Grantee Research Project Results
Publications Details for Grant Number R832721
Environmental Bioinformatics and Computational Toxicology Center
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Computational Toxicology: Environmental Bioinformatics Research Center (2004)
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Reference Type | Citation | Progress Report Year | Document Sources |
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Abstract | Aubramani A, Floutas C. Structure Prediction of Loops with Fixed and Flexible Stems. JOURNAL OF PHYSICAL CHEMISTRY B 2012;116(23):6670-6682 |
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Abstract | Baliban R, Sakellari D, Li Z, DiMaggio P, Garcia B, Floudas C. Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples. JOURNAL OF CLINICAL PERIODONTOLOGY 2012;39(3):203-212 |
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Abstract | Baliban R, DiMaggio P, Plazas-Mayorca M, Garcia B, Floudas C. PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization. JOURNAL OF PROTEOME RESEARCH 2012;11(9):4615-4629 |
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Abstract | Bellows M, Floudas C. Computational Methods for De novo Protein Design and its Applications to the Human Immunodeficiency Virus 1, Purine Nucleoside Phosphorylase, Ubiquitin Specific Protease 7, and Histone Demethylases. CURRENT DRUG TARGETS 2010;11(3):264-278 |
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Abstract | Bellows-Peterson M, Fung H, Floudas C, Kieslich C, Zhang L, Morikis D, Wareham K, Monk P, Hawksworth O, Woodruff T. De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation. JOURNAL OF MEDICINAL CHEMISTRY 2012;55(9):4159-4168 |
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Abstract | Euling SY, White L, Ovacik M, Makris S, Sen B, Androulakis IP, Hester S, Gaido KW, Kim AS, Benson R, Wilson VS, Keshava C, Keshava N, Foster PM, Gray Jr LE, Thompson C, Chiu W. An approach to using genomic data in risk assessment: dibutyl phthalate (DBP) case study. Reproductive Toxicology 2009;28(2):119. |
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Abstract | Foteinou P, Calvano S, Lowry S, Androulakis I. An indirect response model of endotoxin-induced systemic inflammation. Journal of Critical Care 2007;22(4):337-338. |
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Abstract | Lopez de Victoria A, Gorham R, Bellows-Peterson M, Ling J, Lo D, Floudas C, Monrikis D. A New Generation of Potent Complement Inhibitors of the Compstatin Family. CHEMICAL BIOLOGY & DRUG DESIGN 2011;77(6):431-440 |
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Abstract | Orman M, Aria K, Yarmh M, Androulakis I, Berthiaume F, Ierapetritou M. Metabolic Flux Determination in Perfed Livers by Mass Balance Analysis: Effect of Fasting. BIOTECHNOLOGY AND BIOENGINEERING 2010;107(5):825-835 |
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Abstract | Orman M, Berthiaume F, Androulakis I, Ierapetritou M. Pathway analysis of liver metabolism under stressed condition. JOURNAL OF THEORETICAL BIOLOGY 2011;272(1):131-140 |
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Abstract | Rajgaria R, McAllister S, Floudas C. TTowards accurate residue–residue hydrophobic contact prediction for α helical proteins via integer linear optimization. PROTEINS 2008;74(4):929-947. |
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Abstract | Smadbeck J, Peterson M, Kjoury H, Taylor M, Floudas C. Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules. JOVE-JOURNAL OF VISUALIZED EXPERIMENTS 2013;(77):e50476 |
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Abstract | Subramani A, Wei Y, Floudas C. ASTRO-FOLD 2.0: An enhanced framework for protein structure prediction. AICHE JOURNAL 2012;58(5):1619-1637 |
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Abstract | Wei Y, Floudas C. Enhanced inter-helical residue contact prediction in transmembrane proteins. CHEMICAL ENGINEERING SCIENCE 2011;66(19):4356-4369. |
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Book Chapter | Bellows ML, Fung HK, Floudas CA. Recent advances in de novo protein design. In: Pistikopoulos EM, Georgiadis MC, Dua V, Adjiman CS, Galindo A., eds. Process Systems Engineering: Molecular Systems Engineering, Volume 6. Weinheim, Germany: Wiley VCH Verlag GmbH & Co., 2010, Chapter 7, pp. 207-232. |
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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. New York, NY: Oxford University Press, 2006, Chapter 2, pp. 42-66. |
R832721 (2007) R832721C005 (2006) R832721C005 (2007) |
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Book Chapter | Floudas CA, Fung HK, Morikis D, Taylor MS, Zhang L. Overcoming the key challenges in de novo protein design: enhancing computational efficiency and incorporating true backbone flexibility. In: Mondaini RP, Pardalos PM, eds. Mathematical Modelling of Biosystems. Berlin, Germany: Springer-Verlag Berlin-Heidelberg, 2008, pp.133-183. |
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Book Chapter | Georgopoulos PG, Isukapalli SS, Krishnan K. Modeling exposures to chemicals from multiple sources and routes. In: Krishnan K, Andersen ME, eds. Quantitative Modeling in Toxicology. Chichester, UK: John Wiley & Sons, Ltd., 2010, Chapter 16, pp. 315-351. |
R832721 (2008) R832721 (Final) R834547 (2010) R834547 (Final) |
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Book Chapter | Georgopoulos PG, Isukapalli S, Androulakis IP, Ierapetritou MG, Welsh WJ. Multiscale integration of toxicokinetic and toxicodynamic processes: from cell and tissue to organ and “whole body” models. In: Casciano DA, Sahu, SC, eds. Handbook of Systems Toxicology, Volume 2. Hoboken, NJ: John Wiley & Sons, 2011, Chapter 38, pp. 619-668. |
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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. Hoboken, NJ: Wiley, 2007, Chapter 2, pp. 25-52. |
R832721 (2007) R832721C001 (2006) R832721C001 (2007) |
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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. Hoboken, NJ: Wiley, 2007, Chapter 43, pp. 1069-1106. |
R832721 (2007) R832721C001 (2006) R832721C001 (2007) |
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Book Chapter | Isukapalli SS, Spendiff M, Georgopoulos PG, Krishnan K. Uncertainty, variability, and sensitivity analyses in simulation models. In: Krishnan K, Andersen ME, eds. Quantitative Modeling in Toxicology. Chichester, West Sussex, UK: John Wiley & Sons, Ltd., 2010, Chapter 20, pp. 429-458. |
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Book Chapter | Krishnan K, Isukapalli S, Boyd J. Evaluation of toxicological interactions for the dose-response assessment of chemical mixtures. In: Ballantyne B, Marrs TC, Syversen T, eds. General and Applied Toxicology, Volume 1, 3rd Edition. Chichester, UK: John Wiley & Sons, Ltd., 2009, Chapter 9, pp. 211-228. |
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Book Chapter | Krishnan K, Sasso A, Georgopoulos P. Pharmacokinetic mechanisms of interactions in chemical mixtures. In: Mumtaz M, ed. Principles and Practice of Mixtures Toxicology. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co., 2010, Chapter 9, pp. 235-252. |
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Book Chapter | Scheff JD, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Dynamic models of disease progression: toward a multiscale model of systemic inflammation in humans. In: Georgiadis MC, Banga JR, Pistikopoulos EN, eds. Process Systems Engineering, Volume 7: Dynamics Process Modeling. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co., 2010, Chapter 10, pp. 321-368. |
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Book Chapter | Tan MP, Floudas CA. Gene clustering: a novel decomposition-based clustering approach: global optimum search with enhanced positioning. In: Floudas CA, Pardalos PM, eds. Encyclopedia of Optimization, Second edition. New York, NY: Springer, 2009, pp.1134-1145. |
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Book Chapter | Vallero DA, Isukapalli S, Zartarian VG, McCurdy TR, McKone T, Georgopoulos PG, Dary CC. Modeling and predicting pesticide exposures. In: Krieger R, ed. Hayes’ Handbook of Pesticide Toxicology, Third Edition. New York, NY: Elsevier Science, 2010, Chapter 44, pp. 995-1020. |
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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) R832721C004 (2007) |
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Conference Proceedings | Georgopoulos PG. Mechanistic studies of environmental causes of human disease:a bionetwork dynamics modeling approach. In:PRE9:Proceedings of the Protection and Restoration of the Environment IX Conference, Kefalonia, Greece, June 29-July 3, 2008, p. 8. |
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Conference Proceedings | Georgopoulos PG, Isukapalli SS. A unified multiscale field/network/agent based modeling framework for human and ecological health risk analysis. In: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Minneapolis, MN, September 2-6, 2009, pp. 6420-6423. |
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Conference Proceedings | Isukapalli SS, Price K, Georgopoulos PG, Krishnan K. A physiologically-based algorithm for predicting internal dose of inhaled toluene: applications for high dose to low dose and rodent to human extrapolations. In: Rajaei H, Wainer GA, Chinni MJ, eds. Proceedings of the 2008 Spring Simulation Multiconference-SpringSim 2008, The Society for Computer Simulation International, San Diego, CA, April 14-17, 2008, pp. 583-588. |
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Conference Proceedings | McAllister SR, Floudas CA. Alpha-helical topology and tertiary structure prediction in globular proteins. In: Proceedings of the 46th IEEE Conference on Decision and Control, New Orleans, LA, December 12-14, 2007, pp. 4551-4556, doi:10.1109/CDC.2007.4434759. |
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Conference Proceedings | Miller M, Feng X-J, Li G, Rabitz H. Nonlinear bionetwork structure inference using the random sampling-high dimensional model representation (RS-HDMR) algorithm. In: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Minneapolis, MN, September 3-6, 2009, pp. 6412-6415. |
