1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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.
  8. 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.
  9. 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
  10. 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
  11. 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
  12. Koch M, Duigou T, Faulon JL. Reinforcement Learning for Bioretrosynthesis. ACS Synthetic Biology, 9(1): 15, 2020. | DOI: 10.1021/acssynbio.9b00447 | PMID: 31841626
  13. 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
  14. 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
  15. Függer M., Kushwaha M., Nowak T. (2020) Digital Circuit Design for Biological and Silicon Computers. In: Singh V. (eds) Advances in Synthetic Biology. Springer, Singapore | DOI: 10.1007/978-981-15-0081-7_2
  16. 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
  17. 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:
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. Pauthenier C, Faulon JL*. Ingénierie métabolique et biologie de synthèse. Techniques de l’Ingénieur, BIO800, 2013. | link to journal
  60. Pauthenier C, Faulon JL. Composés produits par ingénierie métabolique. Techniques de l’Ingénieur, BIO801, 2013. | link to journal
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. Carbonell P, Faulon JL*. Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics, 26(16): 2012-2019, 2010. | doi: 10.1093/bioinformatics/btq317 | PMID: 20551137
  72. Faulon JL*, Carbonell P. Reaction Network Generation, In Handbook of Chemoinformatics Algorithms. Chapman & Hall/CRC Series in Mathematical & Computational Biology, 2010. |  link to publisher
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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. Epub 2007 Nov 23. | doi:  10.1093/bioinformatics/btm580 | PMID: 18037612
  78. 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
  79. 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
  80. Gaucher SP, Morrow JA, Faulon JL. Use of a designed peptide array to infer dissociation trends for nontryptic peptides in quadrupole ion trap and quadrupole time-of-flight mass spectrometry, Analytical Chemistry, Oct 15;79(20):7822-30, 2007. | doi: 10.1021/ac070557y | PMID: 17854158
  81. Gray GA, Williams PJ, Brown WM, Faulon JL, Sale K. Disparate data fusion for protein phosphorylation prediction, Annals of Operations Research Special Volume on Data Mining, April 2008. | doi: 10.1007/s10479-008-0347-9
  82. Zhang Z, Martino A, Faulon JL. Identification of Expression Patterns of IL-2-Responsive Genes in the Murine T Cell Line CTLL-2, Journal of Interferon & Cytokine Research, 27(12): 991-996,  2007. | doi: 10.1089/jir.2006.0169 | PMID: 18184039
  83. Joo J, Plimpton S, Martin S, Swiler L, Slepoy A, Faulon JL. Sensitivity analysis of  computational model of the NF-κB-IκB-A20 signal transduction network, Annals of NY Academy of Sciences, vol. 1115, pp. 221-239, 2007. | doi: 10.1196/annals.1407.014 | PMID: 17934057
  84. Oprea, T., Tropsha, A., Faulon, J.L. Rintoul M.D. Systems Chemical Biology, Nature chemical biology, 3, 447-50, 2007. | doi: 10.1038/nchembio0807-447 | PMID: 17637771
  85. Martin, S., Zhang, Z., Martino, A., Faulon, J.L. Boolean dynamics of genetic regulatory networks inferred from microarray time series data, Bioinformatics, 23, 866-74, 2007. | doi:  10.1093/bioinformatics/btm021 | PMID: 17267426
  86. del Sol, A., Carbonell, P. The modular organization of domain structures: insights into protein-protein binding. PLoS Computational Biology, Dec ; 3(12): e239, 2007. | doi: 10.1371/journal.pcbi.0030239 | PMID: 18069884
