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Publications

2018

  1. Gasse C, Zaarour M, Noppen S, Abramov M, Marlière P, Liekens S, De Strooper B, Herdewijn P. Modulation of BACE1 activity by chemically modified aptamers.   Chembiochem. 2018, 19(7):754-763. doi: 10.1002/cbic.201700461.
  2. Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers.  Metab Eng. 2018, 45:158-170. doi: 10.1016/j.ymben.2017.12.002.
  3. Koch M, Pandi A, Delépine B, Faulon JL. A dataset of small molecules triggering transcriptional and translational cellular responses. Data Brief. 2018, 17:1374-1378. doi: 10.1016/j.dib.2018.02.061. eCollection 2018 Apr.
  4. Carbonell P, Delépine B, Faulon JL. Extended Metabolic Space Modeling. Methods Mol Biol. 2018, 1671:83-96. doi: 10.1007/978-1-4939-7295-1_6.
  5. Pezo VHassan C, Louis D, Sargueil B, Herdewijn P, Marliere P. Metabolic recruitment and directed evolution of nucleoside triphosphate uptake in Escherichia coli. ACS Synth Biol. 2018, 7(6):1565-1572. doi: 10.1021/acssynbio.8b00048.
  6. Liu C, Cozens C, Jaziri F, Rozenski J, Maréchal A, Dumbre SG, Pezo VMarliere P, Pinheiro VB, Groaz E, Herdewijn P. Phosphonomethyl Oligonucleotides as Backbone Modified Artifi-cial Genetic Polymers.  J Am Chem Soc. 2018, 140:6690-6699. doi: 10.1021/jacs.8b03447.
  7. Trabelsi H, Koch M, Faulon JL. Building a minimal and generalizable model of transcription-factor based biosensors: showcasing flavonoids. Biotechnol Bioeng. 2018, 115:2292-2304. doi: 10.1002/bit.26726.
  8. Jabgunde AM, Jaziri F, Bande O, Froeyen M, Abramov M, Nguyen H, Schepers G, Lescrinier E, Pinheiro VB, Pezo V,Marlière P, Herdewijn P. Methylated nucleobases: Synthesis and evaluation for base pairing in vitro and in vivo. Chemistry 2018, 24:12695-12707. doi: 10.1002/chem.201802304.
  9. Gangwe Nana GY, Ripoll C, Cabin-Flaman A, Gibouin D, Delaune A, Janniere L, Grancher G, Chagny G, Loutelier-Bourhis C, Lentzen E, Grysan P, Audinot JN, Norris V. Division-Based, Growth Rate Diversity in Bacteria. Front Microbiol. 2018, May 11;9:849. doi: 10.3389/fmicb.2018.00849. eCollection 2018.
  10. Nouri H, Monnier AF, Fossum-Raunehaug S, Maciag-Dorszynska M, Cabin-Flaman A, Képès F,Wegrzyn G, Szalewska-Palasz A, Norris V, Skarstad K, Janniere L. Multiple links connect central carbon metabolism to DNA replication initiation and elongation in Bacillus subtilis.  DNA Res. 2018, Sep 26. doi: 10.1093/dnares/dsy031. [Epub ahead of print]
  11. Duigou T, du Lac M, Carbonell P, Faulon JL.  RetroRules: a database of reaction rules for engineering biology. Nucleic Acids Res. 2018, Oct 13. doi: 10.1093/nar/gky940. [Epub ahead of print]
  12. Le Treut G, Képès F, Orland H. A Polymer Model for the Quantitative Reconstruction of Chromosome Architecture from HiC and GAM Data. Biophys J2018 Nov 10. pii: S0006-3495(18)31225-6. doi: 10.1016/j.bpj.2018.10.032. [Epub ahead of print]

  13. de Lorenzo V, Marlière P. The Synthetic Microbiology Caucus: a fresh channel for exploring new ideas, challenging conventional wisdom and fostering community projects.  Microb Biotechnol2018, Oct 25. doi: 10.1111/1751-7915.13331. [Epub ahead of print]
  14. Röthlisberger P, Levi-Acobas F, Sarac I, Marlière P, Herdewijn P, Hollenstein M. Towards the enzymatic formation of artificial metal base pairs with a carboxy-imidazole-modified nucleotide.  J Inorg Biochem2018, Nov 15;191:154-163. doi: 10.1016/j.jinorgbio.2018.11.009. [Epub ahead of print]

 

 

