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Book Chapter (14)
Journal Article (117)
Reference Type Reference Title Journal Author Citation Progress Report Year Document Sources
Book Chapter Recent advances in de novo protein design. None Bellows ML, Fung HK, Floudas CA 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. R832721 (Final)
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Book Chapter Mathematical modeling and optimization methods for de novo protein design. None Floudas CA, Fung HK 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)
Book Chapter Overcoming the key challenges in de novo protein design: enhancing computational efficiency and incorporating true backbone flexibility. None Floudas CA, Fung HK, Morikis D, Taylor MS, Zhang L 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. R832721 (2008)
Book Chapter Modeling exposures to chemicals from multiple sources and routes. None Georgopoulos PG, Isukapalli SS, Krishnan K 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)
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Book Chapter Multiscale integration of toxicokinetic and toxicodynamic processes: from cell and tissue to organ and “whole body” models. None Georgopoulos PG, Isukapalli S, Androulakis IP, Ierapetritou MG, Welsh WJ 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. R832721 (Final)
Book Chapter General principles of programming: computer and statistical. None Isukapalli SS, Roy A 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)
Book Chapter Physiologically based pharmacokinetic modeling: inhalation, ingestion, and dermal absorption. None Isukapalli SS, Roy A, Georgopoulos PG 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)
Book Chapter Uncertainty, variability, and sensitivity analyses in simulation models. None Isukapalli SS, Spendiff M, Georgopoulos PG, Krishnan K 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. R832721 (2008)
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Book Chapter Evaluation of toxicological interactions for the dose-response assessment of chemical mixtures. None Krishnan K, Isukapalli S, Boyd J 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. R832721 (2008)
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Book Chapter Pharmacokinetic mechanisms of interactions in chemical mixtures. None Krishnan K, Sasso A, Georgopoulos PG 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. R832721 (2008)
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Book Chapter Dynamic models of disease progression: toward a multiscale model of systemic inflammation in humans. None Scheff JD, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP 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. R832721 (Final)
Book Chapter Gene clustering: a novel decomposition-based clustering approach: global optimum search with enhanced positioning. None Tan MP, Floudas CA 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. R832721 (2008)
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Book Chapter Modeling and predicting pesticide exposures. None Vallero DA, Isukapalli S, Zartarian VG, McCurdy TR, McKone T, Georgopoulos PG, Dary CC 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. R832721 (Final)
Book Chapter Toxicoinformatics: an introduction. None Welsh WJ, Tong W, Georgopoulos PG 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)
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Journal Article Understanding nuclear receptors using computational methods. DRUG DISCOVERY TODAY Ai N, Krasowski MD, Welsh WJ, Ekins S Ai N, Krasowski MD, Welsh WJ, Ekins S. Understanding nuclear receptors using computational methods. Drug Discovery Today 2009;14(9-10):486-494. R832721 (2008)
Journal Article Relationships between circadian rhythms and modulation of gene expression by glucocorticoids in skeletal muscle. AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY, INTEGRATIVE AND COMPARATIVE PHYSIOLOGY Almon RR, Yang E, Lai W, Androulakis IP, Ghimbovschi S, Hoffman EP, Jusko WJ, DuBois DC 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. R832721 (2008)
Journal Article Circadian variations in liver gene expression: relationships to drug actions. JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS Almon RR, Yang E, Lai W, Androulakis IP, DuBois DC, Jusko WJ 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. R832721 (2008)
Journal Article Analysis of time-series gene expression data: methods, challenges, and opportunities. ANNUAL REVIEW OF BIOMEDICAL ENGINEERING Androulakis IP, Yang E, Almon RR Androulakis IP, Yang E, Almon RR. Analysis of time-series gene expression data:methods, challenges, and opportunities. Annual Review of Biomedical Engineering 2007;9:205-228. R832721 (2007)