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Journal Article | Ai N, Krasowski MD, Welsh WJ, Ekins S. Understanding nuclear receptors using computational methods. Drug Discovery Today 2009;14(9-10):486-494. |
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Journal Article | Almon RR, Yang E, Lai W, Androulakis IP, Ghimbovschi S, Hoffman EP, Jusko WJ, DuBois DC. Relationships between circadian rhythms and modulation of gene expression by glucocorticoids in skeletal muscle. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 2008;295(4):R1031-R1047. |
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Journal Article | Almon RR, Yang E, Lai W, Androulakis IP, DuBois DC, Jusko WJ. Circadian variations in rat liver gene expression: relationships to drug actions. Journal of Pharmacology and Experimental Therapeutics 2008;326(3):700-716. |
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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. |
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Journal Article | Arora S, Wang X, Keenan S, Andaya C, Zhang Q, Peng Y, Welsh W. Novel Microtubule Polymerization Inhibitor with Potent Antiproliferative and Antitumor Activity. CANCER RESEARCH 2009;69(5):1910-1915 |
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Journal Article | Baliban RC, DiMaggio PA, Plazas-Mayorca MD, Young NL, Garcia BA, Floudas CA. A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry. Molecular and Cellular Proteomics 2010;9(5):764-779. |
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Journal Article | Bellows ML, Fung HK, Taylor MS, Floudas CA, Lopez de Victoria A, Morikis D. New compstatin variants through two de novo protein design frameworks. Biophysical Journal 2010;98(10):2337-2346. |
R832721 (Final) |
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Journal Article | Bellows M, Floutas C. Computational Methods for De novo Protein Design and its Applications to the Human Immunodeficiency Vir 1, Purine Nucleoside Phosphorylase, Ubiquitin Specific Protease 7, and Histone Demethylases. CURRENT DRUG TARGETS 2010;11(3):264-278. |
R832721 (Final) |
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Journal Article | Brell G, Li G, Rabitz H. An efficient algorithm to accelerate the discovery of complex material formulations. The Journal of Chemical Physics 2010;132(17):174103-174110. |
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Journal Article | Chekmarev DS, Kholodovych V, Balakin KV, Ivanenkov Y, Ekins S, Welsh WJ. Shape signatures: new descriptors for predicting cardiotoxicity in silico. Chemical Research in Toxicology 2008;21(6):1304-1314. |
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Journal Article | Chekmarev D, Kholodovych V, Kortagere S, Welsh WJ, Ekins S. Predicting inhibitors of acetylcholinesterase by regression and classification machine learning approaches with combinations of molecular descriptors. Pharmaceutical Research 2009;26(9):2216-2224. |
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Journal Article | Chen M, Martin J, Fang H, Isukapalli S, Georgopoulos PG, Welsh WJ, Tong W. ebTrack: an environmental bioinformatics system built upon ArrayTrackTM. BMC Proceedings 2009;3(Suppl 2):S5. |
R832721 (2008) |
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Journal Article | Cohen Hubal EA, Richard A, Aylward L, Edwards S, Gallagher J, Goldsmith M-R, Isukapalli S, Tornero-Velez R, Weber E, Kavlock R. Advancing exposure characterization for chemical evaluation and risk assessment. Journal of Toxicology and Environmental Health-Part B-Critical Reviews 2010;13(2-4):299-313. |
R832721 (Final) |
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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. |
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Journal Article | Davis E, Ierapetritou M. A kriging based method for the solution of mixed-integer nonlinear programs containing black-box functions. JOURNAL OF GLOBAL OPTIMIZATION 2009;43(2-3):191-205. |
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Journal Article | Davis E, Ierapetritou M. A centroid-based sampling strategy for kriging global modeling and optimization. AIChE Journal 2010;56(1):220-240. |
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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 | 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, Lu B, Yates III JR. A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry. Journal of Proteome Research 2008;7(4):1584-1593. |
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Journal Article | DiMaggio Jr PA, McAllister SR, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HA. Optimal methods for re-ordering data matrices in systems biology and drug discovery applications. Biophysical Reviews and Letters 2008;3(1-2):19-42. |
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Journal Article | DiMaggio Jr PA, McAllister SR, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HA. Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. BMC Bioinformatics 2008;9:458-473. |
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Journal Article | DiMaggio Jr. PA, McAllister SR, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HA. Enhancing molecular discovery using descriptor-free rearrangement clustering techniques for sparse data sets. AIChE Journal 2010;56(2):405-418. |
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Journal Article | DiMaggio Jr PA, McAllister SR, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HA. A network flow model for biclustering via optimal re-ordering of data matrices. Journal of Global Optimization 2010;47(3):343-354. |
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Journal Article | DiMaggio Jr. PA, Subramani A, Judson RS, Floudas CA. A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix re-ordering and logistic regression. Toxicological Sciences 2010;118(1):251-265. |
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Journal Article | DiMaggio Jr. PA, Young NL, Baliban RC, Garcia BA, Floudas CA. A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry. Molecular and Cellular Proteomics 2009;8(11):2527-2543. |
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Journal Article | Dong X, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Agent-based modeling of endotoxin-induced acute inflammatory response in human blood leukocytes. PLoS One 2010;5(2):e9249. |
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Journal Article | Efstathiou C, Isukapalli S, Georgopoulos P. A mechanistic modeling system for estimating large scale emissions and transport of pollen and co-allergens. Atmospheric Environment 2011;45(13):2260-2276. |
R832721 (Final) R834547 (2010) R834547 (Final) |
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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. |
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Journal Article | Ekins S, Kholodovych V, Ai N, Sinz M, Gal J, Gera L, Welsh WJ, Bachmann K, Mani S. Computational discovery of novel low micromolar human pregnane X receptor antagonists. Molecular Pharmacology 2008;74(3):662-672. |
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Journal Article | Feng X, Sanchis J, Reetz MT, Rabitz H. Enhancing the efficiency of directed evolution in focused enzyme libraries by the adaptive substituent reordering algorithm. Chemistry-A European Journal 2012;18(18):5646-5654. |
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Journal Article | Floudas CA. Computational methods in protein structure prediction. Biotechnology and Bioengineering 2007;97(2):207-213. |
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Journal Article | Foteinou PT, Yang E, Androulakis IP. Networks, biology and systems engineering: a case study in inflammation. Computers & Chemical Engineering 2009;33(12):2028-2041. |
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Journal Article | Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Translational potential of systems-based models of inflammation. Clinical and Translational Science 2009;2(1):85-89. |
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Journal Article | Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Modeling endotoxin-induced systemic inflammation using an indirect response approach. Mathematical Biosciences 2009;217(1):27-42. |
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Journal Article | Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. In silico simulation of corticosteroids effect on an NFkB-dependent physicochemical model of systemic inflammation. PLoS One 2009;4(3):e4706. |
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Journal Article | Foteinou PT, Yang E, Saharidis GK, Ierapetritou MG, Androulakis IP. A mixed-integer optimization framework for the synthesis and analysis of regulatory networks. Journal of Global Optimization 2009;43(2-3):263-276. |
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Journal Article | Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Multiscale model for the assessment of autonomic dysfunction in human endotoxemia. Physiological Genomics 2010;42(1):5-19. |
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Journal Article | Foteinou P, Calvano S, Lowry S, Androulakis I. A physiological model for autonomic heart rate regulation in human endotoxemia. SHOCK 2011;35(3):229-239. |
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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. |
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Journal Article | Fung HK, Floudas CA, Taylor MS, Zhang L, Morikis D. Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2. Biophysical Journal 2008;94(2):584-599. |
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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):3-21. |
R832721 (2007) R832721 (2008) R832721C001 (2006) R832721C001 (2007) |
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Journal Article | Georgopoulos PG, Sasso AF, Isukapalli SS, Lioy PJ, Vallero DA, Okino M, Reiter L. Response to "µg/kg-day or µg/day? A commentary on Georgopoulos et al., JESEE 2008." Journal of Exposure Science & Environmental Epidemiology 2008;18(6):536-537 (author reply). |
