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PROGRAMME D'EPIGÉNOMIQUE

dernière mise à jour : 01/07/2010

 Créé en 2002, le Programme d'Epigénomique, dont le maître mot est « modéliser pour comprendre », se veut d'abord un lieu de rencontres pour catalyser des recherches autour de problèmes biologiques complexes avec des apports de disciplines différentes : biologie, informatique, mathématiques, physique théorique, chimie artificielle...

C'est à la fois un lieu de formation des chercheurs à une autre discipline que la leur, un programme de visiteurs dont l'une des missions est d'attirer et de stabiliser des chercheurs internationalement reconnus, un réseau (à dominante francophone) de recherches pluridisciplinaires se réunissant régulièrement, un creuset de « défrichage scientifique » suscitant l'invention de nouveaux sujets de recherche et les soutenant par des actions thématiques ciblées, et un service commun local qui centralise les efforts de recherche en modélisation pour la biologie sur le campus évryen.

Les chercheurs peuvent s'y rencontrer selon quatre modes de fonctionnement : les groupes de travail récurrents, l'incubation de jeunes équipes, les actions thématiques ciblées et les conférences nationales et internationales. Chaque action soutenue par le Programme d’Epigénomique est très ciblée au plan thématique, et est centrée autour de quelques chercheurs de haut niveau.

Ce programme hérite des groupes de travail génopolitains qui ont renouvelé depuis 2000 la problématique de la modélisation en fonction de la nouvelle donne en biologie. Ceci représente un «coeur» de 70 chercheurs se réunissant régulièrement, originaires principalement d'Evry, Rouen, Bordeaux, Lyon, Poitiers, Nice, Paris et Montpellier et un « halo » totalisant environ deux cent cinquante personnes lors des manifestations annuelles (écoles thématiques).

Contact
Sylvie Bobelet

Genopole campus 1 - Genavenir 6
5, rue Henri Desbruères
91030 EVRY cedex
Téléphone : 01 69 47 44 30
Fax : 01 69 47 44 37
Contact : sylvie.bobelet@epig
enomique.genopole.fr

THÈMES ET ÉQUIPES

Thèmes :

 

 

 

Membres :

 

 

MEMBRES

Membres :

  •  François Képès - DR CNRS, Directeur du Programme Epigénomique
  • Marc Aiguier - Professeur, École Centrale de Paris
  • Gilles Bernot  Co-directeur, Professeur, Université de  Nice
  • Sylvie Bobelet - Assistante
  • Odile Bronchain - MCF, Université Paris sud 11
  • Bogdana Burlacu - ITA
  • Pablo Carbonell - Post-doc
  • Joelle Compaore - Etudiante PhD
  • Mohamed Elati - MCF, Université d'Evry Val d'Essonne
  • Jean-Loup Faulon - Professeur , Université d'Evry Val d'Essonne
  • Davide Fichera - Post-doc
  • Joan Hérisson - Post-doc CNRS, GENNETEC
  • Alfonso Jaramillo - CR1 CNRS
  • Ivan Junier - Post-doc CNRS, GENNETEC
  • Boris Kirov - Etudiant PhD
  • Thomas Landrain - Etudiant PhD
  • Pascale Le Gall - Professeur, Université d'Évry Val d'Essonne
  • Corine Le Grand - Assistante
  • Matthieu Manceny - Etudiant PhD Université Évry Val d'Essonne
  • Mbarka Mabrouki - Etudiante PhD Université Évry Val d'Essonne
  • Mariel Montesinos -  Chargée de mission
  • Victor Norris - Co-directeur, Université de Rouen
  • Elodie Paillard - Assistante Ingénieure, CDD
  • Nicolas Pollet - CR1 CNRS
  • Sophie Pollet -CR INRA
  • Mathieu Poudret -  PhD, Université Évry Val d'Essonne
  • Thimo Rohlf - Post-doc
  • Vijai Singh - Post-doc
  • Ludivine Sinzelle - Post-doc Genopole

 

PUBLICATIONS

Autres publications

 

