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Publications

2013

 

  1. Elati M, Nicolle R, Junier I, Fernández D, Fekih R, Font J, Képès F. PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION.  Nucleic Acids Res. 2013, 41(3):1406-1415.
  2. Pezo V, Louis D, Guérineau V, Le Caer JP, Gaillon L, Mutzel R, Marlière P. A metabolic prototype for eliminating tryptophan from the genetic code.  Sci Rep. 2013, 3:1359.
  3. Rannou O, Lechatelier E, Larson M, Nouri H, Dalmais B, Laughton C, Janniere L, Soultanas P.  Functional interplay of DnaE polymerase, DnaG primase and DnaC helicase within a ternary complex, and primase to polymerase hand-off during lagging strand DNA replication in Bacillus subtilis. Nucleic Acids Res. 2013, (in press).
  4. Dhorne-Pollet S, Thélie A, Pollet N. Validation of novel reference genes for RT-qPCR studies of gene expression in Xenopus tropicalis during embryonic and post-embryonic development. Dev Dyn. 2013, Apr 5. doi: 10.1002/dvdy.23972. [Epub ahead of print]

 

Book Chapters

  1. Carbonell P, Planson AG, Faulon JL.  Retrosynthetic design of heterologous pathways.  In Systems Metabolic Engineering, Methods Mol Biol.. - 2013; 985:149-173.
  2. Sinzelle L, Pollet N. Designing nonviral targeted integrating vectors for genome engineering in vertebrates. In Site directed insertion of transgenes. Ed. Springer Berlin/Heidelberg. Vol. 23, p41-67, 2013.
  3. Vouillot L., Thelie, A., Scalvenzi, T. and Pollet, N. Genomics and genome engineering in Xenopus. in " Xenopus Development" , Kubiak J. and Kloc M. eds, Wiley-Blackwell, in press

2012

  1. Rodrigo G, Landrain TE, Jaramillo A. De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proc. Natl. Acad. Sci. USA. 2012,  109(38):15271-15276.
  2. Carrera J, Elena SF, Jaramillo A. Computational design of genomic transcriptional networks with adaptation to varying environments. Proc. Natl. Acad. Sci. USA. 2012,  109(38):15277-15282.
  3. Carbonell P, Fichera D, Pandit SB, Faulon JL. Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Syst. Biol., 2012, 6(1):10.
  4. Planson AG, Carbonell P, Grigoras I, Faulon JL.  A retrosynthetic biology approach to therapeutics: from conception to delivery.  Curr. Opin. Biotechnol., 2012, 23(6):948-956.
  5. Planson AG, Carbonell P, Paillard E, Pollet N, Faulon JL. Compound toxicity screening and structure-activity relationship modeling in Escherichia coli.  Biotechnol. Bioeng., 2012, 109(3):846-850.
  6. Peironcely JE, Rojas-Chertó M, Fichera D, Reijmers T, Coulier L, Faulon JL, Hankemeier T.  OMG: open molecule generator. J. Cheminform., 2012, 4(1):21.
  7. Giraut A, Abu El-Asrar R, Marlière P, Delarue M, Herdewijn P. 2'-Deoxyribonucleoside Phosphoramidate Triphosphate Analogues as Alternative Substrates for E. coli Polymerase III.  Chembiochem., 2012, 13(16):2439-2444.
  8. Herdewijn P, Marlière P. Redesigning the leaving group in nucleic acid polymerization.  FEBS Lett., 2012, 586(15):2049-2056.
  9. Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew SY, McLaughlin SH, Herdewijn P, Holliger P. Synthetic genetic polymers capable of heredity and evolution. Science, 2012, 336(6079):341-344.
  10. Maiti M, Siegmund V, Abramov M, Lescrinier E, Rosemeyer H, Froeyen M, Ramaswamy A, Ceulemans A, Marx A, Herdewijn P.  Solution Structure and Conformational Dynamics of Deoxyxylonucleic Acids (dXNA): An Orthogonal Nucleic Acid Candidate.  Chemistry, 2012, 18:869-879.
  11. Rodrigo G, Carrera J, Landrain TE, Jaramillo A.  Perspectives on the automatic design of regulatory systems for synthetic biology.  FEBS Lett., 2012, 586(15):2037-2042.
  12. Carrera J, Fernández Del Carmen A, Fernández-Muñoz R, Rambla JL, Pons C, Jaramillo A, Elena SF, Granell A. Fine-tuning tomato agronomic properties by computational genome redesign. PLoS Comput. Biol., 2012, 8(6):e1002528. doi: 10.1371/journal.pcbi.1002528.
  13. Junier I, Dale RK, Hou C, Képès F, Dean A.  CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus.  Nucleic Acids Res., 2012, 40(16):7718-7727.
  14. Kepes F, Jester BC, Lepage T, Rafiei N, Rosu B, Junier I. The layout of a bacterial genome. FEBS Lett. 2012, 586(15):2043-2048.
  15. Junier I, Hérisson J, Kepes F. Genomic Organization of Evolutionarily Correlated Genes in Bacteria: Limits and Strategies.  J Mol Biol., 2012, 19(5):369-386.
  16. Maciąg-Dorszyńska M, Ignatowska M, Jannière L, Węgrzyn G, Szalewska-Pałasz A.  Mutations in central carbon metabolism genes suppress defects in nucleoid position and cell division of replication mutants in Escherichia coli.  Gene, 2012, 503(1):31-35.
  17. Jester BC, Romby P, Lioliou E. When ribonucleases come into play in pathogens: a survey of gram-positive bacteria. Int. J. Microbiol., 2012, 2012:592196
  18. Sinzelle L, Thuret R, Hwang HY, Herszberg B, Paillard E, Bronchain OJ, Stemple DL, Dhorne-Pollet S, Pollet N.  Characterization of a novel Xenopus tropicalis cell line as a model for in vitro studies. Genesis, 2012, 50:316-324.
  19. Tempel S, Pollet N, Tahi F.  ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins. BMC Bioinformatics, 2012, 13(1):246.
  20. Gilchrist MJ, Pollet N. Databases of gene expression in Xenopus development. Methods Mol. Biol., 2012, 917:319-345.
  21. Parain K, Mazurier N, Bronchain OJ, Borday C, Cabochette P, Chesneau A, Colozza G, el Yakoubi W, Hamdache J, Gilchrist M, Pollet N, Perron M.  A large scale screen for neural stem cell markers in Xenopus retina. Developmental Neurobiology, 2012, 72(4):491-506.

