Team MAGNOME
Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Other Grants and Activities
Dissemination
Bibliography
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Bibliography

Major publications by the team in recent years

[1]
R. 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
http://hal.inria.fr/inria-00202721/en/.
[2]
G. Blandin, P. Durrens, F. Tekaia, M. Aigle, M. Bolotin-Fukuhara, E. Bon, S. Casarégola, 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, p. 31-36.
[3]
B. 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, p. 35-44
http://hal.archives-ouvertes.fr/hal-00104411/en/.
[4]
P. 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
http://hal.inria.fr/inria-00341569/en/.
[5]
H. 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, p. 177-83.
[6]
H. 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.
[7]
M. Nikolski, D. J. Sherman.
Family relationships: should consensus reign?- consensus clustering for protein families, in: Bioinformatics, 2007, vol. 23, p. e71–e76
http://hal.inria.fr/inria-00202434/en/.
[8]
D. 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
http://hal.inria.fr/inria-00341578/en/.
[9]
J.-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. 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, epub ahead of print p
http://hal.inria.fr/inria-00407511/en/.
[10]
M. Taussig, O. Stoevesandt, C. Borrebaeck, A. Bradbury, D. Cahill, C. Cambillau, A. de Daruvar, S. Duebel, J. Eichler, R. Frank, T. Gibson, D. Gloriam, L. Gold, F. Herberg, H. Hermjakob, J. Hoheisel, T. Joos, O. Kallioniemi, M. Koegll, Z. Konthur, B. Korn, E. Kremmer, S. Krobitsch, U. Landegren, S. van der Maarel, J. McCafferty, S. Muyldermans, P.-A. Nygren, S. Palcy, A. Plueckthun, B. Polic, M. Przybylski, P. Saviranta, A. Sawyer, D. J. Sherman, A. Skerra, M. Templin, M. Ueffing, M. Uhlen.
ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome, in: Nature Methods, 2007, vol. 4, no 1, p. 13–17.

Publications of the year

Doctoral Dissertations and Habilitation Theses

[11]
M. Nikolski.
From Genomic to Functional Models, Université Bordeaux 1 Sciences et Technologies, 10 2009
http://www.labri.fr/perso/macha, Habilitation à diriger des recherches.
[12]
H. Soueidan.
Discrete event modeling and analysis for Systems Biology models, Université Bordeaux 1 Sciences et Technologies, 12 2009
http://www.labri.fr/perso/soueidan, Ph. D. Thesis.

Articles in International Peer-Reviewed Journal

[13]
E. Bon, A. Delaherche, E. Bilhere, 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, no 7, p. 2079-90
http://hal.inria.fr/inria-00392015/en/.
[14]
G. 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/.
[15]
C. Payen, G. Fischer, C. Marck, C. Proux, D. J. Sherman, J.-Y. Coppée, M. Johnston, B. Dujon, C. Neuvéglise.
Unusual composition of a yeast chromosome arm is associated with its delayed replication., in: Genome Research, 2009, epub ahead of print p
http://hal.inria.fr/inria-00407518/en/.
[16]
D. J. Sherman.
Minimum information requirements : neither bandits in the Attic nor bats in the belfry, in: New Biotechnology, 2009, vol. 25, no 4, p. 173-4
http://hal.inria.fr/inria-00407505/en/.
[17]
D. 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
http://hal.inria.fr/inria-00341578/en/.
[18]
J.-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. 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, epub ahead of print p
http://hal.inria.fr/inria-00407511/en/.

Invited Conferences

[19]
R. Assar, H. Soueidan, D. J. Sherman.
Hierarchical study of Guyton Circulatory Model, in: Les Journées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2009, France Nantes, I. R. Eric Rivals (editor), Eric Rivals, Irena Rusu, 2009
http://hal.inria.fr/inria-00404135/en/.
[20]
P. Lucas, E. Bon, V. Renouf, M. Dols-Lafargue, C. Le Marrec, A. Lonvaud-Funel.
Oenococcus oeni genomic adaptation to the wine environment, in: SGM-Society for General Microbiology Autumn 2009 Meeting, Royaume-Uni Edinburg, 2009
http://hal.inria.fr/inria-00395530/en/.

