Publications

  1. Orman, M., F. Berthiaume, I.P. Androulakis and M.G. Ierapetritou, Metabolic flux determination in perfused livers by mass balance analysis : Effects of fasting, Biotech.Bioeng , accepted (2010)
  2. Nguyen, T.T., R.R. Almon, D.C. DuBois, W.J. Jusko and I.P. Androulakis, Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures, BMC Bioinformatics , accepted (2010)
  3. Foteinou, P.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, A physiological model for autonomic heart rate regulation in human endotoxemia, SHOCK , accepted (2010)
  4. He, K, I.P. Androulakis and M.G. Ierapetritou, Incorporation of detailed chemical mechanisms in reactive flow simulations using element-flux analysis, I&ECR , doi: 10.1021/ie100490w (2010)
  5. He, K., M.G. Ierapetritou and I.P. Androulakis. Integration of on-the-fly kinetic reduction with multidimensional CFD. AIChE J. , doi: 10.1002/aic.12072 (2010)
  6. Scheff, J. S.C. Calvano, S.F. Lowry and I.P. Androulakis, Modeling the influence of circadian rhythms on the acute inflammatory response, J. Theo. Biol. , 264(3):1068-1076 (2010)
  7. Nguyen, T.T., R.R. Almon, D.C. DuBois, W.J. Jusko and I.P. Androulakis, Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver, BMC Bioinformatics , 11:279 (2010)
  8. Foteinou, P.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, An Integrated Host Response Model for the Assessment of Reduced Heart Rate Variability in Human Endotoxemia, Phys. Genomics , 42:5-19 (2010)
  9. Scheff, J.D., R.R. Almon, D.C. Dubois, W.J. Jusko and I.P. Androulakis, A new symbolic representation for the identification of informative expression motifs in replicated microarray experiments, OMICS , 14(3):239-48, (2010)
  10. Dong, X., P.T. Foteinou, S.E. Calvano, S.F. Lowry and I.P. Androulakis, agent-based simulation of endotoxin induced acute inflammatory response in blood leukocytes, PLoS ONE, 5(2):e9249 (2010)
  11. Treiser, M.D., Yang, E. Gordonov, S., D. Cohen, I.P. Androulakis, J. Kohn and P.M. Mpghe, P.V. Cytoskeleton-based Forecasting of Stem Cell Lineage Fates, Proc Natl Acad Sci USA , 107(2):610 (2010)
  12. Saharidis, G., I.P. Androulakis and M.G. Ierapetritou, Model Building using Bi-level Optimization, J. Global Opt. , DOI: 10.1007/s10898-010-9533-9 (2010)
  13. He, K-Y., I.P. Androulakis and M.G. Ierapetritou, On-the-fly reduction of kinetic mechanisms using element flux analysis, Chem. Eng. Sci., 65(3):1173-1184 (2010)
  14. He, K, I.P. Androulakis and M.G. Ierapetritou, Multi-element flux analysis for the incorporation of detailed kinetic mechanisms in Reactive Simulations, Energy Fuels, 24:309-317 (2010)
  15. Foteinou, P.T., E. Yang and I.P. Androulakis, Networks, Biology and Process Systems Engineering: A Case Study in Inflammation, Comp. Chem. Eng., 33(12):2028-2041 (2009)
  16. Foteinou, P.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, Translational potential of systems-based models of inflammation, Clinical and Translational Science, 2(1):85-89 (2009)
  17. Ierapetritou, M.G., P., Georgopoulos, C.M. Roth and I.P. Androulakis, Tissue-level Modeling of Xenobiotic Metabolism in Liver: An emerging tool for enabling clinical translational research, Clinical Translation Sciences, 2(3):228-237 (2009)
  18. Nguyen, T.T., R. Nowakoski, and I.P. Androulakis, Unsupervised selection of highly coexpressed and non-coexpressed genes, OMICS, 13(3): 219-237 (2009)
  19. Yang, E., R.R. Almon, D.C Dubois, W.J. Jusko and I.P. Androulakis, Identification of Global Transcriptional Dynamics, PLOS ONE 4(7):e5992 (2009)
  20. Foteinou, P.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, in silico simulation of corticosteroids effects on an NFkB-dependent indirect response model of systemic inflammation in peripheral human blood leukocytes, submitted, PLoS ONE, 4(3):e4706 (2009)
  21. Foteinou, P.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, A multiscale model for the assessment of autonomic dysfunction in human endotoxemia, J. Crit. Care, 24(3):e25(2009)
  22. Nguyen T. T. and Androulakis I. P. Recent Advances in the Computational Discovery of Transcription Factor Binding Sites. Algorithms. 2(1):582-605 (2009)