Book chapters

  1. Misra M, Martin S, Faulon JL. Graphs: flexible representations of molecular structures and biological network. In Computational Approaches in Cheminformatics and Bioinformatics, (R. Guha and A. Bender Eds.) John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118131411.ch6, 2012.

                2011

                1. Marlière P, Patrouix J, Döring V, Herdewijn P, Tricot S, Cruveiller S, Bouzon M, Mutzel R.  Chemical evolution of a bacterium's genome.  Angew Chem. Int. Ed. Engl. 2011, 50(31):7109-7114.
                2. Maiti M, Siegmund V, Abramov M, Lescrinier E, Rosemeyer H, Froeyen M, Ramaswamy A, Ceulemans A, Marx A, Herdewijn P.  Solution Structure and Conformational Dynamics of Deoxyxylonucleic Acids (dXNA): An Orthogonal Nucleic Acid Candidate.  Chemistry. 2011, Dec 16. In press
                3. Yang S, Froeyen M, Lescrinier E, Marlière P, Herdewijn P.  3-Phosphono-L-alanine as pyrophosphate mimic for DNA synthesis using HIV-1 reverse transcriptase. Org.  Biomol. Chem. 2011, 9:111-119.
                4. Maiti M, Nauwelaerts K, Lescrinier E, Herdewijn P.  Structural and Binding Study of Modified siRNAs with the Argonaute 2 PAZ Domain by NMR Spectroscopy. Chemistry. 2011, 17:1519-1528.
                5. Jang M, De Jonghe S, Segers K, Anné J, Herdewijn P.  Synthesis of novel 5-amino-thiazolo[4,5-d]pyrimidines as E. coli and S. aureus SecA inhibitors.  Bioorg. Med. Chem. 2011, 19:702-714.
                6. Stella A, Segers K, De Jonghe S, Vanderhoydonck B, Rozenski J, Anné J, Herdewijn P.  Synthesis and Antibacterial Evaluation of a Novel Series of 2-(1,2-Dihydro-3-oxo-3H-pyrazol-2-yl) benzothiazoles. Chem. Biodiv. 2011, 8:253-265.
                7. De Jonghe S, Marchand A, Gao J, Calleja A, Cuveliers E, Sienaert I, Herman J, Clydesdale G, Sefrioui H, Lin Y, Pfleiderer W, Waer M, Herdewijn P. Synthesis and in vitro evaluation of 2-amino-4-N-piperazinyl-6-(3,4-dimethoxyphenyl)-pteridines as dual immunosuppressive and anti-inflammatory agents. Bioorg. Med. Chem. Lett. 2011, 21:145-149.
                8. Jang M, Lin Y, De Jonghe S, Gao L, Vanderhoydonck B, Froeyen M, Rozenski J, Herman J, Louat T, Van Belle K, Waer M, Herdewijn P.  Discovery of 7-N-Piperazinylthiazolo[5,4-d]pyrimidine analogues as a novel class of immunosuppressive agents with in vivo biological activity. J. Med. Chem. 2011, 54:655-668.
                9. Chavain N, Herdewijn P.  2 '-Deoxy-2 '-alpha-C-(hydroxymethyl)adenosine as Potential anti-HCV Agent. Eur. J. Org. Chem. 2011, 6:1140-1147.
                10. Vandooren J, Geurts N, Martens E, Van den Steen PE, De Jonghe S, Herdewijn P, Opdenakker G.  Gelatin degradation assay reveals MMP-9 inhibitors and function of O-glycosylated domain. World J. Biol. Chem. 2011, 2:14-24.
                11. Ovaere M, Herdewijn P, Van Meervelt L.  The crystal structure of the CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC). Chemistry. 2011, 17:7823-7830.
                12. Michielssens S, Moors S, Froeyen M, Herdewijn P, Ceulemans A.  Structural basis for the role of Lys220 as proton donor for nucleotidyl transfer in HIV-1 reverse transcriptase. Biophys. Chem. 2011, 157:1-6.
                13. Huang Q, Herdewijn P.  Synthesis of (E)-3′-phosphonoalkenyl modified nucleoside phosphonates via a highly stereoselective olefin cross-metathesis reaction. J. Org. Chem. 2011, 76:3742-3753.
                14. Kögler M, Vanderhoydonck B, De Jonghe S, Rozenski J, Van Belle K, Herman J, Louat T, Parchina A, Sibley C, Lescrinier E, Herdewijn P.  Synthesis and evaluation of 5-substituted 2'-deoxyuridine monophosphate analogues as inhibitors of flavin-dependent thymidylate synthase in Mycobacterium tuberculosis.  J. Med. Chem. 2011, 54(13):4847-4862.
                15. Song XP, Bouillon C, Lescrinier E, Herdewijn P.  Iminodipropionic acid as leaving group for DNA polymerization by HIV-1 reverse transcriptase. Chem. bio. chem. 2011, 12:1868-1880.
                16. Cocquyt K, Cos P, Herdewijn P, Maes L, Van den Steen PE, Laekeman G.  Ajuga remota benth: from ethnopharmacology to phytomedical perspective in the treatment of malaria. Phytomed., 2011, 18:1229-1237.
                17. Kirkilionis M, Képès F.  Introduction to special issue ECCS'09. Theory in Biosciences 2011, 130:153.
                18. Képès F.  Biologie synthétique et intégrative. C. R. Chimie, 2011, 14:420-423.
                19. Norris V, Zemirline A, Amar P, Audinot JN, Ballet P, Ben-Jacob E, Bernot G, Beslon G, Cabin A, Fanchon E, Giavitto JL, Glade N, Greussay P, Grondin Y, Foster JA, Hutzler G, Jost J, Kepes F, Michel O, Molina F, Signorini J, Stano P, Thierry AR.  Computing with bacterial constituents, cells and populations: from bioputing to bactoputing.  Theory Biosci. 2011, 130(3):211-228.