2017

  1. Jaramillo A.  Synthetic biology: Engineered stable ecosystems. Nat Microbiol. 2017,  2:17119-17120. doi: 10.1038/nmicrobiol.2017.119.
  2. Rodrigo G, Prakash S, Shen S, Majer E, Daròs J-A, Jaramillo A. Model-based design of RNA hybridization networks implemented in living cells. Nucleic Acids Research, 2017. 45(16):9797-9808. http://doi.org/10.1093/nar/gkx698
  3. Banos DT, Trébulle P, Elati M. Integrating transcriptional activity in genome-scale models of metabolism. BMC Syst Biol. 2017, 11(Suppl 7):134. doi: 10.1186/s12918-017-0507-0.
  4. Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0.  J Cheminform. 2017, 9(1):64. doi: 10.1186/s13321-017-0252-9.
  5. Trébulle P, Nicaud JM, Leplat C, Elati M. Inference and interrogation of a coregulatory network in the context of lipid accumulation in Yarrowia lipolyticaNPJ Syst Biol Appl. 2017, Aug 11;3:21. doi: 10.1038/s41540-017-0024-1. eCollection 2017.
  6. Brödel AK, Jaramillo A, Isalan M. Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication. Nature Protocols 2017. 12(9):1830-1843. doi: 10.1038/nprot.2017.084.
  7. Paschalis V, Le Chatelier E, Green M, Képès F, Nouri H, Soultanas P, Jannière L. Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity. Open Biology, 2017. Sep;7(9). pii: 170146. doi: 10.1098/rsob.170146
  8. Eremeeva E, Abramov M, Margamuljana L, Herdewijn P.  Base-Modified Nucleic Acids as a Powerful Tool for Synthetic Biology and Biotechnology.  Chemistry 2017, 23(40):9560-9576. doi: 10.1002/chem.201700679.
  9. Kuenzl T, Sroka M, Srivastava P, Herdewijn P, Marlière P, Panke S. Overcoming the membrane barrier: Recruitment of γ-glutamyl transferase for intracellular release of metabolic cargo from peptide vectors.  Metab Eng., 2017, 39:60-70. doi: 10.1016/j.ymben.2016.10.016.
  10. Singh V, Braddick D, Dhar PK. Exploring the potential of genome editing CRISPR-Cas9 technology. Gene, 2017, 599:1-18. doi: 10.1016/j.gene.2016.11.008. Review.
  11. Celińska E, Ledesma-Amaro R, Larroude M, Rossignol T, Pauthenier C, Nicaud JM. Golden Gate Assembly system dedicated to complex pathway manipulation in Yarrowia lipolytica.  Microb Biotechnol., 2017, 10(2):450-455. doi: 10.1111/1751-7915.12605.
  12. Bronchain OJ, Chesneau A, Monsoro-Burq AH, Jolivet P, Paillard E, Scanlan TS, Demeneix BA, Sachs LM, Pollet N. Implication of thyroid hormone signaling in neural crest cells migration: Evidence from thyroid hormone receptor beta knockdown and NH3 antagonist studies.  Mol Cell Endocrinol., 2017, 439:233-246. doi: 10.1016/j.mce.2016.09.007.
  13. Röthlisberger P, Levi-Acobas F, Sarac I, Marlière P, Herdewijn P, Hollenstein M.  On the enzymatic incorporation of an imidazole nucleotide into DNA.  Org Biomol Chem., 2017, 15(20):4449-4455. doi: 10.1039/c7ob00858a.
  14. Bouzon M, Perret A, Loreau O, Delmas V, Perchat N, Weissenbach J, Taran F, Marlière P.  A Synthetic Alternative to Canonical One-Carbon Metabolism. ACS Synth Biol. 2017, May 3. doi: 10.1021/acssynbio.7b00029.
  15. Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Dunstan M, Jervis AJ, Vinaixa M, Williams AR, Ananiadou S, Faulon JL, Mendes P, Kell DB, Scrutton NS, Breitling R.  biochem4j: Integrated and extensible biochemical knowledge through graph databases. PLoS One, 2017, 12(7):e0179130. doi: 10.1371/journal.pone.0179130
  16. Dhifli W, Da Costa N, Elati M.  An evolutionary schema for mining skyline clusters of attributed graph data.  Congress on Evolutionary Computation At Donostia - San Sebastián, Spain, IEEE, June 2017, pp. 2102-2109. doi: 10.1109/CEC.2017.7969559
  17. Bayer PE, Hurgobin B, Golicz AA, Chan CK, Yuan Y, Lee H, Renton M, Meng J, Li R, Long Y, Zou J, Bancroft I, Chalhoub B, King GJ, Batley J, Edwards D. Assembly and comparison of two closely related Brassica napus genomes.  Plant Biotechnol J. 2017 Apr 12. doi: 10.1111/pbi.12742.
  18. Brödel AK, Isalan M, Jaramillo A. Engineering of biomolecules by bacteriophage directed evolution.  Curr Opin Biotechnol. 2017, 51:32-38. doi: 10.1016/j.copbio.2017.11.004.
  19. Röthlisberger P, Levi-Acobas F, Sarac I, Baron B, England P, Marlière P, Herdewijn P, Hollenstein M. Facile immobilization of DNA using an enzymatic his-tag mimic.  Chem Commun (Camb). 2017, Nov 22. doi: 10.1039/c7cc07207d. 
  20. Röthlisberger P, Gasse C, Hollenstein M. Nucleic Acid Aptamers: Emerging Applications in Medical Imaging, Nanotechnology, Neurosciences, and Drug Delivery. Int J Mol Sci. 2017 Nov 16;18(11). pii: E2430. doi: 10.3390/ijms18112430.
  21. Hurgobin B, Golicz AA, Bayer PE, Chan CK, Tirnaz S, Dolatabadian A, Schiessl SV, Samans B, Montenegro JD, Parkin IAP, Pires JC, Chalhoub B, King GJ, Snowdon R, Batley J, Edwards D. Homoeologous exchange is a major cause of gene presence/ absence variation in the amphidiploid Brassica napus.  Plant Biotechnol J. 2017 Dec 4. doi: 10.1111/pbi.12867.