  87. Brown, W.M., Martin, S., Rintoul, M.D., Faulon, J.L. The Signature Molecular Descriptor. 6. Designing novel polymers with targeted properties using the signature molecular descriptor, Journal of Chemical Information and Modeling, 46(2), 826-835, 2006. | doi: 10.1021/ci0504521 | PMID: 16563014
  88. Brown, W.M., Martin, S., Chabarek, J.P., Strauss, C., Faulon, J.L. Prediction of β-strand packing interactions using the signature product, Journal of Molecular Modeling,12, 355-361, 2006 | doi: 10.1007/s00894-005-0052-4 | PMID: 16365772
  89. Martin, S., Carr, R.D., Faulon, J.L. Random removal of edges from scale free graphs, Physica A.37, 870-876, 2006 | doi: 10.1016/j.physa.2006.04.046
  90. Faulon, J.L., Visco, D., Roe, D. Enumerating Molecules. In: Reviews in Computational Chemistry Vol. 21, Lipkowitz K. Edt., Wiley-VCH, 2005. doi: 10.1002/0471720895.ch3
  91. Faulon, J.L., Brown, W.M., Martin, S. Reverse engineering chemical structures from molecular descriptors: how many solutions? Journal of computer-aided molecular design, 19(9-10):637-650, 2005. | doi: 10.1007/s10822-005-9007-1 | PMID: 16267694
  92. Brown, W.M., Faulon, J.L., Sale, K. A deterministic algorithm for constrained enumeration of transmembrane protein folds. Computational Biology and Chemistry, 29, 143-150, 2005. | doi: 10.1016/j.compbiolchem.2005.03.001 | PMID: 15833442
  93. Weis, D., Faulon, J.L., Visco, D. The Signature Molecular Descriptor. 5. The design of hydrofluoroether foam blowing agents using inverse-QSAR, Industrial & Engineering Chemistry Research, 44, 8883-8891, 2005. | doi: 10.1021/ie050330y
  94. Martin, S., Roe, D., Faulon, J.L. Predicting protein-protein interactions using signature products, Bioinformatics, 21(2):218-226, 2005. | doi: 10.1093/bioinformatics/bth483 | PMID: 15319262
  95. Martin, S., Brown, W.M., Weis, D., Kenneke, J., Visco, D.,  Faulon, J.L. Inverse design of large molecules using linear diophantine equations. Proceedings IEEE CSB2005, 4, 2005. | link to .pdf
  96. Faulon, J.L., Zhang, Z., Martino, A., Timlin, J.A., Haaland, D.M., Martin, S., Davidson, G.,  May, E., Slepoy, A. Reverse engineering biological networks: T-cell response to IL-2 stimulation. SANDIA Report 2005- 5238379, Sandia National Laboratories, Albuquerque, NM. | link to .pdf
  97. Sale, K., Faulon, J.L., Gray, G.A., Schoeniger, J.S., Young, M.M. Optimal bundling of transmembrane helices using sparse distance constraints. Protein Science, 13(10):2613-2627, 2004. | doi: 10.1110/ps.04781504 | PMID: 15340162
  98. Martin, S., Davidson, G., May, E., Werner-Washburne, M., Faulon, J.L. Inferring Genetic Networks from Microarray Data. Proceedings IEEE CSB2004, 3, 566-569, 2004. | doi: 10.1109/CSB.2004.1332498
  99. Faulon, J.L., Martin, S., Carr, R.D.  Dynamical robustness in gene regulatory networks. Proceedings IEEE CSB2004, 3, 595 – 596, 2004. | doi: 10.1109/CSB.2004.1332521
  100. Diallo, M.S., Strachan, A., Faulon, J.L., Goddard, W.A. Properties of Petroleum Geomacromolecules Through Computer Assisted Structure Elucidation and Atomistic Simulations.1. Bulk Arabian Light Asphaltenes, Petroleum Science and Technology, 22, 877-899, 2004. | doi: 10.1016/S0376-7361(09)70276-6
  101. Faulon, J.L., Collins, M., Carr, R.D. The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequence, J. Chem. Inf. Comput. Sci., 44, 427-436, 2004. | doi: 10.1021/ci0341823 | PMID: 15032522
  102. Churchwell, C.J., Rintoul, M.D., Martin, S., Visco, D., Kotu, A., Larson, R.S., Sillerud, L.O., Brown, D.C., Faulon, J.L. The Signature Molecular Descriptor. 3. Inverse Quantitative Structure-Activity Relationship of ICAM-1 Inhibitory Peptides  J. Molecular Graphics & Modelling., 22, 263-273, 2004. [PMID: 15177078]
  103. Faulon, J.L., Visco, D., Roe, D. Molecular Structure Enumeration, SANDIA Report 2004-0960, Sandia National Laboratories, Albuquerque, NM., 2004
