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2010

  1. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam N, Shu S, Taher L, Blitz I, Blumberg B, Dichann D, Dubchak I, Fletcher R, Gerhard D, Goodstein D, Graves T, Grigoriev I, Grimwood J, Kawashima T, Lindquist E, Mead P, Mitros T, Ota Y, Poliakov A, Pollet N, Robert J, Salamov A, Sater A, Schmutz J, Terry A, Vize P, Warren W, Wells D, Wills A, Zimmerman L, Grainger R, Grammer T, Khokha M, Richardson P, Rokhsar D.  The genome of the western clawed frog Xenopus tropicalis. Science 2010, 328:633-636.
  2. Carbonell P, Faulon JL. Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics. 2010, 26:2012-2019.
  3. Sarnowski C, Carbonell P, Elati M, Faulon JL. Prediction of catalytic efficiency to discover new enzymatic activities, Proc. of Machine Learning in Systems Biology 2010, p153-156.
  4. Rodrigo G, Carrera J, Elena SF, Jaramillo A. Robust Dynamical Pattern Formation from a Multifunctional Minimal Genetic Circuit. BMC Systems Biology 2010, 4:48.
  5. Suarez M, Tortosa P, Garcia-Mira MM, Rodríguez-Larrea D, Godoy-Ruiz R, Ibarra-Molero B, Sanchez-Ruiz JM, Jaramillo A. Using multi-objective computational design to extend protein promiscuity. Biophys Chem. 2010, 147(1-2):13-19.
  6. Junier I, Martin O, Képès F.  Spatial and topological organization of DNA chains induced by gene co-localization. PLoS Computational Biology, 2010, 6(2): e1000678.
  7. Bourguignon PY, Samal A, Kepes F, Jost J, Martin OC. Challenges in experimental data integration within genome-scale metabolic models. Algorithms Mol. Biol. 2010, 5:20.
  8. Kirkilionis M, Képès F, Connaughton C.  Editorial - European Conference On Complex Systems 2009. Advances In Complex Systems 2010, 13 #3, 251-252.
  9. Junier I, Hérisson J, Képès F.  Periodic pattern detection in sparse boolean sequences. Algorithms Mol. Biol. 2010, 5:31.
  10. Rohlf T, Junier I, Képès F. Gene regulation in time and space: a model of the interdependence between genome structure and gene network dynamics. Proceedings of the 5th International q-bio Conference, 2010, p123-125.
  11. Ymlahi-Ouazzani Q, Bronchain OJ, Paillard E, Ballagny C, Chesneau A, Jadaud A, Mazabraud A, Pollet N.  Reduced levels of survival motor neuron protein leads to aberrant motoneuron growth in a Xenopus model of muscular atrophy, Neurogenetics, 2010, 11:27-40.
  12. Pollet N. Expression of immune genes during metamorphosis of Xenopus: a survey. Front Biosci. 2010, 15:348-58.
  13. Smelty P, Marchal C, Renard R, Sinzelle L, Pollet N, Dunon D, Jaffredo T, Sire J-Y, Fellah JS.  Identification of the pre–T-cell receptor α chain in non mammalian vertebrates challenges the structure–function of the molecule. PNAS 2010, 107:19991-19996.
  14. Gilbert D, Jaramillo A, Krasnogor N, de Lorenzo V. Editorial: Synthetic biology gains momentum in Europe, Systems and Synthetic Biology 2010, 4:145–147.
  15. Li T, Froeyen M, Herdewijn P.  Insight into ligand selectivity in HCV NS5B polymerase: molecular dynamics simulation, free energy decomposition and docking. J.Mol. Mod. 2010, 16:49–59.
  16. Herdewijn P.  Nucleic acids with a six-membered carbohydrate mimic in the backbone. Chemistry & Biodiversity, 2010, 7:1-59 (cited in faculty of 1000 biology).
  17. Ramaswamy A, Froeyen M, Herdewijn P, Ceulemans A.  The helical structure of xylose-DNA. J. Am. Chem. Soc. 2010,132:587-595.
  18. Giraut A, Song XP, Froeyen M, Marlière P, Herdewijn P.  Iminodiacetic-phosphoramidates as metabolic prototypes for diversifying nucleic acid polymerization in vivo. Nucleic Acids Res. 2010, 38:2541-2550.
  19. Ovaere M, Van Aerschot A, Abramov M, Herdewijn P, Van Meervelt L.  Crystallization and preliminary X-ray study of the D-altritol oligonucleotide GTGTACAC. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010, 66:460-462.
  20. Mattheus W, Gao LJ, Herdewijn P, Landuyt B, Verhaegen J, Masschelein J, Volckaert G, Lavigne R.  Isolation and purification of a new kalimantacin/batumin-related polyketide and elucidation of its biosynthesis gene cluster. Chem. Biol. 2010, 17:149-159.
  21. Abramov M, Herdewijn P.  Synthesis and biological evaluation of inosine phosphonates. New. J. Chem. 2010, 34:875-876.
  22. Maiti M, Nauwelaerts K, Lescrinier E, Schuit FC, Herdewijn P.  Self-complementary sequence context in mature miRNAs. Biochem. Biophys. Res. Commun. 2010, 392:572-576.
  23. Lescrinier E, Duybankova N, Nauwelaerts K, Jones R, Herdewijn P.  Structure determination of the top-loop of the conserved 3’ terminal secondary structure with the genome of flaviviruses. ChemBioChem. 2010, 11:1404-1412.
  24. Bramsen J, Pakula M, Hansen T, Bus C, Langkjær N, Odadzic D, Smicius R, Wengel S, Chattopadhyaya J, Engels J, Herdewijn P, Wengel J, Kjems J.  A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects. Nucleic Acids Res. 2010, 38:5761-5773.
  25. Robeyns K, Herdewijn P, Van Meervelt L.  Comparison between the orthorhombic an tetragonal form of the heptamer sequence d(GCG(XT)GCG)/d(CGCACGC). Acta Crystall. Sect F. 2010, 66:1028-1031.
  26. Giraut A, Herdewijn P.  Influence of the linkage between leaving group and nucleoside on substrate efficiency for incorporation in DNA catalyzed by reverse transcriptase. ChemBioChem 2010, 11:1399-1403.
  27. D’Alonzo D, Guaragna A, Van Aerschot A, Herdewijn P, Palumbo G.  Toward L-homo DNA: stereoselective de novo synthesis of -Lerythro-hexapyranosyl nucleosides as building blocks for the preparation of -L-hoo-DNA. J. Org. Chem. 2010, 75:6402-6410.
  28. Robeyns K, Herdewijn P, Van Meervelt L. Direct observation of two cyclohexenyl (CeNA) ring conformations in duplex DNA.  Artificial DNA, 2010, 1:2-8.
  29. von Kiedrowski G, Otto S, Herdewijn P.  Welcome Home, Systems Chemists! (Editorial). J. Sys. Chem., 2010, 1:1.
  30. Planson AG, Carbonell P, Fichera D, Paillard E, Sarnowski C, Faulon JL. A roadmap to implementing novel therapeutic circuits in E. coli. In ICSynBio, International Conference on Synthetic Biology, Evry (France), Dec. 2010.
  31. Rojas-Chert M, Peironcely J, Kasper P, Bender A, Faulon JL, Reijmers T, Coulier L. Metabolite identification pipeline based on MS fragmentation. American Chemical Society Spring Meeting, San Francisco, March 2010.
  32. Faulon JL, Carbonell P. Molecular signatures of promiscuous enzyme-substrate interactions, American Chemical Society Spring Meeting. San Francisco, March 2010.
  33. Faulon JL, Carbonell P, Fichera D. Probing the evolution of enzymatic reactions with molecular signatures, journee Société Francaise de Chemo-informatique (SFCi), Saint Raphael, March 2010 (invited).
  34. Carbonell P. Systems approach to language networks mapping: pull up by the bootstraps. In Mapping language across cultures: Textual analysis in cross-cultural and intercultural communication (MLAC10), Salamanca (Spain), 2010 (invited).