  23. Yang, E., and I.P. Androulakis, Assessing and Selecting Gene Expression Signals Based Upon the Quality of the Measured Dynamics, BMC Bioinformatics, Feb 10;10(1):55 (2009)
  24. Foteinou, P.T., E. Yang, G.K. Saharidis, M.G. Ierapetritou, and I.P. Androulakis, A systematic framework for the synthesis and analysis of regulatory networks, Journal of Global Optimization, 43(2):263 (2009)
  25. Gerecke, D.R., M. Chen, S. Isukapalli, Y-C-. Chan, W. Tong, I.P. Androulakis and P.G. Georgopoulos, Differential gene expression profiling of mouse skin after sulfur mustard exposure: extended time response and inhibitor effect, Env. Tox. Pharm. 234(2):156-65 (2008)
  26. Yang, E., M.L. Yarmush and I.P. Androulakis, Transcription Factor Network Reconstruction using the Living Cell Array, J. Theor. Biology , 256(3):393-407 (2008)
  27. 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. An approach to using genomics data in risk assessment: Dibutyl phthalate (DBP) case study. Birth Defects Research Part a-Clinical and Molecular Teratology, 82, 296-29 (2008)
  28. Almon, R.R., E. Yang, Lai, W., I.P. Androulakis, D.C. Dubois and W.J. Jusko, Relationships between Circadian Rhythms and Modulation of Gene Expression by Glucocorticoids in Skeletal Muscle, AJP Regulatory, 326(3):700-16 (2008)
  29. Foteinou, P.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, Modeling Endotoxin-Induced Systemic Inflammation Using an Indirect Response Approach, Math. Biosciences, 217(1):27-42 (2008)
  30. Ovacik, M. and I.P. Androulakis, On the potential for integrating gene expression and metabolic flux data: A review, Current Bioinformatics, 3(3):142-148 (2008)
  31. Almon, R.R., E. Yang, W. Lai, I.P. Androulakis, D.C. Dubois and W.J. Jusko, Circadian variations in liver gene expression: Relationships to drug action, J. Pharm. Exp. Therapeutics, 326(3):700-716 (2008)
  32. Yang E, Almon RR, DuBois DC, Jusko WJ, Androulakis IP. Extracting global system dynamics of corticosteroid genomic effects in rat liver. J. Pharm. Exp. Therapeutics 324(3):1243-1254 (2008)
  33. Yang E, Maguire TJ, Yarmush ML, Berthiaume F, Androulakis IP. Identification of regulatory mechanisms of the hepatic response to thermal injury. Comp.& Chem. Eng 32:356-369 (2008)
  34. He, K., M.G. Ierapetritou and I.P. Androulakis, A graph-based approach for developing adaptive representations of complex reaction mechanisms, Comb & Flame, 155(4):585-604 (2008)
  35. Foteinou, P.T., E. Yang, G.K Saharidis, M.G. Ierapetritou and I.P. Androulakis, A Mixed Integer Optimization Algorithm to Reverse Engineer Transcriptional Regulatory Networks, Proceeding of the 5th International Conference on the Foundations of Computer-Aided Process Operations, Cambridge, MA (2008)
  36. Yang, E., P.T. Foteinou, K.R. King, M.L. Yarmush and I.P. Androulakis, Extraction of Transcription Factor Networks via Globally Optimal Biclustering, , Proceeding of the 5th International Conference on the Foundations of Computer-Aided Process Operations, Cambridge, MA (2008)
  37. Yang, E., A. Misra, T.J. Maguire and I.P. Androulakis, Analysis of Regulatory and Interactions Networks from Clusters of co-expressed Genes" in Clustering Challenges, in Biological Networks (S. Butenko and A. Chaovalitwogse, Ed.) Word Scientific Publications (2008)
  38. Foteinou, P.T., E. Yang and I.P. Androulakis, Networks, Biology and Systems Engineering: A Case Study in Inflammation, Proceeding of the 5th International Conference on the Foundations of Computer-Aided Process Operations, Cambridge, MA (2008)
  39. Yang, E. and I.P. Androulakis, Assessing the information content of microarray time series, Encyclopedia of Healthcare Information Systems (Wickramasinghe, Ed.) (2008)
  40. Tung, N.T., E. Yang and I.P. Androulakis Machine learning approaches in promoter sequence analysis, in Machine Learning Research Progress, Nova Science Publishers, Inc. (2008)
  41. Furman, K.C., and I.P. Androulakis, A novel MINLP-based representations of the original complex model for predicting gasoline emissions, Comp.& Chem. Eng. , 32(12)2857-2876 (2008)
