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Environmental Bioinformatics and Computational Toxicology Center – ebCTC » Environmental Bioinformatics Knowledge Base

Blog April 27, 2022

 

Structure of ebCTC research

The Environmental Bioinformatics and Computational Toxicology Center (ebCTC) was established in 2005 with funding from the USEPA as a research consortium of Robert Wood Johnson Medical School, Rutgers and Princeton Universities, and the US Food and Drug Administration’s Center for Toxicoinformatics. During its 5 years of USEPA support, ebCTC researchers produced over 100 peer-reviewed publications and participated in numerous national and international conferences.

William J. Welsh, Ph.D
 Center Director and Principal Investigator
Cheminformatics Tools for Toxicant Characterization
 Department of Pharmacology,
Rutgers-Robert Wood Johnson Medical School

Panos G. Georgopoulos, Ph.D. Center Co-Director and Principal Investigator

Development and Application of Dose-Response Information Analysis (DORIAN) System

Department of Environmental and Occupational Medicine,

Rutgers-Robert Wood Johnson Medical School

Weida Tong, Ph.D.
 Co-Principal Investigator
Development and Application of Dose-Response Information Analysis (DORIAN) System
 Center for Toxicoinformatics, National Center for Toxicological Research, USFDA

Marianthi Ierapetritou, Ph.D. Principal Investigator

Hepatocyte Metabolism Model for Xenobiotics

Department of Chemical & Biochemical Engineering, Rutgers University

Ioannis Androulakis, Ph.D. Co-Principal Investigator

Hepatocyte Metabolism Model for Xenobiotics

Department of Biomedical Engineering, Rutgers University

Herschel Rabitz, Ph.D.
 Principal Investigator
Tools for Optimal Identification of Biological Networks
 Department of Chemistry, Princeton University

Chris A. Floudas, Ph.D. Principal Investigator

Optimization Tools for In Silico Proteomics

Department of Chemical Engineering, Princeton University

Selected peer-reviewed publications

Publications representing results of ebCTC research during 2006-2011, listed alphabetically by lead author; links to abstracts are provided where available. To request an article reprint please contact Linda Everett.

2011

  • Efstathiou C., Isukapalli S.S. and Georgopoulos P.G. (2011). A mechanistic modeling system for estimating large scale emissions and transport of pollen and co-allergens. Atmospheric Environment 45 (13): 2260-2276. DOI:10.1016/j.atmosenv.2010.12.008 [DOI link]
  • Georgopoulos P.G., Isukapalli S., Androulakis I.P., Ierapetritou M.G. and Welsh W.J. (2011). Multiscale integration of toxicokinetic and toxicodynamic processes: From cell and tissue to organ and “whole body” models. In Handbook of Systems Toxicology. Casciano, D. and Sahu, S. (eds.), John Wiley & Sons. pp. 619-668 [publisher link]
  • Isukapalli S.S., Bielory L. and Georgopoulos P.G. (2011). Modeling effects of climate change on allergic illness. In McGraw-Hill Yearbook of Science and Technology 2011 New York, McGraw-Hill: pp.205-208 [publisher link]
  • Ovacik M.A. and Androulakis I.P. (2011). Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison. Toxicology and Applied Pharmacology (advance online publication) DOI: 10.1016/j.taap.2010.09.009 [DOI link]
  • Ovacik M.A., Sen B., Euling S.Y., Gaido K.W., Ierapetritou M.G. and Androulakis I.P. (2011). 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 (advance online publication) DOI: 10.1016/j.taap.2010.09.008 [DOI link]
  • Saharidis G.K.D., Androulakis I.P. and Ierapetritou M.G. (2011). Model building using bi-level optimization. Journal of Global Optimization 49 (1): 49-67. DOI: 10.1007/s10898-010-9533-9 [DOI link]
  • Stamatelos S.K., Brinkerhoff C.J., Isukapalli S.S. and Georgopoulos P.G. (2011). Mathematical model of uptake and metabolism of arsenic(III) in human hepatocytes – Incorporation of cellular antioxidant response and threshold-dependent behavior. BMC Systems Biology 5 (16) DOI: 10.1186/1752-0509-5-16 [Biomed Central link]

