A deterministic global optimization approach for the protein folding problem. - Costas D. Maranas; Ioannis P. Androulakis; Christodoulos A. Floudas (Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995)

αBB: A global optimization method for general constrained nonconvex problems. - Ioannis P. Androulakis; Costas D. Maranas; Christodoulos A. Floudas (J. Glob. Optim., 1995)

Prediction of Oligopeptide Conformations via Deterministic Global Optimization. - Ioannis P. Androulakis; Costas D. Maranas; Christodoulos A. Floudas (J. Glob. Optim., 1997)

"Store and retrieve" representations of dynamic systems motivated by studies in gas phase chemical kinetics. - Ioannis P. Androulakis (Comput. Chem. Eng., 2004)

Selecting maximally informative genes. - Ioannis P. Androulakis (Comput. Chem. Eng., 2005)

Assessing the Information Content of Short Time Series Expression Data. - Eric H. Yang; Ioannis P. Androulakis (EMBC, 2006)

New approaches for representing, analyzing and visualizing complex kinetic transformations. - Ioannis P. Androulakis (Comput. Chem. Eng., 2006)

A novel non-overlapping bi-clustering algorithm for network generation using living cell array data. - Eric Yang; Panagiota T. Foteinou; K. R. King; Martin L. Yarmush; Ioannis P. Androulakis (Bioinform., 2007)

Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. - Eric Yang; Timothy Maguire; Martin L. Yarmush; Francois Berthiaume; Ioannis P. Androulakis (BMC Bioinform., 2007)

A novel MINLP-based representation of the original complex model for predicting gasoline emissions. - Kevin C. Furman; Ioannis P. Androulakis (Comput. Chem. Eng., 2008)

Informative gene selection and design of regulatory networks using integer optimization. - Eric Yang; Timothy Maguire; Martin L. Yarmush; Ioannis P. Androulakis (Comput. Chem. Eng., 2008)

Recent Advances in the Computational Discovery of Transcription Factor Binding Sites. - Tung T. Nguyen; Ioannis P. Androulakis (Algorithms, 2009)

Assessing and selecting gene expression signals based upon the quality of the measured dynamics. - Eric Yang; Ioannis P. Androulakis (BMC Bioinform., 2009)

Networks, biology and systems engineering: A case study in inflammation. - Panagiota T. Foteinou; Eric Yang; Ioannis P. Androulakis (Comput. Chem. Eng., 2009)

A mixed-integer optimization framework for the synthesis and analysis of regulatory networks. - Panagiota T. Foteinou; Eric Yang; Georges K. Saharidis; Marianthi G. Ierapetritou; Ioannis P. Androulakis (J. Glob. Optim., 2009)

Asynchronous Distributed Optimization Algorithms. - Ioannis P. Androulakis (Encyclopedia of Optimization, 2009)

Dynamic Programming: Average Cost Per Stage Problems. - Ioannis P. Androulakis (Encyclopedia of Optimization, 2009)

Dynamic Programming: Discounted Problems. - Ioannis P. Androulakis (Encyclopedia of Optimization, 2009)

Dynamic Programming: Infinite Horizon Problems, Overview. - Ioannis P. Androulakis (Encyclopedia of Optimization, 2009)

Dynamic Programming: Inventory Control. - Ioannis P. Androulakis (Encyclopedia of Optimization, 2009)

Dynamic Programming: Stochastic Shortest Path Problems. - Ioannis P. Androulakis (Encyclopedia of Optimization, 2009)

Dynamic Programming: Undiscounted Problems. - Ioannis P. Androulakis (Encyclopedia of Optimization, 2009)

MINLP: Branch and Bound Global Optimization Algorithm. - Ioannis P. Androulakis (Encyclopedia of Optimization, 2009)

Mathematical Programming for Data Mining. - Ioannis P. Androulakis; Wanpracha Art Chaovalitwongse (Encyclopedia of Optimization, 2009)