Publications François Képès

Articles
  • 1. Képès, F., and Képès, A. (1980). Synchronisation automatique de la croissance de Escherichia coli. Ann. Microbiol. 131, 3-16.
  • 2. Képès, F., and Képès, A. (1981). Long-lasting synchrony of the division of enteric bacteria. Biochem. Biophys. Res. Comm. 99, 761-767.
  • 3. Képès, F., and Képès, A. (1984). Freeze-preservation of synchrony in cultures of Enterobacteriaceae synchronized by continuous phasing in phosphate-limited media. Biotech. Bioeng. 26, 1288-1293.
  • 4. Joseleau-Petit, D., Képès, F., and Képès, A. (1984). Cyclic changes of the rate of phospholipid synthesis during synchronous growth of Escherichia coli. Eur. J. Biochem. 139, 605-611.
  • 5. Képès, F., and Képès, A. (1985). Postponement of cell division by nutritional shift-up in Escherichia coli. J. Gen. Microbiol. 131, 677-685.
  • 6. Képès, F. (1985). Mécanismes d'efflux d'un substrat accumulé par la lactose perméase de Escherichia coli : étude théorique et expérimentale. Biochimie 67, 69-73.
  • 7. Képès, F. (1986). The cell cycle of Escherichia coli and some of its regulatory systems. FEMS Microbiol. Rev. 32, 225-246.
  • 8. Plateau, P., Fromant, M., Képès, F., and Blanquet, S. (1987). Intracellular 5',5'-dinucleoside polyphosphate levels remain constant during the Escherichia coli cell cycle. J. Bacteriol. 169, 419-422.
  • 9. Képès, F., and D'Ari, R. (1987). Involvement of FtsZ protein in shift-up-induced division delay in Escherichia coli. J. Bacteriol. 169, 4036-4040.
  • 10. Joseleau-Petit, D., Képès, F., Peutat, L., D'Ari, R., and Képès, A. (1987). DNA replication initiation, doubling of rate of phospholipid synthesis, and cell division in Escherichia coli. J. Bacteriol. 169, 3701-3706.
  • 11. Képès, F., Joseleau-Petit, D., Legros, M., and Képès, A. (1987). Early increases in the frequency of DNA initiations and of phospholipid synthesis discontinuities after nutritional shift-up in Escherichia coli. Eur. J. Biochem. 164, 205-211.
  • 12. Cook, W. R., Képès, F., Joseleau-Petit, D., MacAlister, T. J., and Rothfield, L. I. (1987). Proposed mechanism for generation and localization of new cell division sites during the division cycle of Escherichia coli. Proc. Natl. Acad. Sci. USA 84, 7144-7148.
  • 13. Képès, F., and Schekman, R. (1988). The yeast SEC53 gene encodes phosphomannomutase. J. Biol. Chem. 263, 9155-9161.
  • 14. Bernstein, M., Képès, F., and Schekman, R. (1989). SEC59 encodes a membrane protein required for core glycosylation in Saccharomyces cerevisiae. Mol. Cell. Biol. 9, 1191-1199.
  • 15. Deshaies, R. J., Képès, F., and Böhni, P. C. (1989). Genetic dissection of the early stages of protein secretion in yeast. TIG 5, 87-93.
  • 16. Joseleau-Petit, D., Képès, F., Peutat, L., D'Ari, R., and Rothfield, L. I. (1990). Biosynthesis of a membrane adhesion zone fraction throughout the cell cycle of Escherichia coli. J. Bacteriol. 172, 6573-6575.
  • 17. Képès, F., Joseleau-Petit, D., Rothfield, L. I., and Plateau, P. (1990). Biochemical analysis of cyclic events involved in bacterial cell division. In Stratégie d'utilisation des substrats pour la production de métabolites microbiens, 13ème colloque. J. M. Lebeault and J. G. Pan, eds. (Paris: Société Française de Microbiologie), pp. 65-84.
  • 18. Liang, S., Lacroute, F., and Képès, F. (1993). Multicopy STS1 restores both protein transport and ribosomal RNA stability in a new yeast sec23 mutant allele. Eur. J. Cell Biol. 62, 270-281.
  • 19. Esnault, Y., Blondel, M.O., Deshaies, R.J., Schekman, R., and Képès, F. (1993). The yeast SSS1 gene is essential for secretory protein translocation and encodes a conserved protein of the endoplasmic reticulum. EMBO J. 12, 4083-4093.
  • 20. Rambourg, A., Clermont, Y., and Képès, F. (1993). Modulation of the Golgi apparatus in Saccharomyces cerevisiae sec7 mutants as seen by three-dimensional electron microscopy. The Anatomical Record 237, 441-452.
  • 21.  Jackson, C.L., and Képès, F. (1994). BFR1, a multicopy suppressor of Brefeldin A-induced lethality, is implicated in secretion and nuclear segregation in S. cerevisiae. Genetics 137, 423-437.
  • 22. Norris, V. et al., Képès, F., et al. (1994). Cell cycle control: prokaryotic solutions to eukaryotic problems? J. theor. Biol.168,227-230
  • 23. Rambourg, A., Clermont, Y., Jackson, C.L., and Képès, F. (1994). Ultrastructural modification of vesicular and Golgi elements in the Saccharomyces cerevisiae sec21 mutant. The Anatomical Record 240, 32-41.
  • 24. Esnault, Y., Feldheim, D., Blondel, M.O., Schekman, R., and Képès, F. (1994). SSS1 encodes a stabilizing component of the Sec61 subcomplex of the protein translocation apparatus. J. Biol. Chem. 269, 27478-27485.
  • 25. Képès, F. (1994). Contributor in "Guidebook to the secretory pathway" (Eds. Rothblatt, J., Novick, P., and Stevens, T.), A Sambrook and Tooze publication at Oxford University Press.
  • 26. Esnault, Y., and Képès, F. (1994). L'appareil eucaryote de translocation des protéines sécrétoires, in "Trafic des Protéines chez les Microorganismes". Les Cahiers IMABIO 11, 45-50.
  • 27. Rambourg, A., Clermont, Y., Jackson, C.L., and Képès, F. (1995). Effects of Brefeldin A on the three-dimensional structure of the Golgi apparatus in a sensitive strain of Saccharomyces cerevisiae. The Anatomical Record 241, 1-9.
  • 28. Rambourg, A., Clermont, Y., Ovtracht, L., and Képès, F. (1995). Three-dimensional structure of tubular networks, presumably Golgi in nature, in various yeast strains: a comparative study. The Anatomical Record 243, 283-293.
  • 29. Rambourg, A., Clermont, Y., Nicaud, J.-M., Gaillardin, C., and Képès, F. (1996). Transformations of membrane-bound organelles in sec14 mutants of the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica. The Anatomical Record 245, 447-458.
  • 30. Rambourg, A., Gachet, E., Clermont, Y., and Képès, F. (1996). Modifications of the Golgi apparatus in Saccharomyces cerevisiae lacking microtubules. The Anatomical Record 246, 162-168.
  • 31. Képès, F. (1996). The '+70 pause' : hypothesis of a translational control of membrane protein assembly. J. Mol. Biol.262, 77-86.
  • 32 Beswick, V., Baleux, F., Huynh-Dinh, T., Képès, F., Neumann, J.M., and Sanson, A. (1996). NMR conformational study of the cytoplasmic domain of the canine Sec61g protein from the protein translocation pore of the endoplasmic reticulum membrane. Biochemistry 35, 14717-14724.
  • 33. Ikonomova, R., Sommer, T., and Képès, F. (1997). The Srp40 protein plays a non-essential role in stable RNA synthesis or assembly, and depends on a novel carboxy-terminal motif for proper localization to skeletal structures within the yeast nucleus. DNA and Cell Biology 16, 1161-1173.
  • 34. Wilkinson, B., Esnault, Y., Craven, R.A., Skiba, F., Fieschi, J., Képès, F., and Stirling, C.J. (1997). Molecular architecture of the ER translocase probed by chemical crosslinking of Sss1p to complementary fragments of Sec61p. EMBO J. 16, 4549-4559.
  • 35. Chabane, S., Gachet, E., and Képès, F. (1998). Overexpression of the yeast BFR2 gene partially suppresses the growth defects induced by Brefeldin A and by four ER-to-Golgi mutations. Curr. Genet. 33, 21-28.
  • 36. Chabane, S., and Képès, F. (1998). Expression of the BFR2 gene is regulated at the transcriptional level and through degradation of its product. Mol. Gen. Genet. 258, 215-221.
  • 37. Morin-Ganet, M.N., Rambourg, A., Clermont, Y., and Képès, F. (1998). Role of ER-derived vesicles in the formation of Golgi elements in sec23 and sec18 Saccharomyces cerevisiae mutants. The Anatomical Record 251, 256-264.
  • 38. Beswick, V., Brodsky, J., Képès, F., Neumann, J.M., Sanson, A., and Garrigos, M. (1998). Expression, purification and characterization of Sss1p, an essential component of the yeast Sec61p protein translocation complex. Protein Expression and Purification 13, 423-432.
  • 39. Ben Mamoun, C., Beckerich, J.-M., Gaillardin, C., and Képès, F. (1999). Disruption of YHC8, a member of the TSR1 gene family, reveals its direct involvement in yeast protein translocation. J. Biol. Chem.274, 11296-11302.
  • 40.  Képès, F. (1999). Le rêve du génomicien. Geninfo 2, 3.
  • 41. Morin-Ganet, M.N., Rambourg, A., Deitz S.B., Franzusoff A., and Képès, F. (2000). Morphogenesis and dynamics of the yeast Golgi apparatus. Traffic 1, 56-68.
  • 42.  Deitz, S.B., Rambourg, A., Képès, F., and Franzusoff, A. (2000). Sec7p directs the transitions required for yeast Golgi biogenesis. Traffic 1, 172-183.
  • 43. Dessen, P., and Képès, F. (2000). The PAUSE software for analysis of translational control over protein targeting: applications to E. nidulans membrane proteins. Gene 244, 89-96.
  • 44. Képès, F. (2001). La simulation à l'ère de la génomique. Biofutur 210, 46-51.
  • 45. Képès, F. (2001). Simulation of biological processes in the genomic context. Biology International 41, 29-38.
  • 46. Mérigout, P., Képès, F., Perret, A.M., Satiat-Jeunemaitre, B., and Moreau, P. (2002). Effects of brefeldin A and nordihydroguaiaretic acid on endomembrane dynamics and lipid synthesis in plant cells. FEBS Letters 518, 88-92.
  • 47. Guelzim, N., Bottani, S., Bourgine, P. and Képès, F. (2002). Topological and causal structure of the yeast transcriptional regulatory network. Nature Genetics 31, 60-63.
  • 48. Képès, F., Delaplace, F., Delosme, J.-M., Guespin, J., Incitti, R. and Norris, V. (2002) Modelling and simulating biological processes in the genomic era: an account of a multidisciplinary seminar held in Autrans (France) in March 2002. J Biol Phys Chem 2, 62-66.