2010

  • Baliban R.C., DiMaggio P.A., Plazas-Mayorca M.D., Young N.L., Garcia B.A. and Floudas C.A. (2010). A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry Molecular and Cellular Proteomics 9: 764-779. DOI: 10.1074/mcp.M900487-MCP200 [DOI link]
  • Bellows M.L., Fung H.K. and Floudas C.A. (2010). Recent advances in de novo protein design. In Process Systems Engineering: Volume 6. Pistikopoulos, E., Georgiadis, M. and Dua, V. (eds.), Wiley: pp.207-226 [publisher link]
  • Bellows M.L., Fung H.K., Taylor M.S., Floudas C.A., López de Victoria A. and Morikis D. (2010). New compstatin variants through two de novo protein design frameworks. Biophysical Journal 98 (10): 2337-2346. DOI: 10.1016/j.bpj.2010.01.057 [DOI link]
  • Brell G., Li G. and Rabitz H. (2010). An efficient algorithm to accelerate the discovery of complex material formulations. The Journal of Chemical Physics 132 (17): 174103-10. DOI: 10.1063/1.3407440 [DOI link]
  • Cohen Hubal E.A., Richard A., Aylward L., Edwards S., Gallagher J., Goldsmith M.-R., Isukapalli S., Tornero-Velez R., Weber E. and Kavlock R. (2010). Advancing exposure characterization for chemical evaluation and risk assessment. Journal of Toxicology and Environmental Health, Part B: Critical Reviews 13 (2): 299 – 313. DOI: 10.1080/10937404.2010.483947 [DOI link]
  • DiMaggio P.A., McAllister S.R., Floudas C.A., Feng X.J., Rabinowitz J.D. and Rabitz H.A. (2010). Enhancing molecular discovery using descriptor-free rearrangement clustering techniques for sparse data sets. AIChE Journal 56 (2): 405 – 418. DOI: 10.1002/aic.11986 6 [DOI link]
  • DiMaggio P.A., McAllister S.R., Floudas C.A., Feng X.J., Rabinowitz J.D. and Rabitz H.A. (2010). A network flow model for biclustering via optimal re-ordering of data matrices. Journal of Global Optimization 47 (3): 343-354. DOI: 10.1007/s10898-008-9349-z [DOI link]
  • DiMaggio P.A., Subramani A., Judson R.S. and Floudas C.A. (2010). 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 118 (1): 251-265. DOI: 10.1093/toxsci/kfq233 [DOI link]
  • Dong X., Foteinou P.T., Calvano S.E., Lowry S.F. and Androulakis I.P. (2010). Agent-based modeling of endotoxin-induced acute inflammatory response in human blood leukocytes. PLoS One 5 (2): e9249. DOI: 10.1371/journal.pone.0009249 [DOI link]
  • Foteinou P.T., Calvano S.E., Lowry S.F. and Androulakis I.P. (2010). Multi-scale model for the assessment of autonomic dysfunction in human endotoxemia. Physiological Genomics 42: 5-19. DOI: 10.1152/physiolgenomics.00184.2009 [DOI link]
  • Foteinou P.T., Scheff J.D., Calvano S.E., Lowry S.F. and Androulakis I.P. (2010). Approaches towards a multi-scale model of systemic inflammation in humans. Chapter 4. In Methods in Bioengineering: Alternative Technologies to Animal Testing. Maguire, T. and Novik, E. (eds.), Artech House Publishers: pp.61-98 [publisher link]
  • Georgopoulos P.G., Isukapalli S. and Krishnan K. (2010). Modeling exposures to chemicals from multiple sources and routes. In Quantitative Modeling in Toxicology. Krishnan, K. and Andersen, M. E. (eds.), John Wiley: pp.315-351 DOI: 10.1002/9780470686263.ch16 [DOI link]
  • Isukapalli S., Spendiff M., Georgopoulos P.G. and Krishnan K. (2010). Uncertainty, variability and sensitivity analyses in simulation models. In Quantitative Modeling in Toxicology. Krishnan, K. and Andersen, M. E. (eds.), John Wiley: pp.429-458 DOI: 10.1002/9780470686263.ch20 [DOI link]
  • Iyer V.V., Androulakis I.P., Roth C.M. and Ierapetritou M.G. (2010). Effects of triadimefon on the metabolism of cultured hepatocytes. Proceedings of the 10th International Conference on Bioinformatics and Bioengineering (BIBE-2010). Philadelphia, PA, May 31-Jun 3, 2010. pp.118-123 DOI: 10.1109/BIBE.2010.28 [DOI link]
  • Iyer V.V., Yang H., Ierapetritou M.G. and Roth C.M. (2010). Effects of glucose and insulin on HepG2-C3A cell metabolism. Biotechnology and Bioengineering 107 (2): 347-356. DOI: 10.1002/bit.22799 [DOI link]
  • Iyer V.V., Ovacik M.A., Androulakis I.P., Roth C.M. and Ierapetritou M.G. (2010). Transcriptional and metabolic flux profiling of triadimefon effects on cultured hepatocytes. Toxicology and Applied Pharmacology 248 (3): 165-177. DOI: 10.1016/j.taap.2010.07.015 5 [DOI link]