Book chapter
Carbonell P, Delépine B, Faulon JL. “Extended metabolic space modeling”, In: Synthetic metabolic pathways: Methods and Protocols, MK Jensen and JD Keasling Eds, Springer, in press, 2017. doi: 10.1007/978-1-4939-7295.

 

2016

  1. Brödel AK, Jaramillo A, Isalan M. Engineering orthogonal dual transcription factors for multi-input synthetic promoters. Nat Commun. 2016, 7:13858. doi: 10.1038/ncomms13858

  2. Le Treut G, Képès F, Orland H. Phase Behavior of DNA in the Presence of DNA-Binding Proteins.  Biophys J. 2016, 110(1):51-62. doi: 10.1016/j.bpj.2015.10.027.
  3. Bande O, Braddick D, Agnello S, Jang M, Pezo V, Schepers G, Rozenski J, Lescrinier E, Marliere P, Herdewijn P. Base pairing involving artificial bases in vitro and in vivo.  Chemical Science, 2016, 7:995–1010  (IF 9.1)
  4. Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TM, Texier T, (.....), Kepes F, et al.  An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.  Nat Commun., 2016. 7:11491. doi: 10.1038/ncomms11491.
  5. Bouyioukos C, Elati M, Képès F. Analysis tools for the interplay between genome layout and regulation. BMC Bioinformatics, 2016. 17 (Suppl 5):191. doi: 10.1186/s12859-016-1047-0.
  6. Delépine B, Libis V, Carbonell P, Faulon JL.  SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic Acids Res. 2016, 44(W1):W226-31. doi: 10.1093/nar/gkw305.
  7. Bouyioukos C, Bucchini F, Elati M, Képès F.  GREAT: a web portal for Genome Regulatory Architecture Tools. Nucleic Acids Res. 2016. 44(W1):W77-82. doi: 10.1093/nar/gkw384
  8. Mellor J, Grigoras I, Carbonell P, Faulon JL.  Semisupervised Gaussian Process for Automated Enzyme Search.  ACS Synth Biol. 2016, 5(6):518-28. doi: 10.1021/acssynbio.5b00294.
  9. Libis V, Delépine B, Faulon JL.  Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways. ACS Synth Biol. 2016, 5(10):1076-1085.
  10. Pasini M, Fernández-Castané AJaramillo A, de Mas C, Caminal G, Ferrer P. Using promoter libraries to reduce metabolic burden due to plasmid-encoded proteins in recombinant Escherichia coli. New Biotechnol. 2016, 33(1):78-90. doi: 10.1016/j.nbt.2015.08.003
  11. Kushwaha M, Rostain W, Prakash S, Duncan JN, Jaramillo A.  Using RNA as Molecular Code for Programming Cellular Function.  ACS Synth Biol. 2016, 5(8):795-809. doi: 10.1021/acssynbio.5b00297.
  12. Libis V, Delépine B, Faulon JL. Sensing new chemicals with bacterial transcription factors.  Curr Opin Microbiol., 2016, 33:105-12. doi: 10.1016/j.mib.2016.07.006. Review.
  13. Eremeeva E, Abramov M, Margamuljana L, Rozenski J, Pezo V, Marlière P, Herdewijn P.  Chemical Morphing of DNA Containing Four Noncanonical Bases.  Angew Chem Int Ed Engl., 2016, 55(26):7515-9. doi: 10.1002/anie.201601529. (IF 11.7)
  14. Bouyioukos C, Reverchon S, Képès F. From multiple pathogenicity islands to a unique organized pathogenicity archipelago.  Sci Rep., 2016. 6:27978. doi: 10.1038/srep27978.