                20. Cabin-Flaman A, Monnier AF, Coffinier Y, Audinot JN, Gibouin D, Wirtz T, Boukherroub R, Migeon HN, Bensimon A, Jannière L, Ripoll C, Norris V.  Combed single DNA molecules imaged by secondary ion mass spectrometry.  Anal. Chem. 2011, 83(18):6940-6947.
                21. Maciąg M, Nowicki D, Jannière L, Szalewska-Pałasz A, Węgrzyn G.  Genetic response to metabolic fluctuations: correlation between central carbon metabolism and DNA replication in Escherichia coli.  Microb. Cell Fact. 2011, 10:19-.
                22. Sinzelle L, Carradec Q, Paillard E, Bronchain OJ, Pollet N.  Characterization of a Xenopus tropicalis Endogenous Retrovirus with Developmental and Stress-Dependent Expression. J Virol. 2011, 85:2167-2179.
                23. Pegoraro C, Pollet N, Monsoro-Burq AH.  Tissue-specific expression of Sarcoplasmic/Endoplasmic Reticulum Calcium ATPases (ATP2A/SERCA) 1, 2, 3 during Xenopus laevis development. Gene Expr Patterns 2011, 11:122-128.
                24. Demattei M-V, Hedhili S, Sinzelle L, Bressac C, Casteret S, Moiré N, Cambefort J, Thomas X, Pollet N, Gantet P, Bigot Y.  Nuclear Importation of Mariner Transposases among Eukaryotes: Motif Requirements and Homo-Protein Interactions. PLoS ONE 2011, 6(8):e23693. doi:10.1371/journal.pone.0023693
                25. Boistel R, Aubin T, Cloetens P, Langer M, Gillet B, Josset P, Pollet N, Herrel A.  Whispering to the Deaf: Communication by a Frog without External Vocal Sac or Tympanum in Noisy Environments. PLoS ONE 2011, 6(7):e22080. doi:10.1371/journal.pone.0022080
                26. Planson AG, Carbonell P, Paillard E, Pollet N, Faulon JL.  Compound toxicity screening and structure-activity relationship modeling in Escherichia coli. Biotechnol. Bioeng. 2011, doi : 10.1002/bit.24356
                27. Planson AG, Carbonell P, Grygoras I, Faulon JL.  Engineering antibiotic production and overcoming bacterial resistance. Biotechnol. J. 2011, 6:812-825. Review
                28. Misra M, Andrienko D, Baumeier B, Faulon JL, von Lilienfeld OA.  Toward Quantitative Structure-Property Relationships for Charge Transfer Rates of Polycyclic Aromatic Hydrocarbons. J. of Chem. Theory and Computation, 2011, 7: 2549-2555.
                29. Carbonell P, Lecointre G, Faulon JL.  Origins of specificity and promiscuity in metabolic networks. J. of Biol. Chem. 2011. 286:43994-44004.
                30. Carbonell P, Planson AG, Fichera D, Faulon JL.  A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Systems Biology, 2011, 5:122.
                31. Carbonell P, Faulon JL.  Using retrosynthetic biology to design metabolic pathways for therapeutics production. In SB5.0: the Fifth International Meeting on Synthetic Biology, Stanford University, Stanford (USA), 2011.
                32. Glykys DJ, Szilvay GR, Tortosa P, Suarez M, Jaramillo A, Banta S.  Pushing the Limits of Automatic Computational Protein Design: Design, Expression, and Characterization of a Large Synthetic Protein based on a Fungal Laccase Scaffold. Systems and Synthetic Biology 2011, 5:45-58.
                33. Camsund D, Lindblad P, Jaramillo A.  Genetically Engineered Light Sensors for Control of Bacterial Gene Expression. Biotechnol. J. 2011, 6:826-836.
                34. Carrera J, Rodrigo G, Singh V, Kirov B, Jaramillo A.  Empirical model and in vivo characterization of the bacterial response to synthetic gene expression show that ribosome allocation limits growth rate. Biotechnol. J. 2011, 6:773-783.
                35. Jaramillo A, Faulon JL. Synthetic Biology - applying new paradigms at the interface of fundamental research and innovation. Biotechnol. J. 2011, 6:766-767.
                36. Rodrigo G, Jaramillo A, Blazquez MA.  Integral control of plant gravitropism through the interplay of hormonal signaling and gene regulation. Biophys. J. 2011, 101:757-763.
                37. Rodrigo G, Carrera J, Jaramillo A.  On the designability of synthetic regulatory networks. Nucl. Acids Res. 2011, 39: e138.
                38. Rodrigo G, Carrera J, Jaramillo A, Elena SF. Optimal viral strategies for bypassing RNA silencing. J.R. Soc. Interface, 2011, 8:257-268.
                39. Vrancken K, Cuypers H, Baelemans W, Gao LJ, Herdewijn P, Anné J.  Genome sequencing based target discovery of batumin. Antimicrob. Agents Chemother. 2011, (submitted).
                40. Crauste C, Froeyen M, Anné J, Herdewijn P.  Asymmetric synthesis of new b-lactam lipopeptides as bacterial signal peptidase I inhibitors. Eur. J. Org. Chem. 2011, (accepted)
                41. Doboszewski B, Herdewijn P.  Simple approach to 1-O-protected (R)- and (S)-glycerols from L- and D-arabinose for Glycerol. Nucleic Acids (GNA) monomers research. Tetrahedron Lett. 2011, (accepted)
                42. Huang Q, Herdewijn P.  Synthesis of 3′-S-phosphonomethyl modified nucleoside phosphonates with a 3′-deoxy-3′-thio-α-L-threosyl sugar moiety. Eur. J. Org. Chem. 2011 (accepted).

