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Published on 11 December 2018


  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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]


  1. 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.
  2. 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.
  3. 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

    Book chapters

  1. 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.


  1. 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.
  2. Mellor J, Grigoras I, Carbonell PFaulon JL.  Semisupervised Gaussian Process for Automated Enzyme Search.  ACS Synth Biol2016, 5(6):518-28. doi: 10.1021/acssynbio.5b00294.
  3. Libis V, Delépine B, Faulon JL.  Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways. ACS Synth Biol. 2016, 5(10):1076-1085.
  4. Libis V, Delépine BFaulon JL. Sensing new chemicals with bacterial transcription factors.  Curr Opin Microbiol., 2016, 33:105-12. doi: 10.1016/j.mib.2016.07.006. Review.


  1. Colombo BM, Scalvenzi T, Benlamara S, Pollet N. Microbiota and mucosal immunity in amphibians. Front. Immunol. 6:111. doi:10.3389/fimmu.2015.00111
  2. 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.
  3. 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, 146(4):657-670.  doi: 10.1111/imm.12533.


  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. 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
  3. 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.
  4. 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.
  5. 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.
  6. Carbonell P, Trosset JY. Overcoming drug resistance through in silico prediction.  Drug Discov Today Technol. 2014, 11:101-107.
  7. 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. 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
  2. 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.


  1. 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.
  2. 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.
  3. Carbonell P, Carlsson L, Faulon JL. Stereo signature molecular descriptor.  J. Chem. Inf. Model. 2013, 53(4):887-897.
  4. 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
  5. 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.
  6. Trosset JY, Carbonell P. Synergistic synthetic biology: units in concert. Frontiers in Bioeng. Biotechnol. 2013, 1:11.
  7. 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
  8. Pauthenier C, Faulon JL. Ingénierie métabolique et biologie de synthèse. Technique de l'ingénieur, article BIO800, nov. 2013.
  9. Pauthenier, C, Faulon JL. Les composés produits par ingénierie métabolique. Technique de l'ingénieur, article BIO801, nov. 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.