  15. Taylor AI, Beuron F, Peak-Chew S-Y, Morris EP, Herdewijn P, Holliger P. Nanostructures from synthetic genetic polymers. ChemBioChem, 2016, 17:1107–1110.  (IF 3.1)
  16. Rodrigo G, Prakash S, Cordero T, Kushwaha M, Jaramillo A.  Functionalization of an Antisense Small RNA. J. Mol. Biol. 2016, 428 (5 PtB):889-892. doi: 10.1016/j.jmb.2015.12.022.
  17.  Lioliou E, Fechter P, Caldelari I, Jester BC, Dubrac S, Helfer AC, Boisset S, Vandenesch F, Romby P, Geissmann T.  Various checkpoints prevent the synthesis of Staphylococcus aureus peptidoglycan hydrolase LytM in the stationary growth phase.  RNA Biol. 2016, 22:1-14.
  18.  Spirhanzlova P, Dhorne-Pollet S, Fellah JS, Da Silva C, Tlapakova T, Labadie K, Weissenbach J, Poulain J, Jaffredo T, Wincker P, Krylov V, Pollet N. Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis.  Dev Biol., 2016. May 30. pii: S0012-1606(16)30050-1. [Epub ahead of print]
  19. Cabin-Flaman A, Monnier A-F, Coffinier Y,
 Audinot J-N, Gibouin D, Wirtz T, Boukherroub R,
Migeon H-N, Bensimon A, Jannière L, Ripoll C, Norris V.  Combining conbing and secondary ion mass spectroscopy to study DNA on chips using 13C and 15N labeling. F1000Res. 2016, 5 :1437. Doi :10.12688/f1000research.8361.1.
  20. Bronchain OJ, Chesneau A, Monsoro-Burq AH, Jolivet P, Paillard E, Scanlan TS, Demeneix BA, Sachs LM, Pollet N.  Implication of thyroid hormone signaling in neural crest cells migration: Evidence from thyroid hormone receptor beta knockdown and NH3 antagonist studies.  Mol. Cell. Endocrinol. 2016, Sep 10. pii: S0303-7207(16)30372-0. doi: 10.1016/j.mce.2016.09.007
  21. de Lorenzo V, Marlière P, Solé R. Bioremediation at a global scale: from the test tube to planet Earth.  Microb Biotechnol. 2016, 9(5):618-25. doi: 10.1111/1751-7915.12399.
  22. Sagona AP, Grigonyte AM, MacDonald PR, Jaramillo A. Genetically modified bacteriophages. Integr. Biol., 2016, 8:465-474.
  23. Dinh Thi VH, Coriton O, Le Clainche I, Arnaud D, Gordon SP, Linc G, Catalan P, Hasterok R, Vogel JP, Jahier J, Chalhoub B.  Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei.  PLoS One. 2016, 11(12):e0167171. doi: 10.1371/journal.pone.0167171.
  24. Eremeeva E, Abramov M, Marlière P, Herdewijn P.  The 5-chlorouracil:7-deazaadenine base pair as an alternative to the dT:dA base pair. Org Biomol Chem. 2016, 15(1)168-176.
  25. Trejo D, Khan S, Trebulle P, Elati M.  Networks interrogation for genotype-phenotype study of the yeast diauxic shift. 17th International conference on systems biology, ICSB Proceedings, Barcelona, p56-59, 2016.
  26. Njah H, Jamoussi S, Mahdi W and Elati M.  A Bayesian approach to construct context-specific gene ontology.  Computational Intelligence in Bioinformatics and Computational Biology, IEEE, pp. 1-6, 2016.

     

     

 