  42. Yan E, Maguire T, Yarmush ML, Androulakis IP. Informative gene selection and design of regulatory networks using integer optimization. Comp.& Chem. Eng 32(4-5):633-649 (2008)
  43. Foteinou, P.T., S. Calvano, S. Lowry and I.P. Androulakis, An indirect response model of endotoxin-induced systemic inflammation, Journal of Critical Care, 22 (4):337-338 (2007)
  44. Androulakis, I.P, Mathematical programming approaches for the analysis of microarray data, Handbook of Optimization in Medicine (E. Romeijn, Ed) (2007)
  45. 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 23:2306-2313 (2007)
  46. Maguire T, Davidovich AE, Wallenstein EJ, Novik E, Sharma N, Pedersen H, Androulakis IP, Schloss R, Yarmush M. Control of hepatic differentiation via cellular aggregation in an alginate microenvironment. Biotechnology & Bioengineering 98:631-644. (2007)
  47. Yang, E., T. Maguire, M.L. Yamush, F. Berthiaume and I.P. Androulakis, Bioinformatics analysis of the early inflammatory response in a rat thermal injury model, BMC Bioinformatics, 8 (10) (2007)
  48. Yang, E., D. Simcha, R.R. Almon, D.C. Dubois, W.J. Jusko, and I.P. Androulakis, Context specific Transcription Factor Prediction, Annals of Biomedical Engineering, 35(6):1053-1067 (2007)
  49. Androulakis, I.P., E. Yang, and R.R. Almon, Analysis of time-series gene expression data: Methods, challenges, and opportunities. Annual Review of Biomedical Engineering, 9: p. 205-228 (2007)
  50. Liang L, Stevens JG, Farrell JT, Huynh PT, Androulakis IP, Ierapetritou MG: An adaptive approach for coupling detailed chemical kinetics and multidimensional CFD, In 5th US National Combustion Meeting; March 25-28; San Diego, CA. March 25-28 (2007)
  51. Androulakis, I.P. and W. Chaovalitwongse, Mathematical programming for data mining, In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.) (2007)
  52. Chaovalitwongse, W., I.P. Androulakis and P.M. Pardalos, Quadratic integer programming: Complexity and equivalent forms, In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.) (2007)
  53. Yang, E., and I.P. Androulakis, Assessing the information content of short time series microarray data, Proceeding of the 28th IEEE EMBS Annual International Conference (2006)
  54. Androulakis, I.P., J.M. Grenda, T.A. Barckholtz, and J.W. Bozzelli, Propagation of uncertainty in chemically activated systems, AIChE J, 50:2956 (2006)
  55. Androulakis IP: New approaches for representing, analyzing and visualizing complex kinetic transformations. Computers & Chemical Engineering, 31:41-50 (2006)
  56. Yang, E., F. Berthiaume, M. Yarmush and I.P. Androulakis, An integrative systems biology approach for analyzing liver hypermetabolism, 9th International Symposium on Process Systems Engineering & 16th European Symposium on Computer Aided Process Design (2006)
  57. Knapinska, A.M., P.I. Irizarry, S.Adusumalli, I.P. Androulakis and G. Brewer, Molecular Mechanisms Regulating mRNA Stability: Physiological and Pathological Significance, Current Genomics, 6(6):471-486 (2005)
  58. Wu, J., and I.P. Androulakis, Selecting maximally informative genes: The interplay between accuracy and complexity, Proceedings of the 18th International Conference on Systems Engineering (ICSEng'05), Special Session on Computer Infrastructure for Systems Biology, Las Vegas (2005)
  59. Wu, J., and I.P. Androulakis, Exploring classifiability metrics for selecting informative genes, Proceeding of 15th European Symposium on Computer Aided Process Engineering, Barcelona (2005)
  60. Androulakis, I.P., New approaches for representing, analyzing and visualizing complex kinetic mechanisms, Proceeding of 15th European Symposium on Computer Aided Process Engineering, Barcelona (2005)
  61. Androulakis, I.P., TA. Barckholtz, and J.W. Bozzelli, Assessing the impact of accuracy of ab initio calculations in describing chemically activated systems, Proceedings of Joint Meeting of the U.S. Section of the Combustion Institution, Philadelphia, PA (2005)
  62. Androulakis, I.P., J. Wu, J. Vitolo and C. Roth, Selecting maximally informative genes to enable temporal expression profiling analysis, Proceedings of Foundations of Systems Biology in Engineering, Santa Barbara, CA, (2005)