Journal Article Novel Microtubule Polymerization Inhibitor with Potent Antiproliferative and Antitumor Activity CANCER RESEARCH Arora S, Wang X, Keenan S, Andaya C, Zhang Q, Peng Y, Welsh W 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 R832721 (Final)
Journal Article A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry. None Baliban RC, DiMaggio PA, Plazas-Mayorca MD, Young NL, Garcia BA, Floudas CA 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. R832721 (Final)
Journal Article New compstatin variants through two de novo protein design frameworks. None Bellows ML, Fung HK, Taylor MS, Floudas CA, Lopez de Victoria A, Morikis D 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)
Journal Article 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 Bellows M, Floutas C 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)
Journal Article An efficient algorithm to accelerate the discovery of complex material formulations. None Brell G, Li G, Rabitz H 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. R832721 (Final)
Journal Article Shape signatures: new descriptors for predicting cardiotoxicity in silico. CHEMICAL RESEARCH IN TOXICOLOGY Chekmarev DS, Kholodovych V, Balakin KV, Ivanenkov Y, Ekins S, Welsh WJ 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. R832721 (2008)
Journal Article Predicting inhibitors of acetylcholinesterase by regression and classification machine learning approaches with combinations of molecular descriptors. PHARMACEUTICAL RESEARCH Chekmarev D, Kholodovych V, Kortagere S, Welsh WJ, Ekins S 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. R832721 (2008)
Journal Article ebTrack: an environmental bioinformatics system built upon ArrayTrackTM. BMC PROCEEDINGS Chen M, Martin J, Fang H, Isukapalli S, Georgopoulos PG, Welsh WJ, Tong W 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)
Journal Article Advancing exposure characterization for chemical evaluation and risk assessment. None Cohen Hubal EA, Richard A, Aylward L, Edwards S, Gallagher J, Goldsmith M-R, Isukapalli S, Tornero-Velez R, Weber E, Kavlock R 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)
Journal Article A kriging method for the solution of nonlinear programs with black-box functions. AICHE JOURNAL Davis E, Ierapetritou M Davis E, Ierapetritou M. A kriging method for the solution of nonlinear programs with black-box functions. AIChE Journal 2007;53(8):2001-2012. R832721 (2007)
Journal Article A kriging based method for the solution of mixed-integer nonlinear programs containing black-box functions JOURNAL OF GLOBAL OPTIMIZATION Davis E, Ierapetritou M 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. R832721 (Final)
Journal Article A centroid-based sampling strategy for kriging global modeling and optimization. AICHE JOURNAL Davis E, Ierapetritou M Davis E, Ierapetritou M. A centroid-based sampling strategy for kriging global modeling and optimization. AIChE Journal 2010;56(1):220-240. R832721 (2008)
Journal Article De novo peptide identification via tandem mass spectrometry and integer linear optimization. ANALYTICAL CHEMISTRY DiMaggio Jr PA, Floudas CA 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)
Journal Article A mixed-integer optimization framework for de novo peptide identification. AICHE JOURNAL DiMaggio Jr PA, Floudas CA DiMaggio Jr PA, Floudas CA. A mixed-integer optimization framework for de novo peptide identification. AIChE Journal 2007;53(1):160-173. R832721 (2007)
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Journal Article 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 DiMaggio Jr PA, Floudas CA, Lu BW, Yates III JR 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. R832721 (2008)
Journal Article Optimal methods for re-ordering data matrices in systems biology and drug discovery applications. BIOPHYSICAL REVIEWS AND LETTERS DiMaggio Jr PA, McAllister SR, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HA 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. R832721 (2008)
Journal Article Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. BMC BIOINFORMATICS DiMaggio Jr PA, McAllister SR, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HA 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. R832721 (2008)
Journal Article Enhancing molecular discovery using descriptor-free rearrangement clustering techniques for sparse data sets. None DiMaggio Jr. PA, McAllister SR, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HA 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. R832721 (Final)
Journal Article A network flow model for biclustering via optimal re-ordering of data matrices. JOURNAL OF GLOBAL OPTIMIZATION DiMaggio Jr PA, McAllister SR, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HA 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. R832721 (2008)