2015

  1. Taylor AI, Pinheiro VB, Smola MJ, Morgunov AS, Peak-Chew S, Cozens C, Weeks KM, Herdewijn P, Holliger P.  Catalysts from synthetic genetic polymers. Nature. 2015, 518(7539):427-430. doi: 10.1038/nature1398
  2. Nicolle R, Radvanyi F, Elati M. COREGNET: reconstruction and integrated analysis of co-regulatory networks. Bioinformatics, 2015, 31(18):3066-3068. doi:10.1093/bioinformatics/btv305
  3. Shen S, Rodrigo G, Prakash S, Majer E, Landrain TE, Kirov B, Daròs JA, Jaramillo A. Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression. Nucleic Acids Res. 2015, 43(10):5158-5170.
  4. Vouillot L, Thélie A, Pollet N. Comparison of T7E1 and Surveyor Mismatch Cleavage Assays To Detect Mutations Triggered by Engineered Nucleases. G3 (Bethesda). 2015, 5(3):407-415. doi: 10.1534/g3.114.015834.
  5. Bande O, Abu El Asrar R, Braddick D, Dumbre S, Pezo V, Schepers G, Pinheiro VB, Lescrinier E, Holliger P, Marlière P, Herdewijn P. Isoguanine and 5-methyl-isocytosine bases, in vitro and in vivo. Chemistry. 2015, 21(13):5009-5022. doi: 10.1002/chem.201406392.
  6. Bougerol M, Auradé F, Lambert FM, Le Ray D, Combes D, Thoby-Brisson M, Relaix F, Pollet N, Tostivint H. (2015) Generation of BAC Transgenic Tadpoles Enabling Live Imaging of Motoneurons by Using the Urotensin II-Related Peptide (ust2b) Gene as a Driver. PLoS One 2015, 10(2):e0117370. doi: 10.1371/journal.pone.0117370
  7. Colombo BM, Scalvenzi T, Benlamara S, Pollet N. Microbiota and mucosal immunity in amphibians. Front. Immunol. 6:111. doi:10.3389/fimmu.2015.00111
  8. Fehér T, Libis V, Carbonell P, Faulon JL. A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli. Front. Bioeng. Biotechnol. 2015, Apr 8;3:46. doi: 10.3389/fbioe.2015.00046. eCollection 2015.
  9. De S, Groaz E, Margamuljana L, Abramov M, Marlière P, Herdewijn P. Sulfonate derived phosphoramidates as active intermediates in the enzymatic primer-extension of DNA. Org. Biomol. Chem., 2015, 13(13):3950-3962. doi: 10.1039/c5ob00157a.
  10. Rodrigo G, Majer E, Prakash S, Daròs JA, Jaramillo A, Poyatos JF. Exploring the Dynamics and Mutational Landscape of Riboregulation with a Minimal Synthetic Circuit in Living Cells.  Biophys J. 2015, 109(5):1070-1076. doi: 10.1016/j.bpj.2015.07.021.
  11. Lepage T, Képès F, Junier I. Thermodynamics of long supercoiled molecules: insights from highly efficient Monte Carlo simulations. Biophys J. 2015, 109(1):135-143. doi: 10.1016/j.bpj.2015.06.005.
  12. Amos M, Axmann IM, Blüthgen N, de la Cruz F, Jaramillo A, Rodriguez-Paton A, Simmel F.  Bacterial computing with engineered populations.  Philos Trans A Math Phys Eng Sci. 2015, 373(2046). pii: 20140218. doi: 10.1098/rsta.2014.0218.
  13. Gottrand G, Courau T, Thomas-Vaslin V, Prevel N, Vazquez T, Ruocco MG, Lambrecht B, Bellier B, Colombo BM, Klatzmann D. Regulatory T cell development and function are impaired in mice lacking membrane expression of full length ICAM-1. Immunology 2015, Sep 14. doi: 10.1111/imm.12533. [Epub ahead of print]
  14. Picchetti T, Chiquet J, Elati M, Neuvial P, Nicolle R, Birmelé E.  A model for gene deregulation detection using expression data.  BMC Systems Biology. 2015; 9 Suppl 6:S6. PMID: 26679516
  15. Singh V, Braddick D. Recent advances and versatility of MAGE towards industrial applications.  Syst. Synth. Biol. 2015 Dec;9(Suppl 1):1-9. doi: 10.1007/s11693-015-9184
  16. Elati M. From biological network reconstruction to data analysis and visualization, 6th Annual World DNA and Genome Day - Phase B04: Bioinformatics/Computational Tools, Big Data Analysis and Visualization, Nanjing, China, 2015.


Book chapters

  1. Rostain W, Landrain TE, Rodrigo G, Jaramillo A. Regulatory RNA design through evolutionary computation and strand displacement. Methods Mol. Biol. 2015, 1244:63-78. doi: 10.1007/978-1-4939-1878-2_4.
  2. Bouyioukos C, Elati M, Képès F.  Protocols for probing genome architecture of regulatory networks in hydrocarbon and lipid microorganisms. in McGenity, T. J.; Timmis, K. N. and Nogales Fernandez, B. (Eds.) Hydrocarbon and Lipid Microbiology Protocols, Springer Protocols Handbooks, DOI 10.1007/8623_2015_92, © Springer-Verlag Berlin Heidelberg 2015.
  3. Hassall J, MacDonald P, Cordero T, Rostain W, Jaramillo A. Design and Characterization of Topological Small RNAs. Methods Mol. Biol.. 2015; 1316:149-167. doi: 10.1007/978-1-4939-2730-2_13.