                 

                Book chapters

                1. Gilchrist MJ, Pollet N. Gene expression databases. In Methods in Molecular Biology (Clifton NJ), 2011. Humana press. In press.
                2. Sinzelle L, Pollet N. Designing nonviral targeted integrating vectors for genome engineering in vertebrates. In Site directed insertion of transgenes. 2011. Springer. In press.
                3. Képès F.  Morphodynamics of secretory endomembranes. In Morphogenesis - Origins of patterns and shapes (eds. Bourgine & Lesne) 2011, p. 119-141. Springer: complexity, New York. ISBN 978-3-642-13173-8.
                4. Rohlf T, Junier I, Képès F. Evolution of spatially optimized gene networks. Proceedings of the Sophia Antipolis Spring School, (eds. Amar P, Képès F & Norris V)
                  2011, p. 75-90 (EDP Sciences). ISBN 978-2-7598-0644-7.
                5. Elati M, Rouveirol C. 
Unsupervised Learning for Gene Regulation Network Inference from Expression Data: A Review. 
In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, (Eds Elloumi M and Zomaya AY) 2011 , Wiley, in press

                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.

                  2009

                  1. Carbonell P, del Sol A. Methyl side-chain dynamics prediction based on protein structure. Bioinformatics, 2009, 25:2552-2558.
                  2. Carbonell P, Nussinov R, del Sol A. Energetic determinants of protein binding specificity: insights into protein interaction networks. Proteomics. 2009, 9:1744-1753.
                  3. Prather KL, Jaramillo A. Editorial: Focus on synthetic biology. Biotechnol J. 2009, 4(10):1367.
                  4. Carrera J, Rodrigo G, Jaramillo A, Elena SF. Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome Biol. 2009, 10(9):R96.
                  5. Landrain TE, Carrera J, Kirov B, Rodrigoand G, Jaramillo A. Modular Model-based Design for Heterologous Bioproduction in Bacteria. Curr. Opinion in Biotechnology 2009, 20:272-279. Review
                  6. Suarez M, Tortosa P, Jaramillo A. PROTDES: CHARMM toolbox for computational protein design. Systems and Synthetic Biology, 2009, DOI:10.1007/s11693-009-9026-7.
                  7. Carrera J, Rodrigo G, Jaramillo A. Towards the automated engineering of a synthetic genome. Mol. Biosystems, 2009, 5(7):733-743.
                  8. Molto G, Suarez M, Tortosa P, Alonso J, Hernandez V, Jaramillo A. Protein Design Based on Parallel Dimensional Reduction. J. Chem. Inf. Model., 2009, 49(5):1261-1271.
                  9. Suarez M, Jaramillo A. Challenges in the computational design of proteins. J. R. Soc. Interface, 2009, 6(S4):S477-491.
                  10. Carrera J, Rodrigo G, Jaramillo A. Model-based redesign of global transcription regulation. Nucleic Acids Research, 2009 37(5):e38.
                  11. Sciretti D, Bruscolini P, Pelizzola A, Pretti M, Jaramillo A. Computational protein design with side-chain conformational entropy. Proteins, 2009, 74(1):176-191.
                  12. Képès F.  Biologie synthétique et intégrative. Médecine / Sciences, 2009
                    25, hors-série n° 2: 39-42. Review
                  13. Gilchrist MJ, Christensen MB, Bronchain O, Brunet F, Chesneau A, Fenger U, Geach TJ, Ironfield HV, Kaya F, Kricha S, Lea R, Masse K, Neant I, Paillard E, Parain K, Perron M, Sinzelle L, Souopgui J, Thuret R, Ymlahi-Ouazzani Q, Pollet N.  Database of Queryable Gene Expression Patterns for Xenopus. Developmental Dynamics, 2009, 238:1379-1388.
                  14. Rodel MO, Kosuch J, Grafe TU, Boistel R, Assemian NE, Kouame NG, Tohe B, Gourene G, Perret JL, Henle K, Tafforeau P, Pollet N, Veith M.  A new tree-frog genus and species from Ivory Coast, West Africa (Amphibia: Anura: Hyperoliidae). Zootaxa, 2009, 2044:23-45.
                  15. Boistel R, Pollet N, Tinevez JY, Cloetens P, Schlenker M.  Irradiation damage to frog inner ear during synchrotron radiation tomographic investigation, J. of Electron Spectroscopy and Related Phenomena, 2009, 170:37- 41.
                  16. Khokha MK, Krylov V, Reilly MJ, Gall JG, Bhattacharya D, Cheung CY, Kaufman S, Lam DK, Macha J, Ngo C, Prakash N, Schmidt P, Tlapakova T, Trivedi T, Tumova L, Abu-Daya A, Geach T, Vendrell E, Ironfield H, Sinzelle L, Sater AK, Wells DE, Harland RM, Zimmerman LB. Rapid gynogenetic mapping of Xenopus tropicalis mutations to chromosomes. Dev Dyn. 2009, 238:1398-1346.
                  17. Faucon F, Rebours E, Bevilacqua C, Helbling JC, Aubert J, Makhzami S, Dhorne-Pollet S, Robin S, Martin, P.  Terminal differentiation of goat mammary tissue during pregnancy requires the expression of genes involved in immune functions. Physiol. Genomics, 2009, 40:61-82.
                  18. Doboszewski D, Herdewijn P.  Carbohydrate chiral-pool approach to four enantiomerically pure 2-naphthylmethyl 3-hydroxy-2- methylbutanoates. Tetrahedron, 2008, 64:5551-5562