  63. Androulakis, I.P., "Store and retrieve representations of dynamic systems motivated by studies in gas phase chemical kinetics", Comp. & Chem. Engng., 28:2141-2155 (2004)
  64. Androulakis, I.P., "Selecting maximally informative genes", Comp. & Chemical Engineering, Special issue on Systems Engineering Challenges and Opportunities in Biology, 29:535-546 (2004)
  65. Androulakis, I.P., J.M. Grenda, and J.W. Bozzelli, "Time-integrated pointers for enabling the analysis of deailed reaction mechanisms", AIChE J., 50(11):2965-2970 (2004)
  66. Androulakis, I.P., J.T. Farrell, C.S. Hsu, K. Qian, and K. Nakakita, "An Integrated Approach for Creating Model Fuels", Energy and Fuels, 19(1):111-119 (2004)
  67. Farrell, J.T., R.J. Johnston, and I.P. Androulakis, "Molecular structure effects on laminar burning velocities at elevated temperature and pressure", SAE Paper 2004-01-2936 (2004)
  68. Grenda, J.M., I.P. Androulakis, A.M. Dean and W.H. Green, "Application of computational kinetic mechanism generation to model the autocatalytic pyrolysis of methane", Ind. & Eng. Chem. Res., 45(5):1000-1010(2003)
  69. Sirdeshpande, I.P. Androulakis and M.G. Ierapetritou, "Design of flexible reduced kinetic models", AIChE J., 47:2461-2474 (2001)
  70. Androulakis, I.P., "Dynamic Programming - Infinite Horizon Problems: Overview", In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.), 1, 514-516, Kluwer Academic Publishers (2001)
  71. Androulakis I.P., "Dynamic Programming - Stochastic Shortest Path Problems", In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.), 1, 526-529, Kluwer Academic Publishers (2001)
  72. Androulakis, I.P., "Dynamic Programming - Discounted Problems", In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.), 1, 502-503, Kluwer Academic Publishers (2001)
  73. Androulakis, I.P., "Dynamic Programming - Un-Discounted Problems", In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.), 1, 529-533, Kluwer Academic Publishers (2001)
  74. Androulakis, I.P., "Dynamic Programming - Average Cost per Stage Problems", In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.), 1, 497-500, Kluwer Academic Publishers (2001)
  75. Androulakis, I.P., "Dynamic Programming - Inventory Control", In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.), 1, 516-519, Kluwer Academic Publisher (2001)
  76. Androulakis, I.P., "MINLP: Branch & Bound Methods", In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.), 3, 325-331, Kluwer Academic Publishers (2001)
  77. Androulakis, I.P., "Asynchronous Distributed Optimization Algorithms", Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.), 1, 68-73, Kluwer Academic Publishers (2001)
  78. Reyes, S.C, I.P. Androulakis, J.H. Sinfelt and M.C. Huff, Some critical issues in the analysis of partial oxidation reactions in monolith reactors, In Studies in Surface Science and Catalysis (E. Iglesia, J.J. Spivey, and T.Z. Fleisch, Eds.), 136, 495-500 (2001)
  79. Grenda, J.M., I.P. Androulakis, and J.W. Bozzelli, The Combined Use of Automated Kinetic Mechanism Generation and Mechanism Reduction in the Development of Chemical Reaction Models, Proceedings of the 2nd Joint Meeting of the US Sections of the Combustion Institute (2001)
  80. Androulakis I.P., Kinetic mechanism reduction based on an integer programming approach, AIChE J., 46, 361-370 (2000)
  81. Huff, M.C., I.P. Androulakis, J.H, Sinfelt, and S.C. Reyes, The contribution of gas phase reactions in the Pt-catalyzed conversion of Ethane-Oxygen mixtures, J. Catal., 191, 46-54 (2000)
  82. Adjiman, C.S., I.P. Androulakis and C.A. Floudas, Global optimization of mixed-integer nonlinear problems, AIChE J., 46, 1796-1798 (2000)
  83. Ierapetritou M.G., I.P. Androulakis, D.S. Monos and C.A. Floudas, "Structure Prediction of Binding Sites of MHC Class II Molecules based on the Crystal of HLA-DR1 and Global Optimization", In Optimization in Computational Chemistry and Molecular Biology (C.A. Floudas and P.M. Pardalos, Eds.), 157-190, Kluwer Academic Publishers (2000)
