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Extramural Research

Environmental Bioinformatics and Computational Toxicology Center

EPA Grant Number: R832721
Center: New Jersey Research Center for Environmental Bioinformatics and Computational Toxicology
Center Director: Welsh, William J.
Title: Environmental Bioinformatics and Computational Toxicology Center
Investigators: Welsh, William J. , Georgopoulos, Panos G.
Institution: University of Medicine and Dentistry of New Jersey , Princeton University , Rutgers University
EPA Project Officer: Pascual, Pasky
Project Period: October 1, 2005 through September 30, 2010
Project Amount: $5,422,135
RFA: Computational Toxicology: Environmental Bioinformatics Research Center (2004)
Research Category: Health Effects , Computational Toxicology

Description:

Objective:

The Research Center will bring together a team of computational scientists, with diverse backgrounds in bioinformatics, cheminformatics and enviroinformatics, from UMDNJ, Rutgers, and Princeton Universities, and the USFDA’s Center for Toxicoinformatics. This team will address, in a systematic and integrative manner, multiple elements of the toxicant Source-to-Outcome sequence ( Investigational Area 1, as identified in the RFA) as well as develop cheminformatics tools for toxicant characterization ( Investigational Area 2, Predictive Models for Hazard Identification ). The computational tools to be developed through this effort will be extensively evaluated and refined through collaborative applications involving Center scientists as well as colleagues from the three universities and USEPA; particular emphasis will be on methods that enhance current quantitative risk assessment practices and reduce uncertainties.

Approach:

The proposed Center will address a wide range of issues in Investigational Areas 1 and 2 and, furthermore, will pursue complementary applications in risk assessment ( Investigational Area 3 ). This will be achieved with the requested resources, by building upon a variety of methods and software systems recently developed at UMDNJ, Rutgers, Princeton (with funding from USEPA, USDOE, NIH and NSF), and USFDA. Research activities over the proposed 5-year effort will be organized in five projects; each project will develop a set of “stand-alone" components addressing specific problems of computational toxicology. Furthermore, Research Project 1 will provide an integrative framework for Investigational Area 1 while Project 4 will address the core issues of Area 2. Extensive interaction as well as public outreach and training activities will constitute essential elements of the Center and will be tightly interwoven with the research activities.

Expected Results:

Research Project 1 (Development and Application of a Dose-Response Information Analysis [DORIAN] System) will provide an integrative framework for the outcomes of the other projects. This framework will include the following components: a web-accessible Environmental Bioinformatics Knowledge Base (EBKB) that will provide a user-oriented interface to an extensive set of information and modeling resources; the ebTrack integrated analysis system that will include linkages to multiple (public and commercial) computational and database systems; Bayesian computational tools for characterizing and reducing uncertainties in mechanistic modeling of toxicity pathways; diagnostic computational tools for sensitivity and stability analysis of mechanistic models and statistical methods for data analysis; and enhanced tools for quantitative risk assessment (QRA) applications (e.g. for cross-species extrapolation, chemical mixtures, and dose-response).

Research Project 2 (Hepatocyte Metabolism Model for Xenobiotics) will develop tools for identifying maximally informative sets of toxicologically relevant genes; tools for analysis of toxicologically relevant regulatory networks; an expanded version of the Rutgers hepatocyte metabolism model that will incorporate transformations of xenobiotics; and tools for the analysis of transcriptional regulation that will allow assessing changes in hepatocyte phenotypic phase space.

Research Project 3 (Tools for Optimal Identification of Biological Networks) will develop efficient identification tools for inferring biological network structure from available laboratory data; optimization tools for extracting quantitative information of biological system parameters (rate constants, diffusion coefficients, binding affinities, etc.); global sensitivity analysis tools for identifying most effective molecular targets or pathways of biological networks and for guiding the design of laboratory experiments; and optimal feedback control tools for inferring networks with feedback loops.

Research Project 4 (Cheminformatics Tools for Toxicant Characterization) will develop an integrative hierarchical decision-forest framework for toxicant characterization that encompasses several novel technologies, including the Shape Signatures tool that rapidly matches organic and organometallic chemicals with each other or, alternatively, against target receptor sites/subsites; the Polynomial Neural Network (PNN) that automatically generates physically-intuitive linear or non-linear QSAR models; and virtual high-throughput screening (vHTS) methods that predict ligand binding affinity and provide mechanistic information (toxicity pathways).