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Journal Article 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. None DiMaggio Jr. PA, Subramani A, Judson RS, Floudas CA 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. R832721 (Final)
Journal Article 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. None DiMaggio PA, Young NL, Baliban RC, Garcia BA, Floudas CA 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. R832721 (Final)
Journal Article Agent-based modeling of endotoxin-induced acute inflammatory response in human blood leukocytes. None Dong X, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP 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. R832721 (Final)
Journal Article A mechanistic modeling system for estimating large-scale emissions and transport of pollen and co-allergens. None Efstathiou C, Isukapalli S, Georgopoulos P 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)
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Journal Article Human pregnane X receptor antagonists and agonists define molecular requirements for different binding sites. MOLECULAR PHARMACOLOGY 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 Ekins S, Chang C, Mani S, Krasowski MD, Reschly EJ, Iyer M, Kholodovych V, Ai N, Welsh WJ, Sinz M, Swaan PW, Patel R, Bachmann K. Human pregnane X receptor antagonists and agonists define molecular requirements for different binding sites. Molecular Pharmacology 2007;72(3):592-603. R832721 (2007)
Journal Article Computational discovery of novel low micromolar human pregnane X receptor antagonists. MOLECULAR PHARMACOLOGY Ekins S, Kholodovych V, Ai N, Sinz M, Gal J, Gera L, Welsh WJ, Bachmann K, Mani S 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. R832721 (2008)
Journal Article Enhancing the efficiency of directed evolution in focused enzyme libraries by the adaptive substituent reordering algorithm. None Feng X, Sanchis J, Reetz MT, Rabitz H 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. R832721 (Final)
Journal Article Computational methods in protein structure prediction. BIOTECHNOLOGY AND BIOENGINEERING Floudas CA Floudas CA. Computational methods in protein structure prediction. Biotechnology and Bioengineering 2007;97(2):207-213. R832721 (2007)
Journal Article Networks, biology and systems engineering: a case study in inflammation. None Foteinou PT, Yang E, Androulakis IP Foteinou PT, Yang E, Androulakis IP. Networks, biology and systems engineering: a case study in inflammation. Computers & Chemical Engineering 2009;33(12):2028-2041. R832721 (Final)
Journal Article Translational potential of systems-based models of inflammation. CLINICAL AND TRANSLATIONAL SCIENCE Foteinou PT, Calvano SE, Lowry SF, Androulakis IP 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. R832721 (2008)
Journal Article Modeling endotoxin-induced systemic inflammation using an indirect response approach. MATHEMATICAL BIOSCIENCES Foteinou PT, Calvano SE, Lowry SF, Androulakis IP 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. R832721 (2008)
Journal Article In silico simulation of corticosteroids effect on an NFkB-dependent physicochemical model of systemic inflammation. PLOS ONE Foteinou PT, Calvano SE, Lowry SF, Androulakis IP 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. R832721 (2008)
Journal Article A mixed-integer optimization framework for the synthesis and analysis of regulatory networks. JOURNAL OF GLOBAL OPTIMIZATION Foteinou PT, Yang E, Saharidis GK, Ierapetritou MG, Androulakis IP 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. R832721 (2008)
Journal Article Multiscale model for the assessment of autonomic dysfunction in human endotoxemia. None Foteinou PT, Calvano SE, Lowry SF, Androulakis IP 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. R832721 (Final)
Journal Article A physiological model for autonomic heart rate regulation in human endotoxemia SHOCK Foteinou P, Calvano S, Lowry S, Androulakis I 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. R832721 (Final)
Journal Article Computational de novo peptide and protein design: rigid templates versus flexible templates. INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH Fung HK, Welsh WJ, Floudas CA Fung HK, Welsh WJ, Floudas CA. Computational de novo peptide and protein design: rigid templates versus flexible templates. Industrial & Engineering Chemistry Research 2008;47(4):993-1001. R832721 (2007)
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Journal Article Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2. BIOPHYSICAL JOURNAL Fung HK, Floudas CA, Taylor MS, Zhang L, Morikis D 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. R832721 (2008)
Journal Article A multiscale approach for assessing the interactions of environmental and biological systems in a holistic health risk assessment framework. WATER, AIR, & SOIL POLLUTION: FOCUS Georgopoulos PG 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)