                  19. Van de Vijver P, Vondenhoff GHM, Denivelle S, Rozenski J, Verhaegen J, Van Aerschot A, Herdewijn P.  Antibacterial 5'-O-(N-dipeptidyl)-sulfamoyladenosines. Bioorg. Med. Chem. 2009, 17:260-269.
                  20. Fisher M, Abramov M, Van Aerschot A, Rozenski J, Dixit V, Juliano RL, Herdewijn P.
                    Biological effects of hexitol and altritol-modified siRNAs targeting B-Raf. Eur. J. Pharmacol. 2009, 606:38-44.
                  21. Herdewijn P, Marlière P.  Toward safe genetically modified organisms through the chemical diversification of nucleic acids. Chem. Biodivers. 2009, 6:791-808.
                  22. Bramsen JB, Laursen MB, Nielsen AF, Hansen TB, Bus C, Langkjaer N, Babu BR, Højland T, Abramov M, Van Aerschot A, Odadzic D, Smicius R, Haas J, Andree C, Barman J, Wenska M, Srivastava P, Zhou C, Honcharenko D, Hess S, Müller E, BobkovGV, Mikhailov SN, Fava E, Mayer TF, Chattopadhyaya J, Zerial M, Engels JW, Herdewijn P, Wengel J, Kjems J.  A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity. Nucleic Acids Res. 2009, 37:2867-2881.
                  23. Wakabayashi T, Bentahir M, Bammens L, Borgions F, Herdewijn P, Staes A, Timmerman E, Vandekerckhove J, Rubinstein E, Boucheix C, Gevaert K, De Stroopere B.  Analysis of the g-secretase interactome and validation of its association with tetraspanin enriched microdomains. Nature, Cell Biol. 2009, 11:1340 – 1346.
                  24. Paeshuyse J, Letellier C, Froeyen M, Dutartre H, Vrancken R, Canard B, De Clercq E, Gueiffier A, Teulade JC, Herdewijn P, Puerstinger G, Koenen F, Kerkhofs P, Baraldi PG, Neyts J.  A pyrazolotriazolopyrimidinamine inhibitor of bovine viral diarrhea virus replication that targets the viral RNA-dependent RNA polymerase. Antiviral Res. 2009, 82:141-147.
                  25. Bockstael K, Geukens N, Channakeshavapura Vijendra Rao SR, Herdewijn P, Anné J, Van Aerschot A.  An easy and fast method for the evaluation of Staphylococcus epidermidis type I signal peptidase inhibitors. J. Microbiol. Methods, 2009, 78:231-237.
                  26. Renders M, Abramov M, Froeyen M, Herdewijn P.  Polymerase-catalysed incorporation of glucose nucleotides into a DNA duplex. Chem. Eur. J. 2009, 15:5463-5470.
                  27. Wang G, Bobkov GV, Mikhailov SN, Schepers G, Van Aerschot A, Rozenski J, Van der Auweraer M, Herdewijn P, De Feyter S.  Detection of RNA hybridization by pyrene-labeled probes. ChemBioChem, 2009, 10:1175-1185.
                  28. Huang Q, Herdewijn P.  Synthesis of 3’-O-phosphonoethyl nucleosides with an adenine and a thymine base moiety. Nucleos. Nucleot. Nucleic Acids, 2009, 28:337-351.
                  29. Deborggraeve S, Coronado X, Solari A, Zulantay I, Apt W, Mertens P, Laurent T, Leclipteux T, Stessens T, Dujardin JC, Herdewijn P, Büscher P.  T.cruzi OligoC-TesT: a simplified and standardized polymerase chain reaction format for diagnosis of Chagas disease. PLoS Negl. Trop. Dis., 2009, 3: e450.
                  30. Buzder-Lantos P, Bockstael K, Anné J, Herdewijn P.  Substrate based peptide aldehyde inhibits bacterial type I signal peptidase. Bioorg. Med. Chem. Lett. 2009, 19:2880-2883.
                  31. Michielssens S, Trung NT, Froeyen M, Herdewijn P, Nguyen MT, Ceulemans A.
                    Hydrolysis of aspartic acid phosphoramidate nucleotides in HIV-RT: a comparative quantum chemical study. Phys. Chem. Chem. Phys. 2009, 11:7274-7285.
                  32. Mikhailov SN, Timofeev EN, Drenichev MS, Efimetseva EV, Herdewijn P, Roesch EB, Lemaitre M.  Oligodeoxynucleotides containing 2’-deoxy-1-methyladenosine and N6-methyl-2’-deoxyadenosine. Curr. Prot. Nucleic Acid Chem. 2009, chapter 4, unit 4.36.
                  33. Bockstael K, Geukens N, Van Mellaert L, Herdewijn P, Anné J, Van Aerschot A.
                    Evaluation of the type I signal peptidases as antibacterial target for biofilm-associated infections of Staphylococcus epidermidis.  Microbiology 2009, 155:3719-3729.
                  34. Giraut A, Dyubankova N, Song XP, Herdewijn P.  Phosphodiester substrates for incorporation of nucleotides in DNA using HIV-1 reverse transcriptase. ChemBio Chem. 2009, 10:2246-2252.
                  35. Abramov M, Renders M, Herdewijn P.  Synthesis of 2’N formamide nucleosides and biological evolution. Nucleos. Nucleot. Nucleic Acids, 2009, 28:1042-1050.
                  36. D’Alonzo D, Van Aerschot A, Guaragna A, Capore S, Palumbo G, Schepers G, Rozenski J, Herdewijn P.  Synthesis and base pairing properties of 1,5-anhydro-L-hexitol nucleic acids (L-HNA). Chemistry, Eur. J. 2009, 15:10121-10131.
                  37. Zlatev I, Giraut A, Morvan F, Herdewijn P, Vasseur JJ.  δ-Di-carboxybutyl phosphoramidate of 2’-deoxycytidine-5’-monophosphate as substrate for DNA polymerization by HIV-1 reverse transcriptase. Bioorg. Med. Chem. 2009, 17:7008-7014.

