Publications supported by UCBREP Training Grants
FY 1999-2000 through FY 2003-2004

• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Williams CL, Boucher PE, Stibitz S, Cotter PA; BvgA functions as both an activator and a repressor to control Bvg phase expression of bipA in Bordetella pertussis; Mol Microbiol, 56(1):175-88, (2005).
   
• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Williams, C. L. and P. A. Cotter; Precise control of bipA expression is important for establishment of tracheal colonization by and induction of humoral immunity to Bordetella bronchiseptica; American Society for Microbiology Annual Meeting, , (2004). Poster Presentation
   
• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Mazar, J., E. L. Benanti, C. B. O'Connell and P. A. Cotter; Variation in maturation and secretion of filamentous hemagglutinin among Bordetella subspecies suggests multiple roles for SphB1 in virulence; American Society for Microbiology Annual Meeting, , (2004). Poster Presentation
   
• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Hernday AD, Braaten BA, Broitman-Maduro G, Engelberts P, Low DA.; Regulation of the pap epigenetic switch by CpxAR: phosphorylated CpxR inhibits transition to the phase ON state by competition with Lrp; Mol Cell, 16(4):537-47, (2004).
   
• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Heithoff DM, Mahan MJ; Vibrio cholerae biofilms: stuck between a rock and a hard place; J Bacteriol, 186(15):4835-7, (2004).
   
• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Badie G, Heithoff DM, Mahan MJ; LcrV synthesis is altered by DNA adenine methylase overproduction in Yersinia pseudotuberculosis and is required to confer immunity in vaccinated hosts; Infect Immun, 72(11):6707-10, (2004).
   
• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Cotter, P. A. and A. M. Jones; Phosphorelay control of virulence gene expression in Bordetella; Trends Microbiol., 11:367-373, (2003).
   
• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Dueger, E. L., J. K. House, D. M. Heithoff, and M. J. Mahan; Salmonella DNA adenine methylase mutants elicit early and late protective immune responses in calves; Vaccine, 21:3249-3258, (2003).
   
• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Inatsuka, C. and P. A. Cotter; Role of the Filamentous Hemagglutinin RGD Triplet in Persistent Respiratory Tract Colonization by B. bronchiseptica; American Society for Microbiology, General Meeting. Washington, D.C., , (2003). Presentation
   
• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Inatsuka, C. and P. A. Cotter; The RGD triplet of filamentous hemagglutinin is required for persistent tracheal colonization of rats by B. bronchiseptica; The 7th International Symposium on Pertussis. Cambridge, England, , (2002). Presentation
   
• Grant 2002-14 – Investigating bacterial-host interactions at mucosal surfaces: A comparative analysis of Bordetella pertussis, Salmonella typhimurium, and uropathogenic Escherichia coli., P.I.: David Low
  Shtrichman, R., D. M. Heithoff, M. J. Mahan, and C. E. Samuel; Tissue selectivity of interferon-stimulated gene (ISG) expression in mice infected with Dam+ versus Dam- Salmonella; Infect. Immun., 70:5579-5588, (2002).
   
• Grant 2002-08 – Arbitrarily Large Spatially Addressable Nanometer Scale Arrays, P.I.: Richard H. Lathrop
  Lathrop J, Hatfield D; A Quick and Easy Method for Producing a Synthetic Gene of any Protein.; A provisional patent was filed by U.C. on synthetic gene self-assembly methodology, May, (2003). Patent
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  Irwin B, Aye M, Baldi P, Beliakova-Bethell N, Cheng H, Dou Y, Liou W, Sandmeyer S.; Retroviruses and yeast retrotransposons use overlapping sets of host genes; Genome Res, 15(5):641-54, (2005).
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  S. Sundaresh , P. Baldi, S. P. Hung, and G. Wesley Hatfield; How noisy and replicable are DNA microarray data?; , , (2004). submitted
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  Dou Y, Baisnee PF, Pollastri G, Pecout Y, Nowick J, Baldi P; ICBS: a database of interactions between protein chains mediated by beta-sheet formation; Bioinformatics, 20(16):2767-77, (2004).
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  P. Baldi, J. Cheng, and A. Vullo; Large-Scale Prediction of Disulphide Bond Connectivity; NIPS (Neural Information Processing Systems Conference), , (2004). Presentation
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  J. Cheng, L . Scharenbroich, P. Baldi, and E. Mjolsness; Sigmoid: Towards a Generative, Scalable Software Infrastructure for Pathway Bioinformatics and Systems Biology; IEEE Intelligent Systems, , (2004). submitted
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  Juskowiak, G. L.; Stachel, S. J.; Tivitmahaisoon, P.; Van Vranken, D. L.; Fluorogenic Peptide Sequences - Transformation of Short Peptides into Fluorophores Under Ambient Photooxidative Conditions; J. Am. Chem. Soc., 126, 550-556, (2004).
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  Murase, K., Poulos, T., Weiss, G.A.; Dissecting binding and multimerization of the nitric oxide synthase inhibitor caveolin-1 through phage-displayed shotgun scanning; , , (2004). in preparation
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  Murase, K., Morrison, K.L., Tam, P.Y., Stafford, R.L., Jurnak, F. & Weiss, G.A.; EF-Tu binding peptides identified, dissected and affinity optimized by phage display; Chem. Biol., 10: 161-168, (2003).
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  P. Baldi, G. Pollastri, P. Frasconi, and A. Vullo; New Machine Learning Methods for the Prediction of Protein Topologies; Artificial Intelligence and Heuristic Methods in Bioinformatics, IOS Press, (2003). Book Chapter
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  S. P. Hung, G. Wesley Hatfield, S. Sundaresh, and P. Baldi; Understanding DNA Microarrays: Sources and Magnitudes of Variances in DNA Microarray Data Sets; Genomics, Proteomics, and Vaccines, John Wiley and Sons, (2003). Book Chapter
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  Chang L, Sundaresh S, Baisnee PF, Baldi P, Licudine A, Vuong T, Hirano M, Olivas T, Mayer M, FitzGerald L, Naliboff B, Mayer E; Altered Diurnal Rhythm of ACTH and Cortisol in Irritable Bowel Syndrome and Fibromyalgia; Presented at conference as a poster. American Gastroenterological association meeting in Orlando, Florida, May, (2003). in preparation
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  P. Baisnee, S. Hampson, and P. Baldi; Why Are Complementary DNA Strands Symmetric?; Bioinformatics, 18, 1021-1033, (2002).
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  G. Pollastri and P. Baldi; Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal Corners. Proceedings of the 2002 Conference on Intelligent Systems for Molecular Biology, ISMB 02; Bioinformatics, 18, Supplement 1, S62-S70, (2002). Nominated for Best Paper Award
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  Avrantinis, S.K. & Weiss, G.A.; Dissecting protein functional epitopes with phage display; In Phage Display in Biotechnology and Drug Discovery, Marcel Dekker, Inc. (Sidhu, S.S., ed.), , (2002). Book Chapter
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  P. Baldi and G. Pollastri; The Principled Design of Large-Scale Recursive Neural Networks Architectures - DAG-RNNs and the Protein Structure Prediction Problem; Journal of Machine Learning Research, , (2002). submitted
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  P. Baldi and G. Pollastri; A Machine Learning Strategy for Protein Analysis; IEEE Intelligent Systems. Special Issue on Intelligent Systems in Biology, 17, 2, 28-35, (2002).
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  G. Pollastri, P. Baldi, P. Fariselli, and R. Casadio; Prediction of Coordination Number and Relative Solvent Accessibility in Proteins; Proteins, 47, 142-153, (2002).
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  G. Pollastri, D. Przybylski, B. Rost, and P. Baldi; Improving the Prediction of Protein Secondary Strucure in Three and Eight Classes Using Recurrent Neural Networks and Profiles; Proteins, 47, 228-235, (2002).
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  G. Pollastri, P. Baldi, A. Vullo, and P. Frasconi; Prediction of Protein Topologies Using GIOHMMs and GRNNs. Advances in Neural Information Processing Systems; MIT Press, Cambridge, MA, , (2002). in press
   