  • Krishnan K., Sasso A. and Georgopoulos P.G. (2010). Pharmacokinetic mechanisms of interactions in chemical mixtures. In Principles and Practice of Mixture Toxicology. Mumtaz, M. (ed.) New York, John Wiley Publishers: pp.235-252 [publisher link]
  • Li C.W., Ai N., Dinh G.K., Welsh W.J. and Chen J.D. (2010). Human ADA3 regulates RAR  transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket. Nucleic Acids Research 38 (16): 5291-5303. DOI: 10.1093/nar/gkq269 [DOI link]
  • Li G., Rabitz H., Yelvington P.E., Oluwole O.O., Bacon F., Kolb C.E. and Schoendorf J. (2010). Global sensitivity analysis for systems with independent and/or correlated inputs. The Journal of Physical Chemistry A 114 (19): 6022-6032. DOI: 10.1021/jp9096919 [DOI link]
  • Li G. and Rabitz H. (2010). D-MORPH regression: Application in modeling with unknown parameters more than observation data. Journal of Mathematical Chemistry 48 (4): 1010-1035. DOI: 10.1007/s10910-010-9722-2 [DOI link]
  • McAllister S.R. and Floudas C.A. (2010). An improved hybrid global optimization method for protein tertiary structure prediction. Computational Optimization and Applications 45 (2): 377-413. DOI: 10.1007/s10589-009-9277-y [DOI link]
  • Nguyen T.T., Almon R.R., DuBois D.C., Jusko W.J. and Androulakis I.P. (2010). Importance of replication in analyzing time-series gene expression data: corticosteroid dynamics and circadian patterns in rat liver. BMC Bioinformatics 11: 279. DOI: 10.1186/1471-2105-11-279 [DOI link]
  • Oelschlaeger P., Ai N., DuPrez K.T., Welsh W.J. and Toney J.H. (2010). Evolving Carbapenemases: Can Medicinal Chemists Advance One Step Ahead of the Coming Storm? Journal of Medicinal Chemistry 53 (8): 3013-3027. DOI: 10.1021/jm9012938 [DOI link]
  • Ovacik M., Sukumaran S., Almon R., DuBois D., Jusko W. and Androulakis I. (2010). Circadian signatures in rat liver: from gene expression to pathways. BMC Bioinformatics 11 (1): 540. DOI: 10.1186/1471-2105-11-540 [DOI link]
  • Rajgaria R., Wei Y. and Floudas C.A. (2010). 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 78 (8): 1825-46. DOI: 10.1002/prot.22696 [DOI link]
  • Sasso A., Isukapalli S. and Georgopoulos P. (2010). A generalized physiologically-based toxicokinetic modeling system for chemical mixtures containing metals. Theoretical Biology and Medical Modelling 7 (1): 17. DOI: 10.1186/1742-4682-7-17 [DOI link]
  • Scheff J.D., Almon R.R., DuBois D.C., Jusko W.J. and Androulakis I.P. (2010). A new symbolic representation for the identification of informative genes in replicated microarray experiments. OMICS: A Journal of Integrative Biology 14 (3): 239-248. DOI: 10.1089/omi.2010.0005 [DOI link]
  • Scheff J.D., Foteinou P.T., Calvano S.E., Lowry S.F. and Androulakis I.P. (2010). Dynamic models of disease progression: Toward a multiscale model of systemic inflammation in humans. In Process Systems Engineering, Volume 7: Dynamics Process Modeling. Banga, J., Georgiadis, M. and Pistikopoulos, S. (eds.) Weinheim, Germany, Wiley VCH: pp.321-368 [publisher link]
  • Vallero D., Isukapalli S., Zartarian V., McCurdy T., McKone T., Georgopoulos P.G. and Dary C. (2010). Modeling and predicting pesticide exposures. Chapter 44. In Hayes’ Handbook of Pesticide Toxicology – Third Edition. Krieger, R. (ed.), Academic Press: pp.995-1020 [publisher link]
  • Xue J., Zartarian V., Wang S.W., Liu S.V. and Georgopoulos P.G. (2010). Probabilistic modeling of dietary arsenic exposure and dose and validation with 2003 NHANES data. Environmental Health Perspectives 118 (3): 345-350. DOI: 10.1289/ehp.0901205 [DOI link]
  • Yang Y., Xu X. and Georgopoulos P.G. (2010). A Bayesian population PBPK model for multiroute chloroform exposure. Journal of Exposure Science and Environmental Epidemiology 20 (4): 326-341. DOI: 10.1038/jes.2009.29 [DOI link]
  • Yang H., Ierapetritou M.G. and Roth C.M. (2010). Effects of amino acid transport limitations on cultured hepatocytes. Biophysical Chemistry 152 (1-3): 89-98. DOI: 10.1016/j.bpc.2010.08.004 [DOI link]

