.fr/inria-00340073/en/
33P. Cliften, P. Sudarsanam, A. Desikan, L. Fulton, R. S. Fulton, J. Majors, R. Waterston, B. A. Cohen, M. Johnston.

Finding functional features in Saccharomyces genomes by phylogenetic footprinting, in: Science, 2003, vol. 301, p. 71–76.
34M. Cvijovic, H. Soueidan, D. J. Sherman, E. Klipp, M. Nikolski.

Exploratory Simulation of Cell Ageing Using Hierarchical Models, in: 19th International Conference on Genome Informatics Genome Informatics, Gold Coast, Queensland Australia, J. Arthur, S.-K. Ng (editors), Genome Informatics, Imperial College Press, London, 2008, vol. 21, p. 114–125, EU FP6 Yeast Systems Biology Network LSHG-CT-2005-018942, EU Marie Curie Early Stage Training (EST) Network “Systems Biology”, ANR-05-BLAN-0331-03 (GENARISE).

http://hal.inria.fr/inria-00350616
35F. S. Dietrich, et al..

The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome, in: Science, 2004, vol. 304, p. 304-7.
36D. Dimova, E. Bon, P. Lucas, R. Beugnot, M. De Leeuw, A. Lonvaud-Funel.

The whole genome of Oenococcus strain IOEB 8413, in: 9th Symposium on Lactic Acid Bacteria, Egmond aan Zee Netherlands, 2008.

http://hal.inria.fr/inria-00340086/en/
37A. Enache-Angoulvant, J. Guitard, F. Grenouillet, T. Martin, P. Durrens, C. Fairhead, C. Hennequin.

Rapid Discrimination between Candida glabrata, Candida nivariensis, and Candida bracarensis by Use of a Singleplex PCR, in: Journal of Clinical Microbiology, September 2011, vol. 49, n^o 9, p. 3375-3379. [ DOI : 10.1128/JCM.00688-11 ]

http://hal.inria.fr/inria-00625115/en
38P. Fickers, A. Marty, J.-M. Nicaud.

The lipases from Yarrowia lipolytica: genetics, production, regulation, biochemical characterization and biotechnological applications, in: Biotechnol Adv., Nov-Dec 2011, vol. 29, n^o 6, p. 632–44.
39R. Fielding, R. Taylor.

Principled design of the modern Web architecture, in: ACM Trans. Internet Technol., 2002, vol. 2, p. 115–150.
40A. 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, P02.446 p, Poster.

http://hal.inria.fr/inria-00529669/en
41D. 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, n^o 1, p. 1-10. [ DOI : 10.1074/mcp.M900185-MCP200 ]

http://hal.inria.fr/inria-00544751/en
42N. Golenetskaya, D. J. Sherman.

Assessing ”last mile” tools for affinity binder databases, in: 5th ESF Workshop on Affinity Proteomics: Ligand Binders against the Human Proteome, Alpbach, Austria, March 2011.

http://hal.inria.fr/hal-00653518/en
43A. Goulielmakis, J. Bridier, A. Barré, O. Claisse, D. J. 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, Dunod, Paris, January 2011.

http://hal.inria.fr/hal-00646867/en
44H. 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, n^o 2, p. 177-83.
45H. Hermjakob, L. Montecchi-Palazzi, C. Lewington, S. Mudali, S. Kerrien, S. Orchard, M. Vingron, B. Roechert, P. Roepstorff, A. Valencia, H. Margalit, J. Armstrong, A. Bairoch, G. Cesareni, D. J. Sherman, R. Apweiler.

IntAct: an open source molecular interaction database, in: Nucleic Acids Res., Jan. 2004, vol. 32, p. D452-5.
46G. 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/
47M. Kellis, B. Birren, E. Lander.

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae, in: Nature, 2004, vol. 428, p. 617-24.
48M. Kellis, N. Patterson, M. Endrizzi, B. Birren, E. Lander.

Sequencing and comparison of yeast species to identify genes and regulatory elements, in: Nature, 2003, vol. 423, p. 241–254.
49S. Kerrien, S. Orchard, L. Montecchi-Palazzi, B. Aranda, A. Quinn, N. Vinod, G. Bader, I. Xenarios, J. Wojcik, D. J. Sherman, M. Tyers, J. Salama, S. Moore, A. Ceol, A. Chatr-Aryamontri, M. Oesterheld, V. Stumpflen, L. Salwinski, J. Nerothin, E. Cerami, M. Cusick, M. Vidal, M. Gilson, J. Armstrong, P. Woollard, C. Hogue, D. Eisenberg, G. Cesareni, R. Apweiler, H. Hermjakob.

Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular, in: BMC Biology, 10 2007, vol. 5, 9;5(1):44 p.

http://hal.archives-ouvertes.fr/hal-00306554/en/
50R. Koszul, S. Caburet, B. Dujon, G. Fischer.

Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments, in: EMBO Journal, 2004, vol. 23, n^o 1, p. 234-43.
51N. 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, P02.602 p, Poster.

http://hal.inria.fr/hal-00652922
52N. 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
53P. Marullo, C. Mansour, M. Dufour, W. Albertin, D. Sicard, M. Bely, D. Dubourdieu.

Genetic improvement of thermo-tolerance in wine Saccharomyces cerevisiae strains by a backcross approach, in: FEMS Yeast Res, 12 2009, vol. 9, n^o 8, p. 1148–60.
54P. Marullo, G. Yvert, M. Bely, I. Masneuf-Pomarède, P. Durrens, M. Aigle.

Single QTL mapping and nucleotide-level resolution of a physiologic trait in wine Sacchar omyces cerevisiae strains, in: FEMS Yeast Res., 2007, vol. 7, n^o 6, p. 941–52.
55I. Masneuf-Pomarède, C. Lejeune, P. Durrens, M. Lollier, M. Aigle, D. Dubourdieu.

Molecular typing of wine yeast strains Saccharomyces uvarum using microsatellite ma rkers, in: Syst. Appl. Microbiol., 2007, vol. 30, n^o 1, p. 75–82.
56D. 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, p. D315-8, GDR CNRS 2354 “Génolevures”. [ DOI : 10.1093/nar/gkh091 ]

http://hal.inria.fr/inria-00407519/en/
57D. 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, n^o Database issue, p. D432-5. [ DOI : 10.1093/nar/gkj160 ]

http://hal.archives-ouvertes.fr/hal-00118142/en/
58D. J. Sherman, N. Golenetskaya.

Databases and Ontologies for Affinity Binders, 05 2010, Overview of advances in defining ontologies and building knowledge bases for affinity binders, over the four years of the ProteomeBinders project. Presented at the Affinomics/ProteomeBinders workshop at the Møller Center, Churchill College, Cambridge University..

http://hal.inria.fr/inria-00563531/en/
59H. Soueidan, M. Nikolski, G. Sutre.

Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models, in: Computational Methods in Systems Biology (CMSB'09), Italie Bologna, Springer Verlag, 2009, vol. 5688, p. 313–327.

http://hal.archives-ouvertes.fr/hal-00408909/en/
60H. Soueidan, D. J. Sherman, M. Nikolski.

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