Publications by Year


2007

    1. Martin S., Brown W. M., Faulon J.L. Using Product Kernels to Predict Protein Interactions. In Advances in Biochemical Engineering/Biotechnology, Eds. H. Seitz and M. Werther, Springer-Verlag. in press, 2007 [PMID: 17922100]
    2. Faulon J.L., Misra M., Martin S., Sale, K., Sapra R.. Genome Scale Enzyme-metabolites and Drug-Target interaction predictions using the signature molecular descriptor, Bioinformatics in press 2007 [PMID: 18037612 ] (link to journal)
    3. Sara P. Gaucher, Jeffrey A. Morrow, and Faulon J.L. Use of a Designed Peptide Array to Infer Dissociation Trends for Non-Tryptic Peptides in Quadrupole Ion Trap and Quadrupole Time of Flight Mass Spectrometry, Analytical Chemistry, in press 2007 [PMID: 17854158 ] (link to journal)
    4. 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, in press 2007
    5. Zhang Z., Martino A., Faulon J.L.. Global analysis of IL-2 responsive genes in murine T Cell, Journal of Interferon & Cytokine Research, in press 2007
    6. 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, in press 2007 [PMID: 17934057] (link to journal)
    7. Oprea T., Tropsha A., Faulon J.L., Rintoul M.D. Systems Chemical Biology, Nature Chem. Bio., 3, 447-50, 2007 [PMID: 17637771] (link to journal)
    8. 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 [PMID: 17267426] (link to journal)

2006

    1. Brown W. M., Martin S., Rintoul M.D., Faulon J.L. The Signature Molecular Descriptor. 6. Designing Novel Polymers with Targeted Properties, J. Chem. Info. & Model., 46, 826-835, 2006 [PMID: 16563014 ] (link to journal)
    2. 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 [PMID: 16365772] (link to journal)
    3. Martin S., R. D. Carr R.D., Faulon J.L. Random Removal of Edges from Scale Free Graphs, Physica A. 37, 870-876, 2006

2005

    1. Faulon J.L., Visco D, Roe D. Enumerating Molecules. In: Reviews in Computational Chemistry Vol. 21, Lipkowitz K. Edt., Wiley-VCH, 2005 (link to amazon.com)
    2. Faulon J.L., Brown W.M., Martin S Reverse engineering chemical structures from molecular descriptors: how many solutions? J. Comput Aided Mol Des. 2005 in press [PMID: 16267694] (link to journal)
    3. Brown W.M., Faulon J.L., Sale K. A deterministic algorithm for constrained enumeration of transmembrane protein folds. Comput Biol Chem., 29, 143-150, 2005. [PMID: 15833442]. (link to journal)
    4. Weis D., Faulon J.L., Visco D. The Signature Molecular Descriptor. 5. The Design of Hydrofluoroether Foam Blowing Agents Using Inverse-QSAR, Ind. Eng. Chem. Res., 44, 8883-8891, 2005. (link to journal)
    5. Martin S., Roe D., Faulon J.L. Predicting Protein-Protein Interactions using Signature Products, Bioinformatics, 21, 218-26, 2005. [PMID: 15319262]. (.pdf manuscript).>
    6. 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.
    7. 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. (.pdf manuscript).

2004

    1. 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, 2613-2627, 2004. [PMID: 15340162]. (.pdf manuscript).
    2. 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. (.pdf manuscript).
    3. Faulon J.L., Martin S., Carr RD. Dynamical Robustness in Gene Regulatory Networks. Proceedings IEEE CSB2004, 3, 626-627, 2004. (.pdf manuscript).>
    4. 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.
    5. 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. [PMID: 15032522]. (.pdf manuscript).
    6. 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]. (.pdf manuscript)
    7. Faulon J.L., Visco D, Roe D. Molecular Structure Enumeration, SANDIA Report 2004-0960, Sandia National Laboratories, Albuquerque, NM., 2004

