You are here: Home RESEARCH - iSSB Publications 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.


    iSSB - CNRS FRE3561
    University of Evry-Val-d'Essonne

    5 rue Henri Desbruères
    Genopole Campus 1, Bât. 6

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

    To come, please follow Genopole access indications.

    On the site, iSSB is located at 1st floor of Genavenir 6 building placed on your left (if you come by pedestrian entry) or on your right (if your come by vehicle entry).


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




      Post-doc proposal in Synthetic Biology.

      Research Thematic School on advances in Systems & Synthetic Biology, March 23-27, 2015, in Strasbourg.

      Abolislogo.jpg iSSB is pleased to announce the creation of the spin-off Abolis . Abolis has won the grand-prize of 200 000 € at the 2030 World Innovation Challenge, and received in 2013 a special prize at the Genopole's White Technologies competition.

      iSSB has received the Genopole award for Research Innovation, which rewards Genopole players achieving major scientific advances. This price has been awarded after selection by an external jury composed of researchers, entrepreneurs and journalists. Please see the video.

      *   logo_iGEM2014.jpg The iGEM-Evry-2014 team , launched by mSSB students and hosted by iSSB, create a new biological system with environmental applications. Please see their "Sponge Patrol" project on their website. The team won a bronze medal at the final jamboree in Boston.

    IronLogo.jpg * The iGEM-Evry 2013 team: "human practice" price, gold medal at the European final. It was one of the 2 French teams selected for the world final in Boston.

    copy_of_IFrog.jpg *  iGEM-Evry-2012 team: two prices (best model, best human practices), gold medal at the European jamboree, selection for the world final.