                  2008

                  1. Faulon JL, Misra M, Martin S, Sale K, Sapra R.  Genome Scale Enzyme-metabolites and Drug-Target interaction predictions using the signature molecular descriptor. Bioinformatics, 2008, 24:225-233.
                  2. Simmons B, Dibble D, Singh S, Aauer M, Jorgens D, Faulon JL.  Utilization of atomic force microscopy, confocal microscopy, and electron microscopy to evaluate biomass pretreatment. Microscopy and microanalysis, 2008, 14 Suppl 2:1492-1493, .
                  3. Weis DC, Visco DP Jr, Faulon JL.  Data mining PubChem using a support vector machine with the Signature molecular descriptor: classification of factor XIa inhibitors. J. Mol. Graph Model. 2008, 27:466-475.
                  4. May E, Leitao A, Faulon JL, Joo J, Misra M, Oprea TI.  Understanding virulence mechanism in M. tuberculosis infection via a circuit-base simulation framework. IEEE Eng. Med. Biol. Soc., 2008, 1:4953-4955.
                  5. Rodrigo G, Carrera J, Prather KJ, Jaramillo A.  DESHARKY: Automatic design of metabolic pathways for optimal cell growth. Bioinformatics, 2008, 24(21):2554-2556.
                  6. Agudelo-Romero P, Carbonell P, de la Iglesia F, Carrera J, Rodrigo G, Jaramillo A, Pérez-Amador MA, Elena SF.  Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Virology Journal 2008, 5:92.
                  7. Suarez M, Tortosa P, Carrera J, Jaramillo A.  Pareto Optimization in Computational Protein Design with Multiple Objectives. J. Comp. Chem. 2008, 29:2704-2711.
                  8. G. Rodrigo, J. Carrera and A. Jaramillo.  Computational design and evolution of the oscillatory response under light-dark cycles. Biochimie. 2008, 90(6):888-897.
                  9. Noirel J, Ow SY, Sanguinetti G, Jaramillo A, Wright PC.  Automated extraction of meaningful pathways from quantitative proteomics data. Briefings in Functional Genomics and Proteomics 2008, 7(2):136-146.
                  10. Bikard D, Képès F.  Succès de la première équipe française lors de la compétition iGEM de biologie synthétique. Médecine / Sciences, 2008, 24:541-544.
                  11. Poudret M, Arnould A, Comet JP, Le Gall P, Meseure P, Képès F.  Topology-based abstraction of complex biological systems: Application to the Golgi apparatus. Theory in Biosciences, 2008, 127:79-88.
                  12. Omont N, Forner K, Lamarine M, Martin G, Képès F, Wojcik J.  Gene-based bin analysis of genome-wide association studies. BMC Proceedings, 2008, 2 (Suppl 4):S6.
                  13. Fierro, AC, Thuret R, Engelen K, Bernot G, Marchal K, Pollet N.  Evaluation of time profile reconstruction from complex two-color microarray designs. BMC Bioinformatics, 2008, 9:1.
                  14. Bowes J, Synder K, Segerdell E, Gibb R, Jarabek C, Noumen E, Pollet N, Vize P. Xenbase: a Xenopus biology and genomics resource. Nucleic Acids Res. 2008, 36 (database issue):D761-767.
                  15. Graindorge A, Le Tonquèze O, Thuret R, Pollet N, Osborne HB, Audic Y. Identification of CUG- BP1/EDEN-BP target mRNAs in Xenopus tropicalis. Nucleic Acids Res. 2008, 36:1861-1870.
                  16. Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD.  Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat. Biotechnol. 2008, 26:305-312.
                  17. Abramov M, Schepers G, Van Aerschot A, Van Hummelen P, Herdewijn P.  HNA and ANA high-affinity arrays for detection of DNA and RNA single-base mismatches. Biosensors Bioelectronics. 2008, 23:1728-1732.
                  18. Li T, Froeyen M, Herdewijn P.  Computational alanine scanning and free energy decomposition for E. coli type 1 signal peptidase with lipopeptide inhibitor complex.  J. Mol. Graph. Model. 2008, 26:813-823.
                  19. Vrancken R, Paeshuyse J, Haegeman A, Puerstinger G, Froeyen M, Herdewijn P, Kerkhofs P, Neyts J, Koenen F.  Imidazo[4,5-c]pyridines inhibit the in vitro replication of the classical swine fever virus and target the viral polymerase. Antiviral Res. 2008, 77:114-119.
                  20. Terrazas M, Marlière P, Herdewijn P.  Enzymatically catalyzed DNA synthesis using L-Asp-dGMP, L-Asp-dCMP and L-Asp-dTMP. Chem. Biodiv., 2008, 5:31-39.
                  21. Robeyns K, Herdewijn P, Van Meervelt L.  Structure of the fully modified left-handed cyclohexene nucleic acid sequence GT GTA CAC.  J. Am. Chem. Soc., 2008, 130:1979-1984.
                  22. Emmerechts G, Maes L, Herdewijn P, Anné J, Rozenski J.  Characterization of the posttranscriptional modifications in Legionella pneumophila small-subunit ribosomal RNA. Chem. Biodivers., 2008, 5:2640-2653.
                  23. Wang G, Abramov M, Van Aerschot A, Rozenski J, Lei S, Klymchenko MA, Van der Auweraer M, De Feyter S, Herdewijn P.  Dendritic nucleotides: interaction with an aliphatic acid monolayer.  Chem. Biodivers., 2008, 5:1675-1682.
                  24. Mikhailov S, Kulikova I, Nauwelaerts K, Herdewijn P.  Synthesis of 2’-O-α-D-ribofuranosyladenosine, monomeric unit of poly(ADP-ribose). Tetrahedron, 2008, 64:2871-2876.
                  25. Deborggraeve S, Koffi M, Jamonneau V, Bonsu FA, Queyson R, Simano PP, Herdewijn P, Büscher P.  Molecular analysis of archived blood slides reveals an atypical human Trypanosoma infection. Diagn. Microbiol. Infect. Dis., 2008, 61:428-433.
                  26. Robeyns K, Herdewijn P, Van Meervelt L.  Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue into the sequence d(CGCGAATTCGCG). Nucleic Acids Res. 2008, 36:1407-1414.
                  27. Li T, Froeyen M, Herdewijn P.  Comparative structural dynamics of tyrosyl-tRNA synthetase complexed with different substrates explored by molecular dynamics. Eur. Biophys. J., 2008, 38:25-35.
                  28. Doboszewski B, Herdewijn P.  Carbohydrate-based approach to four enantiomerically pure 2-naphthylmethyl-3-hydroxy-2-methylbutanoates. Tetrahedron Lett. 2008, 49:1331–1335.
                  29. d’Alonzo D, Guaragna A, Van Aerschot A, Herdewijn P, Palumbo G.  De Novo approach to L-anhydro hexitol nucleoside analogues as building blocks for the synthesis of L-hexitol nucleic acids (L-HNA). Tetrahedon Lett. 2008, 49:6068-6070.
                  30. Van de Vijver P, Ostrowski T, Sproat B, Goebels J, Rutgeerts O, Van Aerschot A, Waer M, Herdewijn P.  Aminoacyl- tRNA synthetase inhibitors as potent and synergistic immunosuppressants. J. Med. Chem. 2008, 51:3020-3029.
                  31. Deborggraeve S, Boelaert M, Rijal S, De Doncker S, Dujardin JC, Herdewijn P, Büscher P.  Diagnostic accuracy of a new Leishmania PCR for clinical visceral leishmaniasis in Nepal and its role in diagnosis of disease. Trop. Med. Int. Health, 2008, 13:1378-1383.
                  32. Deborggraeve S, Laurent T, Espinosa D, Van der Auwera G, Mbuchi M, Wasunna M, El-Safi S, Basheer AA, Arévalo J, Miranda-Verástegui C, Leclipteux T, Mertens P, Dujardin JC, Herdewijn P, Büscher P.  A simplified and standardized polymerase chain reaction format for the diagnosis of Leishmaniasis. J. Infect. Dis., 2008, 198:1565-1572.
                  33. Bobkov GV, Mikhailov SN, Van Aerschot A, Herdewijn P.  Phosphoramidite building blocks for efficient incorporation of 2ʹ′-O-aminoethoxy(and propoxy)methyl nucleosides into oligonucleotides. Tetrahedron, 2008, 64:6238-6251.
                  34. Yang S, Busson R, Herdewijn P.  Synthesis of N-methyl- D-ribopyranuronamide nucleosides. Tetrahedron, 2008, 64:10062-10067.
                  35. Renders M, Lievrouw R, Krecmerová R, Holý A, Herdewijn P.  Enzymatic polymerization of phosphonate nucleosides. ChemBioChem, 2008, 9:2883-2888.
                  36. Paeshuyse J, Vliegen I, Coelmont L, Leyssen P, Tabarrini O, Herdewijn P, Mittendorfer H, Easmon J, Cecchetti V, Bartenschlager R, Puerstinger G.  Comparative in vitro anti-hepatitis C virus activities of a selected series of polymerase, protease and helicase inhibitors. J. Neyts. Antimicrob. Agents Chemother., 2008. 52:3433-3437.
                  37. Liu FW, Di Salvo A, Herdewijn P.  Synthesis of 2'-cyclohexenylnucleosides and corresponding CeNA building blocks. Curr. Protoc. Nucleic Acid Chem, 2008, Chapter 1, Unit 1.20.