  • 49. Képès, F., Delaplace, F., Delosme, J.-M., Guespin, J., Incitti, R. and Norris, V. (2002) Modelling and simulating biological processes in the genomic era. Biology International 43, 36-41.
  • 50. Képès, F., Delaplace, F., Delosme, J.-M., Guespin, J., Incitti, R. and Norris, V. (nov. 2002) Modelling and simulating biological processes in the genomic era. European Communications in Mathematical and Theoretical Biology 4.
  • 51. Képès, F. and Carbone, A. (2002). Modelling macromolecular networks: two meetings in Paris, July, 2002. Bioessays 24,1188-1190.
  • 52. Képès, F. (2002). Secretory compartments as instances of dynamic self-evolving structures. Acta Biotheoretica 50, 209-221.
  • 53. Amar, P. et al., Képès, F. et al. [alphabetical order] (2002). Hyperstructures, genome analysis and I-cells. Acta Biotheoretica 50, 357-373.
  • 54. Képès, F. (2003). Membrane traffic in virtual reality. Traffic 4, 13-17.
  • 55. Flamant, S., Pescher, P., Lemercier, B., Clement-Ziza, M., Képès, F., Fellous, M., Milon, G., Marchal, G. and Besmond, C. (2003). Characterization of a putative type IV aminophospholipid transporter P-type ATPase. Mammalian Genome 14, 21-30.
  • 56. Képès, F. (2003). Integrative biology of molecular networks and beyond. Biology International 44, 48-60.
  • 57. Képès, F., Tracqui, P. and Thellier, M. (2003). Modelling and simulation of biological processes in the context of genomics. C. R. Biologies 326, 457-458.
  • 58. Carbone, A., Zinovyev, A. and Képès, F. (2003). Codon Adaptation Index as a measure of dominating codon bias. Bioinformatics 19, 2005-2015.
  • 59. Képès, F. (2003). Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites. J Mol Biol 329, 859-865.
  • 60. Képès, F. (2003). On the transcription-based solenoidal model of chromosomes. Epigenomics of molecular networks. Proceedings of SNA'03, #143.
  • 61. Norris, V., Amar, P., Bernot, G., Giavitto, J.-L., Godin, C., Guespin, J., Pollard, H., Tracqui, P. and Képès, F. (2003). Modelling and simulation of biological processes in the context of genomics. J Biol Phys Chem 3, 106-110.
  • 62. Képès, F. and Vaillant, C. (2003). Transcription-based solenoidal model of chromosomes. ComPlexUs 1, 171-180.
  • 63. Képès, F. (2004). Periodic transcriptional organization of the E. coli genome. J Mol Biol 340, 957-964.
  • 64. Omont, N. and Képès, F. (2004). Transcription/replication complex collisions cause bacterial transcription units to be longer on the leading strand of replication. Bioinformatics 20, 2719-2725.
  • 65. Képès, F., Amar, P., Barlovatz, G., Bernot, G., Froidevaux, C., Giavitto, J.-L., Guespin, J., Molina, F., Norris, V., Schächter, V., and Tracqui, P. (2004). Modelling and simulating biological processes in the genomic era. J Biol Phys Chem 4, 131-136.
  • 66. Sipos, G., Brickner, J. H., Brace, E. J., Chen, L., Davis, N. G., Rambourg, A., Képès, F. and Fuller, R. S. (2004). Soi3/Rav1p functions at the early endosome to regulate endocytic trafficking to the vacuole and localization of TGN transmembrane proteins. Mol Biol Cell 15, 3196-3209.
  • 67. Bourguignon P.-Y., Guedj M., Képès F., Matias C., Nuel G., Omont N., Prum B. (2004) Recherche de gènes impliqués dans une maladie, Compte Rendu des Journées Math et Industrie, Matapli 74, 33-41.
  • 68. Carbone, A., Képès, F. and Zinovyev, A. (2005). Codon Bias Signatures, Organisation of Microorganisms in Codon Space and Lifestyle. Mol Biol Evol 22, 547-561.
  • 69. Képès, F. (2005). L’épigénétique comme aspect de la postgénomique. Médecine / Sciences 21, 371-376.
  • 70. Omont, N. and Képès, F. (2005). Developmental modularity and evolutionary canalization. BioEssays 27, 667-668.
  • 71. Mercier, G., Berthault, N., Touleimat, N., Képès, F., Fourel, G., Gilson, E. and Dutreix, M. (2005). A haploid-specific transcriptional response to irradiation in Saccharomyces cerevisiae. Nucleic Acids Res. 33, 6635-6643.
  • 72. Schächter, V., Danos, V., Smidtas, S. and Képès, F. (2005). Graph shuffle. In "Computational Methods in Systems Biology". Edinburgh, UK.
  • 73. Bourgine, P., Képès, F. and Schoenauer, M. (2005). Towards a science of complex systems. ComPlexUs 2 (3-4), 109.
  • 74. Hunding, A., Képès, F., Lancet, D., Minsky, A., Norris, V., Raine, D., Sriram, K. and Root-Bernstein, R. (2006). Compositional complementarity and prebiotic ecology in the origin of life. Bioessays 28, 399-412.
  • 75. Matte-Tailliez, O., Hérisson, J. , Ferey, N., Magneau, O., Gros, P. E., Képès, F. and Gherbi, R. (2006). Yeast Naked DNA Spatial Organization Predisposes to Transcriptional Regulation. Lecture Notes in Computer Science 3980, pp. 222 - 231. In "Computational Science and Its Applications - ICCSA 2006: International Conference, Glasgow, UK, May 8-11, 2006. Proceedings, Part I (Editors:  Marina Gavrilova, Osvaldo Gervasi, Vipin Kumar, C. J. Kenneth Tan, David Taniar, Antonio Laganà, Youngsong Mun, Hyunseung Choo).
  • 76. Thierry, A.R., Képès, F., et al. (2006). Modelling of complex biological systems in the context of genomics: an account of a multidisciplinary thematic seminar held in Montpellier (France) in April 2005. J Biol Phys Chem 6, 103-107.
  • 77. Smidtas, S., Schächter, V. and Képès, F. (2006). The adaptive filter of the yeast galactose pathway. J. Theor. Biol. 242, 372-381.
  • 78. Banzhaf, W., Beslon, G., Christensen, S., Foster, J.A., Képès, F., Lefort, V., Miller, J.F., Radman, M. and Ramsden, J.J. (2006). From Artificial Evolution to Computational Evolution:  a research agenda. Nature Reviews Genetics 7, 729-735.
  • 79. Sriram, K., Bernot, G. and Képès, F. (2006). Discrete delay model for the mammalian circadian rhythm. ComPlexUs 3,185-199.
  • 80. Smidtas, S., Yartseva, A., Schächter, V., Képès, F. (2006). Model of interactions in biology and application to heterogeneous network in yeast. C. R. Biol. 329, 945-952.
  • 81. Bourgine, P., Képès, F. and Schoenauer, M. (2006). Towards a science of complex systems. ComPlexUs 3 (1-3), 7.
  • 82. Bourguignon, P.Y., Danos, V., Képès, F., Smidtas, S. and Schächter, V. (2006). Property-driven statistics of biological networks. Transactions on Computational Systems Biology 6, 1-15 (Lecture Notes in Computer Science, Springer-Verlag).
  • 83. Bernot, G. and Képès, F. (2007). Le Programme d'Épigénomique. In "Modélisation et simulation pour la post-génomique" (eds. J.-P. Comet & M. Kaufman). Technique et Science Informatiques 26, 237-240.
  • 84. Sriram, K., Bernot, G. and Képès, F. (2007). A minimal mathematical model combining several regulatory cycles from the budding yeast cell cycle. IET Systems Biology 1, 326-341.
  • 85. Yartseva, A., Devillers, R., Klaudel, H. and Képès, F. (2007). From MIN model to ordinary differential equations. Journal of Integrative Bioinformatics 4, 61. http://journal.imbio.de/index.php?paper_id=61
  • 86. Képès, F. (2007). Le modèle solénoïde des chromosomes. Biofutur 282, 48-51.
  • 87. Yartseva, A., Klaudel, H., Devillers, R. and Képès, F. (2007). Incremental and unifying modelling formalism for biological interaction networks. BMC Bioinformatics 8:433. http://www.biomedcentral.com/1471-2105/8/433
  • 88. Norris, V., Hunding, A., Képès, F., Lancet, D., Minsky, A., Raine, D., Root-Bernstein, R. and Sriram, K. (2007). Question 7: the first units of life were not simple cells. Orig Life Evol Biosph 37, 429-43.
  • 89. Poudret, M., Arnould, A., Comet, J.-P., Le Gall, P., Meseure, P. and Képès, F. (2008). Topology-based abstraction of complex biological systems: Application to the Golgi apparatus. Theory in Biosciences 127, 79-88.
  • 90. Bikard, D. and Képès, F. (2008). Succès de la première équipe française lors de la compétition iGEM de biologie synthétique. Médecine / Sciences 24, 541-544.
BOOK CHAPTERS
  • 1. Rambourg, A., Delosme, J.-M., Incitti, R., Satiat-Jeunemaître, B., Tracqui, P. and Képès, F. (2002). Modeling the dynamics of secretory compartments. Proceedings of the Autrans seminar (eds. Amar, Képès, Norris & Tracqui), p. 147-168.
  • 2. Képès, F., Rambourg, A. and Satiat-Jeunemaître, B. (2005). Morphodynamics of the secretory pathway. International Review of Cytology 242, p. 55-120.
  • 3. Képès, F. (2006). Morphodynamique de la voie sécrétoire. In Morphogenèse, l'origine des formes (eds. Borugine & Lesne), p. 1 29-152 (Belin, Paris).
  • 4. Képès, F. (2007). Transcriptional networks (Chapter 4). In Biological networks (ed. Képès). "Complex systems and inter-disciplinary science" series, Vol. 3, pp. 83-131. World Scientific, Singapour; ISBN 978-981-270-695-9.
  • 5.  Képès, F. (2007). Formalismes mathématiques : des standards de fait. In Biologie systémique, standards et modèles (ed. Roux), pp. 199-214 (Ecrin; Omniscience). ISBN 978-2-916097-12-1.
  • 6. Leclercq, S. and Képès, F. (2008). Épigénomique et Morphodynamique. Proceedings of "Déterminismes et complexités: de la physique à l'éthique (autour d'Henri Atlan)" (eds. Bourgine, Chavalarias, Cohen-Boulakia),  (La Découverte). ISBN 978-2-7071-5090-5.
  • 7. Poudret, M., Comet, J.-P., Le Gall, P., Képès, F., Arnould, A., Meseure, P., Verbavatz, J.-M. and Rambourg, A. (2008). Toward a computer-aided methodology for topology-based simulation of the Golgi apparatus. Proceedings of the Lille Thematic School (eds. Amar, Képès, Norris & Vandenbunder), p. 89-104 (EDP Sciences). ISBN 978-2-7598-0075-9.
  • 8. Rambourg, A., Daraspe, J., Képès, F. and Verbavatz, J.-M. (2008). Morphodynamics of the yeast Golgi apparatus. In "The Golgi complex: the state of the art 110 years after Camillo Golgi's discovery" (eds. Mironov, Pavelka & Luini). In the press.

