Publications

  1. Carbonell P, Delépine B, Faulon JL. “Extended metabolic space modeling”, Synthetic metabolic pathways: Methods and Protocols, MK Jensen and JD Keasling, Springer, in press, 2017. | link to publisher | doi: 10.1007/978-1-4939-7295-1
  2. Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. bioRxiv, 141721, 2017. | doi: 10.1101/141721
  3. Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. bioRxiv, 158147, 2017. | doi: 10.1101/158147
  4. 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. bioRxiv, 188979, 2017. | doi: 10.1101/188979
  5. Swainston NDunstan MJervis AJRobinson CJCarbonell PWilliams ARFaulon JLScrutton NSKell DB. PartsGenie: an integrated tool for optimising and sharing synthetic biology parts. bioRxiv, 189357, 2017. | doi: 10.1101/189357
  6. 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
  7. 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
  8. 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
  9. 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
  10. Libis V, Delépine B, Faulon JL. Expanding biosensing abilities through computer-aided design of metabolic pathways. ACS Synthetic Bioliology, in press, 2016. | doi: 10.1021/acssynbio.5b00225 | PMID: 27028723
  11. 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
  12. 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
  13. 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
  14. Fehér, T., Libis, V., Carbonell, P., Faulon, J.L. 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
  15. Castane, A., Ferer, T. Carbonnell, P, Faulon, J.L. 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
  16. Fehér, T., Planson, A.G., Carbonell, P., Fernández-Castané, A., Grigoras, I., Dariy, E., Perret, A., Faulon, J.L. 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
  17. Carbonell, P., Parutto, P., Baudier, C., Junot, C., Faulon, J.L. Retropath: automated pipeline for embedded metabolic circuits. ACS Synthetic Biology, 3(8): 565-577, 2014. | doi: 10.1021/sb4001273 | PMID: 24131345
  18. Pauthenier, C., Faulon, J.L. 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
  19. Carbonell, P., Parutto, P., Herisson, J., Pandit, S., Faulon, J.L. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Research, 42: W389-394, 2014. | doi: 10.1093/nar/gku362 | PMID: 24792156
  20. Jaghoori, M.M., Jongmans S.T.Q., de Boer, F., Peironcely, J., Faulon, J.L., 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
  21. Joo, J., Plimpton, S.J., Faulon, J.L. 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
  22. Carbonell, P., Carlsson, L., Faulon, J.L. Stereo signature molecular descriptor. Journal of Chemical Information and Modeling, 53(4): 887-897, 2013. | doi: 10.1021/ci300584r | PMID: 23527586
  23. Martiny, V.Y., Carbonell, P., Lagorce, D., Villoutreix, B.O., Moroy, G., Miteva, M.A. 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
  24. Trosset, J.Y, Carbonell, P. Synergistic synthetic biology: units in concert. Frontiers in Synthetic Biology, 1:11, 2013. | doi:  10.3389/fbioe.2013.00011 | PMID: 25022769
  25. 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
  26. Carbonell, P., Planson, A.G., Faulon, J.L. Retrosynthetic design of heterologous pathways. Methods in Molecular Biology, 985: 149-73, 2013. | doi: 10.1007/978-1-62703-299-5_9 | PMID: 23417804
  27. Pauthenier, C., Carbonell, P., Faulon, J.L. 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
  28. Pauthenier, C., Faulon, J.L. Ingénierie métabolique et biologie de synthèse. Techniques de l’Ingénieur, BIO800, 2013. | link to journal
  29. Pauthenier, C., Faulon, J.L. Composés produits par ingénierie métabolique. Techniques de l’Ingénieur, BIO801, 2013. | link to journal
  30. Planson, A.G., Carbonell, P., Grigoras, I., Faulon, J.L. 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
  31. Peironcely, J.E., Rojas-Chertó, M., Fichera, D., Reijmers, T., Coulier, L., Faulon, J.L., Hankemeier, T. OMG: Open Molecule Generator. Journal of Cheminformatics, 4(1): 21. | doi: 10.1186/1758-2946-4-21 | PMID: 22985496
  32. Planson, A.G., Carbonell, P., Paillard, E., Pollet, N., Faulon, J.L. 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
  33. Carbonell, P., Fichera, D., Pandit, S.B., Faulon, J.L. 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
  34. Misra, M., Martin, S., Faulon, J.L. 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
  35. Carbonell, P., Lecointre, G., Faulon, J.L. 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
  36. Carbonell P., Planson A.G., Fichera D., Faulon J.L. 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
  37. Misra, M., Andrienko, D., Baumeier, B., Faulon, J.L., von Lilienfeld, O.A. 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
  38. Jaramillo, A., Faulon, J.L. 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
  39. Planson, A.G., Carbonell, P., Grigoras, I., Faulon, J.L. Engineering antibiotic production and overcoming bacterial resistance. Biotechnology Journal, 6(7): 812-825, 2011. | doi: 10.1002/biot.201100085 | PMID: 21661120
  40. Carbonell, P., Faulon, J.L. Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics, 26(16): 2012-2019, 2010. | doi: 10.1093/bioinformatics/btq317 | PMID: 20551137
  41. Faulon, J.L., Carbonell, P. Reaction Network Generation, In Handbook of Chemoinformatics Algorithms. Chapman & Hall/CRC Series in Mathematical & Computational Biology, 2010. |  link to publisher