  104. Faulon, J.L., Visco, D., Churchwell, C.J. The Signature Molecular Descriptor. 2. Enumerating Molcules from their Extended Valence Sequences,  Journal of Chemical Information and Computer Sciences, 43 (3), 721 -734, 2003. | doi: 10.1021/ci020346o | PMID: 12767130
  105. Faulon, J.L., Visco, D., Pophale, R.S. The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR studies,  Journal of Chemical Information and Computer Sciences, 43, 707-720, 2003. | doi: 10.1021/ci020345w | PMID: 12767129
  106. Faulon, J.L., Sale, K., Young, M.M. Exploring the conformational space of membrane protein folds  matching distance constraints, Protein Science, 12, 1750-1761, 2003. [PMID: 12876324]
  107. Diallo, M.S., Simpson, A., Gassman, P., Faulon, J.L., Johnson, Jr. J.H., Goddard, W.A., Hatcher, P.G. 3-D Structural Modeling of Humic Acids trhough Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Clesea Siol Humic Acid. Environ. Sci. & Technol, 37 (9), 1783 -1793, 2003. [PMID: 12775049]..   (link to journal)
  108. Faulon, J.L., Collins, M., Carr, R.D. Canonizing Molecules Using Extended Valence Sequence, SANDIA Report 2003-3157, Sandia National Laboratories, Albuquerque , NM. , 2003
  109. Faulon, J.L., Rintoul, M.D., Young, M.M. Constrained Self-Avoiding Walks: Implications for Protein Structure Determination,  J. Phys. A: Gen. Math., 34, 1-20, 2002. (link to journal)
  110. Faulon, J.L., Collins, M., Carr, R.D. Canonizing Molecules Using Extended Valence Sequence, SANDIA Report 2003-3157, Sandia National Laboratories, Albuquerque , NM., 2003
  111. Visco, D., Pophale, R.S., Rintoul, M.D., Faulon, J. L. Developing a methodology for an inverse quantitative structure-activity relationship using the signature molecular descriptor, Journal of molecular graphics & modelling, 20, 429-438, 2002. | doi: 10.1016/S1093-3263(01)00144-9 | PMID: 12071277
  112. Heffelfinger, G.S., Martino, A., Gorin, A., Xu, Y., Rintoul, M.D., Geist, A., Al-Hashimi, H.M., Davidson, G.S., Faulon, J.L., Frink, L.J., Haaland, D.M., Hart, W.E., Jakobsson, E., Lane, T., Li, M., LoCascio, P., Olken, F., Olman, V., Palenik, B., Plimpton, S.J., Roe, D.C., Samatova, N.F., Shah, M., Shoshoni, A., Strauss, C., Thomas, E.V., Timlin, J.A., Xu, D. Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling. OMICS 2002, 6, 4, 305-330. [PMID: 12626091]
  113. Diallo, M.S., Faulon, J. L., Goddard, W.A. III., Johnson, J.H. Jr. Binding of Hydrophobic Organic  Compounds to Dissolved Humic Substances: A Predictive Approach Based on Computer Assisted  Structure Elucidation, Atomistic Simulations and Flory-Huggins Solution Theory. In Humic  Substances: Structures, Models and Functions.  Eds. G. Davies and E.A. Ghabbour, Royal Society of  Chemistry, 2001, 221-237.
  114. Faulon, J.L. Stochastic Generator of Chemical Structure. (4) Building Polymeric Systems with  Specified Properties, J. Comput. Chem., 2001, 22, 580-590. (link to journal)
  115. Faulon, J.L., Sault, A.G. Stochastic Generator of Chemical Structure (3) Reaction Network, J.  Chem. Inf. Comput. Sci, 41, 894 -908, 2001. [PMID: 11500106].(link to journal)
  116. Diallo, M.S., Faulon, J.L., Goddard, W.A. III., Johnnson, J.H. Jr., Weber, W.J. Jr. “Molecular  Modeling of Chelsea Humic Acid: A Hierarchical Approach Based on Experimental Characterization,  Computer Assisted Structure Elucidation and Atomistic Simulations”, ACS, Division of  Environmental Chemistry, Preprints of Extended Abstracts, 219th ACS National Meeting, San  Francisco, CA, March 26-30,  Vol, 40, No 1,  2000, 343-347.
  117. Diallo, M.S., Cagin, T., Faulon, J.L., Goddard, W.A. III. Thermodynamic Properties of  Asphaltenes: A predictive Approach Based on Computer Assited Structure Elucidation and Atomistic  Simulation, Asphalts and Asphaltenes II, Development in Petroleum Science 40B, Yen, T.F.  and  Chillingiran, G.V., Edt. Elsevier, Amsterdam, 2000.