Publications JL Faulon

Articles publiés (revues d’audience internationale avec comité de rédaction)

  • 70. Faulon J.L., Misra M., Martin S., Sale, K., Sapra R.. Genome Scale Enzyme-metabolites and Drug-Target interaction predictions using the signature molecular descriptor, Bioinformatics, 24, 225-233, 2008.
  • 69. Sara P. Gaucher, Jeffrey A. Morrow, and J.L. Faulon. Use of a Designed Peptide Array to Infer Dissociation Trends for Non-Tryptic Peptides in Quadrupole Ion Trap and Quadrupole Time of Flight Mass Spectrometry, Analytical Chemistry, 79, 7822-7830, 2007.
    68. Gray G.A. , Williams P.J., Brown W.M., Faulon J.L.,  Sale K. Disparate Data Fusion for Protein Phosphorylation Prediction”, Annals of Operations Research Special Volume on Data Mining, in press 2007.
  • 67. Zhang Z., Martino A., Faulon J.L.. Global analysis of IL-2 responsive genes in murine T Cell, Journal of Interferon & Cytokine Research, 27, 991-995, 2007.
  • 66. Joo J., Plimpton S., Martin S., Swiler L., Slepoy A., Faulon J.L., Sensitivity analysis of  computational model of the NF-κB-IκB-A20 signal transduction network, Annals of NY Academy of Sciences, in press 2007.
  • 65. Oprea T., Tropsha A., Faulon J.L., Rintoul M.D. Systems Chemical Biology, Nature Chem. Bio., 3, 447-50, 2007.
  • 64. Martin S., Zhang Z., Martino A., Faulon J.L. Boolean Dynamics of Genetic Regulatory Networks Inferred from Microarray Time Series Data, Bioinformatics, 23, 866-74, 2007.
  • 63. Brown W. M., Martin S., Rintoul M.D., Faulon J.L. The Signature Molecular Descriptor. 6. Designing Novel Polymers with Targeted Properties, J. Chem. Info. & Model., 46, 826-835, 2006.
  • 62. Brown W. M., Martin S., Chabarek J.P., Strauss C, Faulon J.L. Prediction of β-Strand Packing Interactions using the Signature Product, Journal of Molecular Modeling, 12, 355-361, 2006.
  • 61. Martin S., R. D. Carr R.D., Faulon J.L. Random Removal of Edges from Scale Free Graphs, Physica A. 37, 870-876, 2006.
  • 60. Faulon J.L., Brown W.M., Martin S Reverse engineering chemical structures from molecular descriptors: how many solutions? J. Comput Aided Mol Des., 2005, 1-14.
  • 59. Brown W.M., Faulon J.L., Sale K. A deterministic algorithm for constrained enumeration of transmembrane protein folds. Comput Biol Chem., 29, 143-150, 2005.
  • 58. Weis D., Faulon J.L., Visco D. The Signature Molecular Descriptor. 5. The Design of Hydrofluoroether Foam Blowing Agents Using Inverse-QSAR, Ind. Eng. Chem. Res., 44, 8883-8891, 2005.
  • 57. Sale K, Faulon J.L., Gray G.A., Schoeniger J.S., Young M.M. Optimal bundling of transmembrane helices using sparse distance constraints. Protein Science, 13, 2613-2627, 2004.
  • 56. Martin S., Roe D., Faulon J.L. Predicting Protein-Protein Interactions using Signature Products, Bioinformatics, 21, 218-26, 2005.
  • 55. Faulon J.L., Collins M., Carr R.D.  The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequence, J. Chem. Inf. Comput. Sci., 44, 427-436, 2004.
  • 54. Churchwell C. J., Rintoul M. D, Martin S., Visco D., Kotu, A., Larson R. S., Sillerud L. O. Brown D. C., Faulon J.L.  The Signature Molecular Descriptor. 3. Inverse Quantitative Structure-Activity Relationship of ICAM-1 Inhibitory Peptides  J. Molecular Graphics & Modelling., 22, 263-273, 2004.
  • 53. Diallo M.S, Strachan A., Faulon J.L., Goddard W.A. Properties of Petroleum Geomacromolecules Through Computer Assisted Structure Elucidation and Atomistic Simulations.1. Bulk Arabian Light Asphaltenes, Petroleum Science and Technology, 22, 877-899, 2004.
  • 52. Faulon J.L., Visco D., Churchwell C. J., The Signature Molecular Descriptor. 2. Enumerating Molecules from their Extended Valence Sequences, J. Chem. Inf. Comput. Sci., 43, 721-734, 2003.
  • 51. Faulon J.L., Visco D., Pophale R.S. The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR studies,  J. Chem. Inf. Comput. Sci., 43, 707-720, 2003.
  • 50. Faulon J.L., Sale K, Young M.M., Exploring the conformational space of membrane protein folds matching distance constraints, Protein Science, 12, 1750-1761, 2003.
  • 49. Diallo M.S., Simpson A., Gassman P., Faulon J.L., Johnson Jr. J.H., Goddard W.A., Hatcher P.G. 3-D Structural Modeling of Humic Acids through Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Clesea Soil Humic Acid. Environ. Sci. & Technol 37, 1783-1793, 2003.
  • 48. Faulon J.L., Rintoul M. D., Young, M. M. Constrained Self-Avoiding Walks: Implications for Protein Structure Determination,  J. Phys. A: Gen. Math., 34, 1-20, 2002.
  • 47. Heffelfinger G.S., Martino A., Gorin A., Xu Y., Rintoul M.D., Geist A. Al-Hashimi, H. M. , Davidson, G.S. , Faulon J.-L. , Frink L.J. , Haaland D. M. , Hart W.E. , Jakobsson E. , Lane T.,  Li M., LoCascio P. , Olken F. , Olman V. , Palenik B. , Plimpton S.J. , Roe D.C. , Samatova N. F. , Shah M. , Shoshoni A. , Strauss C.  , Thomas E.V. , Timlin J.A. , Xu D. Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling. OMICS, 6, 4, 305-330, 2002.
  • 46. Visco D, Pophale R.S., Rintoul, M. D., Faulon J. L.,  Developing a Methodology for an Inverse Quantitative Structure-Activity Relationship Using the Signature Molecular Descriptor, J. Molecular Graphics & Modelling, 20, 429-438, 2002.
  • 45. Faulon J. L., Stochastic Generator of Chemical Structure. (4) Building Polymeric Systems with Specified Properties, J. Comput. Chem., 22, 580-590, 2001.
  • 44. Faulon J. L. , Sault A. G. Stochastic Generator of Chemical Structure (3) Reaction Network, J. Chem. Inf. Comput. Sci, 41, 894 -908, 2001.
  • 43. Faulon J. L., Automorphism Partitioning, and Canonical Labeling Can Be Solved in Polynomial-Time for Molecular Graphs, J. Chem. Inf. Comput. Sci., 38, 432-444, 1998.
  • 42. Tokarski J. S., Hopfinger A. J., Hobbs, J. D., Ford D. M., Faulon J. L., Molecular Modeling of Polymer 17.  Simulation and QSPR Analyses of Transport Behavior in Amorphous Polymeric Materials, Computational and Theoretical Polymer Science, 23, 199-214, 1997.
  • 41. Faulon J. L., Stochastic Generator of Chemical Structure. (2) Using Simulated Annealing to Search the Space of Constitutional Isomers, J. Chem. Inf. Comput. Sci., 36, 731-740, 1996.
  • 40. Pohl P. I., Faulon J. L., Smith D. M., Pore Structure of Imogolite Computer Model, Lamgmuir, 12, 4463-4468, 1996.
  • 39. Kowaleski I., Vandenbroucke M., Taylor, J.,  Faulon J. L., Huc, A. , Preliminary Results  on Molecular Modeling of Asphaltene using Structure Elucidation Programs in Conjonction with  Molecular Simulation Programs, Energy and Fuels, 10, 97-107, 1996.
  • 38. Kowaleski I., Vandenbroucke M., Faulon J. L., Taylor J., Behar F., Huc A., Asphaltene Molecular Modeling of Boscan Crude Oil, Revue de l'I.F.P., 51, 161-170, 1996.
  • 37. Faulon J.L., Unraveling complex molecules, CHEMTECH, 25, 16-23, 1995.
  • 36. Faulon J. L., Loy D. A., Carlson G. A., Shea K. J.  Computer-aided Structure  Elucidation for Arylsilsesquioxane Gels, Computational Materials Science, 3,  334-346, 1995.
  • 35. Pohl P. I., Faulon J. L., Smith D. M., Molecular Dynamics Computer Simulations of  Silica Aerogels, J. Non Cryst. Solids, 186, 349-355, 1995.
  • 34. Faulon J. L., Stochastic Generator of Chemical Structure. (1) Application to the  Structure Elucidation of Large Molecules, J. Chem. Inf. Comput. Sci., 34, 1204-1218, 1994.
  • 33. Faulon J. L., Carlson G.A., Hatcher P. G., A Three-Dimensional Model for Lignocellulose from Gymnospermous Wood, Org. Geochem., 211, 1169-1179, 1994.
  • 32. Faulon J.L., Hatcher P. G., Is There Any Order in the Structure of Lignin ?, Energy and Fuels, 8, 402-407, 1994.
  • 31. Faulon J. L., Mathews J. P., Carlson G. A., Hatcher P. G., Correlation Between  Microporosity and Fractal Dimension of Bituminous Coal Based on Computer-Generated  Models, Energy and Fuels, 8, 408-414, 1994.
  • 30. Faulon J. L., Calculating the number averaged molecular weight (Mo) of aromatic and  hydroaromatic clusters in coal using rubber elasticity theory, Energy and Fuels, 8, 1020-1024, 1994.
  • 29. Faulon J. L., Carlson G. A., Hatcher P. G., Statistical Model for Bituminous Coal:  A Three-Dimensional Evaluation of Structural and Physical Properties Based on Computer-Generated Structures, Energy and Fuels, 7, 1062-1072, 1993.
  • 28. Faulon J. L., Hatcher P. G., Carlson, G.A., Wenzel K. A., A computer-aided Molecular Model for High Volatile Bituminous Coal, Fuel Processing Technology, 34, 277-293, 1993.
  • 27. Faulon J.L., On Using the Graph-Equivalent Classes for the Structure Elucidation of Large Molecules, J. Chem. Inf. Comput. Sci., 32, 338-348, 1992.
  • 26. Hatcher P.G, Faulon J.L., Wenzel K. A., Cody G. D., A Structural Model for  Lignin-Derived Vitrinite from High-Volatile Bituminous Coal (Coalified Wood), Energy and Fuel, 6, 813-820, 1992.
  • 25. Faulon J.L., Vandenbroucke M., Drappier J.M., Behar, F., Romero M., 3D Chemical Model for Geological Macromolecules, Org. Geochem., 16, 981-993, 1990.
  • 24. Faulon J.L., Vandenbroucke M., Drappier J.M., Behar F., Romero M., Modeling the Chemical Structures of Sedimentary Macromolecules: The Xmol Software, Revue de l'I.F.P., 45, 161-180, 1989.
  • 23. Faulon J.L., Drappier J.M., Bellevaux C., Elimination des parties cachees par les  silhouettes, Revue Internationale de CFAO et d'Infographie, 3, 57-76, 1988.