 


2014

  1. Fehér T, Planson AG, Carbonell P, Fernández-Castané A, Grigoras I, Dariy E, Perret A, Faulon JL. Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering.  Biotechnol J. 2014, 9(11):1446-1457. doi: 10.1002/biot.201400055.
  2. Scalvenzi T, Pollet N. Insights on genome size evolution from a miniature inverted repeat transposon driving a satellite DNA.  Mol Phylogenet Evol. 2014, 81C:1-9.  doi: 10.1016/j.ympev.2014.08.014.
  3. Plouhinec JL, Roche DD, Pegoraro C, Figueiredo AL, Maczkowiak F, Brunet LJ, Milet C, Vert JP, Pollet N, Harland RM, Monsoro-Burq AH.  Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers. Dev Biol. 2014, 386(2):461-472.
  4. Rodrigo G, Jaramillo A. RiboMaker: computational design of conformation-based riboregulation. Bioinformatics, 2014, 30(17):2508-2510 doi:10.1093/bioinformatics/btu335
  5. Carbonell P, Parutto P, Baudier C, Junot C, Faulon JL. Retropath: automated pipeline for embedded metabolic circuits. ACS Synthetic Biology, 2014, 3(8):565-577. doi: 10.1021/sb4001273
  6. Parutto P, Le Goff L, Léger H, Mercy G, van der Kouwe E, Chhun A, Baudu B, Guillocheau G, Amiot F, Ujéda L, Rostain W, Pauthenier C, Cerisy T, Pollet N, Tolonen A, Jaramillo A. Characterization and modeling of an iron-sensitive system in Escherichia coli. In : Proceedings of the Evry Spring School on advances in Systems and Synthetic Biology. (Eds. Amar P, Képès F, Norris V.), EDP Sciences, 2014, p107-118.
  7. Winterhalter C, Nicolle R, Louis A, To C, Radvanyi F, Elati M. PEPPER: Cytoscape app for Protein complex Expansion using Protein-Protein intERaction networks. Bioinformatics, 2014, 30(23):3419-3420.
  8. Pauthenier C, Faulon JL. PrecisePrimer: an easy to use webserver for designing PCR primers for DNA library cloning and DNA Shuffling. Nucleic Acids Research, 2014, Jul;42(Web Server issue):W205-9. doi: 10.1093/nar/gku393.
  9. Fernandez-Castane A, Feher T, Carbonell P, Pauthenier C, Faulon JL. Computer-aided design for metabolic engineering. J. of Biotechnol., 2014, 192 Pt B:302-13. pii: S0168-1656(14)00159-X.
  10. Carbonell P, Parutto P, Herisson J, Pandit S, Faulon JL. XTMS: Pathway Design in an eXTended Metabolic Space. Nucleic Acids Research, 2014, Jul;42(Web Server issue):W389-94. doi: 10.1093/nar/gku362.
  11. Chebil I, Nicolle R, Santini G, Rouveirol C, Elati M. Hybrid method inference for the construction of cooperative regulatory network in human. IEEE transactions on nanobioscience, 2014, 13(2):97-103.
  12. Pezo V, Schepers G, Lambertucci C, Marlière P, Herdewijn P. Probing Ambiguous Base-Pairs by Genetic Transformation with XNA Templates. ChemBioChem 2014, 15(15):2255-2258. NDOI: 10.1002/cbic.201402226.
  13. De S, Groaz E, Maiti M, Pezo V, Marlière P, Herdewijn P. Synthesis of new biocarrier-nucleotide systems for cellular delivery in bacterial auxotrophic strains. Tetrahedron 2014, 70:8843-8851.
  14. Carbonell P, Trosset JY. Overcoming drug resistance through in silico prediction.  Drug Discov Today Technol. 2014, 11:101-107.
  15. Almelli T, Nuel G, Bischoff E, Aubouy A, Elati M, Wang CW, Dillies MA, Copée JY, Nko Ayissi G, Basco LK, Rogier C, Tuikue Ndam N , Deloron P , Tahar R . Differences in gene transcriptomic pattern of Plasmodium falciparum in children with cerebral malaria and asymptomatic carriers. PLoS One, 2014, 9:e114401.
  16. Koutroumpas K, van Dam TJP, Toedt G, Lu Q, van Reeuwijk J, Boldt K, Ueffing M, Gibson T, Russell R, Roepman R, Huynen M, Elati M, Képès F. A systems biology approach towards the prediction of ciliopathy mechanisms, Conference article, in CILIA2014, Paris, France, November 18-21, 2014.
  17. Delépine B, Carbonell P, Faulon JL. XTMS in Action: Retrosynthetic Design in the Extended Metabolic Space of Heterologous Pathways for High-Value Compounds.  In Computational Methods in Systems Biology - 12th International Conference, CMSB 2014, Proceedings.  Manchester, UK, Nov. 17-19, 2014, p256-259.