• Grant 2002-06 – Biomolecular Interactions in Complex Biological Systems, P.I.: Pierre Baldi
  Y. Guermeur, G. Pollastri, A. Elisseeff, D. Zelus, H. Paugam-Moisy,and P. Baldi; Combining Protein Secondary Structure Prediction Models With Ensemble Methods of Optimal Complexity; Neurocomputing, 2001, Proceedings of the JOBIM01 Conference, , (2001). Presentation
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Riby, J.E., Xue, L., Wu, T., Chatterji, U., Bjeldanes, E.L., Firestone, G.L. and Bjeldanes, L.F.; Activation and Potentiation of Gamma Interferon signaling by 3,3'-diindolylmethane in MCF-7 breast cancer cells; Oncogene, , (2005). submitted
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Xue, L., Firestone, G.L., Bjeldanes, L.F.; DIM stimulates IFN Gamma gene expression in human breast cancer cells via the specific activation of JNK and p38 pathways; Oncogene, 24, 2343-2453, (2005).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Xue L, Schaldach CM, Janosik T, Bergman J, Bjeldanes LF.; Effects of analogs of indole-3-carbinol cyclic trimerization product in human breast cancer cells; Chem Biol Interact, 152(2-3):119-29, (2005).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Davis, S. R., Stacpoole, P. W., Williamson, J., Kick, L. S., Quinlivan, E. P., Coats, B. S., Shane, B., Bailey, L. B. and Gregory, J. F. III.; Tracer-derived total and folate-dependent homocysteine remethylation and synthesis rates in humans indicate that serine is the main one-carbon donor; Am. J. Physiol., 286, E272-279, (2004).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Leong, H., Riby, J., Firestone, G.L. and Bjeldanes, L. F.; Potent ligand-independent estrogen receptor activation by 3,3'-diindolylmethane is mediated by cross-talk between the PKA and MAPK signaling pathways; J. Mol. Endo., 18, 291-302, (2004).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Lei, Z., Chen, W., Zhang, M., and Napoli, J.L.; Reduction of all-trans-retinal in the mouse liver peroxisome fraction by the short-chain dehydrogenase/reductase RRD: induction by the PPARa-ligand clofibrate; Biochemistry, 42, 4190-4196, (2003).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Lin, M., Zhang, M., Abraham, M., Smith, S.M., and Napoli, J.L.; Mouse RALDH4: molecular cloning, cellular expression, and activity in 9-cis-retinoic acid biosynthesis in intact cells; J. Biol. Chem., 278, 9856-9861, (2003).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Song, M.-S., Chen, W., Zhang, M., and Napoli, J.L.; Identification of a mouse short-chain dehydrogenase/reductase gene, RDH-S: function of non-catalytic amino acid residues in enzyme activity; J. Biol. Chem., 278, 40079-40087, (2003).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Zhang, M., Thomas, B.C., and Napoli, J.L.; Gene structure and minimal promoter of mouse rdh1; Gene, 305, 121-131, (2003).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Chatterji, U., Riby, J.E., Taniguchi, T., Bjeldanes, E.L., Bjeldanes, L.F., and Firestone, G.L.; Indole-3-carbinol stimulates transcription of the interferon gamma receptor 1 gene and augments interferon responsiveness in human breast cancer cells; Carcinogenesis, 18, 291-302, (2003).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Prasannan, P., Pike, S., Peng, K., Shane, B. and Appling, D. R.; Human mitochondrial C1-tetrahydrofolate synthase: gene structure, tissue distribution of the mRNA, and immunolocalization in CHO cells; J. Biol. Chem., 278, 43178-43187, (2003).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Stern, L. L., Shane, B., Bagley, P. J., Nadeau, M., Vivian Shih, V. and Selhub, J.; Combined marginal folate and riboflavin status affect homocysteine methylation in cultured immortalized lymphocytes from persons homozygous for the MTHFR C677T mutation; J. Nutr., 133, 2716-2720, (2003).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Zhang, J., Hsu, J.C., Kinseth, M.A., Bjeldanes, L.F., and Firestone, G.L.; Indole-3-carbinol induces a G1 cell cycle arrest and inhibits prostate-specific antigen production in human LNCaP prostate carcinoma cells; Cancer, 98, 2511-2520, (2003).
   