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R832721C001 (2006)
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Journal Article Response to "µg/kg-day or µg/day? A commentary on Georgopoulos et al., JESEE 2008." JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY Georgopoulos PG, Sasso AF, Isukapalli SS, Lioy PJ, Vallero DA, Okino M, Reiter L 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). R832721 (2008)
Journal Article Biologically based modeling of multimedia, multipathway, multiroute population exposures to arsenic. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY Georgopoulos PG, Wang S-W, Yang Y-C, Xue J, Zartarian VG, McCurdy T, Ozkaynak H 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. R832721 (2008)
Journal Article Reconstructing population exposures to environmental chemicals from biomarkers: challenges and opportunities. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY Georgopoulos PG, Sasso AF, Isukapalli SS, Lioy PJ, Vallero DA, Okino M, Reiter L 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. R832721 (2008)
Journal Article Differential gene expression profiling of mouse skin after sulfur mustard exposure: extended time response and inhibitor effect. TOXICOLOGY AND APPLIED PHARMACOLOGY Gerecke DR, Chen M, Isukapalli SS, Gordon MK, Chang Y-C, Tong W, Androulakis IP, Georgopoulos PG 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. R832721 (2008)
Journal Article Derivation of ligands for the complement C3a receptor from the C-termin of C5a EUROPEAN JOURNAL OF PHARMACOLOGY Halai R, Bellows-Peterson M, Branchett W, Smadbeck J, Kieslich C, Croker D, Cooper M, Morikis D, Woodruff T, Floudas C, Monk P 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. R832721 (Final)
Journal Article Mechanistic modeling of emergency events: assessing the impact of hypothetical releases of anthrax. RISK ANALYSIS Isukapalli SS, Lioy PJ, Georgopoulos PG 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. R832721 (2008)
Journal Article Transcriptional and metabolic flux profiling of triadimefon effects on cultured hepatocytes. None Iyer VV, Ovacik MA, Androulakis IP, Roth CM, Ierapetritou MG 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. R832721 (Final)
Journal Article Effects of glucose and insulin on HepG2-C3A cell metabolism. BIOTECHNOLOGY AND BIOENGINEERING Iyer VV, Yang H, Ierapetritou MG, Roth CM 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. R832721 (2008)
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Journal Article A scalable algorithm for molecular property estimation in high dimensional scaffold-based libraries. None Izmailov S, Feng XJ, Li G, Rabitz H 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. R832721 (Final)
Journal Article 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 Jiao Y, Su M, Chen M, Jia W, Chou Y, Huang Z, Yang N, Tong W Jiao Y, Su M, Chen M, Jia W, Chou Y, Huang Z, Yang N, Tong W. LC/ESI-MS method for the determination of trimetazidine in human plasma: application to a bioequivalence study on Chinese volunteers. Journal of Pharmaceutical and Biomedical Analysis 2007;43(5):1804-1807. R832721 (2007)
Journal Article A meta-data based method for DNA microarray imputation. BMC BIOINFORMATICS Jornsten R, Ouyang M, Wang H-Y Jornsten R, Ouyang M, Wang H-Y. A meta-data based method for DNA microarray imputation. BMC Bioinformatics 2007;8:109. R832721 (2007)
Journal Article Mixture models with multiple levels, with application to the analysis of multifactor gene expression data. BIOSTATISTICS Jornsten R, Keles S 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. R832721 (2008)
Journal Article Simultaneous model selection via rate-distortion theory, with applications to cluster and significance analysis of gene expression data. JOURNAL OF COMPUTATIONAL & GRAPHICAL STATISTICS Jornsten R 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. R832721 (2007)
Journal Article Hybrid Scoring and Classification Approaches to Predict Human Pregnane X Receptor Activators PHARMACEUTICAL RESEARCH Kortagere S, Chekmarev D, Welsh W, Ekins S 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 R832721 (Final)
Journal Article New predictive models for blood-brain barrier permeability of drug-like molecules. PHARMACEUTICAL RESEARCH Kortagere S, Chekmarev D, Welsh WJ, Ekins S 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. R832721 (2008)
Journal Article Halogenated ligands and their interactions with amino acids: implications for structure-activity and structure-toxicity relationships. JOURNAL OF MOLECULAR GRAPHICS AND MODELLING Kortagere S, Ekins S, Welsh WJ 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. R832721 (2008)
