ebCTC Publications

Selected peer-reviewed articles and chapters representing published results of ebCTC research during 2006-2008, listed alphabetically by lead author, starting with the current year's publications; links to abstracts are provided where available. To request an article reprint please contact Linda Everett.

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] [download citation to Endnote]
• 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]
• 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]
  
• 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 link]
  
• Foteinou P.T., Yang E., Saharidis G.K., Ierapetritou M.G. and Androulakis I.P. (2008). A mixed-integer optimization framework for the synthesis and analysis of regulatory networks. Journal of Global Optimization (Advance Online Publication) DOI:10.1007/s10898-007-9266-6 [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., Sasso A., Isukapalli S., Lioy P.J., Vallero D., Okino M. and Reiter L. (2008). Reconstructing population exposures to environmental chemicals from biomarkers: Challenges and opportunities. Journal of Exposure Science and Environmental Epidemiology (Advance Online Publication) DOI: 10.1038/jes.2008.9 [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: 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 ]
• 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 barrierpermeability 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 (Advance Online Publication) 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., 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]
• 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]
• 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]

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]
• Davis E. and Ierapetritou M. (2007). A kriging method for the solution of nonlinear programs with black-box functions. AIChE Journal 53 (8): 2001-2012. DOI:10.1002/aic.11228 [DOI 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 [chapter link]
• 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 [chapter link]
• 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
  
• 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. and Androulakis I.P. (2007). 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]
• 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 [chapter link]
• 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]