Publications Alfonso Jaramillo

Articles
  • 1.Guillermo Rodrigo and Alfonso Jaramillo. Computational design of digital and memory biological devices. To appear in the journal Systems and Synthetic Biology 2008.
  • 2.Daniele Sciretti, Pierpaolo Bruscolini, Alessandro Pelizzola, Marco Pretti and Alfonso Jaramillo. Computational protein design with side-chain conformational entropy. To appear in Proteins 2008.
  • 3.G. Rodrigo, J. Carrera and A. Jaramillo. Asmparts: Assembly of Biological Model Parts. journal Systems and Synthetic Biology 2008. DOI: 10.1007/s11693-008-9013-4.
  • 4.M. Suarez, P. Tortosa, J. Carrera and A. Jaramillo. Pareto Optimization in Computational Protein Design with Multiple Objectives. To appear in J. Comp. Chem 2008.
  • 5.G. Rodrigo, J. Carrera and A. Jaramillo. In silico evolution of the oscillatory response under light-dark cycles. Biochimie 2008. DOI: 10.1016/j.biochi.2008.02.012
  • 6.J. Noirel, S.Y. Ow, G. Sanguinetti, A. Jaramillo and P.C. Wright. Automated extraction of meaningful pathways from quantitative proteomics data. To appear in Briefings in Functional Genomics and Proteomics 2008. DOI: 10.1093/bfgp/eln011.
  • 7.G. Rodrigo, J. Carrera et A. Jaramillo, Genetdes: automatic design of transcriptional networks. Bioinformatics 2007 23(14):1857-1858.
  • 8.G. Rodrigo, J. Carrera et A. Jaramillo, Evolutionary mechanisms of circadian clocks. Cent. Eur. J. Biol. 2 (2007) 233-253.
  • 9.G. Rodrigo, A. Montagud, A. Aparici, M.C. Aroca, M. Baguena, J. Carrera, C. Edo, P. Fernandez-de-Cordoba, A. Ferrando, G. Fuertes, D. Gimenez, C. Mata, J.V. Medrano, C. Navarrete, E. Navarro, J. Salgado, P. Tortosa, . UrChudguia et A. Jaramillo. Vanillin Cell Sensor. IET Synthetic Biology, 1 (2007) 74-78.
  • 10.A. Jaramillo et S.J. Wodak. Computational Protein Design Is a Challenge for Implicit Solvation Models. Biophys J. 88 (2005), 156-171.
  • 11.K. Ogata, A. Jaramillo, W. Cohen, J. Briand, F. Connan and S.J. Wodak. Automatic Sequence Design of MHC Class-I Binding Peptides Impairing CD8+T Cell Recognition. J. Biol. Chem. 278 (2003), 1281-1290.
  • 12.A. Jaramillo, L. Wernisch, S. Hery et S.J. Wodak. Folding free energy function selects native-like protein sequences in the core but not on the surface. Proc. Natl. Acad. Sci. 99 (2002), 13554-13559.
  • 13.A. Jaramillo, S.J. Wodak, L. Wernisch et S. Hery. Automatic procedures for protein design. Combinatorial Chemistry and High Throughput Screening 4, 639-655 (2001).
  • 14.A. Jaramillo et P. Mansfield. Finite VEVs from a Large Distance Vacuum Wave Functional. International Journal of Modern Physics 15, 581-600 (2000).
  • 15.A. Jaramillo et P. Mansfield. Non-perturbative VEVs from a local expansion. Acta Physica Polonica B29, 2487-2492 (1998). 
  • 16.M. Baig, J. Clua et A. Jaramillo. Numerical Simulation of Random Paths with a Curvature Dependent Action. Modern Physics Letters A13, 2131 (1998).
  • 17.A. Ferrando and A. Jaramillo. The Role of Temperature in a Dimensional Approach to QCD.Nuclear Physics B457, 57 (1995).
  • 18.A. Ferrando et A. Jaramillo. Two dimensional Quantum Chromodynamics as the limit of higher dimensional theories.Physics Letters B341, 342 (1995).
  • 19.A. Jaramillo, G. Parente, J.L. Diaz-Cruz et O.A. Sampayo. Using F_L as a test of compositeness. Physics Letters B336, 80 (1994).
Manuscripts in peer-review (available upon request)
  • 1.Maria Suarez, Pablo Tortosa and Alfonso Jaramillo. PROTDES: CHARMM toolbox for computational protein design. Submitted to BMC Bioinformatics. MS: 1049743263197735.
  • 2.Maria Suarez, Pablo Tortosa, Maria M. Garcia-Mira, David Rodriguez-Larrea, Raquel Godoy-Ruiz, Beatriz Ibarra-Moreno, J.M. Sanchez-Ruiz, Alfonso Jaramillo, Using multi-objective computational design to extend protein promiscuity. Submitted to PNAS MS#2008-04838.
  • 3.Guillermo Rodrigo, Javier Carrera, Kristala Jones Prather, and Alfonso Jaramillo. DESHARKY: Automatic design of metabolic pathways for optimal cell growth. Submitted to Bioinformatics. MS: BIOINF-2008-0823.
  • 4.Patricia Agudelo-Romero, Pablo Carbonell, Francisca de la Iglesia, Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo, Miguel A. Pérez-Amador and Santiago F. Elena. Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Submitted to Virology Journal. MS: 8477040802031613.