2009

  • Ai N., Krasowski M.D., Welsh W.J. and Ekins S. (2009). Understanding nuclear hormone receptors using computational methods. Drug Discovery Today 14 (9-10): 486-494. DOI: 10.1016/j.drudis.2009.03.003 [DOI link]
  • Arora S., Wang X.I., Keenan S.M., Andaya C., Zhang Q., Peng Y. and Welsh W.J. (2009). Novel microtubule polymerization inhibitor with potent antiproliferative and antitumor activity. Cancer Research 69 (5): 1910-1915. DOI: 10.1158/0008-5472.CAN-08-0877 [DOI link]
  • Chekmarev D., Kholodovych V., Kortagere S., Welsh W.J. and Ekins S. (2009). Predicting inhibitors of acetylcholinesterase by regression and classification machine learning approaches with combinations of molecular descriptors. Pharmaceutical Research 26 (9): 2216-2224. DOI: 10.1007/s11095-009-9937-8 [DOI link]
  • Chen M., Martin J., Fang H., Isukapalli S., Georgopoulos P.G., Welsh W.J. and Tong W. (2009). ebTrack: an environmental bioinformatics system built upon ArrayTrack. BMC Proceedings 3 (Suppl 2): S5. [PubMed link]
  • DiMaggio P.A., Young N.L., Baliban R.C., Garcia B.A. and Floudas C.A. (2009). A mixed-integer linear optimization framework for the identification and quantificationof targeted post-translational modifications of highly modified proteins using multi-plexed electron transfer dissociation tandem mass spectrometry. Molecular and Cellular Proteomics 8 (11): 2527-2543. DOI: 10.1074/mcp.M900144-MCP200 [DOI link]
  • Euling S., Androulakis I., Benson B., Chiu W., Foster P., Gaido K., Gray Jr L.E., Hester S., Keshava C., Keshava N., Kim A., Makris S., Ovacik M., Sen B., Thompson C., White L. and Wilson V. (2009). An Approach to Using Toxicogenomic Data in U.S. EPA Human Health Risk Assessments: A Dibutyl Phthalate (DBP) Case Study (Final Report) Washington DC. U.S. Environmental Protection Agency, National Center for Environmental Assessment. EPA/600/R-09/028F
    [EPA link]
  • Euling S.Y., White L., Ovacik M., Makris S., Sen B., Androulakis I.P., Hester S., Gaido K.W., Kim A.S., Benson R., Wilson V.S., Keshava C., Keshava N., Foster P.M., Gray Jr L.E., Thompson C. and Chiu W. (2009). An approach to using genomic data in risk assessment: Dibutyl phthalate (DBP) case study. Reproductive Toxicology 28 (2): 119-119. DOI: 10.1016/j.reprotox.2009.05.009 [DOI link]
  • Foteinou P.T., Calvano S.E., Lowry S.F. and Androulakis I.P. (2009). Modeling endotoxin-induced systemic inflammation using an indirect response approach. Mathematical Biosciences 217 (1): 27-42. DOI: 10.1016/j.mbs.2008.09.003 [DOI link]
  • Foteinou P.T., Calvano S.E., Lowry S.F. and Androulakis I.P. (2009). Translational potential of systems-based models of inflammation. Clinical and Translational Science 2 (1): 85-89 DOI: 10.1111/j.1752-8062.2008.00051.x [DOI link]
  • Foteinou P.T., Calvano S.E., Lowry S.F. and Androulakis I.P. (2009). In silico simulation of corticosteroids effect on an NFkB-dependent physicochemical model of systemic inflammation. PLoS ONE 4 (3): e4706. DOI: 10.1371/journal.pone.0004706 [DOI link]
  • Foteinou P.T., Yang E. and Androulakis I.P. (2009). Networks, biology and process systems engineering: A case study in inflammation. Computers & Chemical Engineering 33 (12): 2028-2041. DOI: 10.1016/j.compchemeng.2009.06.027
    [DOI link]
  • Foteinou P.T., Yang E., Saharidis G.K., Ierapetritou M.G. and Androulakis I.P. (2009). A mixed-integer optimization framework for the synthesis and analysis of regulatory networks. Journal of Global Optimization 43 (2-3): 263-276. DOI: 10.1007/s10898-007-9266-6 [DOI link]
  • Georgopoulos P.G. and Isukapalli S.S. (2009). A unified multiscale field/network/agent based modeling framework for human and ecological health risk analysis. Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society 1: 6420-6423. DOI: 10.1109/IEMBS.2009.5333795 [DOI link]
  • Georgopoulos P.G., Sasso A.F., Isukapalli S.S., Lioy P.J., Vallero D.A., Okino M. and Reiter L. (2009). Reconstructing population exposures to environmental chemicals from biomarkers: Challenges and opportunities. Journal of Exposure Science and Environmental Epidemiology 19 (2): 149-171. DOI: 10.1038/jes.2008.9 9 [DOI link]
  • Gerecke D., Chen M., Isukapalli S., Gordon M.K., Chang Y.-C., Tong W., Androulakis I. and Georgopoulos P.G. (2009). Differential gene expression profiling of mouse skin after sulfur mustard exposure: extended time response and inhibitor effect. Toxicology and Applied Pharmacology 234 (2): 156-165. DOI: 10.1016/j.taap.2008.09.020 [DOI link]