Journal Article Structure-based Design of Novel Small-Molecule Inhibitors of Plasmodium falciparum JOURNAL OF CHEMICAL INFORMATION AND MODELING Kortagere S, Welsh W, Morrisey J, Daly T, Ejigiri I, Sinnis P, Vaidya A, Bergman L 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 R832721 (Final)
Journal Article Tissue-level modeling of xenobiotic metabolism in liver: an emerging tool for enabling clinical translational research. CLINICAL AND TRANSLATIONAL SCIENCE Lerapetritou MG, Georgopoulos PG, Roth CM, Androulakis IP 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. R832721 (2008)
Journal Article Human ADA3 regulates RARα transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket NUCLEIC ACIDS RESEARCH Li C, Ai N, Dinh G, Welsh W, Chen J 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 R832721 (Final)
Journal Article Human ADA3 regulates RARα transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket. NUCLEIC ACIDS RESEARCH Li C-W, Ai N, Dinh GK, Welsh WJ, Chen JD 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. R832721 (2008)
R832721 (Final)
Journal Article Regularized random-sampling high dimensional model representation (RS-HDMR). JOURNAL OF MATHEMATICAL CHEMISTRY Li G, Rabitz H, Hu J, Chen Z, Ju Y 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. R832721 (2007)
R832721 (2008)
Journal Article Global sensitivity analysis for systems with independent and/or correlated inputs. None Li G, Rabitz H, Yelvington PE, Oluwole OO, Bacon F, Kolb CE, Schoendorf J 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)
Journal Article D-MORPH regression: application to modeling with unknown parameters more than observation data. None Li G, Rabitz H 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)
Journal Article The Major Human Pregnane X Receptor PXR Splice Variant, PXR.2, Exhibits Significantly Diminished Ligand-Activated Transcriptional Regulation None Lin Y, Yassuda K, Assem M, Cline C, Barber J, Li C, Kholodovych V, Ai N, Chen J, Welsh W, Ekins S, Schuetz E 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)
Journal Article Novel approach for α-helical topology prediction in globular proteins: generation of interhelical restraints. PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS McAllister SR, Mickus BE, Klepeis JL, Floudas CA 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)
Journal Article α-helical topology prediction and generation of distance restraints in membrane proteins. None McAllister SR, Floudas CA 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)
Journal Article A path selection approach to global pairwise sequence alignment using integer linear optimization. OPTIMIZATION McAllister SR, Rajgaria R, Floudas CA 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)
Journal Article Descriptor-free molecular discovery in large libraries by adaptive substituent reordering. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS McAllister SR, Feng X-J, DiMaggio Jr PA, Floudas CA, Rabinowitz JD, Rabitz H 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)
Journal Article Enhanced bounding techniques to reduce the protein conformational search space. OPTIMIZATION METHODS & SOFTWARE McAllister SR, Floudas CA 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)
Journal Article Mathematical modeling and efficient optimization methods for the distance-dependent rearrangement clustering problem. JOURNAL OF GLOBAL OPTIMIZATION McAllister SR, DiMaggio Jr PA, Floudas CA 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)
Journal Article An improved hybrid global optimization method for protein tertiary structure prediction. COMPUTATIONAL OPTIMIZATION AND APPLICATIONS McAllister SR, Floudas CA 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)
Journal Article Unsupervised selection of highly coexpressed and noncoexpressed genes using a consensus clustering approach. OMICS Nguyen TT, Nowakowski RS, Androulakis IP 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)
Journal Article Importance of replication in analyzing time-series gene expression data: corticosteroid dynamics and circadian patterns in rat liver. None Nguyen TT, Almon RR, DuBois DC, Jusko WJ, Androulakis IP 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)
Journal Article Computational identification of transcriptional regulators in human endotoxemia. None Nguyen TT, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP 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)
Journal Article Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures BMC BIOINFORMATICS Nguyen T, Almon R, DuBOis D, Jko W, Androulakis I 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)
Journal Article Evolving carbapenemases: can medicinal chemists advance one step ahead of the coming storm? None Oelschlaeger P, Ai N, DuPrez KT, Welsh WJ, Toney JH 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)
