1. Gricourt G, Duigou T, Dérozier S, Faulon JL. neo4jsbml: import systems biology markup language data into the graph database Neo4j. PeerJ, 2024 | DOI: 10.7717/peerj.16726
  2. Faure L, Mollet B, Liebermeister W et al. A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models. Nat Commun, 2023, 14, 4669 | DOI: 10.1038/s41467-023-40380-0
  3. Hérisson J, Duigou T, du Lac M, Bazi-Kabbaj K, Sabeti Azad M, Buldum G, Telle O, El Moubayed Y, Carbonell P, Swainston N, Zulkower V, Kushwaha M, Baldwin GS, Faulon JL. The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering. Nat Commun., 2022, 13(1):5082 | DOI: 10.1038/s41467-022-32661-x | PMID: 36038542
  4. Soudier P, Ana Zuńiga A, Duigou P, Voyvodic PL, Bazi-Kabbaj K, Kushwaha M, Vendrell JA, Solassol J, Bonnet J, and Faulon JL. PeroxiHUB: A Modular Cell-Free Biosensing Platform Using H2O2 as Signal Integrator. ACS Synthetic Biology, 2022, 11(8):2578-2588 | DOI: 10.1021/acssynbio.2c00138 | PMID: 35913043
  5. Pandi A, Diehl C, Yazdizadeh Kharrazi A, Scholz SA, Bobkova E, Faure L, Nattermann M, Adam D, Chapin N, Foroughijabbari Y, Moritz C, Paczia N, Cortina NS, Faulon JL, Erb TJ. A versatile active learning workflow for optimization of genetic and metabolic networks. Nat Commun., 2022, 13(1):3876. | DOI: 10.1038/s41467-022-31245-z | PMID: 35790733
  6. Sabeti Azad M, Cardoso Batista A, Faulon JL, Beisel CL, Bonnet J, Kushwaha, M. Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates. J. Vis. Exp. 2022, (186), e64236 | DOI: 10.3791/64236 | PMID: 36036615
  7. Cardoso Batista A, Levrier A, Soudier P, Voyvodic PL, Achmedov T, Reif-Trauttmansdorff T, DeVisch A, Cohen-Gonsaud M, Faulon JL, Beisel CL, Bonnet J, Kushwaha M. Differentially Optimized Cell-Free Buffer Enables Robust Expression from Unprotected Linear DNA in Exonuclease-Deficient Extracts. ACS Synthetic Biology, 2022, 11(2):732-746. | DOI: 10.1021/acssynbio.1c00448 | PMID: 35034449
  8. Soudier P, Rodriguez Pinzon D, Reif-Trauttmansdorff T, Hijazi H, Cherrière M, Goncalves Pereira C, Blaise D, Pispisa M, Saint-Julien A, Hamlet W, Nguevo M, Gomes E, Belkhelfa S, Niarakis A, Kushwaha M, Grigoras I. Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima. Synth Syst Biotechnol. 2022, 7(2):791-801. | DOI: 10.1016/j.synbio.2022.03.003  | PMID: 35415278
  9. Soudier P, Faure L, Kushwaha M, Faulon JL. Cell-Free Biosensors and AI Integration. Methods Mol Biol. 2022, 2433:303-323. | DOI: 10.1007/978-1-0716-1998-8_19 | PMID: 34985753.
  10. Faulon JL, Faure L. In silico, in vitro, and in vivo machine learning in synthetic biology and metabolic engineering. Curr Opin Chem Biol. 2021, 16;65:85-92. Epub 2021. | DOI: 10.1016/j.cbpa.2021.06.002 | PMID: 34280705.
