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 Publications

  1. 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, accepted (2008)

  2. 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, accepted (2008)

  3. Ovacik, M. and I.P. Androulakis, On the potential for integrating gene expression and metabolic flux data: A review, Current Bioinformatics, accepted (2008)

  4. 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, JPET, accepted for publication, (2008)

  5. Yang, E., R.R. Almon, D.C. DuBois, W.J. Jusko, and I.P. Androulakis, Extracting Global System Dynamics of Corticosteroid Genomic Effects in Rat Liver, JPET, accepted for publication , 324:1243-1254 (2008)

  6. He, K., M.G. Ierapetritou and I.P. Androulakis, A graph-based approach for developing adaptive representations of complex reaction mechanisms, Comb & Flame, accepted for publications (2008)

  7. 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)

  8. 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)

  9. 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)

  10. 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)

  11. Yang, E. and I.P. Androulakis, Assessing the information content of microarray time series, Encyclopedia of Healthcare Information Systems (Wickramasinghe, Ed.) (2008)

  12. 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)

  13. Furman, K.C., and I.P. Androulakis, A novel MINLP-based representations of the original complex model for predicting gasoline emissions, Comp. Chem. Eng., accepted for publication (2007)

  14. 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)

  15. Androulakis, I.P, Mathematical programming approaches for the analysis of microarray data, Handbook of Optimization in Medicine (E. Romeijn, Ed) (2007)

  16. 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, accepted  for publication(2007)

  17. Yang, E., P.T. Foteinou, K.R. King, M.L. Yarmush, and I.P. Androulakis, A novel non-overlapping biclustering algorithm for network generation using Living Cell Array Data, Bioinformatics, accepted for publication (2007)

  18. Maguire, T. A.E. Davidovich, E.J. Wallenstein, E. Novik, N. Sharma, H. Pedersen, I.P. Androulakis, R. Schloss, and M.L. Yarmush, Control of hepatic differentiation via cellular aggregation in an alginate microenvironment, Biotechnology & Bioengineering, accepted for publication (2007)

  19. Yang, E., T.M. Maguire, M.L. Yarmush, F. Berthiaume, and I.P. Androulakis, Identification of Regulatory Mechanisms of the Hepatic Response to Thermal Injury, Comp. Chem. Eng., accepted for publication (2007)  

  20. Yang, E., T. Maguire, M.L. Yamush, F. Berthiaume and I.P. Androulakis, Bionformatics analysis of the early inflammatory response in a rat thermal injury model, BMC Bioinformatics, 8 (10)(2007)

  21. 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)  

  22. Yang, E., T. Maguire, M.L. Yarmush, and I.P. Androulakis, Informative Gene Selection and Design of Regulatory Networks Using Integer Optimization, Comp. Chem. Eng., accepted for publication (2007)

  23. Androulakis, I.P., E. Yang, R.R. Almon, D.C. Dubois, and W.J. Jusko, Analysis of Time-series Gene Expression Data: Methods, Challenges and Opportunities, Annual Review Biomedical Engineering, accepted for publication (2007)

  24. 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)

  25. Androulakis, I.P. and W. Chaovalitwongse, Mathematical programming for data mining, In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.) (2007)

  26. 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)

  27. 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)

  28. 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)

  29. Androulakis IP: New approaches for representing, analyzing and visualizing complex kinetic transformations. Computers & Chemical Engineering, 31:41-50 (2006)

  30. 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)

  31. 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)

  32. 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)

  33. 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)

  34. 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)

  35. 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)

  36. 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)

  37. 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)

  38. Androulakis, I.P., "Selecting maximally informative genes", Comp. & Chemical Engineering, Special issue on Systems Engineering Challenges and Opportunities in Biology, 29:535-546 (2004)

  39. Androulakis, I.P., J.M. Grenda, and J.W. Bozzelli, "Integrated element flux and sensitivity pointers for the analysis and reduction of complex kinetic mechanisms", AIChE J., 50(11):2965-2970  (2004)

  40. 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 )

  41. 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)

  42. 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)

  43. Sirdeshpande, I.P. Androulakis and M.G. Ierapetritou, "Design of flexible reduced kinetic models", AIChE J., 47:2461-2474 (2001)

  44. 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)

  45. 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)

  46. 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)

  47. 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)

  48. 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)

  49. 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)

  50. 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)

  51. 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)

  52. 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)

  53. 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)

  54. Androulakis I.P., Kinetic mechanism reduction based on an integer programming approach, AIChE J., 46, 361-370 (2000)

  55. 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)

  56. Adjiman, C.S., I.P. Androulakis and C.A. Floudas, Global optimization of mixed-integer nonlinear problems, AIChE J., 46, 1796-1798 (2000)

  57. 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)

  58. 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)

  59. Androulakis, I.P and G.V. Reklaitis, Approaches to asynchronous and decentralized decision-making, Comput. & Chem. Engng., 23, 341-355 (1999) 

  60. 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)

  61. 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)

  62. 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)

  63. 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)

  64. Androulakis, I.P., N.N. Nayak, M.G. Ierapetritou, D.S. Monos and C.A. Floudas, Identification of peptide binding specificity for pocket 1 of HLA-DR1 based on global minimization of energy interactions. Proteins: Structure, Function and Genetics, 29, 87-102 (1997)

  65. 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)

  66. 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)

  67. 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)

  68. 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)

  69. 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)

  70. 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)

  71. 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)

  72. 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)

  73. Androulakis, I.P. and G.V. Reklaitis, Analysis of the spurious behavior of asynchronous relaxation algorithms, Comput. Chem. Engng., 19, 827-845 (1995)

  74. 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

  75. Androulakis, I.P. and V. Venkatasubramanian, A genetic algorithmic framework for process design and optimization, Comput. Chem. Engng., 15, 217-228  (1991).

  76. 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)

  77. 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)