  42. Misra, M., Faulon, J.L. 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
  43. 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
  44. 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
  45. Weis, D.C., Visco, D.P. Jr., Faulon J.L. 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
  46. Faulon, J.L., 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
  47. Martin, S., Brown, W.M., Faulon, J.L. Using product kernels to predict protein interactions. Advances in Biochemical Engineering/Biotechnology, 110:215-245, 2008. | doi: 10.1007/10_2007_084 | PMID: 17922100
  48. May, E., Leitao, A., Faulon, J.L., Joo, J., Misra, M., Oprea, T.I. 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
  49. Gaucher, S.P., Morrow, J.A., Faulon J.L. 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
  50. Gray, G.A., Williams, P.J., Brown, W.M., Faulon, J.L.  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
  51. Zhang, Z., Martino, A., Faulon, J.L. 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
  52. Joo, J., Plimpton, S., Martin, S., Swiler, L., Slepoy, A., Faulon, J.L., 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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]
  72. Faulon, J.L., Visco, D., Roe, D. Molecular Structure Enumeration, SANDIA Report 2004-0960, Sandia National Laboratories, Albuquerque, NM., 2004
  73. 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
  74. 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
  75. 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]
  76. 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)
  77. Faulon, J.L., Collins, M., Carr, R.D. Canonizing Molecules Using Extended Valence Sequence, SANDIA Report 2003-3157, Sandia National Laboratories, Albuquerque , NM. , 2003
  78. 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)
  79. Faulon, J.L., Collins, M., Carr, R.D. Canonizing Molecules Using Extended Valence Sequence, SANDIA Report 2003-3157, Sandia National Laboratories, Albuquerque , NM., 2003
  80. 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
  81. 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]
  82. 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.
  83. 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)
  84. 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)
  85. 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.
  86. 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.
  87. 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)
  88. 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.
  89. 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)
  90. 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
  91. Pohl, P.I., Faulon, J.L., Smith, D.M. Pore Structure of Imogolite Computer Model,  Lamgmuir, 12, 4463-4468, 1996. | doi: 10.1021/la9600715
  92. 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)
  93. 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.
  94. 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.
  95. 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.
  96. Faulon, J.L. Unraveling complex molecules, CHEMTECH, 1995,25, 16-23.
  97. 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.
  98. Pohl, P.I., Faulon, J.L., Smith, D.M. Molecular Dynamics Computer Simulations of  Silica  Aerogels, J. Non Cryst. Solids, 1995, 186, 349-355.
  99. 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.
  100. 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
  101. Faulon, J.L., Carlson, G.A., Hatcher, P.G. A Three-Dimensional Model for Lignocellulose  from Gymnospermous Wood, Org. Geochem., 1994, 211, 1169-1179.
  102. Faulon, J.L., Hatcher, P.G. Is There Any Order in the Structure of Lignin ?, Energy and Fuels,  1994, 8, 402-407. (.pdf)
  103. 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)
  104. 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.
  105. 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.
  106. Carlson, G.A., Faulon, J.L. Applications of Molecular Modeling in Coal Research, Am. Chem.  Soc. Div Fuel Chem. Preprints 39, 18-29, 1994.
  107. 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.
  108. 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.
  109. 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)
  110. 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.
  111. 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.
  112. 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.
  113. 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.
  114. 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.
  115. 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)
  116. 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)
  117. 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.
  118. 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.
  119. Faulon, J.L. Prediction Elucidation and Molecular Modeling. Algorithms and Applications in Geochemistry, Ph. D.Thesis, Edited by Ecole des Mines, Paris, 1991.
  120. Faulon, J.L., Vandenbroucke, M., Drappier, J.M., Behar, F., Romero, M. 3D Chemical Model for Geological Macromolecules, Org. Geochem., 1990, 16, 981-993.
  121. 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.
  122. 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.