• Grant 2002-02 – Research and Training Program in Nutritional Genomics, P.I.: Joseph L. Napoli
  Shane, B.; Folate fortification: enough already?; Am. J. Clin. Nutr., 77, 8-9, (2003).
   
• Grant 2001-17 – Structural Determinants of Viral Protein-Nucleic Acid Interactions, P.I.: Bert L. Semler
  Tam, P. Y., Avrantinis, S. K., Zwick, M. B., Scott, J. K., Weiss, G. A.; Modifying the major coat protein of M13 phage for improved phage display; , , (2004). submitted
   
• Grant 2001-17 – Structural Determinants of Viral Protein-Nucleic Acid Interactions, P.I.: Bert L. Semler
  Reinke RA, Lee DJ, McDougall BR, King PJ, Victoria J, Mao Y, Lei X, Reinecke MG, Robinson WE Jr.; L-chicoric acid inhibits human immunodeficiency virus type 1 integration in vivo and is a noncompetitive but reversible inhibitor of HIV-1 integrase in vitro; Virology, 326(2):203-19, (2004).
   
• Grant 2001-17 – Structural Determinants of Viral Protein-Nucleic Acid Interactions, P.I.: Bert L. Semler
  Kuznetsov YG, Victoria JG, Low A, Robinson WE Jr, Fan H, McPherson A.; Atomic force microscopy imaging of retroviruses: human immunodeficiency virus and murine leukemia virus; Scanning, 26(5):209-16, (2004).
   
• Grant 2001-17 – Structural Determinants of Viral Protein-Nucleic Acid Interactions, P.I.: Bert L. Semler
  Cornell, C. T., Perera, R., Brunner, J. E., and Semler, B. L.; Strand-specific RNA synthesis determinants in the RNA-dependent RNA polymerase of poliovirus; J. Virol., 78:4397-4407, (2004).
   
• Grant 2001-17 – Structural Determinants of Viral Protein-Nucleic Acid Interactions, P.I.: Bert L. Semler
  Victoria, J. G., Lee, D. .J., McDougall, B. R., and Robinson, W. E., Jr.; Replication kinetics for divergent type 1 human immunodeficiency viruses using quantitative SYBR green 1 real-time polymerase chain reaction; AIDS Res. Human Retrovirus, 19:865-874, (2003).
   
• Grant 2001-17 – Structural Determinants of Viral Protein-Nucleic Acid Interactions, P.I.: Bert L. Semler
  Kuznetsov, Y. G., Victoria, J. G, Robinson, W. E., Jr., McPherson, A.; Atomic force microscopy investigation of human immunodeficiency virus (HIV) and HIV-infected lymphocytes; J. Virol., 77: 11896-11909, (2003).
   
• Grant 2001-17 – Structural Determinants of Viral Protein-Nucleic Acid Interactions, P.I.: Bert L. Semler
  King, P. J., Lee, D. J., Reinke, R. A., Victoria, J.G., Beale, K., and Robinson, W. E., Jr.; Human immunodeficiency virus type 1 integrase containing a glycine to serine mutation at position 140 is attenuated for catalysis and resistant to integrase inhibitors; Virology, 306:147-161, (2003).
   
• Grant 2001-16 – Nanomaterials through Bioengineering, P.I.: Geoffrey F. Strouse
  Sumerel, Jan L. and D.E. Morse; Biological advances in biosilicification; In: "Silicon biomineralization: Biology - Biochemistry - Molecular Biology - Biotechnology" (W.E. Müller, ed.), John Wiley and Sons, New York, , (2003). Book Chapter
   
• Grant 2001-16 – Nanomaterials through Bioengineering, P.I.: Geoffrey F. Strouse
  Weaver JC, Morse DE; Molecular biology of demosponge axial filaments and their roles in biosilicification; Microsc Res Tech, 62(4):356-67, (2003).
   
• Grant 2001-16 – Nanomaterials through Bioengineering, P.I.: Geoffrey F. Strouse
  Yun, C.S.; Khitrov, G.A.; Vergona, D.E.; Reich, N.O.; Strouse, G.F.; Enzymatic Modulation of DNA-Nanomaterial Constructs.; J. Amer. Chem. Soc., 124, 7644-7645, (2002).
   
• Grant 2001-16 – Nanomaterials through Bioengineering, P.I.: Geoffrey F. Strouse
  N. O. Reich, C.S. Yun, G.F. Strouse; Protein-Nucleic Complexes for Nanomaterial Assembly; , UC Case 2002-446, UC Disclosure filed June, (2002). UC Disclosure
   
• Grant 2001-16 – Nanomaterials through Bioengineering, P.I.: Geoffrey F. Strouse
  D.E. Morse and J.L. Sumerel; Structure-Directing Catalysis for Synthesis of Metal-Oxides, Metal Nitrides Metalloid-oxides, Metalloid Nitrides, Rare-Earth Oxides and Rare-Earth Nitrides for Electronic and Other Applications; , U.C. Disclosure filed June, (2002). UC Disclosure
   
• Grant 2001-15 – Discrete Nanoscale Transport in Biological Systems, P.I.: Samir Mitragotri
  Dinh AT, Theofanous T, Mitragotri S; A Model for Intracellular Trafficking of an Adenovirus; Biophys J, Jun 24; [Epub ahead of print], (2005).
   
• Grant 2001-15 – Discrete Nanoscale Transport in Biological Systems, P.I.: Samir Mitragotri
  Heithoff, D. M. and M. J. Mahan; Vibrio cholerae biofilms: stuck between a rock and a hard place.; J Bacteriol, 186(15):4835-7, (2004).
   
• Grant 2001-15 – Discrete Nanoscale Transport in Biological Systems, P.I.: Samir Mitragotri
  Badie G, Heithoff DM, Mahan MJ; LcrV synthesis is altered by DNA adenine methylase overproduction in Yersinia pseudotuberculosis and is required to confer immunity in vaccinated hosts; Infect Immun, 72(11):6707-10, (2004).
   
