Yannis Androulakis

Ioannis (Yannis) P. Androulakis

Professor

Chemical and Biochemical Engineering

Phone:848-445-6561
Fax:732-445-3753
Email:yannis@rci.rutgers.edu
Office:BME 212
Website: Research Group Webpage

Education

BS, National Technical University of Athens, 1988
MS, Purdue University, 1990
PhD, Purdue University, 1993
Postdoc, Princeton University, 1993-1996
 

Research Interests

Systems Engineering, System Biology, Bioinformatics, Data Mining, Kinetic Modeling

Dr. Androulakis actively pursues research activities in the area of Systems Biology, loosely defined as an integrative modeling and experimental framework that approaches biological entities as "systems" in the physical and engineering sense. Of particular interest are issues related to "functional physiomics" in an attempt to establish functional links between cellular events, such as signaling, transcription and translation, and an expanding envelope of interactions which include the bidirectional links between cells, tissues, organs, environmental signals and physiological responses. The ultimate goal is to develop in silico methodologies that will enable translational research by elucidating putative mechanisms by which macroscopic responses, at the physiome level, can be functionally modulated through mechanistic interventions. Of particular importance are the opportunities of such an integrative approach applied to the inflammatory responses due to the critical role inflammation plays in a number of physiologically and clinically relevant situations. His work integrates a compendium of experimental systems, from cell cultures, to animal models, to human studies in order to address different questions at their appropriate level of detail.

Selected Publications

2012

  • Dick, T.E., Y. Molkov, G. Niemam, Y-H. Hsieh, F.J. Jacono, H. Doyle, S.D. Scheff, S.E. Calvano, I.P. Androulakis and Y. Vodovotz, Linking Inflammation and Cardiorespiratory Variability in Sepsis via Computational Modeling,Front. Physiol., 3:222 (2012) 
  • He, K., M.G. Ierapetritou and I.P. Androulakis, Exploring flux representations of complex kinetics networks, AIChE J58(2):533 (2012) 
  • Yang, Q., J.S. Mattick, M.A. Orma, T.T. Nguyen, M.G. Ierapetritou, F. Berthiaume and I.P. Androulakis, Dynamics of hepatic gene expression profile in a rat cecal ligation and puncture model, J. Surg. Res.176(2):583-600 (2012) 
  • Yang, Q., M.A. Orman, M.G. Ierapetritou, F. Berthiaume and I.P. Androulakis, Dynamics of short-tem gene expression profiling in liver following thermal injury, J. Surg. Res.176(2):549-558 (2012) 
  • Mavroudis, P., J.D. Scheff, S.E. Calvano, S.F. Lowry and I.P. Androulakis, Entrainmenet of peripheral clock genes by cortisol, Phys. Genomics144(11):607 (2012) 
  • Namas, R., R. Zamora, R. Namas, G. An, J. Doyle, T.E. Dick, F.J. Jacono, I.P. Androulakis, G.F. Nieman, S. Chang, T.R. Billiar, J.A. Kellum, D. C. Angus and Y. Vodovotz, Sepsis: Something old, something new and a systems view, J. Crit. Care27:314 (2012) 
  • Orman, M.A, M.G. Ierapetritou, F. Berthiaume and I.P. Androulakis, Long-term dynamics profling of inflammatory mediators in double-hit burn and sepsis animal models, Cytokine58(2):307-315 (2012) 