 

Book chapters

  1. Faulon JL, Carbonell P. Reaction Network Generation,, In Handbook of Chemoinformatics Algorithms. Chapman & Hall/CRC Series in Mathematical & Computational Biology, 2010.
  2. Misra M, Faulon JL. Algorithms to Store and Retrieve 2D Chemical Structures, InHandbook of Chemoinformatics Algorithms. Chapman & Hall/CRC Series in Mathematical & Computational Biology, 2010.
  3. Fichera D, Carbonell P, Faulon JL. Signatures of chemical diversity in metabolic networks. In Modelling Complex Biological Systems in the Context of Genomics, (Eds Amar P, Kepes F, Norris V) Evry (France), 2010.
  4. P. Carbonell, D. Fichera, J.L. Faulon. Predicting heterologous compound-forming reaction pathways through retrosynthesis hypergraphs. In LIX Bioinformatics Colloquium 2010, Ecole Polytechnique, Palaiseau (France), 2010.

    Location - contact

    iSSB
    CNRS FRE3561 - UEVE - GENOPOLE 

    5 rue Henri Desbruères
    Genopole Campus 1, Bât. 6
    F-91030 ÉVRY CEDEX, FRANCE

    contact (at) issb.genopole.fr

    Phone: +33(0)1 69 47 44 30
    Fax: +33(0)1 69 47 44 37

    iSSBbuildingsmall.jpg

    To visit us, please follow Genopole access indications.  Once on Genopole campus 1, iSSB is located on the first floor of Building 6, which is the first building to your left as you cross the pedestrian gate, or to your right as you cross the car gate.

    GPS

    Longitude: E 2° 27' 4''
    Latitude: N 48° 37' 7''

     


    News

    Thematic Research School "advances in Systems & Synthetic Biology" (aSSB): March 13-17, 2017 in Lyon.

      Based on publications in synthetic biology, an independent study (Nov 2015) found that iSSB ranks 3rd lab in Europe and 9th in the world, despite a comparatively small size.

      The European Experience 2016!  The teams iGEM Evry and iGEM IONIS have organized together a thrilling meeting week-end, gathering students from all Europe.