• Grant 2001-15 – Discrete Nanoscale Transport in Biological Systems, P.I.: Samir Mitragotri
  Pangarkar, C., T. Dinh, and S. Mitragotri; Mechanisms of Trafficking of Synthetic Gene Vectors in cells; Gene Therapy, , (2004). submitted
   
• Grant 2001-15 – Discrete Nanoscale Transport in Biological Systems, P.I.: Samir Mitragotri
  Chambers E, Mitragotri S; Prolonged circulation of large polymeric nanoparticles by non-covalent adsorption on erythrocytes; J Control Release, 100(1):111-9, (2004).
   
• Grant 2001-15 – Discrete Nanoscale Transport in Biological Systems, P.I.: Samir Mitragotri
  E. Kisak, B.Coldren, C. Boyer, C. Evans and J. Zasadzinski; The Vesosome - a Multicompartment Drug Delivery Vehicle; Current Medicinal Chemistry, 11, 199-220, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Flinders, J., DeFina, S. C., Brackett, D. M., Baugh, C., Wilson, C. & Dieckmann, T; Recognition of planar and nonplanar ligands in the malachite green-RNA aptamer complex; Chembiochem, 5:62-72, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Endrizzi, J.A., Kim, H., Anderson, P.M., Baldwin, E.P.; Crystal Structure of Escherichia coli Cytidine Triphosphate Synthetase, a Nucleotide-Regulated Glutamine Amidotransferase/ATP-Dependent Amidoligase Fusion Protein and Homologue of Anticancer and Antiparasitic Drug Targets.; Biochemistry, 43:6447-63, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Kim, I. H., Morisseau, C., Watanabe, T. and Hammock, B. D.; Design, synthesis, and biological activity of 1,3-disubstituted ureas as potent inhibitors of the soluble epoxide hydrolase of increased water solubility; J Med Chem, 47: 2110-2122, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Lee, H. J., Shan, G., Ahn, K. C., Park, E. K., Watanabe, T., Gee, S. J. and Hammock, B. D.; Development of an enzyme-linked immunosorbent assay for the pyrethroid cypermethrin.; J Agric Food Chem, 52: 1039-1043, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Zhao, X., Yamamoto, T., Newman, J. W., Kim, I. H., Watanabe, T., Hammock, B. D., Stewart, J., Pollock, J. S., Pollock, D. M. and Imig, J. D.; Soluble epoxide hydrolase inhibition protects the kidney from hypertension-induced damage; J Am Soc Nephrol, 15: 1244-1253, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu R, Hsieh C, Lam KS; New approaches to identifying drugs to inactivate oncogenes; Seminar in Cancer Biology, 14: 13-21, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Peters, L., Van Londen, K., Bergman, A., Bohonowych, J., Denison, M.S., van den Berg, M. and Sanderson, J.T.; Effects of polybrominated diphenyl ethers on basal and TCDD-induced ethoxyresorufin activity and cytochrome P450-1A1 expression in MCF-7, HepG2, and H4IIE cells; Toxicol Sci, 82(2):488-96, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Denison, M.S., Rogers, W.J., Bohonowych, J.E., Ziccardi, M.E. and Zhao, B.; Crude extracts from commercial and consumer products contain agonists for the Ah receptor and Ah receptor-dependent gene expression; , , (2004). in preparation
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Bohonowych, J.E. and Denison, M.S. Bohonowych, J.E. and Denison, M.S.; Binding of 2,3,7,8-tetrachlorodibenzo-p-dioxin to the hepatic cytosolic AhR from various species is essentially irreversible; , , (2004). in preparation
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Kavanagh, K. L., Elling, R. A. and Wilson, D. K.; Structure of Toxoplasma gondii LDH1: active-site differences from human lactate dehydrogenases and the structural basis for efficient APAD+ use; Biochemistry, 43: 879-889, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Lansdon, E. B., Fisher, A. J., and Segel, I. H.; Human PAPS Synthetase (Isoform 1; Brain): Kinetic Properties of the ATP Sulfurylase and APS Kinase Domains; Biochemistry, 43:4356-4365, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Flinders, J. & Dieckmann, T; The Solution Structure of the VS Ribozyme Active Site Loop Reveals a Dynamic "Hotspot"; J Mol Biol, 341(4):935-49, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Kratzer, R., Kavanagh, K. L., Wilson, D. K. and Nidetzky, B.; Studies of the enzymic mechanism of Candida tenuis xylose reductase (AKR 2B5): X-ray structure and catalytic reaction profile for the H113A mutant; Biochemistry, 43: 4944-4954, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu, W. and Toney, M. D.; Kinetic and thermodynamic analysis of the interaction of cations with dialkylglycine decarboxylase; Biochemistry, 43: 4998-5010, (2004).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Vyas, S., Weekley, A. J., Tenn, B. K., Flinders, J. C., Dieckmann, T. & Augustine, M. P.; Using sodium cation organization to study the phase behavior of bicelle solutions; Journal of Physical Chemistry, B 107:10956-10961, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Baldwin, E.P., Martin, S.S., Abel, J., Gelato, K.A., Kim, H., Schultz, P.G., and S.S. Santoro.; A specificity switch in selected Cre recombinase variants is mediated by macromolecular plasticity and water; Chem. Biol., 110:1085-93, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu R, Enstrom A, and Lam KS; Combinatorial peptide library methods for immunobiology research; Experimental Hematology, 31:11-30, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Lam KS, Liu R, Miyamoto S, Lehman A, Tuscano J; Applications of one-bead one-compound combinatorial libraries and chemical microarrays in signal transduction research; Accounts of Chemical Research, 36:370-377, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Marik J, Lau DH, Song A, Wang X, Liu R, and Lam KS; Magnetization of large polystyrene peptide beads for capturing and expanding cancer cells; Journal of magnetism and magnetic materials, 264:153-157, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu R, Marik J, Lam KS; Design, synthesis, screening, and decoding of encoded one-bead one-compound peptidomimetic and small molecule combinatorial libraries; Methods in Enzymology, 369:271-287, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Lam KS, Lehman A, Song A, Doan N, Enstrom A, Liu R; Synthesis and screening of "one-bead one-compound" combinatorial peptide libraries; Methods in Enzymology, 369: 298-322, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Kamath J, Liu R, Endstrom A, Qiang Lou, and Lam KS; Development and characterization of potent pseudosubstrate peptide inhibitors for p60c-src protein tyrosine kinase; The Journal of Peptide Research, 62: 260-268, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Wang X, Peng L, Liu R, Lam KS; Application of topologically segregated bifunctional beads to construct unique combinatorial bead libraries; In Peptide Revolution: Genomics, Proteomics & Therpaeutics (Proceedings of the Eighteenth American Peptide Symposium July 19-23, 2003), Chorev, M and Sawyer, T. (eds), , (2003). Presentation
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Kavanagh, K. L., Klimacek, M., Nidetzky, B. and Wilson, D. K.; Structure of xylose reductase bound to NAD+ and the basis for single and dual co-substrate specificity in family 2 aldo-keto reductases; Biochem J, 373: 319-326, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Klimacek, M., Kavanagh, K. L., Wilson, D. K. and Nidetzky, B.; On the role of Bronsted catalysis in Pseudomonas fluorescens mannitol 2-dehydrogenase; Biochem J, 375: 141-149, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Klimacek, M., Kavanagh, K. L., Wilson, D. K. and Nidetzky, B.; Pseudomonas fluorescens mannitol 2-dehydrogenase and the family of polyol-specific long-chain dehydrogenases/reductases: sequence-based classification and analysis of structure-function relationships; Chem Biol Interact, 143-144: 559-582, (2003).
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu R, Wang J, Marik J, Lam KS; An encoding method for one-bead one-compound beta-turn peptide and peptidomimetic libraries; In Peptide Revolution: Genomics, Proteomics & Therpaeutics (Proceedings of the Eighteenth American Peptide Symposium July 19-23, 2003), Chorev, M and Sawyer, T. (eds), , (2003). Presentation
   