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Journal Article | Georgopoulos PG, Wang S-W, Yang Y-C, Xue J, Zartarian VG, McCurdy T, Ozkaynak H. Biologically based modeling of multimedia, multipathway, multiroute population exposures to arsenic. Journal of Exposure Science & Environmental Epidemiology 2008;18(5):462-476. |
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Journal Article | Georgopoulos PG, Sasso AF, Isukapalli SS, Lioy PJ, Vallero DA, Okino M, Reiter L. Reconstructing population exposures to environmental chemicals from biomarkers: challenges and opportunities. Journal of Exposure Science & Environmental Epidemiology 2009;19(2):149-171. |
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Journal Article | Gerecke DR, Chen M, Isukapalli SS, Gordon MK, Chang Y-C, Tong W, Androulakis IP, Georgopoulos PG. Differential gene expression profiling of mouse skin after sulfur mustard exposure: extended time response and inhibitor effect. Toxicology and Applied Pharmacology 2009;234(2):156-165. |
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Journal Article | Halai R, Bellows-Peterson M, Branchett W, Smadbeck J, Kieslich C, Croker D, Cooper M, Morikis D, Woodruff T, Floudas C, Monk P. Derivation of ligands for the complement C3a receptor from the C-termin of C5a. EUROPEAN JOURNAL OF PHARMACOLOGY 2014;745:176-181. |
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Journal Article | Isukapalli SS, Lioy PJ, Georgopoulos PG. Mechanistic modeling of emergency events: assessing the impact of hypothetical releases of anthrax. Risk Analysis 2008;28(3):723-740. |
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Journal Article | Iyer VV, Ovacik MA, Androulakis IP, Roth CM, Ierapetritou MG. Transcriptional and metabolic flux profiling of triadimefon effects on cultured hepatocytes. Toxicology and Applied Pharmacology 2010;248(3):165-177. |
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Journal Article | Iyer VV, Yang H, Ierapetritou MG, Roth CM. Effects of glucose and insulin on HepG2-C3A cell metabolism. Biotechnology and Bioengineering 2010;107(2):347-356. |
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Journal Article | Izmailov S, Feng XJ, Li G, Rabitz H. A scalable algorithm for molecular property estimation in high dimensional scaffold-based libraries. Journal of Mathematical Chemistry 2012;50(7):1765-1790. |
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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. |
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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. |
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Journal Article | Jornsten R, Keles S. Mixture models with multiple levels, with application to the analysis of multifactor gene expression data. Biostatistics 2008;9(3):540-554. |
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Journal Article | Jornsten R. Simultaneous model selection via rate-distortion theory, with applications to cluster and significance analysis of gene expression data. Journal of Computational & Graphical Statistics 2009;18(3):613-639. |
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Journal Article | Kortagere S, Chekmarev D, Welsh W, Ekins S. Hybrid Scoring and Classification Approaches to Predict Human Pregnane X Receptor Activators. PHARMACEUTICAL RESEARCH 2008;26(4):1001-1011 |
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Journal Article | Kortagere S, Chekmarev D, Welsh WJ, Ekins S. New predictive models for blood-brain barrier permeability of drug-like molecules. Pharmaceutical Research 2008;25(8):1836-1845. |
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Journal Article | Kortagere S, Ekins S, Welsh WJ. Halogenated ligands and their interactions with amino acids: implications for structure-activity and structure-toxicity relationships. Journal of Molecular Graphics and Modelling 2008;27(2):170-177. |
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Journal Article | Kortagere S, Welsh W, Morrisey J, Daly T, Ejigiri I, Sinnis P, Vaidya A, Bergman L. Structure-based Design of Novel Small-Molecule Inhibitors of Plasmodium falciparum. JOURNAL OF CHEMICAL INFORMATION AND MODELING 2010;50(5):840-849 |
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Journal Article | Lerapetritou MG, Georgopoulos PG, Roth CM, Androulakis IP. Tissue-level modeling of xenobiotic metabolism in liver: an emerging tool for enabling clinical translational research. Clinical and Translational Science 2009;2(3):228-237. |
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Journal Article | Li C, Ai N, Dinh G, Welsh W, Chen J. Human ADA3 regulates RARα transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket. NUCLEIC ACIDS RESEARCH 2010;38(16):5291-5303 |
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Journal Article | Li C-W, Ai N, Dinh GK, Welsh WJ, Chen JD. Human ADA3 regulates RARα transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket. Nucleic Acids Research 2010;38(16):5291-5303. |
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Journal Article | Li G, Rabitz H, Hu J, Chen Z, Ju Y. Regularized random-sampling high dimensional model representation (RS-HDMR). Journal of Mathematical Chemistry 2008;43(3):1207-1232. |
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Journal Article | Li G, Rabitz H, Yelvington PE, Oluwole OO, Bacon F, Kolb CE, Schoendorf J. Global sensitivity analysis for systems with independent and/or correlated inputs. Journal of Physical Chemistry A 2010;114(19):6022-6032. |
R832721 (2008) R832721 (Final) R835826 (Final) |
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Journal Article | Li G, Rabitz H. D-MORPH regression: application to modeling with unknown parameters more than observation data. Journal of Mathematical Chemistry 2010;48(4):1010-1035. |
R832721 (Final) |
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Journal Article | Lin Y, Yassuda K, Assem M, Cline C, Barber J, Li C, Kholodovych V, Ai N, Chen J, Welsh W, Ekins S, Schuetz E. The Major Human Pregnane X Receptor PXR Splice Variant, PXR.2, Exhibits Significantly Diminished Ligand-Activated Transcriptional Regulation. DRUG METABOLISM AND DISPOSITION 2009;37(6):1295-1304. |
R832721 (Final) |
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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 | McAllister SR, Floudas CA. α-helical topology prediction and generation of distance restraints in membrane proteins. Biophysical Journal 2008;95(11):5281-5295. |
R832721 (2008) R832721 (Final) |
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Journal Article | McAllister SR, Rajgaria R, Floudas CA. A path selection approach to global pairwise sequence alignment using integer linear optimization. Optimization: A Journal of Mathematical Programming and Operations Research 2008;57(1):101-111. |
R832721 (2008) |
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Journal Article | McAllister SR, Feng X-J, DiMaggio Jr PA, Floudas CA, Rabinowitz JD, Rabitz H. Descriptor-free molecular discovery in large libraries by adaptive substituent reordering. Bioorganic & Medicinal Chemistry Letters 2008;18(22):5967-5970. |
R832721 (2008) |
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Journal Article | McAllister SR, Floudas CA. Enhanced bounding techniques to reduce the protein conformational search space. Optimization Methods & Software 2009;24(4-5):837-855. |
R832721 (2008) |
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Journal Article | McAllister SR, DiMaggio Jr PA, Floudas CA. Mathematical modeling and efficient optimization methods for the distance-dependent rearrangement clustering problem. Journal of Global Optimization 2009;45(1):111-129. |
R832721 (2008) |
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Journal Article | McAllister SR, Floudas CA. An improved hybrid global optimization method for protein tertiary structure prediction. Computational Optimization and Applications 2010;45(2):377-413. |
R832721 (2008) R832721 (Final) |
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Journal Article | Nguyen TT, Nowakowski RS, Androulakis IP. Unsupervised selection of highly coexpressed and noncoexpressed genes using a consensus clustering approach. OMICS 2009;13(3):219-237. |
R832721 (2008) |
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Journal Article | Nguyen TT, Almon RR, DuBois DC, Jusko WJ, Androulakis IP. Importance of replication in analyzing time-series gene expression data: corticosteroid dynamics and circadian patterns in rat liver. BMC Bioinformatics 2010;11:279. |
R832721 (Final) |
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Journal Article | Nguyen TT, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Computational identification of transcriptional regulators in human endotoxemia. PLoS One 2011;6(5):e18889. |
R832721 (Final) |
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Journal Article | Nguyen T, Almon R, DuBOis D, Jko W, Androulakis I. Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver:Transcriptional dynamics and regulatory structures. BMC BIOINFORMATICS 2010;11:515. |
R832721 (Final) |
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Journal Article | Oelschlaeger P, Ai N, DuPrez KT, Welsh WJ, Toney JH. Evolving carbapenemases: can medicinal chemists advance one step ahead of the coming storm? Journal of Medicinal Chemistry 2010;53(8):3013-3027. |
R832721 (Final) |
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Journal Article | Orman M, Arai K, Yarmush M, Androulakis I, Berthiaume F, Ierapetritou M. Metabolic flux determination in perfused livers by mass balance analysis: Effect of fasting. BIOTECHNOLOGY AND BIOENGINEERING 2010;107(5):825-835 |
R832721 (Final) |
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Journal Article | Ovacik MA, Androulakis IP. On the potential for integrating gene expression and metabolic flux data. Current Bioinformatics 2008;3(3):142-148. |
R832721 (2008) |
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Journal Article | Ovacik MA, Sukumaran S, Almon RR, DuBois DC, Jusko WJ, Androulakis IP. Circadian signatures in rat liver: from gene expression to pathways. BMC Bioinformatics 2010;11:540. |