  118. Faulon, J.L. Automorphism Partitioning, and Canonical Labeling Can Be Solved in Polynomial- Time for Molecular Graphs, J. Chem. Inf. Comput. Sci., 1998, 38, 432-444. (link to journal)
  119. Tokarski, J.S., Hopfinger, A.J., Hobbs, J.D., Ford, D.M., Faulon, J.L. Molecular  Modeling of Polymer 17.  Simulation and QSPR Analyses of Transport Behavior in Amorphous  Polymeric Materials, Computational and Theoretical Polymer Science, 1997, 23, 199-214.
  120. Faulon, J.L., Hobbs, J.D., Ford, D.M., Wilcox, R.T. Massively Parallel Simulations of  Diffusion in Dense Polymeric Structures, Proccedings SC97, 1-12,1997. (link to journal)
  121. Faulon, J.L. Stochastic Generator of Chemical Structure. (2) Using Simulated Annealing to Search  the Space of Constitutional Isomers, Journal of Chemical Information and Computer Sciences, 36, 731-740, 1996. | doi: 10.1021/ci950179a
  122. Pohl, P.I., Faulon, J.L., Smith, D.M. Pore Structure of Imogolite Computer Model,  Lamgmuir, 12, 4463-4468, 1996. | doi: 10.1021/la9600715
  123. Kowaleski, I., Vandenbroucke, M., Taylor, J., Faulon, J.L., Huc, A. Preliminary  Results  on Molecular Modeling of Asphaltene using Structure Elucidation Programs in Conjonction  with  Molecular Simulation Programs, Energy and Fuels, 1996, 10, 97-107. (link to journal)
  124. Kowaleski, I., Vandenbroucke, M., Faulon, J.L., Taylor, J., Behar, F., Huc, A. Asphaltene Molecular Modeling of Boscan Crude Oil, Revue de l’I.F.P., 1996, 51, 161-170.
  125. Boduszynski, M.M., Faulon, J.L. Molecular Structure Elucidation of Cycloalkyl- coronenes  found in Hydrocracked Oils, Proceedings of the Dhahran 1996 Lab. RandD Center  Technical  Exchange Meeting, 35-42, 1996.
  126. Boduszynski, M.M., Rechsteiner, C.E., Grudoski, D.A., Iwamoto, J.D., Faulon J.L. The Effect of Molecular Structure on Molecular Weight – Boiling Point Relationship for  Petroleum  Fractions, Proceedings of the Dhahran 1996 Lab. RandD Center  Technical Exchange Meeting, 23-34,  1996.
  127. Faulon, J.L. Unraveling complex molecules, CHEMTECH, 1995,25, 16-23.
  128. Faulon, J.L., Loy, D.A., Carlson, G.A., Shea, K.J. Computer-aided Structure  Elucidation forArylsilsesquioxane Gels, Computational Materials Science, 1995, 3,  334-346.
  129. Pohl, P.I., Faulon, J.L., Smith, D.M. Molecular Dynamics Computer Simulations of  Silica  Aerogels, J. Non Cryst. Solids, 1995, 186, 349-355.
  130. Faulon, J.L., Carlson, G.A. CAMD Studies of Coal Structure and Coal Liquefaction, Proceedings  of the Coal Liquefaction and Gas Conversion Contractors’ Review Conference, 619-635, 1994.
  131. Faulon, J.L. Stochastic Generator of Chemical Structure. (1) Application to the  Structure Elucidation  of Large Molecules, Journal of Chemical Information and Computer Sciences, 34, 1204-1218, 1994. | doi: 10.1021/ci00063a012
  132. Faulon, J.L., Carlson, G.A., Hatcher, P.G. A Three-Dimensional Model for Lignocellulose  from Gymnospermous Wood, Org. Geochem., 1994, 211, 1169-1179.
  133. Faulon, J.L., Hatcher, P.G. Is There Any Order in the Structure of Lignin ?, Energy and Fuels,  1994, 8, 402-407. (.pdf)
  134. Faulon, J.L., Mathews, J.P., Carlson, G.A., Hatcher, P.G. Correlation Between Microporosity and Fractal Dimension of Bituminous Coal Based on Computer-Generated  Models,  Energy and Fuels, 1994, 8, 408-414. (.pdf)
  135. Faulon, J.L. Calculating the number averaged molecular weight (Mo) of aromatic and  hydroaromatic  clusters in coal using rubber elasticity theory, Energy and Fuels, 1994, 8, 1020-1024.