• Grant 2001-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu R, Lam KS; Increase diversity of sone-bead one-compound combinatorial peptide libraries with side-chain derivatization; In Peptide Revolution: Genomics, Proteomics & Therpaeutics (Proceedings of the Eighteenth American Peptide Symposium July 19-23, 2003), Chorev, M and Sawyer, T. (eds), , (2003). Presentation
   
• Grant 2000-13 – Training Program in Biosensor Design, Delivery and Use, P.I.: Ehud Y. Isacoff
  Kratz, E., Dugas, J.C., and Ngai, J.; Odorant receptor gene regulation: implications from genomic organization.; Trends Genet., 18: 29-34, (2002).
   
• Grant 2000-13 – Training Program in Biosensor Design, Delivery and Use, P.I.: Ehud Y. Isacoff
  Guerrero G, Siegel MS, Roska B, Loots E, Isacoff EY; Tuning FlaSh: redesign of the dynamics, voltage range, and color of the genetically encoded optical sensor of membrane potential; Biophys J, 83(6):3607-18, (2002).
   
• Grant 2000-13 – Training Program in Biosensor Design, Delivery and Use, P.I.: Ehud Y. Isacoff
  Wang, J. and R. S. Zucker; Photolysis-induced suppression of inhibition in rat hippocampal CA1 pyramidal neurons; J. Physiol., 533: 757-763, (2001).
   
• Grant 2000-13 – Training Program in Biosensor Design, Delivery and Use, P.I.: Ehud Y. Isacoff
  Balya. D., Roska, B., Roska, T. and Werblin, F.S.; A CNN Model of a mammalian Retina; Int. N. Circuit Theory and Applications, , (2001). in press
   
• Grant 2000-13 – Training Program in Biosensor Design, Delivery and Use, P.I.: Ehud Y. Isacoff
  Roska, B. & Werblin, F.S.; Vertical Interactions Across Ten Parallel Stacked Representations in the Mammalian Retina; Nature, 410, 583-587, (2001).
   
• Grant 2000-13 – Training Program in Biosensor Design, Delivery and Use, P.I.: Ehud Y. Isacoff
  Werblin, F., Roska, B. & Balya, D.; Parallel processing in the mammalian retina: lateral and vertical interactions across stacked representations.; In Kolb, Ripps and Wu (Eds.) Progress in Brain Research, 131: 229-238, (2001).
   
• Grant 2000-13 – Training Program in Biosensor Design, Delivery and Use, P.I.: Ehud Y. Isacoff
  Parnas, D., Haghighi, P., Fetter, R.D., Kim, S.W. and Goodman, C.S.; Regulation of Postsynaptic Structure and Protein Localization by the Rho-Type Guanine Nucleotide Exchange Factor dPix; Neuron, 32: 415-424, (2001).
   
• Grant 2000-12 – Diagnostic Analysis of Microbial Communitites, P.I.: James Borneman
  Jampachaisri K, Valinsky L, Borneman J, Press SJ; Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses.; Bioinformatics, 21(14):3122-30, (2005).
   
• Grant 2000-12 – Diagnostic Analysis of Microbial Communitites, P.I.: James Borneman
  Jampachaisri K, Valinsky L, Borneman J, Press SJ; Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses; Bioinformatics, 21(14):3122-30, (2005).
   
• Grant 2000-12 – Diagnostic Analysis of Microbial Communitites, P.I.: James Borneman
  Figueroa A, Borneman J, Jiang T; Clustering binary fingerprint vectors with missing values for DNA array data analysis; J Comput Biol, 11(5):887-901, (2004).
   
• Grant 2000-12 – Diagnostic Analysis of Microbial Communitites, P.I.: James Borneman
  Yin, B., A. J. Scupham, J. A. Menge, J. Borneman; Shift in bacterial community composition associated with a Phytophthora cinnamomi epidemic: disease and suppressiveness; Plant and Soil, , (2003). submitted
   
• Grant 2000-12 – Diagnostic Analysis of Microbial Communitites, P.I.: James Borneman
  Yin B, Valinsky L, Gao X, Becker JO, Borneman J; Bacterial rRNA genes associated with soil suppressiveness against the plant-parasitic nematode Heterodera schachtii; Appl Environ Microbiol, 69(3):1573-80, (2003).
   