R832721 (2008) R832721 (Final) |
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Journal Article | Ovacik MA, Androulakis IP. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison. Toxicology and Applied Pharmacology 2013;271(3):363-371. |
R832721 (2008) R832721 (Final) |
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Journal Article | Ovacik MA, Sen B, Euling SY, Gaido KW, Ierapetritou MG, Androulakis IP. Pathway modeling of microarray data: a case study of pathway activity changes in the testis following in utero exposure to dibutyl phthalate (DBP). Toxicology and Applied Pharmacology 2013;271(3):386-394. |
R832721 (Final) |
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Journal Article | Piazza M, Feng X-J, Rabinowitz JD, Rabitz H. Diverse metabolic model parameters generate similar methionine cycle dynamics. Journal of Theoretical Biology 2008;251(4):628-639. |
R832721 (2008) |
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Journal Article | Rabinowitz JD, Hsiao JJ, Gryncel KR, Kantrowitz ER, Feng X-J, Li G, Rabitz H. Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase. Biochemistry 2008;47(21):5881-5888. |
R832721 (2008) |
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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 2006;65(3):726-741. |
R832721 (2007) R832721C005 (2006) R832721C005 (2007) |
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Journal Article | Rajgaria R, McAllister SR, Floudas CA. Distance dependent centroid to centroid force fields using high resolution decoys. Proteins: Structure, Function, Bioinformatics 2008;70(3):950-970. |
R832721 (2008) |
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Journal Article | Rajgaria R, McAllister SR, Floudas CA. Towards accurate residue-residue hydrophobic contact prediction for α helical proteins via integer linear optimization. Proteins: Structure, Function, Bioinformatics 2009;74(4):929-947. |
R832721 (2008) R832721 (Final) |
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Journal Article | Rajgaria R, Wei Y, Floudas CA. Contact prediction for beta and alpha-beta proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO-FOLD. Proteins 2010;78(8):1825-1846. |
R832721 (Final) |
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Journal Article | Reschly EJ, Ai N, Ekins S, Welsh WJ, Hagey LR, Hofmann AF, Krasowski MD. Evolution of the bile salt nuclear receptor FXR in vertebrates. Journal of Lipid Research 2008;49(7):1577-1587. |
R832721 (2008) |
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Journal Article | Reschly EJ, Ai N, Welsh WJ, Ekins S, Hagey LR, Krasowski MD. Ligand specificity and evolution of liver X receptors. Journal of Steroid Biochemistry and Molecular Biology 2008;110(1-2):83-94. |
R832721 (2008) |
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Journal Article | Saharidis GK, Ierapetritou MG. Resolution method for mixed integer bi-level linear problems based on decomposition technique. Journal of Global Optimization 2009;44(1):29-51. |
R832721 (2008) |
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Journal Article | Saharidis G, Androulakis I, Ierapetritou M. Model building using bi-level optimization. JOURNAL OF GLOBAL OPTIMIZATION 2011;49(1):49-67. |
R832721 (Final) |
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Journal Article | Sasso AF, Isukapalli SS, Georgopoulos PG. A generalized physiologically-based toxicokinetic modeling system for chemical mixtures containing metals. Theoretical Biology and Medical Modelling 2010;7:17. |
R832721 (Final) |
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Journal Article | Sasso AF, Georgopoulos PG, Isukapalli SS, Krishnan K. Bayesian analysis of a lipid-based physiologically based toxicokinetic model for a mixture of PCBs in rats. Journal of Toxicology 2012;2012:895391, doi:10.1155/2012/895391. |
R832721 (2008) |
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Journal Article | Scheff JD, Almon RR, DuBois DC, Jusko WJ, Androulakis IP. A new symbolic representation for the identification of informative genes in replicated microarray experiments. OMICS–A Journal of Integrative Biology 2010;14(3):239-248. |
R832721 (Final) |
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Journal Article | Schnackenberg LK, Chen M, Sun J, Holland RD, Dragan Y, Tong W, Welsh W, Beger RD. Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies. Toxicology and Applied Pharmacology 2009;235(1):25-32. |
R832721 (2008) |
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Journal Article | Stamatelos SK, Brinkerhoff CJ, Isukapalli SS, Georgopoulos PG. Mathematical model of uptake and metabolism of arsenic(III) in human hepatocytes – incorporation of cellular antioxidant response and threshold-dependent behavior. BMC Systems Biology 2011;5:16. |
R832721 (Final) |
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Journal Article | Stamatelos S, Androulakis I, Kong A, Georgopoulos P. A semi-mechanistic integrated toxicokinetic-toxicodynamic (TK/TD) model for arsenic(III) in hepatocytes. JOURNAL OF THEORETICAL BIOLOGY 2013;317:244-256 |
R832721 (Final) |
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Journal Article | Subramani A, DiMaggio P, Floudas C. Selecting High Quality Protein Structures from Diverse Conformational Ensembles. BIOPHYSICAL JOURNAL 2009;97(6):1728-1736. |
R832721 (Final) |
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Journal Article | Sun JJ, Abdeljabbar DM, Clarke N, Bellows ML, Floudas CA, Link AJ. Reconstitution and engineering of apoptotic protein interactions on the bacterial cell surface. Journal of Molecular Biology 2009;394(2):297-305. |
R832721 (Final) |
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Journal Article | Tan MP, Smith EN, Broach JR, Floudas CA. Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures. BMC Bioinformatics 2008;9:268-289. |
R832721 (2008) |
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Journal Article | Taylor MS, Fung HK, Rajgaria R, Filizola M, Weinstein H, Floudas CA. Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework. Biophysical Journal 2008;94(7):2470-2481. |
R832721 (2008) |
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Journal Article | Xue J, Zartarian V, Wang S-W, Liu SV, Georgopoulos P. Probabilistic modeling of dietary arsenic exposure and dose and evaluation with 2003-2004 NHANES data. Environmental Health Perspectives 2010;118(3):345-350. |
R832721 (Final) |
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Journal Article | Yang EH, Almon RR, Dubois DC, Jusko WJ, Androulakis IP. Identification of global transcriptional dynamics. PLoS One 2009;10;4(7):e5992. |
R832721 (2008) |
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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, 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, Androulakis IP. Informative gene selection and design of regulatory networks using integer optimization. Computers & Chemical Engineering 2008;32(4-5):633-649. |
R832721 (2007) R832721 (2008) |
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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) R832721 (2008) |
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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) R832721 (2008) |
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Journal Article | Yang E, Androulakis IP. Assessing and selecting gene expression signals based upon the quality of the measured dynamics. BMC Bioinformatics 2009;10:55-67. |
R832721 (2008) |
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Journal Article | Yang E, Yarmush ML, Androulakis IP. Transcription factor network reconstruction using the living cell array. Journal of Theoretical Biology 2009;256(3):393-407. |
R832721 (2008) |
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Journal Article | Yang H, Roth CM, Ierapetritou MG. A rational design approach for amino acid supplementation in hepatocyte culture. Biotechnology and Bioengineering 2009;103(6):1176-1191. |
R832721 (2008) R832721 (Final) |
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Journal Article | Yang H, Ierapetritou MG, Roth CM. Effects of amino acid transport limitations on cultured hepatocytes. Biophysical Chemistry 2010;152(1-3):89-98. |
R832721 (2008) R832721 (Final) |
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Journal Article | Yang H, Roth CM, Ierapetritou MG. Analysis of amino acid supplementation effects on hepatocyte cultures using flux balance analysis. OMICS 2011;15(7-8):449-460. |
R832721 (2008) |
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Journal Article | Yang Y, Xu X, Georgopoulos PG. A Bayesian population PBPK model for multiroute chloroform exposure. Journal of Exposure Science & Environmental Epidemiology 2010;20(4):326-341. |
R832721 (2008) R832721 (Final) |
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Journal Article | Yuan J, Doucette C, Fowler W, Feng X, Piazza M, Rabitz H, Wingreen N, Rabinowitz J. Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. MOLECULAR SYSTEMS BIOLOGY 2009;5(302). |
R832721 (Final) |
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Presentation | Ai N, Yu S-J, Delisle RK, Welsh WJ. Computational models for predicting the binding affinities of ligands for the androgen receptor. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R826133 (Final) R832721 (2007) |
not available |
Presentation | Ai N, Chekmarev D, Zhang P, Kholodovych V, Welsh WJ. Shape signatures database of PDB-extracted ligands for computational toxicology. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Ai N, Reschly EJ, Krasowski MD, Hagey LR, Hoffman AF, Welsh WJ, Ekins S. Understanding co-evolution of nuclear receptors using computational methods. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Androulakis I. From data to models: systems toxicology linkages to toxicoinformatics. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Androulakis I. From data to models: systems biology methods and potential applications to toxicoinformatics. Presented at the Computational Toxicology Seminar Series, U.S. EPA National Center for Computational Toxicology, Research Triangle Park, NC, March 12, 2008. |
R832721 (2008) |