  11. Batista AC , Soudier P, Kushwaha M, Faulon JL. Optimising protein synthesis in cell‐free systems, a review, Engineering Biology 5 (1), 10-19. | DOI: 10.1049/enb2.12004
  12. Borkowski O, Koch M, Zettor A, Pandi A, Cardoso Batista A, Soudier P & Faulon JL. Large scale active-learning-guided exploration for in vitro protein production optimization. Nature Communications, 11(1): 1872, 2020. | DOI: 10.1038/s41467-020-15798-5 | PMID: 32312991
  13. Castaño-Cerezo S, Fournié M, Urban P, Faulon JL, Truan G. Development of a Biosensor for Detection of Benzoic Acid Derivatives in Saccharomyces cerevisiae. Frontiers in Bioengineering and Biotechnology, 7: 372, 2020. | DOI: 10.3389/fbioe.2019.00372 | PMID: 31970152
  14. Koch M, Duigou T, Faulon JL. Reinforcement Learning for Bioretrosynthesis. ACS Synthetic Biology, 9(1): 15, 2020. | DOI: 10.1021/acssynbio.9b00447 | PMID: 31841626
  15. Dunstan MS, Robinson CJ, Jervis AJ, Yan C, Carbonell P, Hollywood KA, Vinaixa M, Currin A, Swainston N, Rattray NJW, Le Feuvre R, Mickefield J, Faulon JL, Breitling R, Turner, N, Takano E, Scrutton NS. Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol.  Synthetic Biology (Oxford), ysaa012, 2020. | DOI: 10.1093/synbio/ysaa012
  16. Pandi A., Trabelsi H. (2020) Current Progress in Synthetic Genetic Networks. In: Singh V. (eds) Advances in Synthetic Biology. Springer, Singapore | DOI: 10.1007/978-981-15-0081-7_2
  17. Pandi A., Borkowski O., Faulon JL. (2020) Synthetic Biology at the Hand of Cell-Free Systems. In: Singh V. (eds) Advances in Synthetic Biology. Springer, Singapore | DOI: 10.1007/978-981-15-0081-7_2
  18. Faulon, JL, du Lac, M, Duigou, T., Carbonell, P., Herisson, J. Design Automation Workflows for Synthetic Biology and Metabolic Engineering: The Galaxy SynBioCAD portal, of 12th IWBDA-2020, 25-26, 2020. DOI:
  19. Armetta J, Berthome R, Cros A, Pophillat C, Colombo B, Pandi A, Grigoras I. Biosensor-based enzyme engineering approach applied to psicose biosynthesis. Synthetic Biology, 4(1): ysz028, 2019. | DOI: 10.1093/synbio/ysz028
  20. Pandi A, Koch M, Voyvodic PL, Soudier P, Bonnet J, Kushwaha M*, Faulon JL*. Metabolic Perceptrons for Neural Computing in Biological Systems. Nature Communications, 10: 3880, 2019. | DOI: 10.1038/s41467-019-11889-0 | PMID: 31462649
  21. Carbonell, P. Faulon JL, Breitling, R. Efficient learning in metabolic designs through optimal assembling. IFAC-PapersOnLine, 52(26): 7-22 , 2019. | DOI: 10.1016/j.ifacol.2019.12.228
  22. Pandi A, Grigoras I, Borkowski O*, Faulon JL*. Optimizing Cell-Free Biosensors to Monitor Enzymatic Production. ACS Synth Biol. 8(8):1952-1957, 2019 | DOI: 10.1021/acssynbio.9b00160 | PMID: 31335131
  23. Voyvodic PL, Pandi A, Koch M, Conejero I, Valjent E, Courtet P, Renard E, Faulon JL*, Bonnet J*. Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors. Nature Communications, 10(1):1697, 2019. | DOI: 10.1038/s41467-019-09722-9 | PMID: 30979906
  24. Koch M, Pandi A, Borkowski O, Cardoso Batista A, Faulon JL*. Custom-made transcriptional biosensors for metabolic engineering. Current Opinion in Biotechnology, 59:78-84, 2019. | DOI: 10.1016/j.copbio.2019.02.016 | PMID: 30921678
  25. Duigou T, du Lac M, Carbonell P, Faulon JL*. RetroRules: a database of reaction rules for engineering biology. Nucleic Acids Research, 47(D1): D1229-1235, 2019. | DOI: 10.1093/nar/gky940 | PMID: 30321422
  26. Salvador M, Abdulmutalib U, Gonzalez J, Kim J, Smith AA, Faulon JL, Wei R, Zimmermann W, Jimenez JI. Microbial Genes for a Circular and Sustainable Bio-PET Economy. Genes (Basel). 2019 May 16;10(5). pii: E373. | DOI: 10.3390/genes10050373 | PMID: 31100963
  27. Jervis AJ, Carbonell P, Vinaixa M, Dunstan MS, Hollywood KA, Robinson CJ, Rattray NJW, Yan C, Swainston N, Currin A, Sung R, Toogood HS, Taylor S, Faulon JL, Breitling R, Takano E, Scrutton NS. Machine learning of designed translational control allows predictive pathway optimisation in Escherichia coli. ACS Synthetic Biology, 18; 8(1):127-136, 2018. | DOI: 10.1021/acssynbio.8b00398 | PMID: 30563328