                  2007

                  1. Rodrigo G, Jaramillo A.  Computational design of digital and memory biological devices. Systems and Synthetic Biology, 2007, 1:183-195.
                  2. Rodrigo G, Carrera J, Jaramillo A.  Asmparts: Assembly of biological model parts. Systems and Synthetic Biology, 2007, 1:167-170.
                  3. Rodrigo G, Carrera J, Jaramillo A.  Genetdes: automatic design of transcriptional networks. Bioinformatics, 2007, 23(14):1857-1858.
                  4. Rodrigo G, Carrera J, Jaramillo A. Evolutionary mechanisms of circadian clocks. Cent. Eur. J. Biol. 2007, 2:233-253.
                  5. Rodrigo G, Montagud A, Aparici A, Aroca MC, Baguena B, Carrera J, Edo C, Fernandez-de-Cordoba P, Ferrando A, Fuertes G, Gimenez D, Mata C, Medrano JV, Navarrete C, Navarro E, Salgado J, Tortosa P, Urchueguia J, Jaramillo A.  Vanillin Cell Sensor. IET Synthetic Biology, 2007, 1:74-78.
                  6. Norris V, Hunding A, Képès F, Lancet D, Minsky A, Raine D, Root-Bernstein R, Sriram K.  Question 7: the first units of life were not simple cells. Orig. Life Evol. Biosph.  2007, 37:429-443.
                  7. Sriram K, Bernot G, Képès F.  A minimal mathematical model combining several regulatory cycles from the budding yeast cell cycle. IET Systems Biology, 2007, 1:326-341.
                  8. Yartseva A, Devillers R, Klaudel H, Képès F.  From MIN model to ordinary differential equations. J. of Integrative Bioinformatics, 2007, 4:61.
                  9. Yartseva A, Klaudel H, Devillers R, Képès F.  Incremental and unifying modelling formalism for biological interaction networks. BMC Bioinformatics, 2007, 8:433.
                  10. Bronchain O, Pollet N, Ymlahi-Ouazzani Q, Dhorne-Pollet S, Helbling JC, Lecarpentier JE, Percheron K, Wegnez M.  The Olig family: phylogenetic analysis and early gene expression in Xenopus tropicalis. Development, Genes and Evolution, 2007, 217:485-497.
                  11. Fierro AC, Thuret R, Coen L, Perron M, Demeneix BA, Wegnez M, Gyapay G, Weissenbach J, Wincker P, Mazabraud A, Pollet N.  Exploring the nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis. BMC Genomics, 2007, 8:118.
                  12. Du Pasquier D, Chesneau A, Ymlahi-Ouazzani Q, Boistel R, Pollet N, Ballagny C, Sachs LM, Demeneix B, Mazabraud A.  TBid mediated Activation of the Mitochondrial Death Pathway leads to Genetic Ablation of the lens in Xenopus laevis. Genesis, 2007, 45:1-10.
                  13. Troncale S, Thuret R, Ben C, Pollet N, Comet JP, Bernot G.  Modelling of the TH-dependent regulation of tadpole tail resorption. J. of Biol. Phys. Chem. 2007, 7:45-50.
                  14. Vörbruggen H, Lagoja I, Herdewijn P.  Synthesis of ribonucleosides by condensation using trimethylsilyl triflate. Curr. Protoc. Nucleic Acid Chem. 2007, 1.13.1-1.13.16.
                  15. Mikhailov SN, Efimtseva EV, Rodionov AA, Bobkov GV, Kulikova IV, Herdewijn P.
                    Synthesis of 2’-O-β-D-ribofuranosyl nucleosides. Curr. Protoc. Nucleic Acid Chem. 2007, 1.14.1-1.14.19.
                  16. Lambertucci C, Schepers G, Cristalli G, Herdewijn P, Van Aerschot A.  Synthesis and evaluation of hexitol nucleoside congeners as ambiguous nucleosides. Tetrahedron  Lett. 2007, 48:2143-2145.
                  17. Fisher M, Abramov M, Van Aerschot A, Xu D, Juliano R, Herdewijn P.  Inhibition of MDR1 expression with altritol modified siRNA. Nucleic Acids Res. 2007, 35:1064-1074.
                  18. Herdewijn P, Juliano R.  Nucleic acids with a six-membered carbohydrate mimic and RNA interference. Blood Cells, Mol. Dis. 2007, 38:100-101.
                  19. Viña D, Wu T, Renders M, Laflamme G, Herdewijn P.  Synthesis of 3’-O phosphonomethyl nucleosides with adenine base moiety. Tetrahedron, 2007, 63:2634-2646.
                  20. Nauwelaerts K, Lescrinier E, Herdewijn P.  Structure of α-homo DNA:RNA duplex and the function of twist and slide to catalogue nucleic acids duplexes. Chem. Eur. J. 2007, 13:90-98.
                  21. Renders M, Emmerechts G, Rozenski J, Krecmerová M, Holý A, Herdewijn P.  Enzymatic synthesis of phosphonomethyl oligonucleotides by therminator polymerase. Angewandte Chem. Int. Ed. 2007, 46:2501-2504.
                  22. Nauwelaerts K, Fisher M, Froeyen M, Lescrinier E, Van Aerschot A, Xu DG, De Long R, Kang H, Juliano RL, Herdewijn P.  Structural characterization and biological evaluation of small interfering RNAs containing cyclohexenyl nucleosides. J. Am. Chem.Soc. 2007, 129:9340-9348.
                  23. Timofeev E, Mikhailov S, Zuev A, Efimtseva E, Somers R, Herdewijn P, Lemaitre M.
                    Oligodeoxynucleotides containing N1-Me deoxyadenosine and their Dimroth rearrangement. Helv. Chim. Acta, 2007, 90:928-937.
                  24. Zhou D, Froeyen M, Rozenski J, Van Aerschot A, Herdewijn P.  Chemical etiology of nucleic acids: aminopropyl nucleic acids. Chem. Biodiv. 2007, 4:740-761.