International Peer-Reviewed Conference/Proceedings

[21]
T. Martin, M. Nikolski, D. J. Sherman, J.-L. Souciet, P. Durrens.
The Génolevures online database, in: Second German/ French/European/ Meeting Yeast and Filamentous Fungi, France Strasbourg, 2009
http://hal.inria.fr/inria-00409534/en/.
[22]
H. Soueidan, G. Sutre, M. Nikolski.
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/.
[23]
N. 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, Canada Montréal, F. Rothlauf (editor), ACM, ACM SIGEVO, 2009
http://hal.inria.fr/inria-00407508/en/.

National Peer-Reviewed Conference/Proceedings

[24]
E. Bon, A. Delaherche, E. Bilhere, C. Miot-Sertier, P. Durrens, A. De Daruvar, A. Lonvaud-Funel, C. Le Marrec.
Oenococcus oeni genome plasticity associated with adaptation to wine, an extreme ecological niche, in: JOBIM-10èmes Journées Ouvertes en Biologie, Informatique et Mathématiques, France Nantes, E. Rivals, I. Rusu (editors), 2009, p. 121-122
http://hal.inria.fr/inria-00392020/en/.
[25]
E. Bon, C. Miot-Sertier, M. Dols-Lafargue, G. Morel, A. Lonvaud-Funel, C. Le Marrec.
A 24 kb-genomic island contributing to Oenococcus oeni adaptation to wine can excise from the chromosome, in: 16th CBL-Club des Bactéries Lactiques Meeting, France Toulouse, 2009
http://hal.inria.fr/inria-00392022/en/.
[26]
F. El Garniti, C. Miot-Sertier, M. Dols-Lafargue, E. Bon, A. Lonvaud-Funel, C. Le Marrec.
IS30 elements as mediators of strain diversity in Oenococcus oeni, in: 16th CBL- Club des Bactéries Lactiques Meeting, France Toulouse, 2009
http://hal.inria.fr/inria-00396032/en/.
[27]
T. Martin, D. J. Sherman, M. Nikolski, J.-L. Souciet, P. Durrens.
Base de données Génolevures : génomique comparative des Hemiascomycetes, in: Journée Ouvertes Biologie Informatique Mathématiques, JOBIM 2009, France Nantes, E. Rivals, I. Rusu (editors), 2009, p. 181-182
http://hal.inria.fr/inria-00401915/en/.

Other Publications

[28]
H. Soueidan.
Extending Discrete Event Systems for the Hierarhical Specification, Analysis and Simulation of Systems Biology Models, in: Séminaire équipe INRIA IBIS, France, 2009
http://hal.archives-ouvertes.fr/hal-00407522/en/.