not available |
Presentation | Bellows ML, Floudas CA. A novel framework for de novo protein design and its applications. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Brinkerhoff CJ, Stamatelos S, Isukapalli SS, Georgopoulos PG. Pharmacokinetic model of uptake and metabolism of arsenicals in hepatocytes with implications for reactive oxygen species generation and hepatocarcinogenesis. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Brinkerhoff CJ, Georgopoulos PG. Linking exposure dynamics with health effects through biological modeling: case study with TCE exposure and oxidative stress. Presented at the Integrative Exposure Biology and Computational Toxicology for Risk Assessment Symposium, 2009 Annual Conference of ISES, Minneapolis, MN, November 1-5, 2009. |
R832721 (Final) |
not available |
Presentation | Brinkerhoff CJ, Isukapalli SS, Georgopoulos PG. Integrative modeling of chemically induced oxidative stress: a case study with trichloroethylene. Presented at the 4th International Conference on Oxidative/Nitrosative Stress and Disease, New York Academy of Sciences (NYAS), New York, NY, October 28-30, 2009. |
R832721 (Final) |
not available |
Presentation | Chekmarev D, Ai N, Kholodovych V, Kortagere S, Welsh WJ. Shape signatures: a novel tool for computational toxicology. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Chekmarev D, Ai N, Kholodovych V, Kortagere S, Welsh WJ. Progress in development of the shape signatures tool for computational toxicology. Systems Toxicology: Presented at the Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Chen M, Tong W, Welsh W, Georgopoulos PG. Gene expression profiles of rodent pulmonary tissue following sulfur mustard exposure using ArrayTrack. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Chen M, Isukapalli SS, Georgopoulos PG, Welsh WJ, Tong W. ebTrack: an environmental bioinformatics system built upon ArrayTrack. Presented at the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES), Raleigh, NC, October 25-26, 2007. |
R832721 (2008) |
not available |
Presentation | Chen M, Schnackenberg L, Guo L, Holland R, Beger R, Shi Q, Isukapalli SS, Georgopoulos PG, Welsh WJ, Tong W. Progress in developing infrastructure for a virtual liver II: multi-scale studies of hepatotoxicants for elucidating potential biomarkers and important pathways related to hepatotoxicity. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Chen M, Schnackenberg LK, Guo L, Holland R, Beger RD, Shi Q, Isukapalli S, Georgopoulos PG, Welsh W, Tong W. Toxicogenomic studies reveal biosynthetic pathway of S-adenosylmethione as a possible hepatotoxic mechanism. Presented at the MidSouth Computational Biology and Bioinformatics Society-MCBIOS 2008 Conference, Oklahoma City, OK, February 23-24, 2008. |
R832721 (2008) |
not available |
Presentation | Chen M, Schnackenberg LK, Holland R, Beger RD, Isukapalli S, Georgopoulos PG, Welsh WJ, Tong W. Toxicogenomics studies of the transsulfuration pathway as a possible mechanism for liver toxicity. Presented at the Society of Toxicology (SOT) Annual Meeting and ToxExpo, Seattle, WA, March 16-20, 2008. |
R832721 (2008) |
not available |
Presentation | Dary CC, Geogopoulus PG, Vallero DA, Tornero-Velez R, Morgan MO, Dellarco M, Power F, Blancato JN. Characterizing chemical exposure from biomonitoring data using the Exposure Related Dose Estimating Model (ERDEM). Presented at the 17th Annual International Society of Exposure Assessment (ISEA) Conference, Durham, NC, October 14-18, 2007. |
R832721 (2008) |
not available |
Presentation | DiMaggio PA, Floudas CA. De novo peptide identification via tandem mass spectrometry and mixed-integer linear optimization. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | DiMaggio PA, Tan MP, Floudas CA. Optimization tools for the identification of (I) peptides and proteins, and (II) gene clusters. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | DiMaggio PA, Floudas CA. Optimization tools for in silico proteomics. Info on Informatics Seminar Series. Presented at the USEPA National Center for Computational Toxicology, Research Triangle Park, NC, March 14, 2007. |
R832721 (2007) |
not available |
Presentation | DiMaggio PA, Floudas CA, Salinas K, Hemmer M, Serrano J. In silico and experimental methodologies for tandem mass spectrometry-based proteomics. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | DiMaggio PA, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HA. Biclustering via optimal re-ordering of data matrices in systems biology. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Dong X, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Agent-based imulation of endotoxin induced acute inflammatory response in human blood leukocytes. Presented at the American Institute of Chemical Engineers (AIChE) National Meeting, Nashville, TN, November 8-13, 2009. |
R832721 (Final) |
not available |
Presentation | Dong X, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Agent-based simulation of endotoxin induced acute inflammatory response in human blood leukocytes. Presented at the Biomedical Engineering Society Annual Meeting, Pittsburgh, PA, October 7-10, 2009. |
R832721 (Final) |
not available |
Presentation | Ekins S. Computational toxicology: new methods and models at the molecular level. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Euling SY, Makris S, Sen B, Kim AS, Benson B, Gaido KW, Wilson VS, Keshava C, Keshava N, White L, Foster PM, Androulakis IP, Ovacik M, Ierapetritou MG, Gray LE, Thompson C, Barone S, Chiu W, Welsh W, Georgopoulos PG. Use of toxicogenomics data in risk assessment: a case study on dibutyl phthalate and male reproductive developmental effects. Presented at the Society of Toxicology Annual Meeting and ToxExpo, Charlotte, NC, March 25-29, 2007. |
R832721 (2007) |
not available |
Presentation | Euling S, Sen B, Welsh W, Georgopoulos PG, Ovacik M, Ierapetritou MG, Androulakis I. Expression profiling to assess developmental effects of exposure to DBP. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Euling S, Sen B, Welsh W, Georgopoulos PG, Ovacik M, Ierapetritou MG, Androulakis I. Temporal expression profiling to assess dynamics of exposure to DBP. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Euling S, Makris S, Sen B, White L, Benson B, Gaido KW, Kim AS, Hester S, Wilson V, Keshava C, Keshava N, Foster PM, Androulakis IP, Ovacik M, Ierapetritou MG, Gray Jr LE, Thompson C, Chiu W, Welsh WJ, Georgopoulos PG. Use of toxicogenomics data in risk assessment: a case study on dibutyl phthalate and male reproductive developmental effects. Presented at the 2007 International Science Forum on Computational Toxicology, Research Triangle Park, NC, May 21-23, 2007. |
R832721 (2007) |
not available |
Presentation | Euling S, Makris S, Sen B, White L, Benson B, Gaido K, Kim A, Hester S, Keshava C, Foster P, Androulakis IP, Ovacik M, Ierapetritou MG, Gray LE, Thompson C, Chiu W. An approach to using genomics data in risk assessment. Presented at the 48th Teratology Society Annual Meeting, Monterey, CA, June 28-July 2, 2008. |
R832721 (2008) |
not available |
Presentation | Feng XJ, Rabitz H. Development of computational tools for optimal identification of biological networks. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Feng X-J. Optimal identification of complex biological networks. Presented at the IEEE International Parallel and Distributed Processing Symposium, Miami, FL, April 13-18, 2008. |
R832721 (2008) |
not available |
Presentation | Feng X-J, Rabinowitz JD. System identification tools for metabolic engineering. Presented at the Interagency Conference on Metabolic Engineering, North Bethesda, MD, February 11, 2008. |
R832721 (2008) |
not available |
Presentation | Feng X-J, Li G, Rabitz H. A closed-loop identification protocol (CLIP) for nonlinear biological networks. Presented at the Info on Informatics Seminar Series, USEPA National Center for Computational Toxicology, Research Triangle Park, NC, October 11, 2006. |
R832721 (2007) R832721C003 (2006) |
not available |
Presentation | Floudas CA. Dynamics of macromolecules: optimization methods and tools for in silico proteomics. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Floudas CA, DiMaggio PA, McAllister SR, Feng XJ, Rabinowitz JD, Rabitz HR. Optimal methods for re-ordering data matrices in systems biology and drug discovery applications. Presented at the International Symposium on Mathematical and Computational Biology-BIOMAT 2007 Conference, Buzios, Brazil, November 24-29, 2007. |
R832721 (2008) |
not available |
Presentation | Floudas CA, Fung HK, Morikis D. De novo protein design with flexible backbone templates and its application to the redesign of complement C3a. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
not available |
Presentation | Floudas CA, Rajgaria R, McAllister SR. A new optimization based approach for protein residue contact prediction. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
not available |
Presentation | Floudas CA, McAllister SR, DiMaggio PA, Feng XJ, Li G, Rabinowitz JD, Rabitz HR. A novel approach for accelerating molecular discovery of sparsely sampled libraries. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
not available |
Presentation | Floudas CA. Biclustering via optimal ordering. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
not available |
Presentation | Floudas CA, Tan MP, Broach JR. Inferring large scale gene regulatory structures using optimization based approaches. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
not available |
Presentation | Floudas CA, DiMaggio PA. Peptide identification via integer linear optimization, local alignment database search and tandem mass spectrometry. Presented at the American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
not available |
Presentation | Floudas CA. De novo protein design in computational genomics. Presented at Tufts University, Medford, MA, October 2007. |
R832721 (2008) |
not available |
Presentation | Floudas CA. De novo protein design in computational genomics: advances and challenges. Presented at the Distinguished Lecture Series in Systems Biology, Georgia Institute of Technology, Atlanta, GA, October 16, 2007. |
R832721 (2008) |
not available |
