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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. 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.
  3. 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).
  4. Ramaswamy A, Froeyen M, Herdewijn P, Ceulemans A.  The helical structure of xylose-DNA. J. Am. Chem. Soc. 2010,132:587-595.
  5. Jang M, De Jonghe S, Van Belle K, Louat T, Waer M, Herdewijn P.  Synthesis, immunosuppressive activity and structure-activity relationship study of a new series of 4-N- piperazinyl-thino [2,3-d] pyrimidine analogues. Bioorg. Med. Chem. Lett. 2010, 1:844-847.
  6. 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.
  7. 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.
  8. 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.
  9. Abramov M, Herdewijn P.  Synthesis and biological evaluation of inosine phosphonates. New. J. Chem. 2010, 34:875-876.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. Robeyns K, Herdewijn P, Van Meervelt L. Direct observation of two cyclohexenyl (CeNA) ring conformations in duplex DNA.  Artificial DNA, 2010, 1:2-8.
  17. Mattheus W, Maschelein J, Gao L-J, Herdewijn P, Landuyt B, Volckaert G, Lavigne R.
    The kalimantacin/batumin biosynthesis operon encodes a self-resistance isoform of the FabI bacterial target. Chem. Biol. 2010, 17:1067-1071.
  18. Kaptein S, De Burghgraeve T, Froeyen M, Pastorino B, Alen M, Mondotte JA, Herdewijn P, Jacobs M, de Lamballerie X, Schols D, Gamarnik AV, Sztaricskai F, Neyts J.  A derivative of the antibiotic Doxorubicin is a selective inhibitor of Dengue and Yellow Fever Virus replication in vitro. Antimicrobial Agents and Chemotherapy, 2010, 54:5269-5280.
  19. SAlim MTA, Goto Y, Hamasaki T, Okamoto M, Aoyama H, Hashimoto Y, Musiu S, Paeshuyse J, Neyts J, Froeyen M, Herdewijn P, Baba M.  Highly potent and selective inhibition of bovine viral diarrhea virus replication by g-carboline derivatives.  Antiviral Res., 2010, 88:263-268.
  20. Hean J, Crowther C, Ely A, ul Islam R, Barichievy S, Bloom K, Weinberg M, van Otterlo W, de Koning C, Salazar F, Marion P, Roesch E, Lemaitre M, Herdewijn P, Arbuthnot P.  Inhibition of hepatitis B virus replication in vivo using lipoplexes containing altritol-modified antiviral siRNA’s. Artificial DNA, 2010, 1:17-26.
  21. Cesnek M, Herdewijn P.  Synthesis and anti-HIV activity of new 3’-O-Phosphonomethyl nucleosides. Heterocycles 2010, 82:663-687.
  22. von Kiedrowski G, Otto S, Herdewijn P.  Welcome Home, Systems Chemists! (Editorial). J. Sys. Chem., 2010, 1:1.
  23. Carbonell P, Faulon JL. Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics. 2010, 26:2012-2019.
  24. 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.
  25. 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), 2010.
  26. 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.
  27. Faulon JL, Carbonell P. Molecular signatures of promiscuous enzyme-substrate interactions, American Chemical Society Spring Meeting. San Francisco, March 2010.
  28. 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).
  29. 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).
  30. Rodrigo G, Carrera J, Elena SF, Jaramillo A. Robust Dynamical Pattern Formation from a Multifunctional Minimal Genetic Circuit. BMC Systems Biology 2010, 4:48.
  31. 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):13-9.
  32. 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.
  33. 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.
  34. Kirkilionis M, Képès F, Connaughton C.  Editorial - European Conference On Complex Systems 2009. Advances In Complex Systems 2010, 13 #3, 251-252.
  35. Junier I, Hérisson J, Képès F.  Periodic pattern detection in sparse boolean sequences. Algorithms Mol. Biol. 2010, 5:31.
  36. 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.
  37. 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.
  38. Pollet N.  Expression of immune genes during metamorphosis of Xenopus: a survey. Front Biosci. 2010, 15:348-58.
  39. 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.
  40. Gilbert D, Jaramillo A, Krasnogor N, de Lorenzo V. Editorial: Synthetic biology gains momentum in Europe, Systems and Synthetic Biology 2010, 4:145–147.

 

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

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

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

    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).

    GPS

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

     

    iSSBbuildingsmall.jpg

    News

    * Dr. Alfonso Jaramillo wins the 3d prize in the synthetic biology Gen9-prize 2012 contest

    *  IFrog.jpg L'équipe iGEM-Evry recrute ! / the iGEM-Evry team is recruiting!

    The iGEM-Evry-2012 team has won two prices (best model, best human practices) and got a gold medal at the European jamboree. It was selected for the world championship in Boston.


    *  Press file on Synthetic Biology
    To learn more about Synthetic Biology: its origins, applications and potential, the biotech companies and the laboratories on the Genopole biopark working in this field.