  • Ierapetritou M.G., Georgopoulos P.G., Roth C.M. and Androulakis I.P. (2009). Tissue-level modeling of xenobiotic metabolism in liver: An emerging tool for enabling clinical translational research. Clinical and Translational Science 2 (3): 228-237. DOI: 10.1111/j.1752-8062.2009.00092.x
    [DOI link]
  • Kortagere S., Chekmarev D., Welsh W.J. and Ekins S. (2009). Hybrid scoring and classification approaches to predict human pregnane x receptor activators. Pharmaceutical Research 26 (4): 1001-1011. DOI: 10.1007/s11095-008-9809-7 [PubMed link]
  • Krishnan K., Isukapalli S. and Boyd J. (2009). Evaluation of toxicological interactions for the dose-response assessment of chemical mixtures. In General and Applied Toxicology. Ballantyne, B., Marrs, T. C. and Turner, P. (eds.), Wiley/Blackwell [Publisher link]
  • Lin Y., Yasuda K., Assem M., Cline C., Barber J., Li C.W., Kholodovych V., Ai N., Chen J.D., Welsh W.J., Ekins S. and Schuetz E. (2009). The major human PXR splice variant, PXR.2, exhibits significantly diminished ligand-activated transcriptional regulation. Drug Metabolism and Disposition 37 (6): 1295-1304. DOI: 10.1124/dmd.108.025213 [DOI link]
  • McAllister S., DiMaggio P. and Floudas C. (2009). Mathematical modeling and efficient optimization methods for the distance-dependent rearrangement clustering problem. Journal of Global Optimization 45 (1): 111-129. DOI: 10.1007/s10898-008-9393-8 [DOI link]
  • McAllister S.R. and Floudas C.A. (2009). Enhanced bounding techniques to reduce the protein conformational search space. Optimization Methods and Software 24 (4-5): 837-855. DOI: 10.1080/10556780902753486
    [DOI link]
  • Miller M., Feng X., Li G. and Rabitz H. (2009). Nonlinear bionetwork structure inference using the random sampling-high dimensional model representation (RS-HDMR) algorithm. Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society 1: 6412-6415. DOI: 10.1109/IEMBS.2009.5333798 [DOI link]
  • Nguyen T.T., Nowakowski R.S. and Androulakis I.P. (2009). Unsupervised selection of highly coexpressed and noncoexpressed genes using a consensus clustering approach. OMICS: A Journal of Integrative Biology 13 (3): 219-237. DOI: 10.1089/omi.2008.0074 [DOI link]
  • Rajgaria R., McAllister S.R. and Floudas C.A. (2009). Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization. Proteins: Structure, Function, and Bioinformatics 74 (4): 929-947. DOI: 10.1002/prot.22202 [DOI link]
  • Saharidis G. and Ierapetritou M. (2009). Resolution method for mixed integer bi-level linear problems based on decomposition technique. Journal of Global Optimization 44 (1): 29-51. DOI: 10.1007/s10898-008-9291-0 [DOI link]
  • Schnackenberg L.K., Chen M., Sun J., Holland R.D., Dragan Y., Tong W., Welsh W. and Beger R.D. (2009). Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies. Toxicology and Applied Pharmacology 235 (1): 25-32. DOI: 10.1016/j.taap.2008.11.015 [DOI link]
  • Subramani A., DiMaggio P.A. and Floudas C.A. (2009). Selecting high quality protein structures from diverse conformational ensembles. Biophysical Journal  97 (6): 1728-1736. DOI: 10.1016/j.bpj.2009.06.046 [DOI link]
  • Sun J., Abdeljabbar D.M., Clarke N., Bellows M.L., Floudas C.A. and Link A.J. (2009). Reconstitution and engineering of apoptotic protein interactions on the bacterial cell surface. Journal of Molecular Biology 394 (2): 297-305. DOI: 10.1016/j.jmb.2009.09.023 [DOI link]
  • Yang E. and Androulakis I.P. (2009). Assessing and selecting gene expression signals based upon the quality of the measured dynamics. BMC Bioinformatics 10: 55. DOI: 10.1186/1471-2105-10-55 [DOI link]
  • Yang E., Yarmush M.L. and Androulakis I.P. (2009). Transcription factor network reconstruction using the living cell array. Journal of Theoretical Biology 256 (3): 393-407. DOI: 10.1016/j.jtbi.2008.09.040 [DOI link]
  • Yang H., Roth C.M. and Ierapetritou M.G. (2009). A rational design approach for amino acid supplementation in hepatocyte culture. Biotechnology and Bioengineering 103 (6): 1176-1191. DOI: 10.1002/bit.22342
    [DOI link]
  • Yang E., Almon R.R., Dubois D.C., Jusko W.J. and Androulakis I.P. (2009). Identification of Global Transcriptional Dynamics. PLoS ONE 4 (7): e5992. DOI: 10.1371/journal.pone.0005992 [DOI link]
  • Yuan J., Doucette C.D., Fowler W.U., Feng X.-J., Piazza M., Rabitz H.A., Wingreen N.S. and Rabinowitz J.D. (2009). Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Molecular Systems Biology 5: 302. DOI: 10.1038/msb.2009.60 [DOI link]