Presentation | Floudas CA. De novo protein design. Presented to the Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, April 2008 (George T. Piercy Lecture). |
R832721 (2008) |
not available |
Presentation | Floudas CA. De novo protein design: advances and challenges. Presented to the Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY, April 2008. |
R832721 (2008) |
not available |
Presentation | Floudas CA. Discovery in proteomics: de novo and hybrid methods via tandem mass spectrometry. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Floudas CA. Structure prediction in protein folding, de novo protein design and proteomics. Presented at the Pan American Advanced Studies Institute on Emerging Trends in Process Systems Engineering (PASI-2008), Mar del Plata, Argentina, August 12-21, 2008 (invited). |
R832721 (2008) |
not available |
Presentation | Floudas CA. Prediction of interhelical contacts and tertiary structure in alpha helical globular proteins. Presented at the IMA Annual Program Year Workshop-Protein Folding, University of Minnesota, Twin Cities Campus, Minneapolis, MN, January 14-18, 2008 (invited). |
R832721 (2008) |
not available |
Presentation | Floudas CA. De novo protein design in computational genomics: advances and challenges. Presented at the 2nd International Conference on Control and Optimization with Industrial Applications-COIA-2008, Baku, Azerbaijan, June 2-4, 2008 (keynote lecture). |
R832721 (2008) |
not available |
Presentation | Floudas CA. Recent advances in deterministic global optimization. Presented at the Advanced Optimization Methods and Algorithms for the Design of Electronic Circuits and Devices, MOMiNE, Ragusa, Italy, June 21-28, 2008 (plenary lecture). |
R832721 (2008) |
not available |
Presentation | Floudas CA. Deterministic global optimization. Presented at the 14th Latin-Ibero-American Conference on Operations Research (CLAIO-2008), Cartagena, Colombia, November 9-12, 2008 (plenary lecture). |
R832721 (2008) |
not available |
Presentation | Foteinou PT, Yang E, Calvano SE, Lowry SF, Androulakis IP. Transcriptional analysis of the genome-wide response of leukocytes in an in vivo human model of systemic inflammation. Presented at the First International Conference on Biomolecular Engineering, Coronado, CA, January 14-18, 2007. |
R832721 (2007) |
not available |
Presentation | Foteinou PT, Ierapetritou MG, Androulakis IP. A mixed-integer optimization model for the design of gene regulatory networks. Presented at the 4th International Conference on Advances in Global Optimization, Mykonos, Greece, June 12-17, 2007. |
R832721 (2007) |
not available |
Presentation | Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. In silico simulation of corticosteroids effect on a nuclear factor-kB dependent indirect response model of systemic inflammation in peripheral human blood leukocytes. Presented at the 7th Annual Colloquium on Systems Biology and Molecular Diagnostics in Sepsis, Chapel Hill, NC, May 12-14, 2008. |
R832721 (2008) |
not available |
Presentation | Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Approaches toward a reverse engineering model of system inflammation in humans. Presented at the NIH Quantitative and Systems Pharmacology Workshop, Bethesda, MD, September 25-26, 2008. |
R832721 (2008) |
not available |
Presentation | Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. A multi-scale model for the assessment of autonomic dysfunction in human endotoxemia. Presented at the American Institute of Chemical Engineers (AIChE) National Meeting, Nashville, TN, November 8-13, 2009. |
R832721 (Final) |
not available |
Presentation | Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. A multi-scale model for the assessment of autonomic dysfunction in human endotoxemia. Presented at the Biomedical Engineering Society Annual Meeting, Pittsburgh, PA, October 7-10, 2009. |
R832721 (Final) |
not available |
Presentation | Fung HK, Floudas CA. A novel computational framework for de novo protein design. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Fung HK, McAllister SR, Rajgaria R, Floudas CA. Protein structure prediction and de novo protein design. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Fung HK, Floudas CA, Ault AD, Broach JR. A novel computational framework for the optimal design of a protein biosensor that recognizes a known set of ligands. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
not available |
Presentation | Fung HK, Welsh WJ, Floudas CA. Full-sequence design of human beta defensin-2. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Georgopoulos PG, Isukapalli S, Wang SW, Sasso A. An overview of MENTOR and DORIAN. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Georgopoulos PG. An integrative framework for systems toxicology. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Georgopoulos PG, Welsh WJ, Isukapalli S, Ierapetritou M, Androulakis I, Roth CM, Tong W. Infrastructure for a virtual liver I: essential concepts and modules systems toxicology. Presented at the Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Georgopoulos PG, Isukapalli S, Wang SW. Overview of an integrated modeling system for supporting multiscale source-to-effect studies of human health risks. Presented at the USEPA Integrated Modeling Workshop, Research Triangle Park, NC, January 30, 2007. |
R832721 (2007) |
not available |
Presentation | Georgopoulos PG, Lioy PJ, Welsh WJ, Isukapalli S, Wang SW. Integrating enviroinformatic and bioinformatic approaches for the systematic analysis of environmentally related human health risks. Presented at the Meadowlands Symposium II, Lyndhurst, NJ, May 15-17, 2007. |
R832721 (2007) |
not available |
Presentation | Georgopoulos PG, Isukapalli S, Wang SW, Sasso A, Chen M, Tong W. Environmental systems biology framework for human health risk analysis. Presented at the 2007 International Science Forum on Computational Toxicology, Research Triangle Park, NC, May 21-23, 2007. |
R832721 (2007) |
not available |
Presentation | Georgopoulos PG, Wang SW, Sasso AF, Isukapalli SS. Characterizing exposures to arsenic and co-occurring contaminants using the Modeling Environment for TOtal Risk studies (MENTOR). Presented at the 17th Annual International Society of Exposure Assessment (ISEA) Conference, Durham, NC, October 14-18, 2007. |
R832721 (2008) |
not available |
Presentation | Georgopoulos PG, Isukapalli SS, Tong W, Lioy PJ, Welsh WJ. Exposure biology for a systems approach in studying environmental health risks. Presented at the 17th Annual International Society of Exposure Assessment (ISEA) Conference, Durham, NC, October 14-18, 2007. |
R832721 (2008) |
not available |
Presentation | Georgopoulos PG. A multiscale framework for environmental systems toxicology. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Georgopoulos PG, Welsh WJ, Isukapalli SS, Ierapetritou M, Androulakis I, Roth CM, Tong W. Progress in developing infrastructure for a virtual liver I: essential concepts and modules. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Georgopoulos PG. Mechanistic studies of environmental causes of human disease: a bionetwork dynamics modeling approach. Presented at the Protection and Restoration of the Environment IX (PRE9) Conference, Kefalonia, Greece, June 29-July 3, 2008. |
R832721 (2008) |
not available |
Presentation | Georgopoulos PG, Isukapalli SS. Integrative source-to-dose-to-effect modeling for interpreting biomonitoring data in an exposure context. Presented at the Integrative Exposure Biology and Computational Toxicology for Risk Assessment Symposium, 2009 Annual Conference of ISES, Minneapolis, MN, November 1-5, 2009. |
R832721 (Final) |
not available |
Presentation | Georgopoulos PG. A multiscale integrated model-based approach for the analysis of exposure risks. Presented at the USFDA Center for Food Safety and Applied Nutrition Seminar, College Park, MD, April 20, 2010. |
R832721 (Final) |
not available |
Presentation | Gerecke DR, Chen M, Isukapalli S, Tong W, Ovacik MA, Foteinou PT, Androulakis IP, Welsh W, Georgopoulos PG. Differential gene expression profiling of mouse skin after sulfur mustard exposure: extended time response and inhibitor effect. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Gerecke DR, Chen M, Isukapalli S, Chang Y-C, Tong W, Androulakis IP, Georgopoulos PG. Gene expression studies of mouse skin response to sulfur mustard exposure for evaluating efficacy of inhibitors. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Guzikowski SA, Roth CM, Ierapetritou MG, Isukapalli S, Georgopoulos PG. Infrastructure for a virtual liver III: methods for metabolic analysis of xenobiotic interactions. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Guzikowski SA, Ierapetritou MG, Roth CM. Metabolic analysis of xenobiotic interactions in hepatocytes. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
not available |
Presentation | Guzikowski S, Ierapetritou MG, Roth CM. Modeling metabolic relationships in acetaminophen-induced hepatotoxicity. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Isukapalli SS, Sasso AF, Okino M, Georgopoulos PG. Evaluation of methods for reconstructing exposures from biomarkers via PBTK models. Presented at the 17th Annual International Society of Exposure Assessment (ISEA) Conference, Durham, NC, October 14-18, 2007. |
R832721 (2008) |
not available |
Presentation | Isukapalli SS, Price K, Georgopoulos PG, Krishnan K. A physiologically-based algorithm for predicting internal dose of inhaled toluene: applications for high dose to low dose and rodent to human extrapolations. Presented at the International Conference on Health Sciences Simulation, Ottawa, Ontario, Canada, April 14-17, 2008. |
R832721 (2008) |
not available |
Presentation | Isukapalli SS, Sasso AF, Georgopoulos PG, Krishnan K. Efficient physiologically-based algorithms for estimating internal doses occurring due to chronic exposures of organics. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Isukapalli SS, Brinkerhoff CJ, Sasso AF, Georgopoulos PG. Progress in developing infrastructure for a virtual liver V: PBTK/TD models with zonal and distributed parameters for metabolism of environmental toxins. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Isukapalli SS. Multiscale mechanistic models in exposure assessment: case studies with virtual organs. Presented at the Integrative Exposure Biology and Computational Toxicology for Risk Assessment Symposium at the 2009 Annual Conference of ISES, Minneapolis, MN, November 1-5, 2009. |
