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)


    1. 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)
    2. Martin S., R. D. Carr R.D., Faulon J.L. Random Removal of Edges from Scale Free Graphs, Physica A. 37, 870-876, 2006


    1. 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)
    2. Martin S., Roe D., Faulon J.L. Predicting Protein-Protein Interactions using Signature Products, Bioinformatics, 21, 218-26, 2005. [PMID: 15319262]. (.pdf manuscript).>
    3. 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.
    4. 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).


    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. 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)


  1. 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)


  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. 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]

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