2008

  • Chekmarev D.S., Kholodovych V., Balakin K.V., Ivanenkov Y., Ekins S. and Welsh W.J. (2008). Shape Signatures: New descriptors for predicting cardiotoxicity in silico. Chemical Research in Toxicology 21 (6): 1304-1314. DOI:10.1021/tx800063r
    [DOI link]
  • DiMaggio P.A., Floudas C.A., Lu B.W. and Yates J.R. (2008). 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 7 (4): 1584-1593. DOI:10.1021/pr700577z [DOI link]
  • DiMaggio P.A., McAllister S.R., Floudas C.A., Feng X.J., Rabinowitz J.D. and Rabitz H.A. (2008). Optimal methods for re-ordering matrices in systems biology and drug discovery applications. Biophysical Reviews and Letters (Special Issue – Proceedings of the International Symposium on Mathematical and Computational Biology – BIOMAT 2007) 3 (1/2): 19-42. DOI: 10.1142/S1793048008000605 [DOI link]
  • DiMaggio P., McAllister S., Floudas C., Feng X.-J., Rabinowitz J. and Rabitz H. (2008). Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. BMC Bioinformatics 9 (1): 458. DOI: 10.1186/1471-2105-9-458 [DOI link]
  • Ekins S., Kholodovych V., Ai N., Sinz M., Gal J., Gera L., Welsh W.J., Bachmann K. and Mani S. (2008). Computational discovery of novel low micromolar human pregnane X receptor antagonists. Molecular Pharmacology 74 (3): 662-672. DOI: 10.1124/mol.108.049437 [DOI link]
  • Euling S.Y., Makris S., Sen B., White L., Benson R., Gaido K.W., Kim A.S., Hester S., Wilson V.S., Keshava C., Keshava N., Foster P.M., Androulakis I.P., Ovacik M., Ierapetritou M.G., Gray L.E., Thompson C. and Chiu W. (2008). An approach to using genomics data in risk assessment: Dibutyl phthalate (DBP) case study. Birth Defects Research Part A – Clinical and Molecular Teratology 82 (5): 296. DOI: 10.1002/bdra.20475 [DOI link]
  • Floudas C.A., Fung H.K., Morikis D., Taylor M.S. and Zhang L. (2008). Overcoming the key challenges in de novo protein design: Enhancing computational efficiency and incorporating true backbone flexibility. In Mathematical Modelling of Biosystems. Mondaini, R. P. and Pardalos, P. M. (eds.) Berlin Heidelberg, Springer. 102: pp.133-183. DOI: 10.1007/978-3-540-76784-8_4 [DOI link]
  • Fung H.K., Floudas C.A., Taylor M.S., Zhang L. and Morikis D. (2008). Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2. Biophysical Journal 94 (2): 584-599. DOI:10.1529/biophysj.107.110627 [DOI link]
  • Fung H.K., Welsh W.J. and Floudas C.A. (2008). Computational de novo peptide and protein design: Rigid templates versus flexible templates. Industrial and Engineering Chemistry Research 47(4): 993-1001. DOI: 10.1021/ie071286k [DOI link]
  • Georgopoulos P.G. (2008). Mechanistic studies of environmental causes of human disease: a bionetwork dynamics modeling approach. In: Proceedings of the Protection and Restoration of the Environment 9. Kefalonia, Greece, June 29-July 3, 2008.
  • Georgopoulos P.G., Sasso A.F., Isukapalli S.S., Lioy P.J., Vallero D.A., Okino M. and Reiter L. (2008). Response to “µg//kg-day or µg//day: A commentary on Georgopoulos et al., JESEE 2008”. Journal of Exposure Science and Environmental Epidemiology 18 (6): 536-537. DOI: 10.1038/jes.2008.54 [DOI link]
  • Georgopoulos P.G., Wang S.-W., Yang Y.-C., Xue J., Zartarian V.G., McCurdy T. and Ozkaynak H. (2008). Biologically based modeling of multimedia, multipathway, multiroute population exposures to arsenic. Journal of Exposure Science and Environmental Epidemiology 18 (5): 462-476.
    DOI:10.1038/sj.jes.7500637 [DOI link]
  • Georgopoulos P. (2008). A multiscale approach for assessing the interactions of environmental and biological systems in a holistic health risk assessment framework. Water, Air, and Soil Pollution: Focus 8(1): 3-21. DOI:10.1007/s11267-007-9137-7 [DOI link]
  • Isukapalli S.S., Lioy P.J. and Georgopoulos P.G. (2008). Mechanistic modeling of emergency events: Assessing the impact of hypothetical releases of anthrax. Risk Analysis 28 (3): 723-740. DOI:10.1111/j.1539-6924.2008.01055.x [DOI link ]
  • Isukapalli S., Price K., Georgopoulos P.G. and Krishnan K. (2008). A physiologically-based algorithm for predicting internal dose of inhaled toluene: applications for high dose to low dose and rodent to human extrapolations. In: Proceedings of the 2008 Spring Simulation Multiconference – SpringSim 2008. (ISBN 1-56555-000-X). Rajaei, H., Wainer, G. A. and Chinni, M. J. (eds.) Ottawa, Canada, April 14-17, 2008. The Society for Computer Simulation International, San Diego. pp.583-588. [ACM link]