  28. Koch M, Faulon JL*, Borkowski O*. Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster. Frontiers in Bioengineering and Biotechnology, 6: 182, 2018. | DOI: 10.3389/fbioe.2018.00182 | PMID: 30555825
  29. Carbonell P, Jervis AJ, Robinson CJ, Yan C, Dunstan M, Swainston N, Vinaixa M, Hollywood KA, Currin A, Rattray NJW, Taylor S, Spiess R, Sung R, Williams AR, Fellows D, Stanford NJ, Mulherin P, Le Feuvre R, Barran P, Goodacre R, Turner NJ, Goble C, Chen GG, Kell DB, Micklefield J, Breitling R, Takano E, Faulon JL, Scrutton NS. An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals. Communications Biology, 1:66, 2018. | DOI: 10.1038/s42003-018-0076-9 | PMID: 30271948
  30. Koch M, Pandi A, Delépine B, Faulon JL*. A dataset of small molecules triggering transcriptional and translational cellular responses. Data in Brief, 17: 1374-1378, 2018. | DOI: 10.1016/j.dib.2018.02.061 | PMID: 29556520
  31. Trabelsi H, Koch M, Faulon JL*. Building a minimal and generalizable model of transcription-factor based biosensors: showcasing flavonoids. Biotechnology and Bioengineering, 115(9): 2292-2304, 2018. | DOI: 10.1002/bit.26726 | PMID: 29733444
  32. Carbonell P*, Wong J, Swainston N, Takano E, Turner NJ, Scrutton NS, Kell DB, Breitling R, Faulon JL*. Selenzyme: enzyme selection tool for pathway design. Bioinformatics, 34(12): 2153-2154, 2018. | DOI: 10.1093/bioinformatics/bty065
  33. Delépine B, Duigou T, Carbonell P, Faulon JL*. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. | DOI: 10.1016/j.ymben.2017.12.002 | PMID: 29233745
  34. Carbonell P, Koch M, Duigou T, Faulon JL*. Enzyme discovery: Enzyme selection and pathway design, In: Enzymes in Synthetic Biology. Series in Methods in Enzymology, 608: 3-27, 2018. | doi: 10.1016/bs.mie.2018.04.005
  35. Swainston N, Dunstan M, Jervis AJ, Robinson CJ, Carbonell P, Williams AR, Faulon JL, Scrutton NS, Kell DB. PartsGenie: an integrated tool for optimising and sharing synthetic biology parts. Bioinformatics, 34(13): 2327-2329, 2018. | DOI: 10.1093/bioinformatics/bty105
  36. Koch M, Duigou T, Carbonell P, Faulon JL*. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9(1): 64, 2017. | DOI: 10.1186/s13321-017-0252-9
  37. Carbonell P, Delépine B, Faulon JL*. Extended metabolic space modeling, In: Synthetic metabolic pathways: Methods and Protocols, MK Jensen and JD Keasling, Springer, 1671: 83-96, 2017. | doi: 10.1007/978-1-4939-7295-1_6 | link to publisher
  38. Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Vinaixa M, Ananiadou S, Faulon JL, Mendes P, Kell DB, Breitling R. biochem4j: integrated and extensible biochemical knowledge through graph databases. PLoS One, 12(7): e0179130, 2017. | doi: 10.1371/journal.pone.0179130 | PMID: 28708831
  39. Carbonell P, Gök A, Shapira P, Faulon JL*. Mapping the patent landscape of synthetic biology for fine chemical production pathways. Microbial Biotechnology, 9(5): 687-695, 2016. | doi: 10.1111/1751-7915.12401 | PMID: 27489206
  40. Libis V, Delépine B, Faulon JL*. Sensing new chemicals with bacterial transcription factors. Current opinion in microbiology, 33: 105-112, 2016. | doi: 10.1016/j.mib.2016.07.006 | PMID: 27472026
  41. Delépine B, Libis V, Carbonell P, Faulon JL*. SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic Acids Research, 44: W226-231, 2016. | doi: 10.1093/nar/gkw305  | PMID: 27106061
  42. Libis V, Delépine B, Faulon JL*. Expanding biosensing abilities through computer-aided design of metabolic pathways. ACS Synthetic Bioliology, 5(10): 1076-1085, 2016. | doi: 10.1021/acssynbio.5b00225 | PMID: 27028723