• Grant 2000-12 – Diagnostic Analysis of Microbial Communitites, P.I.: James Borneman
  Jampachaisri, Katechan, and Press, S. James; Statistical Modeling Using Singular Value Decomposition in Biology; presented at Annual Meeting Amer. Stat. Assoc., Aug. 2002, appear in Proceedings Bayesian Statistical Science Section Amer. Stat. Assoc., , (2002). Poster Presentation
   
• Grant 2000-12 – Diagnostic Analysis of Microbial Communitites, P.I.: James Borneman
  Smith, D. A., S. Alvey, C. Yang, D. D. Focht, D. E. Crowley; Kinetic Analysis of Atrazine Degradation by an Atrazine Degrading Bacterial Consortium; American Society for Microbiology, 102nd General Meeting, Salt Lake City, Utah, , (2002). Poster Presentation
   
• Grant 2000-12 – Diagnostic Analysis of Microbial Communitites, P.I.: James Borneman
  L. Valinsky, G. Della Vedova, A. J Scupham, S. Alvey, A. Figueroa, B. Yin, R. J. Hartin, M. Chrobak, D. E. Crowley, T. Jiang, and J. Borneman; Analysis of bacterial community composition using oligonucleotide fingerprinting of ribosomal RNA genes; Applied and Environmental Microbiology, 68:3243-3250, (2002).
   
• Grant 2000-12 – Diagnostic Analysis of Microbial Communitites, P.I.: James Borneman
  Valinsky L, Della Vedova G, Jiang T, Borneman J; Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition; Appl Environ Microbiol, 68(12):5999-6004, (2002).
   
• Grant 2000-12 – Diagnostic Analysis of Microbial Communitites, P.I.: James Borneman
  Borneman, J., M. Chrobak, G. Della Vedova, A. Figueroa, and T. Jiang; Probe selection algorithms with applications in the analysis of microbial communities; Bioinformatics, 17(Suppl. 1):S39-S48, (2001).
   
• Grant 2000-08 – Graduate Training in Signal Transduction in Biotechnology, P.I.: Laurence L. Brunton
  Gustafsson ÅB and Brunton LL; Attenuation of cyclic AMP accumulation in adult rat cardiac fibroblasts by IL-1b and nitric oxide: role of cGMP-stimulated phosphodisterase (PDE2); Am J Physiol Cell Physiol, 283: C463-C471, (2002).
   
• Grant 2000-08 – Graduate Training in Signal Transduction in Biotechnology, P.I.: Laurence L. Brunton
  Prowse CN, Lew J; Mechanism of activation of ERK2 by dual phosphorylation; J Biol Chem, 276(1):99-103, (2001).
   
• Grant 2000-08 – Graduate Training in Signal Transduction in Biotechnology, P.I.: Laurence L. Brunton
  Prowse CN, Deal MS, Lew J; The complete pathway for catalytic activation of the mitogen-activated protein kinase, ERK2; J Biol Chem, 276(44):40817-23, (2001).
   
• Grant 2000-08 – Graduate Training in Signal Transduction in Biotechnology, P.I.: Laurence L. Brunton
  Prowse CN, Hagopian JC, Cobb MH, Ahn NG, Lew J; Catalytic reaction pathway for the mitogen-activated protein kinase ERK2; Biochemistry, 39(45):14002, (2000).
   
• Grant 2000-08 – Graduate Training in Signal Transduction in Biotechnology, P.I.: Laurence L. Brunton
  Gustafsson ÅB and Brunton LL; Regulation of the Expression of Inducible Nitric Oxide Synthase in Adult Rat Cardiac Fibroblasts by IL-1b and b-Adrenergic Stimulation; Mol Pharmacol, 58:1470-1478, (2000).
   
• Grant 2000-08 – Graduate Training in Signal Transduction in Biotechnology, P.I.: Laurence L. Brunton
  Prowse CN, Hagopian JC, Cobb MH, Ahn NG, Lew J; Catalytic reaction pathway for the mitogen-activated protein kinase ERK2; Biochemistry, 39(20):6258-66, (2000).
   
• Grant 2000-08 – Graduate Training in Signal Transduction in Biotechnology, P.I.: Laurence L. Brunton
  Gustafsson ÅB and Brunton LL; Differential and Selective Inhibition of PKA and PKC in Intact Cells by Balanol Congeners; Mol. Pharmacol, 56: 377-382, (1999).
   