  • Jornsten R. and Keles S. (2008). Mixture models with multiple levels, with application to the analysis of multifactor gene expression data. Biostatistics 9 (3): 540-554. DOI: 10.1093/biostatistics/kxm051
    [DOI link]
  • Kortagere S., Chekmarev D., Welsh W.J. and Ekins S. (2008). New predictive models for blood-brain barrier permeability of drug-like molecules. Pharmaceutical Research 25 (8): 1836-1845. DOI: 10.1007/s11095-008-9584-5
    [DOI link]
  • Kortagere S., Ekins S. and Welsh W.J. (2008). Halogenated ligands and their interactions with amino acids: Implications for structure-activity and structure-toxicity relationships. Journal of Molecular Graphics and Modelling 27 (2): 170-177. DOI: 10.1016/j.jmgm.2008.04.001 [DOI link]
  • Li G., Rabitz H., Hu J., Chen Z. and Ju Y. (2008). Regularized random-sampling high dimensional model representation (RS-HDMR). Journal of Mathematical Chemistry 43 (3): 1207-1232. DOI: 10.1007/s10910-007-9250-x
    [DOI link]
  • McAllister S.R., Feng X.-J., DiMaggio Jr P.A., Floudas C.A., Rabinowitz J.D. and Rabitz H. (2008). Descriptor-free molecular discovery in large libraries by adaptive substituent reordering. Bioorganic & Medicinal Chemistry Letters 18 (22): 5967-5970. DOI: 10.1016/j.bmcl.2008.09.068 [DOI link]
  • McAllister S.R. and Floudas C.A. (2008). Alpha-helical topology prediction and generation of distance restraints in membrane proteins. Biophysical Journal 95: 5281-5295. DOI: 10.1529/biophysj.108.132241 [DOI link]
  • McAllister S.R., Rajgaria R. and Floudas C.A. (2008). A path selection approach to global pairwise sequence alignment using integer linear optimization. Optimization 57 (1): 101-111. DOI:10.1080/02331930701778940 [DOI link]
  • Ovacik M.A. and Androulakis I.P. (2008). On the potential for integrating gene expression and metabolic flux data. Current Bioinformatics 3 (3): 142-148. DOI: 10.2174/157489308785909223 [DOI link]
  • Piazza M., Feng X.J., Rabinowitz J.D. and Rabitz H. (2008). Diverse metabolic model parameters generate similar methionine cycle dynamics. Journal of Theoretical Biology 251 (4): 628-639. DOI: 10.1016/j.jtbi.2007.12.009 [DOI link]
  • Rabinowitz J.D., Hsiao J.J., Gryncel K.R., Kantrowitz E.R., Feng X.-J., Li G. and Rabitz H. (2008). Dissecting enzyme regulation by multiple allosteric effectors: Nucleotide regulation of aspartate transcarbamoylase. Biochemistry 47 (21): 5881-5888. DOI: 10.1021/bi8000566 [DOI link]
  • Rajgaria R., McAllister S.R. and Floudas C.A. (2008). Distance dependent centroid to centroid force fields using high resolution decoys. Proteins-Structure Function and Bioinformatics 70 (3): 950-970. DOI: 10.1002/prot.21561 [DOI link]
  • Reschly E.J., Ai N., Ekins S., Welsh W.J., Hagey L.R., Hofmann A.F. and Krasowski M.D. (2008). Evolution of the bile salt nuclear receptor FXR in vertebrates. Journal of Lipid Research 49: 1577-1587. DOI:10.1194/jlr.M800138-JLR200
    [pubmed link]
  • Reschly E.J., Ai N., Welsh W.J., Ekins S., Hagey L.R. and Krasowski M.D. (2008). Ligand specificity and evolution of liver X receptors. Journal of Steroid Biochemistry and Molecular Biology 110 (1-2): 83-94. DOI: 10.1016/j.jsbmb.2008.02.007 [DOI link]
  • Tan M.P., Smith E.N., Broach J.R. and Floudas C.A. (2008). Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures. BMC Bioinformatics 9: 268. DOI: 10.1186/1471-2105-9-268 [DOI link]
  • Taylor M.S., Fung H.K., Rajgaria R., Filizola M., Weinstein H. and Floudas C.A. (2008). Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework. Biophysical Journal 94 (7): 2470-2481. DOI:10.1529/biophysj.107.117622 [DOI link]
  • Yang E., Almon R.R., DuBois D.C., Jusko W.J. and Androulakis I.P. (2008). Extracting global system dynamics of corticosteroid genomic effects in rat liver. Journal of Pharmacology and Experimental Therapeutics 324(3):1243-1254. DOI:10.1124/jpet.107.133074 [pubmed link]
  • Yang E., Maguire T.M., Yarmush M.L., Berthiaume F. and Androulakis I.P. (2008). Identification of regulatory mechanisms of the hepatic response to thermal injury. Computers and Chemical Engineering 32(1-2): 356-369. DOI:10.1016/j.compchemeng.2007.02.009 [DOI link]
  • Yang E., Maguire T., Yarmush M.L. and Androulakis I.P. (2008). Informative gene selection and design of regulatory networks using integer optimization. Computers and Chemical Engineering 32(4-5) 633-649. DOI:10.1016/j.compchemeng.2007.01.009 [DOI link]