  43. Le Feuvre RA, Carbonell P, Currin A, Dunstan M, Fellows D, Jervis AJ, Rattray NJW, Robinson CJ, Swainston N, Vinaixa M, Williams A, Yan C, Barran P, Breitling R, Chen GG, Faulon JL, et al. SYNBIOCHEM Synthetic Biology Research Centre, Manchester e A UK foundry for fine and speciality chemicals production. Synthetic and systems biotechnology, 1(4): 271–275, 2016. | doi: 10.1016/j.synbio.2016.07.001
  44. Carbonell P, Currin A, Dunstan M, Fellows D, Jervis A, Rattray NJ, Robinson CJ, Swainston N, Vinaixa M, Williams A, Yan C, Barran P, Breitling R, Chen GG, Faulon JL, Goble C, Goodacre R, Kell DB, Feuvre RL, Micklefield J, Scrutton NS, Shapira P, Takano E, Turner NJ. SYNBIOCHEM-a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals. Biochemical Society transactions, 44(3): 675-677, 2016. | doi: 10.1042/BST20160009 | PMID: 27284023
  45. Mellor J, Grigoras I, Carbonell P, Faulon JL*. Semi-supervised Gaussian Process for automated enzyme search. ACS Synthetic Biology, 5(6): 518-528, 2016. | doi: 10.1021/acssynbio.5b00294 | PMID: 27007080
  46. Fehér T, Libis V, Carbonell P, Faulon JL*. A sense of balance: experimental investigation and modeling of a malonyl-CoA sensor in Escherichia coli. Frontiers in Bioengineering and Biotechnology, 3: 46, 2015. | doi: 10.3389/fbioe.2015.00046 | PMID: 25905101
  47. Castane A, Ferer T, Carbonnell P, Faulon JL*. Computer-aided design for metabolic engineering. Journal of Biotechnology, 192(Part B): 302-313, 2014. | doi: 10.1016/j.jbiotec.2014.03.029 | PMID: 24704607
  48. 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. Biotechnology Journal, 9(11): 1446-1457, 2014. | doi: 10.1002/biot.201400055 | PMID: 25224453
  49. Carbonell P, Parutto P, Baudier C, Junot C, Faulon JL*. Retropath: automated pipeline for embedded metabolic circuits. ACS Synthetic Biology, 3(8): 565-577, 2014. | doi: 10.1021/sb4001273 | PMID: 24131345
  50. Pauthenier C, Faulon JL*. PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling. Nucleic Acids Research, 42: W205-W209, 2014. | doi: 10.1093/nar/gku393 | PMID: 24829457
  51. Carbonell P, Parutto P, Herisson J, Pandit S, Faulon JL*. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Research, 42: W389-394, 2014. | doi: 10.1093/nar/gku362 | PMID: 24792156
  52. 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, 299: 53-60, 2013. | doi: 10.1016/j.entcs.2013.11.005
  53. Joo J*, Plimpton SJ, Faulon JL*. Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κB signaling networks. BMC Systems Biology, 7: 45, 2013. | doi: 10.1186/1752-0509-7-45 | PMID: 23742268
  54. Carbonell P, Carlsson L, Faulon JL*. Stereo signature molecular descriptor. Journal of Chemical Information and Modeling, 53(4): 887-897, 2013. | doi: 10.1021/ci300584r | PMID: 23527586
  55. 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, 8(9): e73587, 2013. | doi: 10.1371/journal.pone.0073587 | PMID: 24039991
  56. Trosset JY, Carbonell P. Synergistic synthetic biology: units in concert. Frontiers in Synthetic Biology, 1:11, 2013. | doi:  10.3389/fbioe.2013.00011 | PMID: 25022769
  57. 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. | doi: 10.1155/2013/504728
  58. Carbonell P, Planson AG, Faulon JL*. Retrosynthetic design of heterologous pathways. Methods in Molecular Biology, 985: 149-73, 2013. | doi: 10.1007/978-1-62703-299-5_9 | PMID: 23417804
  59. 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, 375: 30-36, 2013. | link to journal
  60. Pauthenier C, Faulon JL*. Ingénierie métabolique et biologie de synthèse. Techniques de l’Ingénieur, BIO800, 2013. | link to journal
  61. Pauthenier C, Faulon JL. Composés produits par ingénierie métabolique. Techniques de l’Ingénieur, BIO801, 2013. | link to journal
  62. Planson AG, Carbonell P, Grigoras I, Faulon JL*. A retrosynthetic biology approach to therapeutics: from conception to delivery. Current Opinion in Biotechnology, 23(6): 948-956, 2012. | doi: 10.1016/j.copbio.2012.03.009 | PMID: 22475981