• Grant 2000-08 – Graduate Training in Signal Transduction in Biotechnology, P.I.: Laurence L. Brunton
  Gustafsson ÅB and Brunton LL; Interactions of the Cyclic AMP and Nitric Oxide Pathways in Cardiac Fibroblasts; ISHR Proceedings, , (). in press
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu W, Peterson PE, Carter RJ, Zhou X, Langston JA, Fisher AJ, Toney MD.; Crystal structures of unbound and aminooxyacetate-bound Escherichia coli gamma-aminobutyrate aminotransferase; Biochemistry, 43(34):10896-905, (2004).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Jeuken A, Keser BJ, Khan E, Brouwer A, Koeman J, Denison MS.; Activation of the Ah receptor by extracts of dietary herbal supplements, vegetables, and fruits.; J Agric Food Chem., 51(18):5478-87, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Wheelock, C. E., Wheelock, Å. M., Zhang, R., Stok, J. E., Morisseau, C., LeValley, S. E., Green, C., Hammock, B. D.; Evaluation of a-cyanoesters as fluorescent substrates for examining interindividual variation in general and pyrethroid-specific esterases in human liver microsomes; Analytical Biochemistry, 315:208-222, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Newman, J.W., Morisseau, C., Harris, T.R., and Hammock, B.D.; The soluble epoxide hydrolase encoded by EPXH2 is a bifunctional enzyme with novel lipid phosphate phosphatase activity; PNAS, 100(4):1558-1563, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Wilson, D. K., Kavanagh, K. L., Klimacek, M., Nidetzky, B.; The xylose reductase (AKR2B5) structure: homology and divergence from other aldo-keto reductases and opportunities for protein engineering; Chemico-Biological Interactions, 143:515-521, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Klimacek, M., Wuehrer, F., Kavanagh, K. L., Wilson, D. K., Nidetzky, B.; Altering dimer contacts in xylose reductase from Candida tenuis by site-directed mutagenesis: structural and functional properties of R180A mutant.; Chemico-Biological Interactions, 143:523-532, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Kavanagh, K. L., Klimacek, M., Nidetzky, B., Wilson, D. K.; Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase: evidence for a very divergent long-chain dehydrogenase family.; Chemico-Biological Interactions, 143: 551-558, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Klimacek, M., Kavanagh, K. L., Wilson, D. K. and Nidetzky, B.; Systematic classification of the family of long-chain D-mannitol dehydrogenases.; Chemico-Biological Interactions, 143: 559-582, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Franz, A. H., Liu, R., Song A., Lam, K. S., Lebrilla, C. B.; High-Throughput One-Bead-One-Compound Approach to Peptide-Encoded Combinatorial Libraries: MALDI-MS Analysis of Single TentaGel Beads.; J. Comb. Chem., 5: 125-137, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu, R., Marik, J., Lam, K. S.; Design, synthesis, screening, and decoding of encoded one-bead one-compound peptidomimetic and small molecule combinatorial libraries.; Methods in Enzymology, 369:271-87, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Lam, K. S., Lehman, A. L., Song, A., Doan, N., Enstrom, A. M., Liu, R.; Synthesis and screening of "one-bead one-compound" combinatorial peptide libraries.; Methods in Enzymology, 369:298-322, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Kamita, S.G., Hinton, A.C., Wheelock, C.E., Wogulis, M.D., Wilson, D.K., Wolf, N.M., Hock, B., and Hammock, B.D.; Juvenile hormone (JH) esterase: why are you so JH specific?; Insect Biochem Mol Biol., 33(12):1261-73, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Kavanagh, K. L., Klimacek, M., Nidetzky, B., Wilson, D. K.; Structure of xylose reductase bound to NAD+ and the basis for single and dual co-substrate specificity in family 2 aldo-keto reductases.; Biochem J., 15;373(Pt 2):319-26, (2003).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu, R., Lam, K. S.; Increase diversity of one-bead one-compound combinatorial peptide libraries with side chain derivatization.; , , (2003). Manuscript in preparation
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu, R., Wang, X., Marik, J. Lam, K. S.; A general approach to synthesize peptide libraries with non-sequenceable building blocks in certain positions and N-terminally blocked peptidomimetic libraries.; J. Comb. Chem., , (2003). Manuscript in preparation
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu, R., Marik, J., and Lam, K. S.; A novel peptide-based encoding system for "one-bead one-compound" peptidomimetic and small molecule combinatorial libraries; J. Am. Chem. Soc., 124:7678-7680, (2002).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Lansdon, E. B., Segel, I. H., and Fisher, A. J.; Ligand-Induced Structural Changes in Adenosine 5´-Phosphosulfate Kinase from Penicillium chrysogenum; Biochemistry, 41:13672-13680, (2002).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Liu, W., Rogers, C. J., Fisher, A. J., Toney, M. D.; Aminophosphonate inhibitors of dialkylglycine decarboxylase: Structural basis for slow, tight binding inhibition; Biochemistry, 41:12320-12328, (2002).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Denison, M. S., Pandini, A., Nagy, S. R., Baldwin, E. P., and Bonati, L.; Ligand Binding and Activation of the Ah Receptor; Chemico Biological Interactions, 141:3-24, (2002).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Wheelock, C. E., Colvin, M. E., Uemura, I., Olmstead, M. M., Sanborn, J. R., Nakagawa, Y., Jones, A. D, Hammock, B. D.; Use of ab initio calculations to predict the biological potency of carboxylesterase inhibitors; Journal of Medicinal Chemistry, 45(25):5576-5593, (2002).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Kavanagh, K. L., Klimacek, M., Nidetzky, B., Wilson, D. K.; The structure of apo and holo forms of xylose reductase, a dimeric aldo-keto reductase from Candida tenuis; Biochemistry, 41:8785-8795, (2002).
   
• Grant 2000-07 – Training Program in Structure-Assisted Drug Discovery, P.I.: Andrew Fisher
  Kavanagh, K. L., Klimacek, M., Nidetzky, B., Wilson, D. K.; Crystal Structure of Pseudomonas fluorescens Mannitol 2-Dehydrogenase Binary and Ternary Complexes: Specificity and catalytic mechanism; J. Biol. Chem., 277: 43433-43442, (2002).
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  S. Brown, J. L. Chang, Wolfgang Sadee, and Patricia C. Babbitt; A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes.; AAPS PharmSci, 5(1):E1, (2003).
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  F. Horn, G. Vriend and F. E. Cohen; Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems; Nucleic Acids Res, 29: 346-349, (2001).
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  J.S. Cantwell, W.R Novak, P-F. Wang, M.J. McLeish, G.L. Kenyon, and Babbitt, P.C.; Mutagenesis of two acidic active site residues in human muscle creatine kinase: Implications for the catalytic mechanism; Biochem, 40:3056-3061, (2001).
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  D.R Banatao, C.C. Huang, P.C. Babbitt, RB. Altman, RB. and T.E. Klein; ViewFEATURE: Integrated FEATURE analysis and visualization; R B. World Interscience, Singapore, Pacific Symposium on Biocomputing (Eds. RB. Altman, T.E. Klein, L. Hunter, A.K. Dunker) Vol. 5, (2001). Poster Presentation
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  Zhang. H., Lou, S.L.. Sickles, E.A.. Huang, H.K.; Building an intranet digital mammography case library; Proc. Med. Imaging, , (2000).
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  F. Horn, M. Mokrane, J. Weare, and G. Vriend; G protein-coupled receptors, or the power of data; Genomics and Proteomics (Ed. S. Suhai), 191-215, (2000). Book Chapter
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  F. Horn, E. van der Wenden, L. Oliveira A.P. Dzermann and G. Vriend; Receptors coupling to G proteins: Is there a signal behind the sequence?; Proteins: Structure, Function, and Genetics, 41:448-459, (2000).
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  Walther. D., Cohen, F.E., and Doniach, S.; Reconstruction of low resolution three-dimensional density maps form one-dimensional small angle X-ray scattering data for biomolecules in solution; J. of Applied Crystall., , (1999). submitted
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  Novak. C. F., Young, M., Ferrin, T. E. and Babbitt, P. C.; Towards automated generation of protein superfamily relationships; , , (1999). Poster presentation for the Pacific Symposium on Biocomputing. Mauna Lani, HI. World Scientific
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  Yan. O. and Sadee. W.; HTD: a relational database for pharmacogenetics of human membrane transporters; , , (1999). Poster presentation at Second AAPS Frontier Symposium
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  Yan. O. and Hunt, C.A.; An informatics approach to study drug resistance in breast cancer therapy; , , (1999). Poster presentation at Eighth annual Bioinformatics and Genome Research
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  Zhang. H., Lou. S-L.. Hoogstrate. D.R. Sickles, E.A.. Hunga, H.K.. Wong, A.W.; DICOM image transmission for real-time telemanagement of fullfield digital mamography (FFDM); Proc. Med. Imaging, 3662,225-230, (1999).
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  Walther. D. and Cohen, F.E.; Helix-helix packing angle preferences for finite helix axes; Acta Crystal, 55,506-517, (1998).
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  Han, H.-K, de Vrueh, R.L.A., Rhie, J.K., Covitz. M.Y., Smith, C., Lee, D.M., Oh, W., Sadee, W., and Amidon, G.L.; 5'-Amino acid esters of antiviral nucleosides, acyclovier and AXT, are absorbed by the intestinal PEPT1 peptide transporter; Pharm. Res., 15. 1154-1159, (1998).
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  Covitz. M.Y., Amidon, G.L., and Sadee, W.; Membrane topology of the human dipeptide transporter. hPepT1, determined by epitope insertions.; Biochem., 37, 15214-15221, (1998).
   