Journal Article Metabolic flux determination in perfused livers by mass balance analysis: Effect of fasting BIOTECHNOLOGY AND BIOENGINEERING Orman M, Arai K, Yarmush M, Androulakis I, Berthiaume F, Ierapetritou M 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)
Journal Article On the potential for integrating gene expression and metabolic flux data. CURRENT BIOINFORMATICS Ovacik MA, Androulakis IP Ovacik MA, Androulakis IP. On the potential for integrating gene expression and metabolic flux data. Current Bioinformatics 2008;3(3):142-148. R832721 (2008)
Journal Article Circadian signatures in rat liver: from gene expression to pathways. BMC BIOINFORMATICS Ovacik MA, Sukumaran S, Almon RR, DuBois DC, Jusko WJ, Androulakis IP 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)
Journal Article Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison. TOXICOLOGY AND APPLIED PHARMACOLOGY Ovacik MA, Androulakis IP 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)
Journal Article Pathway modeling of microarray data: a case study of pathway activity changes in the testis following in utero exposure to dibutyl phthalate (DBP). None Ovacik MA, Sen B, Euling SY, Gaido KW, Ierapetritou MG, Androulakis IP 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)
Journal Article Diverse metabolic model parameters generate similar methionine cycle dynamics. JOURNAL OF THEORETICAL BIOLOGY Piazza M, Feng XJ, Rabinowitz JD, Rabitz H 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)
Journal Article Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase. BIOCHEMISTRY Rabinowitz JD, Hsiao JJ, Gryncel KR, Kantrowitz ER, Feng X-J, Li G, Rabitz H 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)
Journal Article A novel high resolution Cα—Cα distance dependent force field based on a high quality decoy set. PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS Rajgaria R, McAllister SR, Floudas CA 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)
Journal Article Distance dependent centroid to centroid force fields using high resolution decoys. PROTEINS: STRUCTURE, FUNCTION, BIOINFORMATICS Rajgaria R, McAllister SR, Floudas CA 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)
Journal Article Towards accurate residue-residue hydrophobic contact prediction for α helical proteins via integer linear optimization. PROTEINS: STRUCTURE, FUNCTION, BIOINFORMATICS Rajgaria R, McAllister SR, Floudas CA 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)
Journal Article 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. None Rajgaria R, Wei Y, Floudas CA 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)
Journal Article Evolution of the bile salt nuclear receptor FXR in vertebrates. JOURNAL OF LIPID RESEARCH Reschly EJ, Ai N, Ekins S, Welsh WJ, Hagey LR, Hofmann AF, Krasowski MD 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)
Journal Article Ligand specificity and evolution of liver X receptors. JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY Reschly EJ, Ai N, Welsh WJ, Ekins S, Hagey LR, Krasowski MD 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)
Journal Article Resolution method for mixed integer bi-level linear problems based on decomposition technique. JOURNAL OF GLOBAL OPTIMIZATION Saharidis GK, Ierapetritou MG 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)
Journal Article Model building using bi-level optimization JOURNAL OF GLOBAL OPTIMIZATION Saharidis G, Androulakis I, Ierapetritou M Saharidis G, Androulakis I, Ierapetritou M. Model building using bi-level optimization. JOURNAL OF GLOBAL OPTIMIZATION 2011;49(1):49-67. R832721 (Final)
Journal Article A generalized physiologically-based toxicokinetic modeling system for chemical mixtures containing metals. None Sasso AF, Isukapalli SS, Georgopoulos PG 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)
Journal Article Bayesian analysis of a lipid-based physiologically based toxicokinetic model for a mixture of PCBs in rats. JOURNAL OF TOXICOLOGY Sasso AF, Georgopoulos PG, Isukapalli SS, Krishnan K 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)
Journal Article A new symbolic representation for the identification of informative genes in replicated microarray experiments. None Scheff JD, Almon RR, DuBois DC, Jusko WJ, Androulakis IP 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)
Journal Article Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies. TOXICOLOGY AND APPLIED PHARMACOLOGY Schnackenberg LK, Chen M, Sun J, Holland RD, Dragan Y, Tong W, Welsh W, Beger RD 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)
Journal Article Mathematical model of uptake and metabolism of arsenic(III) in human hepatocytes – incorporation of cellular antioxidant response and threshold-dependent behavior. None Stamatelos SK, Brinkerhoff CJ, Isukapalli SS, Georgopoulos PG 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)