  84. Androulakis, I.P. and S.C. Reyes, Role of distributed oxygen addition and product removal in the oxidative coupling of methane, AIChE J., 45, 360-379 (1999)
  85. Androulakis, I.P and G.V. Reklaitis, Approaches to asynchronous and decentralized decision-making, Comput. & Chem. Engng., 23, 341-355 (1999)
  86. Ierapetritou, M.G., I.P. Androulakis, Uncertainty considerations in the reduction of chemical reaction mechanisms, Proceedings of the 5th International Conference on Foundations of Computer-Aided Process Design, 96, 406-410 (1999)
  87. Adjiman, C.S., I.P. Androulakis I.P., and C.A. Floudas, A global optimization method, aBB, for general twice differentiable constrained NLPs – II Implementation and computational results, Comp. Chem. Engng., 22, 1159-1179 (1998)
  88. Klepeis, J.L., I.P. Androulakis, M.G. Ierapetritou, and C.A. Floudas, Predicting solvated peptide conformations via global minimization of energetic atom-to-atom interactions, Comp. Chem. Engng., 22, 765-788 (1998)
  89. Androulakis I.P., and C.A. Floudas, "Distributed Branch and Bound-based Algorithms for Global Optimization", In Institute for Mathematics and its Applications: Parallel Processing of Discrete Problems, 106, 1-36, Kluwer Academic Publishers (1998)
  90. Androulakis, I.P., N.N. Nayak, M.G. Ierapetritou, D.S. Monos and C.A. Floudas, A Predictive Method for the Evaluation of Peptide Binding in Pocket 1 of HLA-DRB1 via Global Minimization of Energy Interactions. Proteins: Structure, Function and Genetics, 29, 87-102 (1997)
  91. Maranas, C.D., I.P. Androulakis IP, C.A. Floudas, A.J. Berger, and J.M. Mulvey, Solving long-term financial planning problems via global optimization, J. Econ. Dyn. Control, 1997, 21, 1405-1425 (1997)
  92. Androulakis, I.P., C.D. Maranas, and C.A. Floudas, Prediction of oligopeptide conformations via deterministic global optimization, J. Glob. Optim., 11, 1-34 (1997)
  93. Adjiman, C.S., I.P. Androulakis, and C.A. Floudas, Global optimization of MINLP problems in process synthesis and design, Comp. Chem. Engng, 21, S445-S450 (1997)
  94. Monos D., A.Soulika, E.Argyris, J. Corga, L. Stern, P. Cordopatis, I.P. Androulakis, V. Magafa and C.A. Floudas, HLA-Peptide Interactions: Theoretical and Experimental Approaches, In HLA Diversity: Functional and Medical Implications (D. Charron, Eds.), EDK Sevres, 451-455 (1997)
  95. Adjiman, C.S., I.P. Androulakis, C.D. Maranas, and C.A. Floudas, A global optimization method, aBB, for process design, Comput. Chem. Engng., 20, S419-S424, (1996)
  96. Monos, D.S., A. Soulika, E. Argyris, J. Corga, L. Stern, V. Magafa, P. Cordopatis, I.P. Androulakis, and C.A. Floudas, HLA-Peptide interactions: theoretical and experimental approaches, Proceedings of the 12th International Histocompatibility Conference, (1996)
  97. Maranas C.D., I.P. Androulakis and C.A. Floudas, A Deterministic Global Optimization Approach for the Protein Folding Problem, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 133-150, (1995)
  98. Androulakis I.P., C.D. Maranas, and C.A. Floudas, aBB A global optimization method for general constrained nonconvex problems, J. Glob. Optim., 7, 337-363 (1995)
  99. Androulakis, I.P. and G.V. Reklaitis, Analysis of the spurious behavior of asynchronous relaxation algorithms, Comput. Chem. Engng., 19, 827-845 (1995)
  100. Androulakis I.P., V. Visweswaran and C.A. Floudas, "Distributed Decomposition-based Approaches in Global Optimization", State of the Art in Global Optimization, Kluwer Academic Publishers, 1995
  101. Androulakis, I.P. and V. Venkatasubramanian, A genetic algorithmic framework for process design and optimization, Comput. Chem. Engng., 15, 217-228 (1991).
  102. Kalospiros, N.YAS., G.M. Misseyannis, I.P. Androulakis, and D.P. Tassios, Application of the VdW-711 equation of state to polar mixtures – Correlation of binary and prediction of multicomponent vapor-liquid equilibria, Fluid Phase Equil., 64, 173-184 (1991)
  103. Androulakis, I.P., N.S. Kalospiros, and D.P. Tassios, Thermophysical properties of pure polar and nonpolar compounds with a modified VdW-711 equation of state, Fluid Phase Equil., 45, 135-163 (1989)