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New Jersey Research Center for Environmental Bioinformatics and Computational Toxicology

Grant Number R832721


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  • Book Chapter (4)
  • Journal Article (20)
    • Reference Type Citation Progress Report Year Document Sources
    Book Chapter Floudas CA, Fung HK. Mathematical modeling and optimization methods for de novo protein design. In: Rigoutsos I, Stephanopoulos G, eds. Systems Biology, Volume II: Networks, Models, and Applications. Chapter 2. USA: Oxford University Press, 2006, pp. 42-66. R832721 (2007)
    R832721C005 (2006)
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    • Book Chapter Isukapalli SS, Roy A. General principles of programming (computer and statistical). In: Ette EI, Williams PJ, eds. Pharmacometrics: The Science of Quantitative Pharmacology. Chapter 2. Wiley, 2007, pp. 25-52. R832721 (2007)
    R832721C001 (2006)
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    • Book Chapter Isukapalli SS, Roy A, Georgopoulos PG. Physiologically based pharmacokinetic modeling: inhalation, ingestion, and dermal absorption. In: Ette EI, Williams PJ, eds. Pharmacometrics: The Science of Quantitative Pharmacology. Chapter 43. Wiley, 2007, pp. 1069-1106. R832721 (2007)
    R832721C001 (2006)
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    • Book Chapter Welsh WJ, Tong W, Georgopoulos PG. Toxicoinformatics: an introduction. In: Ekins S, ed. Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals. Chapter 6. Wiley, 2007, pp. 151-181. R832721 (2007)
    R832721C001 (2006)
    R832721C004 (2006)
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    • Journal Article Androulakis IP, Yang E, Almon RR. Analysis of time-series gene expression data: methods, challenges, and opportunities. Annual Review of Biomedical Engineering 2007;9:205-228. R832721 (2007)
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    • Journal Article Davis E, Ierapetritou M. A kriging method for the solution of nonlinear programs with black-box functions. AIChE Journal 2007;53(8):2001-2012. R832721 (2007)
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    • Journal Article DiMaggio Jr PA, Floudas CA. A mixed-integer optimization framework for de novo peptide identification. AIChE Journal 2007;53(1):160-173. R832721 (2007)
    R832721C005 (2006)
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    • Journal Article DiMaggio Jr PA, Floudas CA. De novo peptide identification via tandem mass spectrometry and integer linear optimization. Analytical Chemistry 2007;79(4):1433-1446. R832721 (2007)
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    • Journal Article Ekins S, Chang C, Mani S, Krasowski MD, Reschly EJ, Iyer M, Kholodovych V, Ai N, Welsh WJ, Sinz M, Swaan PW, Patel R, Bachmann K. Human pregnane X receptor antagonists and agonists define molecular requirements for different binding sites. Molecular Pharmacology 2007;72(3):592-603. R832721 (2007)
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    • Journal Article Floudas CA. Computational methods in protein structure prediction. Biotechnology and Bioengineering 2007;97(2):207-213. R832721 (2007)
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    • Journal Article Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. An indirect response model of endotoxin-induced systemic inflammation. Journal of Critical Care 2007;22(4):337-338. R832721 (2007)
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    • Journal Article Fung HK, Welsh WJ, Floudas CA. Computational de novo peptide and protein design: rigid templates versus flexible templates. Industrial & Engineering Chemistry Research 2008;47(4):993-1001. R832721 (2007)
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    • Journal Article Georgopoulos PG. A multiscale approach for assessing the interactions of environmental and biological systems in a holistic health risk assessment framework. Water, Air, & Soil Pollution: Focus 2008;8(1):1567-7230. R832721 (2007)
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    • Journal Article Jiao Y, Su M, Chen M, Jia W, Chou Y, Huang Z, Yang N, Tong W. LC/ESI-MS method for the determination of trimetazidine in human plasma: application to a bioequivalence study on Chinese volunteers. Journal of Pharmaceutical and Biomedical Analysis 2007;43(5):1804-1807. R832721 (2007)
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    • Journal Article Jornsten R, Ouyang M, Wang H-Y. A meta-data based method for DNA microarray imputation. BMC Bioinformatics 2007;8:109. R832721 (2007)
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    • Journal Article McAllister SR, Mickus BE, Klepeis JL, Floudas CA. Novel approach for α-helical topology prediction in globular proteins: generation of interhelical restraints. Proteins: Structure, Function, and Bioinformatics 2006;65(4):930-952. R832721 (2007)
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    • Journal Article Rajgaria R, McAllister SR, Floudas CA. A novel high resolution Cα—Cα distance dependent force field based on a high quality decoy set. Proteins: Structure, Function, and Bioinformatics 2006;65(3):726-741. R832721 (2007)
    R832721C005 (2006)
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    • Journal Article Wang CY, Ai N, Arora S, Erenrich E, Nagarajan K, Zauhar R, Young D, Welsh WJ. Identification of previously unrecognized antiestrogenic chemicals using a novel virtual screening approach. Chemical Research in Toxicology 2006;19(12):1595-1601. R832721C004 (2006)
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    Journal Article Yang E, Foteinou PT, King KR, Yarmush ML, Androulakis IP. A novel non-overlapping bi-clustering algorithm for network generation using living cell array data. Bioinformatics 2007;23(17):2306-2313. R832721 (2007)
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    • Journal Article Yang E, Maguire T, Yarmush ML, Berthiaume F, Androulakis IP. Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. BMC Bioinformatics 2007;8:10. R832721 (2007)
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    • Journal Article Yang E, Simcha D, Almon RR, Dubois DC, Jusko WJ, Androulakis IP. Context specific transcription factor prediction. Annals of Biomedical Engineering 2007;35(6):1053-1067. R832721 (2007)
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    • Journal Article Yang E, Almon RR, DuBois DC, Jusko WJ, Androulakis IP. Extracting global system dynamics of corticosteroid genomic effects in rat liver. Journal of Pharmacology and Experimental Therapeutics 2008;324(3):1243-1254. R832721 (2007)
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    • Journal Article Yang E, Maguire TJ, Yarmush ML, Berthiaume F, Androulakis IP. Identification of regulatory mechanisms of the hepatic response to thermal injury. Computers & Chemical Engineering 2008;32(1-2):356-369. R832721 (2007)
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    • Journal Article Yang E, Maguire T, Yarmush ML, Androulakis IP. Informative gene selection and design of regulatory networks using integer optimization. Computers & Chemical Engineering 2008;32(4-5):633-649. R832721 (2007)
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