2007

  • Androulakis I.P., Yang E. and Almon R.R. (2007). Analysis of time-series gene expression data: Methods, challenges, and opportunities. Annual Review of Biomedical Engineering 9: 205-228. DOI:10.1146/annurev.bioeng.9.060906.151904 [pubmed link]
  • DiMaggio P.A. and Floudas C.A. (2007). A mixed-integer optimization framework for de novo peptide identification. AIChE Journal 53 (1): 160-173. DOI:10.1002/aic.11061 [DOI link]
  • DiMaggio P.A. and Floudas C.A. (2007). De novo peptide identification via tandem mass spectrometry and integer linear optimization. Analytical Chemistry 79 (4): 1433-1446. DOI:10.1021/ac0618425 [pubmed link]
  • Ekins S., Chang C., Mani S., Krasowski M.D., Reschly E.J., Iyer M., Kholodovych V., Ai N., Welsh W.J., Sinz M., Swaan P.W., Patel R. and Bachmann K. (2007). Human pregnane X receptor antagonists and agonists define molecular requirements for different binding sites. Molecular Pharmacology 72 (3): 592-603. DOI:10.1124/mol.107.038398 [pubmed link]
  • Floudas C.A. (2007). Computational methods in protein structure prediction. Biotechnology and Bioengineering 97 (2): 207-213. DOI:10.1002/bit.21411 [pubmed link]
  • Isukapalli S.S. and Roy A. (2007). General principles of programming (computer and statistical). In Pharmacometrics: the Science of Quantitative Pharmacology. Ette, E. I. and Williams, P. J. (eds.), Wiley: pp.25-52
  • Isukapalli S.S., Roy A. and Georgopoulos P.G. (2007). Physiologically Based Pharmacokinetic Modeling: Inhalation, Ingestion, and Dermal Absorption. In Pharmacometrics: the Science of Quantitative Pharmacology. Ette, E. I. and Williams, P. J. (eds.), Wiley: pp.1069-1108
  • Jiao Y., Su M., Chen M., Jia W., Chou Y., Huang Z., Yang N. and Tong W. (2007). 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 43 (5): 1804-7. DOI:10.1016/j.jpba.2006.11.040 [pubmed link]
  • Jornsten R., Ouyang M. and Wang H.Y. (2007). A meta-data based method for DNA microarray imputation. BMC Bioinformatics 8: 109. DOI:10.1186/1471-2105-8-109 [pubmed link]
  • McAllister S.R. and Floudas C.A. (2007). Alpha helical topology and tertiary structure prediction in globular proteins. In: Proceedings of the 46th IEEE Conference on Decision and Control. New Orleans, LA, December 12-14, 2007. pp.4551-4556 DOI: 10.1109/CDC.2007.4434759 [DOI link]
  • Welsh W.J., Tong W. and Georgopoulos P.G. (2007). Toxicoinformatics: An Introduction. In Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals. Ekins, S. (ed.), Wiley: pp.153-182 [book link]
  • Yang E., Foteinou P.T., King K.R., Yarmush M.L. and Androulakis I.P. (2007). A novel non-overlapping bi-clustering algorithm for network generation using living cell array data. Bioinformatics 23 (17): 2306-13. DOI:10.1093/bioinformatics/btm335 [pubmed link]
  • Yang E., Maguire T., Yarmush M.L., Berthiaume F. and Androulakis I.P. (2007). Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. BMC Bioinformatics 8 (10) DOI:10.1186/1471-2105-8-10 [pubmed link]
  • Yang E., Simcha D., Almon R.R., Dubois D.C., Jusko W.J. and Androulakis I.P. (2007). Context specific transcription factor prediction. Annals of Biomedical Engineering 35 (6): 1053-1067. DOI:10.1007/s10439-007-9268-z [pubmed link]

2006

  • Floudas C.A. and Fung H.K. (2006). Mathematical Modeling and Optimization Methods for De Novo Protein Design. In Systems Biology, Volume II: Networks, Models, and Applications. Rigoutsos, I. and Stephanopoulos, G. (eds.) USA, Oxford University Press: pp.42-66. [book link]
  • Georgopoulos P.G. (2006). A holistic multiscale approach for assessing the interactions of environmental and biological systems. In Proceedings of Protection and Restoration of the Environment VIII (PRE8) Conference. Chania, Greece. July 3-7, 2006
  • Kortagere S. and Welsh W.J. (2006). Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors. Journal of Computer Aided Molecular Design 20 (12): 789-802. DOI:10.1007/s10822-006-9077-8 [pubmed link]
  • McAllister S.R., Mickus B.E., Klepeis J.L. and Floudas C.A. (2006). Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints. Proteins 65 (4): 930-52. DOI: 10.1002/prot.21095 [pubmed link]
  • Rajgaria R., McAllister S.R. and Floudas C.A. (2006). A novel high resolution C-alpha-C-alpha distance dependent force field based on a high quality decoy set. Proteins-Structure Function and Bioinformatics 65 (3): 726-741. DOI:10.1002/prot.21149 [pubmed link]
  • Wang C.Y., Ai N., Arora S., Erenrich E., Nagarajan K., Zauhar R., Young D. and Welsh W.J. (2006). Identification of previously unrecognized antiestrogenic chemicals using a novel virtual screening approach. Chemical Research in Toxicology 19 (12): 1595-601. DOI:10.1021/tx060218k [pubmed link]
  • Yang E., Berthiaume F., Yarmush M.L. and Androulakis I.P. (2006). An integrative systems biology approach for analyzing liver hypermetabolism. In Proceedings of the 16th European Symposium on Computer Aided Process Engineering and 9th International Symposium on Process Systems Engineering. (ISBN 0444529691). Marquardt, W. and Pantelides, C. (eds.) Garmish-Partenkirchen, Germany, July 9-13, 2006. Elsevier. pp.1655-1660 [book link]
  • Yang H., Yarmush M.L., Roth C. and Ierapetritou M.G. (2006). Minimal reaction sets and metabolic pathways for cultured hepatocytes. In Proceedings of the 16th European Symposium on Computer Aided Process Engineering and 9th International Symposium on Process Systems Engineering. (ISBN 0444529691). Marquardt, W. and Pantelides, C. (eds.) Garmisch-Partenkirchen, Germany, July 9-13, 2006. Elsevier. pp.1711-1716 [book link]

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