  136. Hatcher, P.G., Faulon, J.L. Coalification of Lignin from Vitrinite: A New Structural  Template  Based on a Helical Structure, Am. Chem. Soc. Div Fuel Chem. Preprints 39, 7-17, 1994.
  137. Carlson, G.A., Faulon, J.L. Applications of Molecular Modeling in Coal Research, Am. Chem.  Soc. Div Fuel Chem. Preprints 39, 18-29, 1994.
  138. Faulon, J.L., Carlson, G.A. CAMD Studies of Coal Structure and Coal Liquefaction, Proceedings of the Coal Liquefaction and Gas Conversion Contractors’ Review Conference, 619-635, 1994.
  139. Carlson, G.A., Faulon, J.L., Pohl, P.I., Shelnutt, J. A. Applications of Molecular  Modeling to the Design and Characterization of Materials, Proceedings of the 93′ Science and Technology Materials Conference, 12-21, 1993.
  140. Faulon, J.L., Carlson, G.A., Hatcher, P.G. Statistical Model for Bituminous Coal:  A Three- Dimensional Evaluation of Structural and Physical Properties Based on Computer-Generated  Structures, Energy and Fuels, 1993, 7, 1062-1072. (.pdf)
  141. Faulon, J.L., Hatcher, P.G., Carlson, G.A., Wenzel K.A. A computer-aided Molecular  Model for High Volatile Bituminous Coal, Fuel Processing Technology, 1993, 34, 277-293.
  142. Mathews, J.P., Scaroni, A., Faulon, J.L., Hatcher, P.G. A Structural Model for Coalified  Wood (Vitrinite) from Medium Volatile Bituminous Coal, Proceedings of the 7th International  Conference on Coal Science, 128-138, Michaeliam, K. H. Edt, 1993.
  143. Hatcher, P.G., Faulon, J.L., Clifford, D.A., Mathews, J.P. A Three-dimensional  Structural Model for Humic Acids from Oxidized Soil, Proccedings of the 6th IHSS Int. Meeting, 436-446, Elsevier, Amsterdam, 1993.
  144. Hatcher, P.G., Wenzel, K.A., Faulon, J.L. Reaction of Wood During Early  Coalification, A  Clue to the Structure of Vitrinite, Am. Chem. Soc. Div Fuel Chem. Preprints 38, 412-419, 1993.
  145. Faulon, J.L., Carlson, G.A., Mathews, J.P., Hatcher, P.G. Statistical Evaluation of  Physical Properties for Coal based on Computer-generated Models, Am. Chem. Soc. Div Fuel Chem.  Preprints 38, 420-430, 1993.
  146. Faulon, J.L. On Using the Graph-Equivalent Classes for the Structure Elucidation of  Large  Molecules, J. Chem. Inf. Comput. Sci., 1992, 32, 338-348.(.pdf)
  147. Hatcher, P.G, Faulon, J.L., Wenzel, K.A., Cody, G.D. A Structural Model for  Lignin-Derived Vitrinite from High-Volatile Bituminous Coal (Coalified Wood), Energy and Fuel, 1992, 6, 813-820. (.pdf)
  148. Faulon, J.L., Hatcher, P.G, Wenzel, K.A. A Computer Assisted-Structural Elucidation for Coal Macromolecule, Am. Chem. Soc. Div. Fuel Chem. Preprints 37, 900-910, 1992.
  149. Hatcher, P.G., Faulon, J.L., Wenzel, K.A., Cody, G.D. A Three Dimensional Structural Model for Vitrinite from High Volatile Bituminous Coal, Am. Chem. Soc. Div. Fuel Chem. Preprints 37, 886-896, 1992.
  150. Faulon, J.L. Prediction Elucidation and Molecular Modeling. Algorithms and Applications in Geochemistry, Ph. D.Thesis, Edited by Ecole des Mines, Paris, 1991.
  151. Faulon, J.L., Vandenbroucke, M., Drappier, J.M., Behar, F., Romero, M. 3D Chemical Model for Geological Macromolecules, Org. Geochem., 1990, 16, 981-993.
  152. Faulon, J.L., Vandenbroucke, M., Drappier, J.M., Behar, F., Romero, M. Modeling the Chemical Structures of Sedimentary Macromolecules: The Xmol Software, Revue de l’I.F.P., 1989, 45, 161-180.
  153. Faulon, J.L., Drappier, J.M., Bellevaux, C. Elimination des parties cachees par les  silhouettes, Revue Internationale de CFAO et d’Infographie, 1988, 3, 57-76.