References in notes

[29]
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[30]
A. Bairoch, R. Apweiler, C. Wu, W. Barker, B. Boeckmann, e. al..
The Universal Protein Resource (UniProt), in: Nucleic Acids Res., 2005, vol. 33, p. D154–D159.
[31]
G. Blandin, P. Durrens, F. Tekaia, M. Aigle, M. Bolotin-Fukuhara, E. Bon, S. Casarégola, 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, p. 31-36.
[32]
J. Cherry, C. Adler, C. Ball, S. Chervitz, S. Dwight, E. Hester, Y. Jia, G. Juvik, T. Roe, M. Schroeder, S. Weng, D. Botstein.
SGD: Saccharomyces Genome Database, in: Nucleic Acids Res., 1998, vol. 26, p. 73–79.
[33]
P. Cliften, P. Sudarsanam, A. Desikan, L. Fulton, B. 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.
[34]
P. Cousot, R. Cousot.
Abstract interpretation: a unified lattice model for static analysis of programs by construction or approximation of fixpoints, in: Conference Record of the Fourth ACM Symposium on Principles of Programming Languages, January 1977, p. 238–252.
[35]
F. S. Dietrich, e. al..
The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome, in: Science, 2004, vol. 304, p. 304-7.
[36]
B. Dujon, D. J. Sherman, e. al..
Genome Evolution in Yeasts, in: Nature, 2004, vol. 430, p. 35–44.
[37]
P. 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
http://hal.inria.fr/inria-00341569/en/.
[38]
K. Eilbeck, S. Lewis, C. Mungall, M. Yandell, L. Stein, R. Durbin, M. Ashburner.
The Sequence Ontology: a tool for the unification of genome annotations, in: Genome Biology, 2005, vol. 6, R44 p.
[39]
R. Fielding, R. Taylor.
Principled design of the modern Web architecture, in: ACM Trans. Internet Technol., 2002, vol. 2, p. 115–150.
[40]
A. 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/.
[41]
M. Hucka, e. al..
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, in: Bioinformatics, 2003, vol. 19, no 4, p. 524-31.
[42]
F. Iragne, M. Nikolski, B. Mathieu, D. Auber, D. J. Sherman.
ProViz: protein interaction visualization and exploration, in: Bioinformatics, 2005, vol. 21, p. 272-274
http://hal.inria.fr/inria-00202436/en/.
[43]
C. Kanz, P. Aldebert, N. Althorpe, W. Baker, A. Baldwin, K. Bates, e. al..
The EMBL Nucleotide Sequence Database, in: Nucleic Acids Res., 2005, vol. 33 database issue, p. D29–D33.
[44]
M. 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.
[45]
M. Kellis, N. Patterson, M. Endrizzi, B. Birren, E. S. Lander.
Sequencing and comparison of yeast species to identify genes and regulatory elements, in: Nature, 2003, vol. 423, p. 241–254.
[46]
E. Korobkova, T. Emonet, J. Vilar, T. Shimizu, P. Cluzel.
From molecular noise to behavioural variability in a single bacterium., in: Nature, 2004, vol. 428, p. 574–578.
[47]
R. Koszul, S. Caburet, B. Dujon, G. Fischer.
Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments, in: EMBO Journal, 2004, vol. 23, no 1, p. 234-43.
[48]
H. Mewes, D. Frischman, U. Guldener, G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Munsterkotter, S. Rudd, B. Weil.
MIPS: a database for genomes and protein sequences, in: Nucleic Acids Res., January 2002, vol. 30, no 1, p. 31–34.
[49]
M. Nikolski, D. J. Sherman.
Family relationships: should consensus reign?- consensus clustering for protein families, in: Bioinformatics, 2007, vol. 23, p. e71–e76
http://hal.inria.fr/inria-00202434/en/.
[50]
D. 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
http://hal.inria.fr/inria-00407519/en/, GDR CNRS 2354 "Génolevures".
[51]
D. 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, no Database issue, p. D432-5
http://hal.archives-ouvertes.fr/hal-00118142/en/.
[52]
D. 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), 11 2008
http://hal.inria.fr/inria-00341578/en/, epub ahead of print.
[53]
T. F. Smith, M. Waterman.
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[54]
J.-L. Souciet, e. al..
FEBS Letters Special Issue: Génolevures, in: FEBS Letters, December 2000, vol. 487, no 1.
[55]
H. Soueidan, M. Nikolski, G. Sutre.
Syntaxe, Sémantique et abstractions de programmes AltaRica Dataflow, Université de bordeaux 1, 2005
http://www.labri.fr/~soueidan/, Masters thesis.
[56]
H. 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/.
[57]
J. Stajich, D. Block, K. Boulez, S. Brenner, S. Chervitz, e. al..
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L. D. Stein.
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Integrative Analysis of Cell Cycle Control in Budding Yeast, in: Mol. Biol. Cell, 2004, vol. 15, no 8, p. 3841-3862
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PIRSF: family classification system at the Protein Information Resource, in: Nucleic Acids Res., 2004, vol. 32, p. D315–D318.

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