Selection of Maximally Informative Genes. - Ioannis P. Androulakis; Eric Yang (Encyclopedia of Optimization, 2009)

Quadratic Integer Programming: Complexity and Equivalent Forms. - Wanpracha Art Chaovalitwongse; Ioannis P. Androulakis; Panos M. Pardalos (Encyclopedia of Optimization, 2009)

Effects of Triadimefon on the Metabolism of Cultured Hepatocytes. - Vidya V. Iyer; Ioannis P. Androulakis; Charles M. Roth; Marianthi G. Ierapetritou (BIBE, 2010)

Dynamic Complexity of the Temporal Transcriptional Regulation Program in Human Endotoxemia. - Tung T. Nguyen; Panagiota T. Foteinou; Ioannis P. Androulakis; Steve E. Calvano; Stephen F. Lowry (BIBE, 2010)

Modeling Circadian Rhythms in Inflammation. - Jeremy D. Scheff; Ioannis P. Androulakis; Steve E. Calvano; Stephen F. Lowry (BIBE, 2010)

Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver. - Tung T. Nguyen; Richard R. Almon; Debra C. DuBois; William J. Jusko; Ioannis P. Androulakis (BMC Bioinform., 2010)

Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures. - Tung T. Nguyen; Richard R. Almon; Debra C. DuBois; William J. Jusko; Ioannis P. Androulakis (BMC Bioinform., 2010)

Circadian signatures in rat liver: from gene expression to pathways. - Meric A. Ovacik; Siddharth Sukumaran; Richard R. Almon; Debra C. DuBois; William J. Jusko; Ioannis P. Androulakis (BMC Bioinform., 2010)

Model building using bi-level optimization. - Georges K. Saharidis; Ioannis P. Androulakis; Marianthi G. Ierapetritou (J. Glob. Optim., 2011)

Pulsatile Glucocorticoid Secretion: Origins and Downstream Effects. - Jeremy D. Scheff; Alyssa K. Kosmides; Steve E. Calvano; Stephen F. Lowry; Ioannis P. Androulakis (IEEE Trans. Biomed. Eng., 2011)

A multiscale modeling approach to inflammation: A case study in human endotoxemia. - Jeremy D. Scheff; Panteleimon D. Mavroudis; Panagiota T. Foteinou; Gary An; Steve E. Calvano; John Doyle 001; Thomas E. Dick; Stephen F. Lowry; Yoram Vodovotz; Ioannis P. Androulakis (J. Comput. Phys., 2013)

Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver. - Tung T. Nguyen; John S. A. Mattick; Qian Yang; Mehmet A. Orman; Marianthi G. Ierapetritou; Francois Berthiaume; Ioannis P. Androulakis (BMC Bioinform., 2014)

A chemical engineer's perspective on health and disease. - Ioannis P. Androulakis (Comput. Chem. Eng., 2014)

Biosystems modeling and engineering. - Andreas A. Linninger; Ioannis P. Androulakis (Comput. Chem. Eng., 2014)

On the analysis of complex biological supply chains: From process systems engineering to quantitative systems pharmacology. - Rohit T. Rao; Megerle L. Scherholz; Clara Hartmanshenn; Seul-A. Bae; Ioannis P. Androulakis (Comput. Chem. Eng., 2017)

The quest for digital health: From diseases to patients. - Ioannis P. Androulakis (Comput. Chem. Eng., 2019)

The Impact of Stochasticity and Its Control on a Model of the Inflammatory Response. - Panteleimon D. Mavroudis; Jeremy D. Scheff; John C. Doyle 001; Yoram Vodovotz; Ioannis P. Androulakis (Comput., 2019)

HPA axis differential flatness and Liouvillian study for higher resiliency investigations. - Florentina Nicolau; Hugues Mounier; Ioannis P. Androulakis (IMA J. Math. Control. Inf., 2023)