 

Book Chapters

  1. Vouillot L, Thelie A, Scalvenzi T, Pollet N. Genomics and genome engineering in Xenopus. in " Xenopus Development" , Kloc M. and Kubiak J.Z.  (eds), John Wiley & Sons. Vol 20, p383-401, 2014.
  2. Elati M, To C, Bouyioukos C. Evolutionary computation for pattern recognition-based inference of functional biological circuits. In book "Pattern Recognition in Computational Molecular Biology: Techniques and Approaches", M. Elloumi, Costas S. IIiopouos, Jason T. L. Wang and A. Y. Zomaya (Eds), Wiley, 2014
  3. Bouyioukos C, Elati  M, Képès F. Genome regulatory and architecture analysis Tools. In "Protocols for Hydrocarbon Microbiology, Higher structure genomic organization", vol 8,  K. Timmis, T. McGenity (Eds), Springer Protocols Series, in press, 2014
  4. Carbonell P, Feher T, Grigoras I, Faulon JL. RetroPath: Retrosynthesis design of metabolic pathways. Proceedings of the Evry Spring School on advances in Systems and Synthetic Biology. (Eds. Amar P, Képès F, Norris V.), EDP Sciences, 2014, p49-56
  5. Bouyioukos C, Elati M, Kepes F. GREAT: Genome REgulatory and Architecture analysis Tools. Proceedings of the Evry Spring School on advances in Systems and Synthetic Biology. (Eds. Amar P, Képès F, Norris V.), EDP Sciences, 2014, p39-48.

2013

  1. Boistel R, Aubin T, Cloetens P, Peyrin F, Scotti T, Herzog P, Gerlach J, Pollet N, Aubry J-F.  How minute sooglossid frogs hear without a middle ear. Proc. Natl. Acad. Sci. 2013, 110(38):15360-15364.    doi: 10.1073/pnas.1302218110
  2. 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.
  3. Joo J, Plimpton SJ, Faulon JL. Statistical Ensemble Analysis for Simulating Extrinsic Noise-driven Response in NF-kappaB Signaling Network. BMC Systems Biology, 2013, 7:45.
  4. Rodrigo G, Landrain TE, Shen S, Jaramillo A. A new frontier in synthetic biology: Automated design of small RNA devices in bacteria. Trends in Genetics 2013, 29:529-536.  Doi: 10.1016/j.tig.2013.06.005
  5. Carrera J, Jaramillo A.  Automated design of bacterial genome sequences. BMC Systems Biology 2013, 7:108.    Doi: 10.1186/1752-0509-7-108
  6. Rodrigo G, Jaramillo A.  AutoBioCAD: Full bio-design automation of genetic circuits. ACS Synthetic Biology 2013, 2(5):230-236. doi: 10.1021/sb300084h
  7. Rodrigo G, Landrain TE, Majer E, Daròs JA, Jaramillo A. Full design automation of multi-state RNA devices to program gene expression using energy-based optimization. PLOS Comp. Biol. 2013, 9: e1003172. doi:10.1371/journal.pcbi.1003172
  8. Pauthenier C, Carbonell P, Faulon JL. La conception rationnelle de ferments biologiques : comment concevoir un micro-organisme pour produire un composé chimique spécifique. l'Actualité Chimique, 2013, 375:30-36.
  9. Suárez-Diez M, Pujol AM, Matzapetakis M, Jaramillo A, Iranzo O.  Computational protein design with electrostatic focusing and experimental characterization of a conditionally folded helical protein domain with a reduced amino acid alphabet. Biotechnology J. 2013, 8:855-864. doi: 10.1002/biot.201200380.
  10. 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.
  11. 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, 41:5303-5320.
  12. 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, 242(6):709-717.
  13. Carbonell P, Carlsson L, Faulon JL. Stereo signature molecular descriptor.  J. Chem. Inf. Model. 2013, 53(4):887-897.
  14. Rodrigo G, Kirov B, Shen S, Jaramillo A. Theoretical and experimental analysis of the forced LacI-AraC oscillator with a minimal gene regulatory model. Chaos 2013, 23(2):025109. doi: 10.1063/1.4809786.
  15. Pezo V, Liu FW, Abramov M, Froeyen M, Herdewijn P, Marlière P. Binary Genetic Cassettes for Selecting XNA-Templated DNA Synthesis In Vivo.  Angew Chem. Int. Ed. Engl. 2013, 52(31):8139-8143. doi: 10.1002/anie.201303288.
  16. Martiny VY, Carbonell P, Lagorce D, Villoutreix BO, Moroy G, Miteva MA. In Silico Mechanistic Profiling to Probe Small Molecule Binding to Sulfotransferases. PLoS ONE 2013, 8(9): e73587. doi:10.1371/journal.pone.0073587
  17. Rodrigo G, Elena SF.  MicroRNA Precursors Are Not Structurally Robust but Plastic. Genome Biol. Evol. 2013; 5(1): 181–186.
  18. Jaghoori MM, Jongmans STQ, de Boer F, Peironcely J, Faulon JL, Reijmers T, Hankemeier T. PMG: Multi-core metabolite identification. Electronic Notes in Theoretical Computer Science, 2013, 299: 53-60.
  19. Trosset JY, Carbonell P. Synergistic synthetic biology: units in concert. Frontiers in Bioeng. Biotechnol. 2013, 1:11.
  20. Xu S, Ying H, Carbonell P, Hu J, Lee C, Wu W. Fuzzy logic applications in control theory and systems biology. Advances in Fuzzy Systems, 504728, 2013
  21. Kepes F.  [Scientific and technological conditions of the emergence of synthetic biology]. Med Sci (Paris). 2013, Spec No 2:13-15.
  22. Pauthenier C, Faulon JL. Ingénierie métabolique et biologie de synthèse. Technique de l’ingénieur, article BIO800, nov. 2013.
  23. Pauthenier, C, Faulon JL. Les composés produits par ingénierie métabolique. Technique de l’ingénieur, article BIO801, nov. 2013.
  24. To C, Elati M. A parallel genetic programming for single class classification. In Genetic and evolutionary computation (GECCO), ACM Companion, pp 1579-1586, 2013
  25. Chebil I, Elati M, Santini G, Rouveirol C. SETNET: Ensemble Method techniques for Learning Regulatory Networks. In Machine Learning and Applications (ICMLA), IEEE, vol.1, pp.34-39, 2013
  26. Elati M, To C, Nicolle R. Multi-objective optimization for relevant sub-graph extraction. Learning and Intelligent OptimizatioN (LION), LNCS, pp 104-109, 2013