Publications Nicolas Pollet

Revues internationales

2010

  • Pollet, N. Expression of immune genes during metamorphosis of Xenopus : a survey. (2010) Frontiers in Bioscience 15:348-358.

 2009

  • Ymlahi-Ouazzani, Q., Bronchain, O.J., Paillard, E., Ballagny, C., Chesneau, A., Jadaud, A., Mazabraud, A. and Pollet, N. Reduced levels of survival motor neuron protein leads to aberrant motoneuron growth in a Xenopus model of muscular atrophy. Neurogenetics in press doi : 10.1007/s10048-009-0200-6
  • Khokha, M.K., V. Krylov, M.J. Reilly, J.G. Gall, D. Bhattacharya, C.Y. Cheung, S. Kaufman, D.K. Lam, J. Macha, C. Ngo, N. Prakash, P. Schmidt, T. Tlapakova, T. Trivedi, L. Tumova, A. Abu-Daya, T. Geach, E. Vendrell, H. Ironfield, L. Sinzelle, A.K. Sater, D.E. Wells, R.M. Harland, and L.B. Zimmerman. (2009). Rapid gynogenetic mapping of Xenopus tropicalis mutations to chromosomes. Dev Dyn 238 : 1398-1346.doi:10.1002/dvdy.21965
  • Gilchrist, M.J., Christensen, M.B., Bronchain, O., Brunet, F., Chesneau, A., Fenger, U., Geach, T.J., Ironfield, H.V., Kaya, F., Kricha, S., Lea, R., Massé, K., Néant, I., Paillard, E., Parain, K., Perron, M., Sinzelle, L., Souopgui, J., Thuret, R., Ymlahi-Ouazzani, Q. and Pollet, N. (2009) Database of queryable gene expression patterns for Xenopus. Dev Dyn. 238:1379-88. doi:10.1002/dvdy.21940
  • Boistel, R., Pollet, N., Tinevez, J-Y., Cloetens, P. and Schlenker, M. Irradiation damage to frog inner ear during synchrotron radiation tomographic investigation. (2009) Journal of Electron Spectroscopy and Related Phenomena - Radiation damage special issue. 170:37-41. doi:10.1016/j.elspec.2008.09.004
  • Rödel, M.O., Kosuch, J., Grafe, T.U.,Boistel,R., Assemian, N.E., Kouamé, N.G., Tohé, B., Gourène, G., Perret, J.-L., Henle, K., Tafforeau, P., Pollet, N. and Veith, M. (2009) A new tree-frog genus and species from Ivory Coast, West Africa (Amphibia : Anura : Hyperoliidae). Zootaxa 2044:23-45.

 2008

  • Chesneau, A., Sachs, L.M., Chai, N., Chen, Y., Du Pasquier, L., Loeber, J., Pollet, N., Reilly, M., Weeks, D.L. and Bronchain, O.J. (2008) Transgenesis procedures in Xenopus. Biol Cell 100:503-21.
  • Fierro, A.C., Thuret, R., Engelen, K., Bernot, G., Marchal, K. and Pollet, N. (2008) Evaluation of time profile reconstruction from complex two-color microarray designs. BMC Bioinformatics 9:1. online.
  • Bowes, J., Synder, K., Segerdell, E., Gibb, R., Jarabek, C., Noumen, E., Pollet, N. and Vize, P. (2008) Xenbase : a Xenopus biology and genomics resource. Nucleic Acids Res. doi : 10.1093/nar/gkm826.online
  • Graindorge, A., Le Tonquèze, O., Thuret, R., Pollet, N., Osborne, H.B. and Audic Y. (2008) Identification of CUG-BP1/EDEN-BP target mRNAs in Xenopus tropicalis. Nucleic Acids Research. doi:10.1093/nar/gkn031
  • Deutsch, E.W., Ball, C.A., Berman, J.J., Bova, G.S., Brazma, A., Bumgarner, R.E., Campbell, D., Causton, H.C., Christiansen, J.H., Daian, F., Dauga, D., Davidson, D.R., Gimenez, G., Goo, Y.A., Grimmond, S., Henrich, T., Herrmann, B.G., Johnson, M.H., Korb, M., Mills, J.C., Oudes, A.J., Parkinson, H.E., Pascal, L.E., Pollet, N., Quackenbush, J., Ramialison, M., Ringwald, M., Salgado, D., Sansone, S.A., Sherlock, G., Stoeckert, C.J. Jr, Swedlow, J., Taylor, R.C., Walashek, L., Warford, A., Wilkinson, D.G., Zhou, Y., Zon, L.I., Liu, A.Y., True, L.D. (2008) Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat. Biotechnol. 26:305-12.
  • Segerdell, E., Bowes, J.B., Pollet, N. and Vize, P.D. (2008) An ontology for Xenopus anatomy and development. BMC Developmental Biology 8:92. doi:10.1186/1471-213X-8-92 online
  • Gilchrist, M.J., Christensen, M.B., Harland, R., Pollet, N., Smith, J.C., Ueno, N. and Papalopulu, N. (2008) Evading the annotation bottleneck : using sequence similarity to search non-sequence gene data. BMC Bioinformatics 9:442. doi:10.1186/1471-2105-9-442 highly accessed

 2007

  • Troncale, S., Thuret, R., Ben, C., Pollet, N., Comet, J.-P. and Bernot, G. (2007) Modelling of the TH-dependent regulation of tadpole tail resorption. Journal of Biological Physics and Chemistry 7:45-50.
  • Bronchain, O. [°], Pollet, N. [°], Ymlahi-Ouazzani, Q., Dhorne-Pollet, S., Helbling, J.C., Lecarpentier, J.E., Percheron, K., Wegnez, M. (2007) The Olig family : phylogenetic analysis and early gene expression in Xenopus tropicalis. Development, Genes and Evolution. 217:485-97.
  • Fierro, A.C. [°], Thuret, R., [°] Coen, L., Perron, M., Demeneix, B.A., Wegnez, M., Gyapay, G., Weissenbach, J., Wincker, P., Mazabraud, A., Pollet, N. (2007) Exploring the nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis. BMC Genomics 8:118. online.
  • Du Pasquier, D., Chesneau, A., Ymlahi-Ouazzani, Q., Boistel, R., Pollet, N., Ballagny, C., Sachs, L.M., Demeneix, B., Mazabraud, A. (2007) TBid mediated Activation of the Mitochondrial Death Pathway leads to Genetic Ablation of the lens in Xenopus laevis. Genesis 45:1-10.