Journal Article A semi-mechanistic integrated toxicokinetic-toxicodynamic (TK/TD) model for arsenic(III) in hepatocytes. JOURNAL OF THEORETICAL BIOLOGY Stamatelos S, Androulakis I, Kong A, Georgopoulos P 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)
Journal Article Selecting High Quality Protein Structures from Diverse Conformational Ensembles BIOPHYSICAL JOURNAL Subramani A, DiMaggio P, Floudas C Subramani A, DiMaggio P, Floudas C. Selecting High Quality Protein Structures from Diverse Conformational Ensembles. BIOPHYSICAL JOURNAL 2009;97(6):1728-1736. R832721 (Final)
Journal Article Reconstitution and engineering of apoptotic protein interactions on the bacterial cell surface. None Sun J, Abdeljabbar DM, Clarke N, Bellows ML, Floudas CA, Link AJ 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)
Journal Article Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures. BMC BIOINFORMATICS Tan MP, Smith EN, Broach JR, Floudas CA 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)
Journal Article Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework. BIOPHYSICAL JOURNAL Taylor MS, Fung HK, Rajgaria R, Filizola M, Weinstein H, Floudas CA 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)
Journal Article Probabilistic modeling of dietary arsenic exposure and dose and evaluation with 2003-2004 NHANES data. None Xue J, Zartarian V, Wang S-W, Liu SV, Georgopoulos P 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)
Journal Article Identification of global transcriptional dynamics. PLOS ONE Yang EH, Almon RR, Dubois DC, Jusko WJ, Androulakis IP Yang EH, Almon RR, Dubois DC, Jusko WJ, Androulakis IP. Identification of global transcriptional dynamics. PLoS One 2009;10;4(7):e5992. R832721 (2008)
Journal Article Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. BMC BIOINFORMATICS Yang E, Maguire T, Yarmush ML, Berthiaume F, Androulakis IP 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)
Journal Article Context specific transcription factor prediction. ANNALS OF BIOMEDICAL ENGINEERING Yang E, Simcha D, Almon RR, Dubois DC, Jusko WJ, Androulakis IP 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)
Journal Article A novel non-overlapping bi-clustering algorithm for network generation using living cell array data. BIOINFORMATICS Yang E, Foteinou PT, King KR, Yarmush ML, Androulakis IP 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)
Journal Article Informative gene selection and design of regulatory networks using integer optimization. COMPUTERS & CHEMICAL ENGINEERING Yang E, Maguire T, Yarmush ML, Androulakis IP 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)
Journal Article Identification of regulatory mechanisms of the hepatic response to thermal injury. COMPUTERS & CHEMICAL ENGINEERING Yang E, Maguire TJ, Yarmush ML, Berthiaume F, Androulakis IP 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)
Journal Article Extracting global system dynamics of corticosteroid genomic effects in rat liver. JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS Yang E, Almon RR, DuBois DC, Jusko WJ, Androulakis IP 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)
Journal Article Assessing and selecting gene expression signals based upon the quality of the measured dynamics. BMC BIOINFORMATICS Yang E, Androulakis IP 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)
Journal Article Transcription factor network reconstruction using the living cell array. JOURNAL OF THEORETICAL BIOLOGY Yang E, Yarmush ML, Androulakis IP 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)
Journal Article A rational design approach for amino acid supplementation in hepatocyte culture. BIOTECHNOLOGY AND BIOENGINEERING Yang H, Roth CM, Ierapetritou MG 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)
Journal Article Effects of amino acid transport limitations on cultured hepatocytes. BIOPHYSICAL CHEMISTRY Yang H, Ierapetritou MG, Roth CM 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)
Journal Article Analysis of amino acid supplementation effects on hepatocyte cultures using flux balance analysis. OMICS Yang H, Roth CM, Ierapetritou MG 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)
Journal Article A Bayesian population PBPK model for multiroute chloroform exposure. JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY Yang Y, Xu X, Georgopoulos PG 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)
Journal Article Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli MOLECULAR SYSTEMS BIOLOGY Yuan J, Doucette C, Fowler W, Feng X, Piazza M, Rabitz H, Wingreen N, Rabinowitz J 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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