R832721 (Final) |
not available |
Presentation | Isukapalli S, Sasso A, Wang SW, Ierapetritou MG, Georgopoulos PG. Optimized Bayesian inversion of biological data using mechanistic models. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Iyer VV, Roth CM, Ierapetritou MG. Progress in developing infrastructure for a virtual liver IV: effects of glucose and insulin levels on HepG2 cell metabolism. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Iyer VV, Ierapetritou MG, Roth CM. Understanding mechanisms of conazole toxicity in cultured hepatocytes. Presented at the American Institute of Chemical Engineers (AIChE) National Meeting, Nashville, TN, November 8-13, 2009. |
R832721 (Final) |
not available |
Presentation | Iyer VV, Androulakis IP, Roth CM, Ierapetritou MG. Effects of triadimefon on the metabolism of cultured hepatocytes. Presented at the 10th International Conference on Bioinformatics and Bioengineering (BIBE-2010), Philadelphia, PA, May 31-June 3, 2010. |
R832721 (Final) |
not available |
Presentation | Jornsten R. Flexible mixture modeling, with applications to gene clustering and the selection of differentially expressed genes. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Jornsten R. Simultaneous model selection via rate-distortion theory, with applications to the analysis of gene expression data. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Kholodovych V, Tabb MM, Blumberg B, Welsh WJ. Regulation of the clearance mechanism of environmental pollutants and xenobiotic chemicals by the Pregnane X Receptor (PXR): structural requirements and species to species extrapolation. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Kholodovych V, Tabb MM, Blumberg B, Welsh WJ. Structural characteristics of the pregnane X receptor in regulation of the clearance mechanism of environmental pollutants and xenobiotic chemicals. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Kholodovych V, Ai N, Welsh WJ, Chang C, Mani S, Krasowski MD, Reschly EJ, Iyer M, Sinz M, Swaan PW, Patel R, Bachmann K, Ekins S. Human pregnane X receptor antagonists and agonists define molecular requirements for different binding sites. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Kholodovych V, Chekmarev D, Welsh WJ. Biological spectra profile analysis in computational toxicology: linking the bioactivities and molecular structures of chemical datasets. Presented at the Integrative Exposure Biology and Computational Toxicology for Risk Assessment Symposium, 2009 Annual Conference of ISES, Minneapolis, MN, November 1-5, 2009. |
R832721 (Final) |
not available |
Presentation | Kortagere S, Welsh WJ. Structural analysis of toxicophore interactions with biomolecules. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Kortagere S, Welsh WJ. Structural analysis of toxicophore interactions with biomolecules. Presented at the 2007 International Science Forum on Computational Toxicology, Research Triangle Park, NC, May 21-23, 2007. |
R832721 (2007) |
not available |
Presentation | Kortagere S, Chekmarev D, Welsh WJ, Ekins S. New predictive models for blood-brain barrier permeability of drug-like molecule. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Li G, Feng X. Dynamics of bionetworks: tools for network identification and high-dimensional data analysis. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Lioy PJ, Weisel C, Georgopoulos PG. Activities on environmental exposure and sampling issues. Presented at the National Children’s Study Queens Vanguard Center Meeting, New York, NY, April 19, 2010. |
R832721 (Final) |
not available |
Presentation | McAllister SR, Mickus BE, Klepeis JL, Floudas CA. A novel approach for α-helical topology prediction in globular proteins. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Miller M, Feng XJ, Li G, Rabitz HA. Nonlinear bionetwork structure inference. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Orman MA, Berthiaume F, Androulakis IP, Ierapetritou MG. Optimization based pathway analysis to elucidate the effects of burn injury on the hepatic metabolism. Presented at the American Institute of Chemical Engineers (AIChE) National Meeting, Nashville, TN, November 8-13, 2009. |
R832721 (Final) |
not available |
Presentation | Ovacik MA, Ierapetritou MG, Nesnow IPS, Hester S, Welsh W, Georgopoulos PG. Classification of triazole conazole fungicides: pathway analysis. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Ovacik MA, Androulakis IP, Ierapetritou MG, Euling S, Sen B, Gaido KW, Welsh WJ, Georgopoulos PG. Transcriptional analysis following in utero exposure to dibutyl phthalate (DBP) esters. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Ovacik MA, Ierapetritou MG, Sen B, Euling S, Georgopoulos PG, Welsh W, Gaido KW, Androulakis IP. Toxicogenomics analysis following in utero exposure to di-butyl-phthalate. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
not available |
Presentation | Ovacik MA, Ierapetritou MG, Georgopoulos PG, Welsh W, Euling S, Sen B, Gaido K, Androulakis IP. Pathway activity analysis for transcriptional profiling of in utero exposure to d-n-butyl phthalate. Presented at the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES), Raleigh, NC, October 25-26, 2007. |
R832721 (2008) |
not available |
Presentation | Ovacik MA, Ierapetritou MG, Georgopoulos PG, Welsh WJ, Androulakis IP. The indirect response model of arsenic exposure on gene expression. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Ovacik M, Ierapetritou MG, Androulakis IP, Sen B, Euling S, Gaido K, Georgopoulos PG, Welsh W. Incorporating toxicogenomic data and approaches in risk assessment: case study-phthalate esters. Presented at the Info on Informatics Seminar Series, USEPA National Center for Computational Toxicology, Research Triangle Park, NC, April 11, 2007. |
R832721 (2007) |
not available |
Presentation | Ovacik M, Ierapetritou MG, Androulakis IP, Sen B, Euling S, Gaido K, Welsh W, Georgopoulos PG. Gene expression profiling following exposure to phthalate esters: an integrative toxicogenomics approach. Presented at the 2007 International Science Forum on Computational Toxicology, Research Triangle Park, NC, May 21-23, 2007. |
R832721 (2007) |
not available |
Presentation | Ovacik M, Ierapetritou MG, Georgopoulos P, Welsh W, Euling S, Sen B, Gaido K, Androulakis IP. Pathway modeling of microarray data of the rat testes after in utero DBP exposure. Presented at the Integrative Exposure Biology and Computational Toxicology for Risk Assessment Symposium, 2009 Annual Conference of ISES, Minneapolis, MN, November 1-5, 2009. |
R832721 (Final) |
not available |
Presentation | Ovacik M, Androulakis IP. Species comparison analysis based on pathways. Presented at the American Institute of Chemical Engineers (AIChE) National Meeting, Nashville, TN, November 8-13, 2009. |
R832721 (Final) |
not available |
Presentation | Rabitz H, Feng X, Miller M, Li G. Reverse engineering of quantitative bionetwork architecture. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Rabitz H, Feng X-J. Optimal identification and analysis of bionetworks and biomolecules. Presented at the Computational Toxicology Seminar Series, U.S. EPA National Center for Computational Toxicology, Research Triangle Park, NC, December 20, 2007. |
R832721 (2008) |
not available |
Presentation | Rajgaria R, McAllister SR, Floudas CA. High resolution Cα—Cα and side chain centroid based distance dependent force fields. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Rajgaria R, Floudas CA. Optimization models in novel force field generation. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Roth C. Computational modeling of liver function. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) SU835083 (Final) |
not available |
Presentation | Sasso AF, Isukapalli SS, Georgopoulos PG. Physiologically based toxicokinetic modeling for mixtures of toxic metals. Presented at the 17th Annual International Society of Exposure Assessment (ISEA) Conference, Durham, NC, October 14-18, 2007. |
R832721 (2008) |
not available |
Presentation | Sasso AF, Isukapalli SS, Kenyon E, Georgopoulos PG. Sensitivity analysis for studying impacts of aging on population toxicokinetics and toxicodynamics. Presented at the 17th Annual International Society of Exposure Assessment (ISEA) Conference, Durham, NC, October 14-18, 2007. |
R832721 (2008) |
not available |
Presentation | Sasso AF, Isukapalli SS, Georgopoulos PG. Consistent physiologically based toxicokinetic modeling for mixtures of toxic metals and metalloids. Presented at the Society of Environmental Toxicology and Chemistry (SETAC) Fall Workshop-Environmental Risk Assessment of Metals and Metalloids, Camden, NJ, October 26, 2007. |
R832721 (2008) |
not available |
Presentation | Sasso AF, Georgopoulos PG. User oriented implementation of a generalized physiologically-based toxicokinetic (PBTK) modeling framework for mixtures. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Sasso AF, Krishnan K, Isukapalli SS. Integrated computational models for supporting risk assessment: case studies with chemical mixtures. Presented at the Integrative Exposure Biology and Computational Toxicology for Risk Assessment Symposium, 2009 Annual Conference of ISES, Minneapolis, MN, November 1-5, 2009. |
R832721 (Final) |
not available |
Presentation | Sasso A, Georgopoulos PG. Physiologically-based toxicokinetic models for toxic metal mixtures: development and demonstration of a mechanistically consistent framework. Presented at the SRA 2006 Annual Meeting-Risk Analysis in a Dynamic World: Making a Difference, Baltimore, MD, December 3-6, 2006. |
R832721 (2007) |
not available |
