Publications prior 2008 (Jean-Loup Faulon)

 

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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]
  24. Faulon, J.L., Visco, D., Roe, D. Molecular Structure Enumeration, SANDIA Report 2004-0960, Sandia National Laboratories, Albuquerque, NM., 2004
  25. 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
  26. 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
  27. 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]
  28. 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)
  29. Faulon, J.L., Collins, M., Carr, R.D. Canonizing Molecules Using Extended Valence Sequence, SANDIA Report 2003-3157, Sandia National Laboratories, Albuquerque , NM. , 2003
  30. 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)
  31. Faulon, J.L., Collins, M., Carr, R.D. Canonizing Molecules Using Extended Valence Sequence, SANDIA Report 2003-3157, Sandia National Laboratories, Albuquerque , NM., 2003
  32. 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
  33. 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]
  34. 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.
  35. 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)
  36. 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)
  37. 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.
  38. 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.
  39. 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)
  40. 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.
  41. 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)
  42. 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
  43. Pohl, P.I., Faulon, J.L., Smith, D.M. Pore Structure of Imogolite Computer Model,  Lamgmuir, 12, 4463-4468, 1996. | doi: 10.1021/la9600715
  44. 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)
  45. 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.
  46. 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.
  47. 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.
  48. Faulon, J.L. Unraveling complex molecules, CHEMTECH, 1995,25, 16-23.
  49. 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.
  50. Pohl, P.I., Faulon, J.L., Smith, D.M. Molecular Dynamics Computer Simulations of  Silica  Aerogels, J. Non Cryst. Solids, 1995, 186, 349-355.
  51. 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.
  52. 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
  53. Faulon, J.L., Carlson, G.A., Hatcher, P.G. A Three-Dimensional Model for Lignocellulose  from Gymnospermous Wood, Org. Geochem., 1994, 211, 1169-1179.
  54. Faulon, J.L., Hatcher, P.G. Is There Any Order in the Structure of Lignin ?, Energy and Fuels,  1994, 8, 402-407. (.pdf)
  55. 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)
  56. 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.
  57. 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.
  58. Carlson, G.A., Faulon, J.L. Applications of Molecular Modeling in Coal Research, Am. Chem.  Soc. Div Fuel Chem. Preprints 39, 18-29, 1994.
  59. 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.
  60. 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.
  61. 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)
  62. 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.
  63. 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.
  64. 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.
  65. 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.
  66. 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.
  67. 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)
  68. 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)
  69. 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.
  70. 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.
  71. Faulon, J.L. Prediction Elucidation and Molecular Modeling. Algorithms and Applications in Geochemistry, Ph. D.Thesis, Edited by Ecole des Mines, Paris, 1991.
  72. Faulon, J.L., Vandenbroucke, M., Drappier, J.M., Behar, F., Romero, M. 3D Chemical Model for Geological Macromolecules, Org. Geochem., 1990, 16, 981-993.
  73. 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.
  74. 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.