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.

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.
  22. Nicolle R, Elati M, Radvanyi F. Network transformation of gene expression for feature extraction. Machine Learning and Applications (ICMLA), IEEE vol 1: pp 108-113, 2012.

 

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. Carrera J, Rodrigo G, Singh V, Kirov B, Jaramillo A.  Empirical model and in vivocharacterization of the bacterial response to synthetic gene expression show that ribosome allocation limits growth rate. Biotechnol. J. 2011, 6:773-783.
                3. Jaramillo A, Faulon JL. Synthetic Biology - applying new paradigms at the interface of fundamental research and innovation. Biotechnol. J. 2011, 6:766-767.
                4. 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.
                5. Rodrigo G, Carrera J, Jaramillo A.  On the designability of synthetic regulatory networks. Nucl. Acids Res. 2011, 39: e138.
                6. 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.
                7. 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.
                8. 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.
                9. 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.
                10. 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
                11. 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
                12. Planson AG, Carbonell P, Grigoras I, Faulon JL.  Engineering antibiotic production and overcoming bacterial resistance. Biotechnol. J. 2011, 6:812-825. Review
                13. 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.
                14. Carbonell P, Lecointre G, Faulon JL. Origins of specificity and promiscuity in metabolic networks. J. of Biol. Chem. 2011. 286:43994-44004.
                15. 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.
                16. 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.
                17. 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.
                18. Camsund D, Lindblad P, Jaramillo A.  Genetically Engineered Light Sensors for Control of Bacterial Gene Expression. Biotechnol. J. 2011, 6:826-836.
                19. Rodrigo G, Carrera J, Jaramillo A, Elena SF. Optimal viral strategies for bypassing RNA silencing. J.R. Soc. Interface, 2011, 8:257-268.
                20. 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.
                21. 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.
                22. Chavain N, Herdewijn P. 2 '-Deoxy-2 '-alpha-C-(hydroxymethyl)adenosine as Potential anti-HCV Agent. Eur. J. Org. Chem. 2011, 6:1140-1147.
                23. 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.
                24. Kirkilionis M, Képès F.  Introduction to special issue ECCS'09. Theory in Biosciences 2011, 130:153.
                25. Képès F.  Biologie synthétique et intégrative. C. R. Chimie, 2011, 14:420-423.
                26. 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.
                27. Elati M, Fekih R, Nicolle R, Junier I, Herisson J, Képès F. Boosting binding sites prediction using gene’s positions. Algorithms in Bioinformatics (WABI), LNCS, 2011, 6833:92-103.

                 

                Book chapters

                1. 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.
                2. 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.
                3. 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) Jan 2011,  John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470892107.ch41.

                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 UMR8030 - UEVE - CEA - 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

                     Congratulations to the iGEM-Evry 2018 team that was nominated for the "best composite part" price, and that won a Gold Medal at the final world iGEM jamboree. To follow their work, please visit their wiki.

                   

                   The annual spring School on advances in Systems and Synthetic Biology (aSSB) becomes an autumn School, on November 18-22, 2019.

                   iSSB is pleased to announce the creation of the spin-off Synovance, founded by two former iSSB researchers.

                   The spin-off of iSSB Inovactis, founded by two former mSSB students, won the national competition I-Lab 2017 organized each year by the Ministry of Higher Education and Research to encourage the most innovative technologies.

                    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.