Presentation | Sasso A, Shade P, Isukapalli SS, Georgopoulos PG. Age and gender considerations in physiologically based population toxicokinetics. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Sasso A, Isukapalli SS, Georgopoulos PG. Physiologically-based population toxicokinetic models for mixtures of metals. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Sasso A, Isukapalli S, Georgopoulos PG. Biologically based Bayesian reconstruction of human exposures from biomarker data: application to chlorpyrifos. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Sasso A, Isukapalli S, Georgopoulos PG. Mechanistically consistent PBTK modeling framework for mixtures: application to toxic metals. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
not available |
Presentation | Sasso A, Isukapalli SS, Georgopoulos PG. Assessing exposure and dose of VOCs using physiologically-based toxicokinetic models. Presented at the ACC-LRI Workshop on VOC Exposure Modeling, Piscataway, NJ, June 20, 2007. |
R832721 (2007) |
not available |
Presentation | Sasso A, Isukapalli S, Georgopoulos PG. Mechanistically consistent PBTK modeling framework for mixtures of toxic metals. Presented at the 2007 International Science Forum on Computational Toxicology, Research Triangle Park, NC, May 21-23, 2007. |
R832721 (2007) |
not available |
Presentation | Sasso A, Isukapalli SS, Georgopoulos PG. A systematic toxicokinetic modeling framework for mixtures of toxic metals. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
not available |
Presentation | Shade P, Georgopoulos PG. Physiologically based inhalation dosimetry modeling for nanoparticles: considerations of activity, age and gender. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Subramani A, Floudas CA. Single sequence alpha-helix and beta-strand prediction for globular proteins. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Swiss V, Nguyen T, Androulakis IP, Casaccia-Bonnefil P. The E2 family of transcription factors mediate the transcriptional regulation necessary for oligodendrocyte differentiation. Presented at the 6th Meeting on Dynamic Organization of Nuclear Function, Cold Spring Harbor, NY, September 17-21, 2008. |
R832721 (2008) |
not available |
Presentation | Tan MP, Broach JR, Floudas CA. A novel optimization-based iterative clustering approach to uncover biologically coherent structures. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Tong W. Toxicogenomics: technology, application and challenges. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Wang SW, Yan Y, Georgopoulos PG. Comparative evaluation of three statistical data mining techniques (CART, MARS, and Random Forest) and their applications in analyzing the NHANES VOC project data. Presented at the 17th Annual International Society of Exposure Assessment (ISEA) Conference, Durham, NC, October 14-18, 2007. |
R832721 (2008) |
not available |
Presentation | Wang SW, Sasso A, Yang YC, Georgopoulos PG, Xue J, McCurdy T, Ozkaynak H. Modeling dietary human exposures to mercury and methylmercury using a probabilistic source-to-dose approach. Presented at the U.S. EPA Region 2 Seminar-Evaluating Fish Consumption Guidelines: A Qualitative and Quantitative Approach for High Risk Ethnic Groups, New York, NY, April 15, 2008. |
R832721 (2008) |
not available |
Presentation | Welsh WJ. Dynamics of small molecules: Cheminformatics tools for predictive toxicology. Presented at the Systems Toxicology: Multiscale Modeling of Environmental Impacts on Bionetworks-an ebCTC Workshop, EOHSI and DIMACS, Piscataway, NJ, April 26-27, 2007. |
R832721 (2007) |
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Presentation | Welsh WJ, Kholodovych V, Chekmarev D, Georgopoulos PG. Shape signatures: a powerful new technology for risk assessment. Presented at the 2007 International Science Forum on Computational Toxicology, Research Triangle Park, NC, May 21-23, 2007. |
R832721 (2007) |
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Presentation | Welsh WJ, Georgopoulos PG. Multiscale modeling of environmental impacts on bionetworks. Presented at the 17th Annual International Society of Exposure Assessment (ISEA) Conference, Durham, NC, October 14-18, 2007. |
R832721 (2008) |
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Presentation | Welsh WJ. Computational toxicology from a cheminformatics perspective. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Welsh WJ, Georgopoulos PG. Environmental Bioinformatics and Computational Toxicology Center (ebCTC): research in multiscale modeling of the effects of environmental toxicants. Presented at the Computational Toxicology Centers Science To Achieve Results (STAR) Progress Review Workshop, USEPA Main Campus, Research Triangle Park, NC, October 1, 2009. |
R832721 (Final) |
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Presentation | Welsh W. Cheminformatics tools for toxicant identification and characterization. Presented at the Info on Informatics Seminar Series, USEPA National Center for Computational Toxicology, Research Triangle Park, NC, December 13, 2006. |
R832721 (2007) |
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Presentation | Welsh W, Ekins S. Molecular modeling studies of interactions between xenobiotics and liver nuclear receptors. Presented at the Computational Toxicology Seminar Series, U.S. EPA National Center for Computational Toxicology, Research Triangle Park, NC, December 20, 2007. |
R832721 (2008) |
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Presentation | Yang E, Androulakis IP. A non-independent model for transcription factor binding prediction. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
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Presentation | Yang E, Foteinou PT, King KR, Yarmush ML, Androulakis IP. Extraction of transcriptional signaling networks via globally optimal biclustering. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
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Presentation | Yang E, Androulakis IP. A non-independent model for transcription factor binding. Presented at the Biomedical Engineering Society (BMES) Fall Meeting, Los Angeles, September 2007. |
R832721 (2007) |
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Presentation | Yang E, Foteinou PT, King KR, Yarmush ML, Androulakis IP. Extraction of transcriptional signaling networks via globally optimal biclustering. Presented at the Biomedical Engineering Society (BMES) Fall Meeting, Los Angeles, CA, September 2007. |
R832721 (2007) |
not available |
Presentation | Yang H, Roth CM, Ierapetritou MG. Reaction and pathway analysis of hepatic metabolism. Presented at the ebCTC Overview Workshop, Piscataway, NJ, November 17, 2006. |
R832721 (2007) |
not available |
Presentation | Yang H, Roth CM, Ierapetritou M. Effects of amino acid supplementation in optimal liver specific functions of hepatocytes. Presented at the 2007 American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt Lake City, UT, November 4-9, 2007. |
R832721 (2008) |
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Presentation | Yang H, Roth CM, Ierapetritou MG. Progress in developing infrastructure for a virtual liver III: effects of amino acid supplementation in hepatic metabolism. Presented at the 2nd Annual Systems Toxicology Symposium: Multiscale Modeling, from Molecules to Organisms, Piscataway, NJ, April 30-May 1, 2008. |
R832721 (2008) |
not available |
Presentation | Yang H, Roth CM, Ierapetritou MG. Analysis of amino acids supplementation in hepatocyte culture using optimization modeling. Presented at the American Institute of Chemical Engineers (AIChE) National Meeting, Nashville, TN, November 8-13, 2009. |
R832721 (Final) |
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Presentation | Yang H, Roth CM, Ierapetritou MG. Design and analysis of amino acid supplementation in hepatocyte culture using optimization modeling. Presented at the Chinese Institute of Engineers-USA/Greater New York Chapter Annual Convention, Marriott Hotel, Newark, NJ, October 31, 2009. |
R832721 (Final) |
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Presentation | Yang YC, Xu X, Georgopoulos PG. Improving assessments of residential human exposures to chloroform via Bayesian PBTK modeling. Presented at the ACC-LRI Workshop on VOC Exposure Modeling, Piscataway, NJ, June 20, 2007. |
R832721 (2007) |
not available |
Proceedings | Fung H, Floudas C, Taylor M, Siliciano R. A New De Novo Approach for Optimizing Peptides that Inhibit HIV-1 Entry. 17TH EUROPEAN SYMPOSIUM ON COMPUTER AIDED PROCESS ENGINEERING 2017;1-6 |
R832721 (Final) |
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Proceedings | Georgopoulos PG. A holistic multiscale approach for assessing the interactions of environmental and biological systems. In: Proceedings of the Protection and Restoration of the Environment VIII (PRE8) Conference, Chania, Greece, July 3-7, 2006. |
R832721 (2007) R832721C001 (2006) |
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Proceedings | McAlister S, Floudas C. Alpha-helical topology and tertiary structure prediction in globular proteins. PROCEEDINGS OF THE 46TH IEEE CONFERENCE ON DECISION AND CONTROL, VOLS 1-14 2007;9885857:4599+ |
R832721 (Final) |
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Proceedings | Miller M, Feng X, Li G, Rabitz H. Nonlinear bionetwork structure inference using the random sampling-high dimensional model representation (RS-HDMR) algorithm. In: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Piscataway, NJ, 2009, 6412-6415. |
R832721 (Final) |
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Proceedings | Yang E, Berthiaume F, Yarmush ML, Androulakis IP. An integrative systems biology approach for analyzing liver hypermetabolism. In: Proceedings of the 16th European Symposium on Computer Aided Process Engineering and 9th International Symposium on Process Systems Engineering, Garmish-Partenkirchen, Germany, July 9-13, 2006, pp. 1655-1660. |
R832721 (2007) R832721C002 (2006) |
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Proceedings | Yang H, Yarmush ML, Roth C, Ierapetritou MG. Minimal reaction sets and metabolic pathways for cultured hepatocytes. In: Proceedings of the 16th European Symposium on Computer Aided Process Engineering and 9th International Symposium on Process Systems Engineering, Garmisch-Partenkirchen, Germany, July 9-13, 2006, pp. 1711-1716. |
R832721 (2007) R832721C002 (2006) |
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The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.