  63. Peironcely JE, Rojas-Chertó M, Fichera D, Reijmers T, Coulier L, Faulon JL, Hankemeier T. OMG: Open Molecule Generator. Journal of Cheminformatics, 4(1): 21. | doi: 10.1186/1758-2946-4-21 | PMID: 22985496
  64. Planson AG, Carbonell P, Paillard E, Pollet N, Faulon JL*. Compound toxicity screening and structure-activity relationship modeling in Escherichia coli. Biotechnology and Bioengineering, 109(3): 846-850, 2012. | doi: 10.1002/bit.24356 | PMID: 22038678
  65. Carbonell P, Fichera D, Pandit SB, Faulon JL*. Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Systems Biology, 6: 10, 2012. | doi: 10.1186/1752-0509-6-10 | PMID: 22309974
  66. Misra M, Martin S, Faulon JL*. Graphs: Flexible Representations of Molecular Structures and Biological Networks, in Computational Approaches in Cheminformatics and Bioinformatics, Guha R., Bender, A. Edts, Wiley, 2012. | doi: 10.1002/9781118131411.ch6
  67. Carbonell P, Lecointre G, Faulon JL*. Origins of specificity and promiscuity in metabolic networks. Journal of Biological Chemistry, 286(51): 43994-44004, 2011. | doi: 10.1074/jbc.M111.274050 | PMID: 22052908
  68. Carbonell P, Planson AG, Fichera D, Faulon JL*. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Systems Biology, 5: 122, 2011. | doi: 10.1186/1752-0509-5-122 | PMID: 21819595
  69. Misra M, Andrienko D, Baumeier B, Faulon JL, von Lilienfeld OA. Toward quantitative structure-property relationships for charge transfer rates of polycyclic aromatic hydrocarbons. Journal of Chemical Theory and Computation, 7(7): 2094-2103, 2011. | doi: 10.1021/ct200231z | PMID: 26606628
  70. Jaramillo A, Faulon JL. Synthetic Biology – applying new paradigms at the interface of fundamental research and innovation. Biotechnology Journal, 6(7): 766-767, 2011. | doi: 10.1002/biot.201100254 | PMID: 21728241
  71. Planson AG, Carbonell P, Grigoras I, Faulon JL*. Engineering antibiotic production and overcoming bacterial resistance. Biotechnology Journal, 6(7): 812-825, 2011. | doi: 10.1002/biot.201100085 | PMID: 21661120
  72. Carbonell P, Faulon JL*. Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics, 26(16): 2012-2019, 2010. | doi: 10.1093/bioinformatics/btq317 | PMID: 20551137
  73. Faulon JL*, Carbonell P. Reaction Network Generation, In Handbook of Chemoinformatics Algorithms. Chapman & Hall/CRC Series in Mathematical & Computational Biology, 2010. |  link to publisher
  74. Misra M, Faulon JL*. Algorithms to Store and Retrieve 2D Chemical Structures, In Handbook of Chemoinformatics Algorithms. Chapman & Hall/CRC Series in Mathematical & Computational Biology, 2010. |  link to publisher
  75. Carbonell P, del Sol A. Methyl side-chain dynamics prediction based on protein structure. Bioinformatics, 25(19): 2552-8, 2009. | doi: 10.1093/bioinformatics/btp463 | PMID: 19648137
  76. Carbonell P, Nussinov R, del Sol A. Energetic determinants of protein binding specificity: insights into protein interaction networks. Proteomics, 9(7): 1744-1753, 2009. | doi: 10.1002/pmic.200800425 | PMID: 19253304
  77. 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 Nov;27(4):466-75. Epub 2008 Aug 27. | doi: 10.1016/j.jmgm.2008.08.004 | PMID: 18829357
  78. Faulon JL*, Misra M, Martin S, Sale K, Sapra R. Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor. Bioinformatics. 2008 Jan 15;24(2):225-33.  | doi:  10.1093/bioinformatics/btm580 | PMID: 18037612
  79. Martin S, Brown WM, Faulon JL*. Using product kernels to predict protein interactions. Advances in Biochemical Engineering/Biotechnology, 110:215-245, 2008. | doi: 10.1007/10_2007_084 | PMID: 17922100
  80. May E, Leitao A, Faulon JL, Joo J, Misra M, Oprea TI. Understanding virulence mechanisms in M. tuberculosis infection via a circuit-based simulation framework. Conference proceedings : Annual International Conference of the IEEE Engineering in Medicine and Biology Society. 2008;2008:4953-5. | doi: 10.1109/IEMBS.2008.4650325 | PMID: 19163828

Publications prior 2008 (Jean-Loup Faulon)