Publications
- Gricourt G, Meyer P, Duigou T, Faulon JL. Artificial Intelligence Methods and Models for Retro-Biosynthesis. ACS Synth Biol. 2024 Aug 16;13(8):2276-2294. doi: 10.1021/acssynbio.4c00091. Epub 2024 Jul 24. PMID: 39047143; PMCID: PMC11334239.
- Faulon JL, Ahavi P, Hoang A, Reservoir Computing with Bacteria, bioRxiv 2024 | DOI: 10.1101/2024.09.12.612674
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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.
- 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.
- 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
- 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
- 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
- Koch M, Duigou T, Faulon JL. Reinforcement Learning for Bioretrosynthesis. ACS Synthetic Biology, 9(1): 15, 2020. | DOI: 10.1021/acssynbio.9b00447 | PMID: 31841626
- 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
- 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
- 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
- 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: https://www.iwbdaconf.org/2020/#proceedings
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Pauthenier C, Faulon JL*. Ingénierie métabolique et biologie de synthèse. Techniques de l’Ingénieur, BIO800, 2013. | link to journal
- Pauthenier C, Faulon JL. Composés produits par ingénierie métabolique. Techniques de l’Ingénieur, BIO801, 2013. | link to journal
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Carbonell P, Faulon JL*. Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics, 26(16): 2012-2019, 2010. | doi: 10.1093/bioinformatics/btq317 | PMID: 20551137
- Faulon JL*, Carbonell P. Reaction Network Generation, In Handbook of Chemoinformatics Algorithms. Chapman & Hall/CRC Series in Mathematical & Computational Biology, 2010. | link to publisher
- 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
- 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
- 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
- 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
- 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
- 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
- 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)