2011

  • Nguyen, T.T., P.T. Foteinou, S.E. Calvano, S.F. Lowry and I.P. Androulakis, Computational identification of transcriptional regulators in human endotoxemia, PLoS ONE6(5):e18889 (2011) 
  • Scheff, J.D., P. Mavroudis, S.E. Calvano, S.F. Lowry and I.P. Androulakis, Modeling autonomic regulation of cardiac function and heart rate variability in human endotoxemia, Phys. Genomics43(16):951 (2011) 
  • Orman, M.A., I.P. Androulakis , F. Berthiaume and M.G. Ierapetritou, Metabolic Network Analysis of Perfused Livers under Fed and Fasted States: Incorporating Thermodynamic and Futile-Cycle-Associated Regulatory Constraints, J. Theo. Biol.293:101 (2011) 
  • Yang, Q., S.C. Calvano, S.F. Lowry and I.P. Androulakis, A Dual Negative Regulation Model of Toll-Like Receptor 4 Signaling for Endotoxin Preconditioning in Human Endotoxemia, Math. Biosc.232(2):151 (2011) 
  • Orman, M.A., I.P. Androulakis, M.G. Ierapetritou and F. Berthiaume, Metabolic Response of Perfused Livers to Various Oxygenation Conditions, Biotech. Bioeng.108(12):2947 (2011) 
  • Ovacik, M., S. Sukumaran, R. R. Almon, D.C. Dubois, W.J. Jusko and I.P. Androulakis, Circadian signatures in rat liver: From gene expression to pathways, BMC Bionformatics11:540 (2011) 
  • Orman, M.A., F. Berthiaume, I.P. Androulakis and M.G. Ierapetritou, Advanced stoichiometric analysis of metabolic networks of mammalian cells, Crit. Rev. Biomedical Eng.39(6):511 (2011) 
  • Orman, M.A., T.T. Nguyen, M.G. Ierapetritou, F. Berthiaume and I.P. Androulakis, Comparison of Cytokine Dynamics of the Early Inflammatory Response in Models of Burn Injury and Infection, Cytokine55(3):362 (2011)
  • Scheff, J.D., A.K. Kosmides, S.E. Calvano, S.F. Lowry and I.P. Androulakis, Pulsatile glucocorticoid secretion: origins and downstream effects, IEEE Trans. Biomed. Eng.58(12):3504 (2011) 
  • Swiss, V.A., T.T. Nguyen, J. Dugas, A. Ibrahim, b. Barres, I.P. Androulakis and P. Casaccia, Identification of a gene regulatory network necessary for the initiation of oligodendrocyte differentiation, PLoS One6(4):e18088 (2011) 
  • Scheff, J.D., D.C. DuBois, R.R. Almon, W.J. Jusko and I.P. Androulakis, Assessment of pharmacologic area under the curve when baselines are variable, J Pharmacokinetics Pharmacodynamics28(5):1081-1089 (2011)
  • Orman, M.A., M.G. Ierapetritou, F. Berthiaume and I.P. Androulakis, The Dynamics of the Early Inflammatory Response in Double-hit Burn and Sepsis Animal Models, Cytokine56(2):494 (2011) 
  • Nguyen, T.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, Agent based model of human endotoxemia accounting for circadian variability, J. Critical Care:e6-e7 (2011)
  • Scheff, J.D., S.E. Calvano, S.F. Lowry and I.P. Androulakis, Decreased communication leads to diminished physiologic variability in a multiscale model of inflammation, J. Critical Care:e3 (2011)
  • Foteinou, P.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, A physiologic model for autonomic heart rate regulation in human endotoxemia, J. Critical Care:e2-e3 (2011)

2010

  • Foteinou, P.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, A physiological model for autonomic heart rate regulation in human endotoxemia, SHOCK35(3):229-239 (2010) 
  • Orman, M., F. Berthiaume, I.P. Androulakis and M.G. Ierapetritou, Pathway Analysis of Liver Metabolism under Stressed Condition , J. Theo. Biol.272(1):131-140 (2010) 
  • 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) 
  • 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) 
  • 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) 
  • Yang, Q., F. Berthiaume and I.P. Androulakis, A quantitative model of thermal injury-induced acute inflammation , Math. Biosci.229(2):135-148 (2010) 
  • Iyer, V., M.A. Ovacik, I.P. Androulakis, C.M Roth and M.G. Ierapetritou, Transcriptional and Metabolic Flux Profiling of Triadimefon Effects on Cultured Hepatocytes, Toxicology and Applied Pharmacology248(3):1665-177 (2010) 
  • 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 11:515 (2010) 
  • 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) 
  • 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) 
  • 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) 
  • 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 ONE5(2):e9249 (2010) 
  • 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) 
  • 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 107(5):825-835 (2010) 
  • 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) 
  • 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) 
  • He, K, I.P. Androulakis and M.G. Ierapetritou, Multi-element flux analysis for the incorporation of detailed kinetic mechanisms in Reactive Simulations, Energy Fuels24:309-317 (2010) 

2009

  • 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) 
  • Foteinou, P.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, Translational potential of systems-based models of inflammation, Clinical and Translational Science2(1):85-89 (2009) 
  • 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) 
  • Nguyen, T.T., R. Nowakoski, and I.P. Androulakis, Unsupervised selection of highly coexpressed and non-coexpressed genes, OMICS13(3): 219-237 (2009) 
  • 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) 
  • 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 ONE4(3):e4706 (2009) 
  • 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. Care24(3):e25 (2009)
  • Nguyen T. T. and Androulakis I. P. Recent Advances in the Computational Discovery of Transcription Factor Binding Sites. Algorithms2(1):582-605 (2009) 
  • Yang, E., and I.P. Androulakis, Assessing and Selecting Gene Expression Signals Based Upon the Quality of the Measured Dynamics, BMC Bioinformatics10(1):55 (2009) 
  • 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 Optimization43(2):263 (2009) 