 2006

  • Pasquet, S., Naye, F., Faucheux, C., Bronchain, O., Chesneau, A., Thiebaud, P., Theze, N. (2006) TEF-1 dependent expression of the alpha-tropomyosin gene in the three muscle cell types. J Biol Chem. 281:34406-20. online.
  • Petit, A., Rouleux-Bonnin, F., Lambelé, M., Pollet, N., Bigot, Y. Properties of the various Botmar1 transcripts in imagoes of the bumble bee, Bombus terrestris (Hymenoptera : Apidae). Gene 390:52-66.
  • Sinzelle, L., Vallin, J., Coen, L., Chesneau, A., Du Pasquier, D., Pollet, N., Demeneix, B., Mazabraud, A. (2006) Generation of transgenic Xenopus laevis using the Sleeping Beauty transposon. Transgenic Research. 15:751-60.
  • Du Pasquier, D., Rincheval, V., Sinzelle, L., Chesneau, A., Ballagny, C., Sachs, L.M., Demeneix, B., Mazabraud , A. (2006) Developmental cell death during Xenopus metamorphosis involves BID cleavage and caspase 2 and 8 activation.Dev Dyn. (8):2083-94.
  • Du Pasquier D., Chesneau Phung A., Ymlahi Ouazzani Q., Sinzelle L., Ballagny C., Bronchain O., Du Pasquier L., Mazabraud A. (2006) Survivin increased vascular development during Xenopus ontogenesis. Differentiation 73:1-10.
  • Van Campenhout, C., Nichane, M., Antoniou, A, Pendeville, H., Bronchain, O., Marine, J.-C., Mazabraud, A., Voz, M., Bellefroid, E.J. (2006) Evi1 has a conserved restricted expression profile in vertebrate embryos and regulates pronephros development. Dev. Biol. 294:203-19.
  • Sinzelle, L., Chesneau, A., Bigot, Y., Mazabraud, A. and Pollet, N. (2006) The mariner transposons belonging to the irritans subfamily were maintained in chordate genomes by vertical transmission. J. Mol. Evol. 62:53-65.
  • Graindorge, A., Thuret, R., Pollet, N., Osborne, B and Audic, Y. (2006) Identification of post-transcriptionally regulated Xenopus tropicalis maternal mRNAs by microarray. Nucleic Acids Res. 34:986-95.
  • Pollet, N. and Mazabraud, A. (2006) "The Xenopus genomes" in Volff J-N "Vertebrate Genomes." Genome dynamics Basel, Karger, 2006, vol 2, pp 138-153.

 2005

  • Osborne, H.B., Gautier-Courteille, C., Graindorge, A., Barreau, C., Audic, Y., Thuret, R., Pollet, N. and Paillard, L. (2005) Post-transcriptional regulation in Xenopus embryos : role and targets of EDEN-BP. Biochem Soc Trans. 33:1541-3.
  • Coolen, M., Sii-Felice, K., Bronchain, O., Mazabraud, A., Bourrat, F., Retaux, S., Felder-Schmittbuhl, M.P., Mazan, S., Plouhinec, J.L.. (2005) Phylogenomic analysis and expression patterns of large Maf genes in Xenopus tropicalis provide new insights into the functional evolution of the gene family in osteichthyans. Dev Genes Evol 215:327-39.
  • Sinzelle, L., Pollet, N., Bigot, Y. and Mazabraud, A. (2005) Characterization of multiple lineages of Tc1-like elements within the genome of the amphibian Xenopus tropicalis. Gene 349:187-196.Sinzelle et al., Gene 2005 349:187-96
  • Pollet, N., Muncke, N., Verbeek, B., Li, Y., Fenger, U., Delius, H. and Niehrs, C. (2005) An atlas of differential gene expression during early Xenopus embryogenesis. Mech. Dev. 122:365-439.Pollet et al., Mech Dev. 2005 ; 122(3):365-439.

 2004

  • Konig, R., Baldessari, D., Pollet, N., Niehrs, C. and Eils, R. (2004) Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design. Nucleic Acids Res. 32:29.
  • Bottcher, R.T., Polmet,N.( Delius, H. and Niehrs, C. (6004)"Txe transmembrane protein XFLRT3 forms a complex with FGF receptors and promotes FGF signalling. Nat Cell Biol. 6:38-44.

 2003

  • Li, Y, Fenger, U., Niehrs, C. and Pollet, N. (2003) Cyclic expression of esr9 gene in Xenopus presomitic mesoderm. Differentiation. 71 :83-89.
  • Pollet, N., Delius, H. and Niehrs, C. (2003) Analyse In Situ de l’expression des gènes dans les embryons de Xénope. Comptes Rendus Biologies. 326:1011-1017.

 2001

  • du Pasquier D., Coen L., Le Mével S., Brown S., Tata J., Mazabraud A. and Demeneix B. (2001). Metamorphic degeneration of Rohon-Beard and Mauthner neurons is delayed by overexpression of a Xenopus Bcl-XL homologue, XR11, Proc. Natl. Acad. Sci. USA, 98, 7869-7874.
  • Nutt SL, Bronchain OJ, Hartley KO, Amaya E. (2001) Comparison of morpholino based translational inhibition during the development of Xenopus laevis and Xenopus tropicalis. Genesis. 30:110-3.
  • Chen, Y., Pollet, N., Niehrs, C. and Pieler, T. (2001). Increased XRALDH2 activity has a posteriorizing effect on the central nervous system of Xenopus embryos. Mech. Dev. 101 :91-103.
  • Lamar, E., Deblandre, G., Wettstein, D., Gawantka, V., Pollet, N., Niehrs, C. and Kintner, C. (2001). Nrarp is a novel intracellular component of the Notch signaling pathway. Genes Dev. 15 :1885-99.
  • Duncan, P. I., Pollet, N., Niehrs, C. and Nigg, E. A. (2001) Cloning and characterization of Plx2 and Plx3, two additional Polo-like kinases from Xenopus laevis. Exp Cell Res.270:78-87.

 2000

  • Pollet, N., Schmidt, H.A., Gawantka, V., Vingron, M. and Niehrs, C. (2000) Axeldb : a Xenopus laevis database focusing on gene expression. Nucleic Acids Res. 28 :139-140.
  • Demattei, M. V., Auge-Gouillou, C., Pollet, N., Hamelin, M. H., Meunier-Rotival, M. and Bigot, Y. (2000). Features of the mammal mar1 transposons in the human, sheep, cow, and mouse genomes and implications for their evolution. Mamm. Genome 11 :1111-6.

 1999

  • Bronchain OJ, Hartley KO, Amaya E. (1999) A gene trap approach in Xenopus. Curr Biol. 9:1195-8.
  • Crosnier, C., Driancourt., C., Raynaud, N., Dhorne-Pollet, N., Pollet, N., Bernard, O., Hadchouel, M. et Meunier-Rotival, M. (1999) Mutations in JAGGED1 gene are predominantly sporadic in Alagille syndrome. Gastroenterology. 116 :1141-1148.
  • Jen, W.C., Gawantka, V., Pollet, N., Niehrs, C. and Kintner, C. (1999). Periodic repression of Notch pathway genes governs the segmentation of Xenopus embryos. Genes Dev. 13 :1486-1499.
  • Niehrs, C. and Pollet, N. (1999) Synexpression groups in eukaryotes. Nature 402 :483-487.

