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.
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, n^o 7, p. 650-3. [ DOI : 10.1038/nbt0710-650 ]

http://hal.inria.fr/inria-00544750/en
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, n^o 9, 145 p. [ 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, n^o 6995, p. 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, e1000200 p. [ 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, p. 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, p. e71–e76. [ 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, p. D550-D554. [ DOI : 10.1093/nar/gkn859 ]

http://hal.inria.fr/inria-00341578/en/
10J.-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. 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

11R. Assar.

Modeling and simulation of Hybrid Systems and Cell factory applications, Université Sciences et Technologies - Bordeaux I, October 2011.

http://hal.inria.fr/tel-00635273/en

Articles in International Peer-Reviewed Journal

12P. Durrens, T. Martin, D. J. Sherman.

The Génolevures database, in: Comptes Rendus de l'Académie des Sciences, Série Biologies, 2011.

http://hal.inria.fr/inria-00539200/en
13A. 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

Invited Conferences

14T. Martin.

Genolevures: automated annotation of yeast genome sequences, in: Comparative Genomics of Eukaryotic Microorganisms, Sant Feliu de Guixols, Spain, October 2011.

http://hal.inria.fr/hal-00640571/en
15D. J. Sherman, N. Golenetskaya.

Addressing scaling-out challenges for comparative genomics, in: Moscow Conference on Computational Molecular Biology, Moscow, Russian Federation, July 2011.

http://hal.inria.fr/hal-00649189/en

International Conferences with Proceedings

16A. 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
17T. Martin, P. Durrens.

Génolevures: Policy for Automated Annotation of Genome Sequences, in: JOBIM 2011, Paris, France, June 2011.

http://hal.inria.fr/inria-00614485/en
18T. Martin, D. J. Sherman, P. Durrens.

Genolevures : automated annotation of yeast genome sequences, in: Comparative Genomics of Eukaryotic Microorganisms, Sant Feliu de Guixols, Spain, October 2011.

http://hal.inria.fr/hal-00640575/en

National Conferences with Proceeding

19R. 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
20C. Blanchet, C. Gauthey, C. Caron, O. Collin, S. Delmotte, T. Martin, A. Roult, F. Samson, B. Spataro.

RENABI GRISBI Infrastructure Distribuée pour la Bioinformatique, in: JOBIM 2011 - Journées Ouvertes Biologie Informatique Mathématique, Paris, France, June 2011.

http://hal.inria.fr/hal-00640007/en

Conferences without Proceedings

21N. 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
22N. Golenetskaya, D. J. Sherman.

Rethinking global analyses and algorithms for comparative genomics in a functional MapReduce style, in: Algorithmique, combinatoire du texte et applications en bio-informatique (SeqBio 2011), Lille, France, December 2011.

http://hal.inria.fr/hal-00654797/en
23T. Martin, P. Durrens.

Un polymorphisme suspect, in: Unithé ou Café, Talence, France, June 2011.

http://hal.inria.fr/inria-00614484/en
24D. J. Sherman, N. Golenetskaya, T. Martin, P. Durrens.

Comparative annotation and scaling-out challenges for paraphyletic strategies, in: EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Understanding the Complexity of Diversity, San Feliu de Guixols, Spain, EMBO, October 2011.

http://hal.inria.fr/hal-00652903/en

References in notes

25R. 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
26A. 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/
27R. 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/
28E. 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/
29P. 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.
30M. 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
31J. Dean, S. Ghemawat.

MapReduce: simplified data processing on large clusters, in: Proceedings of the 6th conference on Symposium on Operating Systems Design and Implementation (OSDI'04), San Francisco, CA, 2004.
32F. 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.
33D. 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/
34P. 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.
35R. Fielding, R. Taylor.

Principled design of the modern Web architecture, in: ACM Trans. Internet Technol., 2002, vol. 2, p. 115–150.
36A. 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
37D. 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
38H. 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.
39H. 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.
40G. 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/
41M. 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.
42M. 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.
43S. 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/
44R. 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.
45N. 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/en
46N. 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
47P. 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.
48P. 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.
49I. 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.
50D. 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/
51D. 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/
52D. 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/
53H. 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/
54H. Soueidan, D. J. Sherman, M. Nikolski.

BioRica: A multi model description and simulation system, in: F0SBE, Allemagne, 2007, p. 279-287.

http://hal.archives-ouvertes.fr/hal-00306550/en/
55L. D. Stein.

The Generic Genome Browser: A building block for a model organism system database, in: Genome Res., 2002, vol. 12, p. 1599-1610.
56N. 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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