2003

    1. Faulon J. L., Visco D. Churchwell, C. J., The Signature Molecular Descriptor. 2. Enumerating Molcules from their Extended Valence Sequences, J. Chem. Inf. Comput. Sci., 43 (3), 721 -734, 2003. [PMID: 12767130]. (link to journal)
    2. Faulon J.L., Visco D., Pophale R.S. The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR studies, J. Chem. Inf. Comput. Sci., 43, 707-720, 2003. [PMID: 12767129]. (link to journal)
    3. 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]. (.pdf)
    4. 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)
    5. Faulon J.L., Collins M., Carr R.D. Canonizing Molecules Using Extended Valence Sequence, SANDIA Report 2003-3157, Sandia National Laboratories, Albuquerque, NM., 2003

2002

    1. 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)
    2. Faulon J.L., Collins M., Carr R.D. Canonizing Molecules Using Extended Valence Sequence, SANDIA Report 2003-3157, Sandia National Laboratories, Albuquerque, NM., 2003
    3. 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, J. Molecular Graphics & Modelling, 20, 429-438, 2002. [PMID: 12071277]. (link to journal)
    4. 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]

2001

    1. 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.
    2. 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)
    3. 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)

2000

    1. 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.
    2. Diallo, M. S. ; Cagin, T..; Faulon, J. L.; Goddard, III, W. A., 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.

prior 2000

    1. 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)
    2. 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.
    3. 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)
    4. Faulon, J. L., Stochastic Generator of Chemical Structure. (2) Using Simulated Annealing to Search the Space of Constitutional Isomers, J. Chem. Inf. Comput. Sci., 1996, 36, 731-740. (link to journal)
    5. Pohl, P. I.; Faulon, J. L.; Smith, D. M., Pore Structure of Imogolite Computer Model, Lamgmuir, 1996, 12, 4463-4468. (link to journal)
    6. 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)
    7. 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.
    8. 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.
    9. 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.
    10. Faulon, J.L., Unraveling complex molecules, CHEMTECH, 1995,25, 16-23.
    11. 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.
    12. Pohl, P. I. ; Faulon, J. L. ; Smith, D. M., Molecular Dynamics Computer Simulations of Silica Aerogels, J. Non Cryst. Solids, 1995, 186, 349-355.
    13. 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.
    14. Faulon, J. L., Stochastic Generator of Chemical Structure. (1) Application to the Structure Elucidation of Large Molecules, J. Chem. Inf. Comput. Sci., 1994, 34, 1204-1218. (.pdf)
    15. Faulon, J. L. ; Carlson, G.A. ; Hatcher, P. G., A Three-Dimensional Model for Lignocellulose from Gymnospermous Wood, Org. Geochem., 1994, 211, 1169-1179.
    16. Faulon, J.L. ; Hatcher, P. G., Is There Any Order in the Structure of Lignin ?, Energy and Fuels, 1994, 8, 402-407. (.pdf)
    17. Faulon, J. L. ; Mathews, J. P. ; Carlson, G. A. and 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)
    18. 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.
    19. 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.
    20. Carlson, G. A. ; Faulon, J. L., Applications of Molecular Modeling in Coal Research, Am. Chem. Soc. Div Fuel Chem. Preprints 39, 18-29, 1994.
    21. Faulon J. L. and 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.
    22. 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.
    23. 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)
    24. 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.
    25. 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.
    26. 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.
    27. 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.
    28. 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.
    29. 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)
    30. 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)
    31. 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.
    32. 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.
    33. Faulon, J. L., Prediction Elucidation and Molecular Modeling. Algorithms and Applications in Geochemistry, Ph. D.Thesis, Edited by Ecole des Mines, Paris, 1991.
    34. Faulon, J.L. ; Vandenbroucke, M. ; Drappier, J.M. ; Behar, F. and Romero, M., 3D Chemical Model for Geological Macromolecules, Org. Geochem., 1990, 16, 981-993.
    35. Faulon, J.L. ; Vandenbroucke, M. ; Drappier, J.M. ; Behar, F. and Romero, M., Modeling the Chemical Structures of Sedimentary Macromolecules: The Xmol Software, Revue de l'I.F.P., 1989, 45, 161-180.
    36. 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.

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