Research Project 5 (Optimization Tools for In Silico Proteomics) will customize computational methods for protein structure prediction and de novo protein design, with specific focus on the important families of Glutathione Transferases (GST) (cytosolic, mitochondrial and microsomal GST); develop and implement computational methods for elucidating the topology of signal transduction networks and addressing uncertainties in experimental data and models; and develop de novo computational proteomics methods for peptide and protein identification via tandem mass spectroscopy.


Journal Articles: 103 Displayed | Download in RIS Format

Other center views: All 301 publications 117 publications in selected types All 103 journal articles

Type Citation Sub Project Document Sources
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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2008)
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  • Journal Article Androulakis IP, Yang E, Almon RR. Analysis of time-series gene expression data:methods, challenges, and opportunities. Annual Review of Biomedical Engineering 2007;9:205-228. R832721 (2007)
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  • Journal Article 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)
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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 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)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2007)
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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. R832721 (2008)
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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)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (Final)
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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. R832721 (2008)
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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. R832721 (Final)
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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. R832721 (Final)
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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. R832721 (Final)
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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)
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  • Journal Article Ekins S, Chang C, Mani S, Krasowski MD, Reschly EJ, Iyer M, Kholodovych V, Ai N, Welsh WJ, Sinz M, Swaan PW, Patel R, Bachmann K. Human pregnane X receptor antagonists and agonists define molecular requirements for different binding sites. Molecular Pharmacology 2007;72(3):592-603. R832721 (2007)
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  • Journal Article 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)
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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. R832721 (Final)
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  • Journal Article Floudas CA. Computational methods in protein structure prediction. Biotechnology and Bioengineering 2007;97(2):207-213. R832721 (2007)
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  • Journal Article Foteinou PT, Yang E, Androulakis IP. Networks, biology and systems engineering: a case study in inflammation. Computers & Chemical Engineering 2009;33(12):2028-2041. R832721 (Final)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (Final)
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  • Journal Article Fung HK, Welsh WJ, Floudas CA. Computational de novo peptide and protein design: rigid templates versus flexible templates. Industrial & Engineering Chemistry Research 2008;47(4):993-1001. R832721 (2007)
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  • Journal Article 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)
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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)
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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). R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (Final)
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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. R832721 (2008)
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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. R832721 (Final)
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  • Journal Article Jiao Y, Su M, Chen M, Jia W, Chou Y, Huang Z, Yang N, Tong W. LC/ESI-MS method for the determination of trimetazidine in human plasma: application to a bioequivalence study on Chinese volunteers. Journal of Pharmaceutical and Biomedical Analysis 2007;43(5):1804-1807. R832721 (2007)
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  • Journal Article Jornsten R, Ouyang M, Wang H-Y. A meta-data based method for DNA microarray imputation. BMC Bioinformatics 2007;8:109. R832721 (2007)
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  • Journal Article 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)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2008)
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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. R832721 (2007)
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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)
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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 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, 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)
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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 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 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)
    R832721 (Final)
    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)
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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 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 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 Wang CY, Ai N, Arora S, Erenrich E, Nagarajan K, Zauhar R, Young D, Welsh WJ. Identification of previously unrecognized antiestrogenic chemicals using a novel virtual screening approach. Chemical Research in Toxicology 2006;19(12):1595-1601. R832721C004 (2006)
    R832721C004 (2007)
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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)
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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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  • Supplemental Keywords:

    computational toxicology, bioinformatics, proteomics, metabonomics, physiomics, cytomics, genomics, transcriptomics, enviroinformatics, cheminformatics, biologically based dose response-modeling, cross-species extrapolation, risk assessment,, Health, Scientific Discipline, Geographic Area, State, Risk Assessments, Biochemistry, Environmental Monitoring, Biology, ecological risk assessment, computational toxicology, toxicology, biopollution, dose-response, environmental risks, outreach and training, chemical composition, New Jersey (NJ), human exposure, bioinformatics, human health risk

    Progress and Final Reports:
    2006 Progress Report
    2007 Progress Report
    2008 Progress Report
    Final Report

    Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
    R832721C001 Development and Application of the DORIAN (Dose-Response Information Analysis) System
    R832721C002 Hepatocyte Metabolism Model for Xenobiotics
    R832721C003 Development of Computational Tools for Optimal Identification of Biological Networks
    R832721C004 Cheminformatics Tools for Toxicant Characterization
    R832721C005 Optimization Tools for In Silico Structural Proteomics

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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.

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