2008

  • 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. Pharm234(2):156-65 (2008) 
  • 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) 
  • 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 Teratology82, 296-29 (2008)
  • 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) 
  • Foteinou, P.T., S.E. Calvano, S.F. Lowry and I.P. Androulakis, Modeling Endotoxin-Induced Systemic Inflammation Using an Indirect Response Approach, Math. Biosciences217(1):27-42 (2008) 
  • Ovacik, M. and I.P. Androulakis, On the potential for integrating gene expression and metabolic flux data: A review, Current Bioinformatics3(3):142-148 (2008) 
  • 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. Therapeutics326(3):700-716 (2008) 
  • 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) 
  • 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) 
  • He, K., M.G. Ierapetritou and I.P. Androulakis, A graph-based approach for developing adaptive representations of complex reaction mechanisms, Comb & Flame155(4):585-604 (2008) 
  • 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) 
  • 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) 
  • 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) 
  • 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) 
  • Yang, E. and I.P. Androulakis, Assessing the information content of microarray time series, Encyclopedia of Healthcare Information Systems (Wickramasinghe, Ed.) (2008) 
  • 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) 
  • 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) 
  • 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) 

2007

  • Foteinou, P.T., S. Calvano, S. Lowry and I.P. Androulakis, An indirect response model of endotoxin-induced systemic inflammation, Journal of Critical Care22 (4):337-338 (2007) 
  • Androulakis, I.P, Mathematical programming approaches for the analysis of microarray data, Handbook of Optimization in Medicine (E. Romeijn, Ed) (2007) 
  • 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) 
  • 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) 
  • 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 Bioinformatics8 (10) (2007) 
  • 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 Engineering35(6):1053-1067 (2007) 
  • Androulakis, I.P., E. Yang, and R.R. Almon, Analysis of time-series gene expression data: Methods, challenges, and opportunities. Annual Review of Biomedical Engineering9: p. 205-228 (2007) 
  • 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 MeetingMarch 25-28; San Diego, CA. March 25-28 (2007) 
  • Androulakis, I.P. and W. Chaovalitwongse, Mathematical programming for data mining, In Encyclopedia of Optimization (C.A. Floudas and P.M. Pardalos, Eds.) (2007) 
  • 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) 

2006

  • 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) 
  • Androulakis, I.P., J.M. Grenda, T.A. Barckholtz, and J.W. Bozzelli, Propagation of uncertainty in chemically activated systems, AIChE J50:2956 (2006) 
  • Androulakis IP: New approaches for representing, analyzing and visualizing complex kinetic transformations.Computers & Chemical Engineering, 31:41-50 (2006) 
  • 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) 

2005

  • Knapinska, A.M., P.I. Irizarry, S.Adusumalli, I.P. Androulakis and G. Brewer, Molecular Mechanisms Regulating mRNA Stability: Physiological and Pathological Significance, Current Genomics6(6):471-486 (2005) 
  • 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) 
  • Wu, J., and I.P. Androulakis, Exploring classifiability metrics for selecting informative genes, Proceeding of 15thEuropean Symposium on Computer Aided Process Engineering, Barcelona (2005) 
  • 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) 
  • 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) 
  • 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) 

2004

  • 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) 
  • Androulakis, I.P., "Selecting maximally informative genes", Comp. & Chemical EngineeringSpecial issue on Systems Engineering Challenges and Opportunities in Biology29:535-546 (2004) 
  • 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) 
  • Androulakis, I.P., J.T. Farrell, C.S. Hsu, K. Qian, and K. Nakakita, "An Integrated Approach for Creating Model Fuels", Energy and Fuels19(1):111-119 (2004) 
  • 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) 

2003

  • 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)

2001

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

2000

  • Androulakis I.P., Kinetic mechanism reduction based on an integer programming approach, AIChE J., 46, 361-370 (2000) 
  • 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) 
  • Adjiman, C.S., I.P. Androulakis and C.A. Floudas, Global optimization of mixed-integer nonlinear problems,AIChE J., 46, 1796-1798 (2000) 
  • 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)

1999

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

1998

  • 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) 
  • 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) 
  • Androulakis I.P., and C.A. Floudas, "Distributed Branch and Bound-based Algorithms for Global Optimization", InInstitute for Mathematics and its Applications: Parallel Processing of Discrete Problems106, 1-36, Kluwer Academic Publishers (1998) 

1997

  • 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 Genetics29, 87-102 (1997) 
  • 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) 
  • 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) 
  • Adjiman, C.S., I.P. Androulakis, and C.A. Floudas, Global optimization of MINLP problems in process synthesis and design, Comp. Chem. Engng21, S445-S450 (1997) 
  • 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)

1996

  • 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) 
  • 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 12thInternational Histocompatibility Conference, (1996)

1995

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

1991

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

1989

  • 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)