                  25. Marchand A, Marchand D, Busson R, Marlière P, Herdewijn P.  Synthesis of a Pyridoxine–Peptide Based Delivery System for Nucleotides. Chem. Biodiv. 2007, 4:1450-1465.
                  26. Horvath A, Ruttens B, Herdewijn P.  Stereoselective synthesis of (-)ara-cyclohexenyladenine. Tetrahedron Lett. 2007, 48:3621-3623.
                  27. Lagoja I, Herdewijn P.  Preparation of guanine and diaminopurine from biuret. Chem. Biodiv. 2007, 4:818-822.
                  28. Adelfinskaya O, Herdewijn P.  Amino Acid Phosphoramidate Nucleotides as Alternative Substrates for HIV-1 Reverse Trancriptase. Angewandte Chem. Int. Ed. 2007, 46:4365-4368.
                  29. Mikhailov SN, Bobkov GV, Brilliantov KV, Rozenski J, Van Aerschot A, Herdewijn P, Fisher MH, Juliano RL.  2’-O-hydroxyalkoxymethylribonucleosides and their incorporation into oligoribonucleotides. Nucleosides, Nucleotides and Nucleic Acids, 2007, 26:1509-1512.
                  30. Margineanu A, De Feyter S, Melnikov S, Marchand D, Van Aerschot A, Herdewijn P, Habuchi S, De Schryver FC, Hofkens J.  Complexation of lipofectamine and cholesterol-modified DNA sequences studied by single molecule fluorescence techniques. Biomacromolecules. 2007, 8:3382-3392.
                  31. Froeyen M, Morvan F, Vasseur JJ, Nielsen P, Van Aerschot A, Rosemeyer H, Herdewijn P.  Conformational and chiral selection of oligonucleotides. Chem. Biodiv. 2007, 4:803-817.
                  32. Emmerechts G, Barbé S, Herdewijn P, Anné J, Rozenski J.  Post-transcriptional modification mapping in the clostridium actobutylicum 16S rRNA by masspectrometry and reversed transcriptase assays. Nucleic Acids Res. 2007, 35:3494-3503.
                  33. Goulioukina N, Wehbe J, Marchand D, Busson R, Lescrinier E, Heindl D, Herdewijn P.  Synthesis of NAD analogues with a sugar modified nicotinamide moiety. Helv. Chim. Acta, 2007, 90:1266-1278.
                  34. Paeshuyse J, Chezal JM, Froeyen M, Leyssen P, Dutartre H, Vrancken R, Canard B, Letellier C, Li T, Mittendorfer H, Koenen F, Kerkhofs P, De Clercq E, Herdewijn P, Puerstinger G, Gueiffier A, Chavignon O, Teulade JC, Neyts J. The imidazopyrrolopyridine analogue AG110 is a novel, highly selective inhibitor of pestiviruses that targets the viral RNA-dependent RNA polymerase at a hot spot for inhibition of viral replication. J. Virol. 2007, 81:11046-11053.
                  35. Stevens M, Balzarini J, Lagoja I, Noppen B, François K, Van Aerschot A, Herdewijn P, De Clercq E, Pannecouque C.  Inhibition of human immunodeficiency virus type 1 transcription by N-amino imidazole derivatives. Virology, 2007, 365:220-237.
                  36. Lagoja I, Herdewijn P.  Use of RNA in drug design. Expert Opinion on Drug Discovery, 2007, 2:889-903. 
                  37. Novoa de Armas H, Doboszewski B, Herdewijn P, Blaton N.  3-Deoxy-1,2-O-isopropylidene-3-C-methyl-5-O-(p-tolylsulfonyl)-D-ribofuranose. Acta Crystallographica, 2007, E63, 2678-2680.
                  38. Abramov M, Herdewijn P.  Synthesis of altritol nucleoside phosphoramidites for oligonucleotide synthesis. Curr. Protoc. Nucleic Acids Chem. 2007, 1.18.1-1.18.21.
                  39. Adelfinskaya O, Terrazas M, Froeyen M, Marlière P, Nauwelaerts K, Herdewijn P.  Polymerase-catalyzed synthesis of DNA from phosphoramidate conjugates of deoxynucleotides and amino acids. Nucleic Acids Res., 2007, 35:5060-5072.
                  40. Rosemeyer H, Stürenberg EM, Herdewijn P.  Nucleolipids as potential organogelators. Nucleosides Nucleotides Nucleic Acids, 2007, 26:995-999.
                  41. Voight-Goffmann F, Hengesbach M, Kobitski AY, Van Aerschot A, Herdewijn P, Nienhaus GU, Helm M.  A methyl group controls conformational equilibrium in human tRNALys. J. Am. Chem. Soc., 2007, 129:13382-13383.
                  42. Gaucher SP, Morrow JA, Faulon JL.  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, 2007, 79:7822-7830.
                  43. Gray GA, Williams PJ, Brown WM, Faulon JL, Sale K.  Disparate Data Fusion for Protein Phosphorylation Prediction”, Annals of Operations Research Special Volume on Data Mining, 2007.
                  44. Zhang Z, Martino A, Faulon JL.  Global analysis of IL-2 responsive genes in murine T Cell. J. of Interferon & Cytokine Res., 2007, 27:991-995.
                  45. Joo J, Plimpton S, Martin S, Swiler L, Slepoy A, Faulon JL.  Sensitivity analysis of computational model of the NF-κB-IκB-A20 signal transduction network. Annals of NY Academy of Sciences, 2007, 1115:221-239.
                  46. Oprea T, Tropsha A, Faulon JL, Rintoul MD.  Systems Chemical Biology. Nature Chem. Biol., 2007, 3:447-450.
                  47. Martin S, Zhang Z, Martino A, Faulon JL.  Boolean Dynamics of Genetic Regulatory Networks Inferred from Microarray Time Series Data. Bioinformatics, 2007, 23:866-874.
                  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.