• Grant 2000-04 – Training in Bioinformatics and Biocomputing, P.I.: Patricia C. Babbitt
  Gonzalez. D.E., Covitz. M.Y., Sadee, W., and Mrsny. Rj.; An oligopeptide transporter is expressed at high levels in the pancreatice carcinoma cell lines AsPc-1 and Capan-2.; Cancer Res., 58. 519-525, (1998).
   
• Grant 1999-14 – A Biotechnology Training Program on Developing Miniaturized Hybrid Biomaterials, P.I.: Cyrus Safinya
  A. W. C. Lau, D. B. Lukatsky, P. Pincus, S. A. Safran; Charge Fluctuations and Counterion Condensation; Phys Rev E Stat Nonlin Soft Matter Phys., 65(5 Pt 1):051502, (2002).
   
• Grant 1999-14 – A Biotechnology Training Program on Developing Miniaturized Hybrid Biomaterials, P.I.: Cyrus Safinya
  T. Pfohl, J. H. Kim, M. Yasa, H. P. Miller, G. C. L. Wong, F. Bringezu, Z. Wen, L. Wilson, Y. Li, M. W. Kim, and C. R. Safinya; Controlled Modification of Microstructured Silicon Surfaces for Confinement of Biological Macromolecules and Liquid Crystals; Langmuir, 17, 5343-5351, (2001).
   
• Grant 1999-14 – A Biotechnology Training Program on Developing Miniaturized Hybrid Biomaterials, P.I.: Cyrus Safinya
  C. R. Safinya; Structures of Lipid-DNA Complexes: Supramolecular Assembly and Gene Delivery; Current Opinion in Structural Biology, 11 (4) 440-448, (2001).
   
• Grant 1999-14 – A Biotechnology Training Program on Developing Miniaturized Hybrid Biomaterials, P.I.: Cyrus Safinya
  Cheng, J.; Deming, T. J.; Controlled Polymerization of b-Lactams Using Metal-Amido Complexes. Synthesis of Block Copoly(b-Peptides); J. Am. Chem. Soc., 123, 9457-9458, (2001).
   
• Grant 1999-14 – A Biotechnology Training Program on Developing Miniaturized Hybrid Biomaterials, P.I.: Cyrus Safinya
  Cheng, J.; Deming, T. J.; Synthesis and Conformational Analysis of Optically Active Poly(b-peptides); Macromolecules, 34, 5169-5174, (2001).
   
• Grant 1999-14 – A Biotechnology Training Program on Developing Miniaturized Hybrid Biomaterials, P.I.: Cyrus Safinya
  G. C. L. Wong, Jay X. Tang, Alison Lin, Youli Li, P. A. Janmey, C. R. Safinya; Hierarchical Self-Assembly of F-Actin and Cationic Lipid Complexes: Stacked Three-Layer Tubule Networks; Science, 288 2035-2039, (2000). This publication has been further highlighted in Chemical & Engineering News [http://pubs.acs.org/cen, "News of the Week", June 19, 2000]
   
• Grant 1999-14 – A Biotechnology Training Program on Developing Miniaturized Hybrid Biomaterials, P.I.: Cyrus Safinya
  Alison J. Lin , N. L. Slack , A. Ahmad, I. Koltover, C. X. George, C. E. Samuel, C. R. Safinya; Structure-Function Studies of Lipid-DNA Nonviral Gene Delivery Systems; Journal of Drug Targeting, 8 (1), pp.13-27, (2000).
   
• Grant 1999-14 – A Biotechnology Training Program on Developing Miniaturized Hybrid Biomaterials, P.I.: Cyrus Safinya
  Deming, T. J.; Living Polymerization of a-Amino Acid-N-Carboxyanhydrides; J. Polym. Sci. Polym. Chem. Ed., 38, 3011-3018, (2000).
   
• Grant 1999-14 – A Biotechnology Training Program on Developing Miniaturized Hybrid Biomaterials, P.I.: Cyrus Safinya
  A. W. C. Lau, Dov Levine, P. Pincus; Novel Electrostatic Attraction from Plasmon Fluctuations; PRL, 84, 4116-4119, (2000).
   
• Grant 1999-14 – A Biotechnology Training Program on Developing Miniaturized Hybrid Biomaterials, P.I.: Cyrus Safinya
  W. C. Lau, P. Pincus; Bonding of oppositely charged membranes and membrane reorganization; E. Phys. J., B, 10, 175-180, (1999).
   
• Grant 1997-15 – Characterization of the Physical and Functional Properties of Plant Dehydration-Associated Proteins, P.I.: Timothy J. Close
  Koag MC, Fenton RD, Wilkens S, Close TJ; The binding of maize DHN1 to lipid vesicles. Gain of structure and lipid specificity.; Plant Physiol., 131:309-316, (2003).