 1998

  • Pollet, N., Gawantka, V. , Delius, H., Vingron, M., Pfister, R., Nitsch, R., Blumenstock, C. and Niehrs C. (1998) Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning. Mech. Dev. 77 :95-141.
  • Ouatas T., Sélo M., Sadji Z., Hourdry J., Denis H. and Mazabraud A (1998) Xenopus nucleoside diphosphate kinases (NDPK/NM23) are heterogeously expressed during early development. Int. J. Dev. Biol, 42 : 43-52.

 1997

  • Ouatas, T., Abdallah, B., Gasmi, L., Bourdais, J., Postel, E. and Mazabraud, A. (1997) Three genes encode NM23/nucleoside diphosphate kinase of Xenopus laevis. Gene, 194 : 215-225.
  • Pollet, N., Boccaccio, C., Dhorne-Pollet, S., Driancourt, C., Raynaud, N., Auffray, C., Hadchouel, M. et Meunier-Rotival, M. (1997) Construction of an integrated physical and gene map of human chromosome 20p12 providing candidate genes for Alagille syndrome. Genomics 42 :489-498.

 1996

  • Abdallah B., Sachs L., Hourdry J., Wegnez M., Demeneix B.A. and Mazabraud A. (1996) Thyroid hormone regulation of germ cell-specific EF-1alpha expression during metamorphosis of Xenopus laevis. Int. J. Dev. Biol., 40, 507-514,.

 1995

  • Pollet, N., Dhorne-Pollet, S., Deleuze, J.-F., Boccaccio, C., Driancourt C, Raynaud, N., Le Paslier, D., Hadchouel, M. and Meunier-Rotival, M. (1995) Construction of a 3.7-Mb physical map within human chromosome 20p12 ordering 18 markers in the Alagille syndrome locus. Genomics 27 :467-474.
  • Auge-Gouillou, C., Bigot, Y., Pollet, N., Hamelin, M.-H., Meunier-Rotival, M. and Periquet, G. (1995) Human and other mammalian genomes contain transposons of the mariner family. FEBS Letters 368 :541-546.

 1994

  • Deleuze, J.-F., Dhorne, S., Hazan, J., Borghi, E., Raynaud, N., Pollet, N., Meunier-Rotival, M., Deschatrette, J., Alagille, D. and Hadchouel, M. (1994) Deleted chromosome 20 from a patient with Alagille syndrome isolated in a cell hybrid through leucine transport selection : Exclusion of three candidates genes. Mamm. Genome 5 :663-669.

 1991

  • Cormier P, Osborne HB, Morales J, Bassez T, Poulhe R, Mazabraud A, Mulner-Lorillon O, Belle R. (1991) Molecular cloning of Xenopus elongation factor 1 gamma, major M-phase promoting factor substrate. Nucleic Acids Res.19:6644.
  • Abdallah B, Hourdry J, Deschamps S, Denis H, Mazabraud A. (1991) The genes encoding the major 42S storage particle proteins are expressed in male and female germ cells of Xenopus laevis. Development. 113:851-6.
  • Abdallah B, Hourdry J, Krieg PA, Denis H, Mazabraud A. Germ cell-specific expression of a gene encoding eukaryotic translation elongation factor 1 alpha (eEF-1 alpha) and generation of eEF-1 alpha retropseudogenes in Xenopus laevis. Proc Natl Acad Sci U S A. 88:9277-81.
  • Deschamps S, Morales J, Mazabraud A, le Maire M, Denis H, Brown DD. (1991) Two forms of elongation factor 1 alpha (EF-1 alpha O and 42Sp50), present in oocytes, but absent in somatic cells of Xenopus laevis. J Cell Biol. 114:1109-11.
  • Viel A, le Maire M, Philippe H, Morales J, Mazabraud A, Denis H. (1991) Structural and functional properties of thesaurin a (42Sp50), the major protein of the 42 S particles present in Xenopus laevis previtellogenic oocytes. J Biol Chem. 266:10392-9.

 1990

  • Dje MK, Mazabraud A, Viel A, le Maire M, Denis H, Crawford E, Brown DD. (1990) Three genes under different developmental control encode elongation factor 1-alpha in Xenopus laevis. Nucleic Acids Res. 18:3489-93.


Publications Pacale Le Gall

Revues
  • M. Poudret, J.-P. Comet, P. Le Gall, F. Képès, A. Arnould, P. Meseure. Topology- based abstraction of complex biological systems: Application to the Golgi apparatus. in Biosciences, 127:79-88, 2008.
  • D. Mateus, J.-P. Gallois, J.-P. Comet, and P. Le Gall, Symbolic modeling of genetic regulatory networks.  Journal of Bioinformatics and Computational Biology, 5(2B):627-640, 2007.
  • M. Aiguier and D. Bahrami. Structures for abstract rewriting Journal of Automated Reasoning, 38(4):303-351, 2007
  • M. Aiguier and F. Barbier. An institution-independent Proof of the Beth Definability Studia Logica, 85(3):333-359, 2007
  • M. Aiguier and R. Diaconescu. Stratified institutions and elementary homomorphisms Information Processing Letters, 103(1):5-13, 2007
Chapitres de livres
  • M. Poudret, J.-P. Comet, P. Le Gall, F. Képès, A. Arnould, P. Meseure, J.-M. Verbavatz, A. Rambourg. Toward a computer-aided methodology for topology-based simulation of the Golgi apparatus. In Proc. of the Lille Spring school on Modelling and simulation of biological processes in the context of genomics (eds. P. Amar, F. Képès, V. Norris and P. Tracqui). pp. 89-104, EDP Science, ISBN : 978-2-7598-0075-9, 2008.        
  • D. Mateus, J.-P. Comet, J.-P. Gallois and P. Le Gall. Chapter : Inferring parameters of genetic regulatory networks with symbolic formal methods. In Proc. of the Evry Spring school on Modelling and simulation of biological processes in the context of genomics (eds. P. Amar, F. Képès, V. Norris and P. Tracqui). pp. 51-70, EDP Science, ISBN : 978-2-7598-0019-3, 2007.

 

MANIFESTATIONS

Autres manifestations

 École Thématique "Modélisation de systèmes biologiques complexes dans le contexte de la génomique" : du 3 au 7 mai 2010 à Evry

La compréhension des mécanismes qui sous-tendent les fonctions biologiques s'enracine dans celle de la morphodynamique des réseaux d'interaction moléculaires et cellulaires. Cette dernière devient aujourd'hui accessible, grâce aux progrès des méthodes de la biologie moléculaire à grande échelle (génomique, transcriptomique, protéomique), mais également à l'émergence de nouveaux outils théoriques permettant d'intégrer les données expérimentales au sein de modèles quantitatifs ou qualitatifs, permettant simulations, analyses et prédictions.
Ce programme de recherche requiert un effort commun des informaticiens, mathématiciens, physiciens et biologistes, que l'École «Modélisation de systèmes biologiques complexes dans le contexte de la génomique» a pour objectif de faciliter.

Largement ouverte aux doctorants, post-doctorants et chercheurs, l'École s'articulera cette année autour de cinq axes d'intérets principaux :
Réseaux moléculaires et Modélisation
Approches discrètes des réseaux de régulation
Métabolisme à l'échelle du génome
Biophysique de la cellule
Traitement de l'information par les bactéries

Informations et inscription : http://epigenomique.free.fr/fr/index.php

 

 

 

COLLABORATIONS

Réseau de recherche

 

Collaborations internationales

 

 

Plateforme scientifique

 

FORMATIONS

Formations attachées

Ecole doctorale

 Ecole doctorale des Génomes Aux Organismes.

Masters attachés

 

 Master 2 de Biologie Systémique et Synthétique :

www.mssb.fr

Thèses en cours

  • Vieira Gilles - Paris 11
  • Carrera Javier - Universidad Poltecnica de Valencia
  • Rodrigo Guillermo - Universidad Politecnica de Valencia
  • Pinto Filipe - Universidad de Poto
  • Landrain Thomas
  • Kirov Boris
  • Mabrouki Mbarka

 

Supports et matériels pédagogiques

 

 

INFORMATIONS PRATIQUES

Responsable du laboratoire : François KEPES

Tél. : 01 69 47 44 30

 

 

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