A Geometric Terrain Methodology for Global Optimization. - Angelo Lucia; Peter A. DiMaggio Jr.; P. Depa (J. Glob. Optim., 2004)

The phase behavior of n-alkane systems. - Angelo Lucia; Peter A. DiMaggio; Meghan L. Bellows; Leah M. Octavio (Comput. Chem. Eng., 2005)

Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. - Peter A. DiMaggio Jr.; Scott R. McAllister; Christodoulos A. Floudas; Xiao-Jiang Feng; Joshua D. Rabinowitz; Herschel Rabitz (BMC Bioinform., 2008)

Mathematical modeling and efficient optimization methods for the distance-dependent rearrangement clustering problem. - Scott R. McAllister; Peter A. DiMaggio Jr.; Christodoulos A. Floudas (J. Glob. Optim., 2009)

Peptide Identification via Mixed-Integer Optimization. - Peter A. DiMaggio Jr.; Christodoulos A. Floudas (Encyclopedia of Optimization, 2009)

A network flow model for biclustering via optimal re-ordering of data matrices. - Peter A. DiMaggio Jr.; Scott R. McAllister; Christodoulos A. Floudas; Xiao-Jiang Feng; Joshua D. Rabinowitz; Herschel Rabitz (J. Glob. Optim., 2010)

A Nash Equilibrium Approach to Metabolic Network Analysis. - Angelo Lucia; Peter A. DiMaggio (MOD, 2016)

On the Explicit Use of Enzyme-Substrate Reactions in Metabolic Pathway Analysis. - Angelo Lucia; Edward Thomas; Peter A. DiMaggio (MOD, 2017)

Metabolic pathway analysis using a nash equilibrium approach. - Angelo Lucia; Peter A. DiMaggio; Diego Alonso-Martinez (J. Glob. Optim., 2018)

A Multi-Scale Computational Approach to Understanding Cancer Metabolism. - Angelo Lucia; Peter A. DiMaggio (Data Science for Healthcare, 2019)

HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs. - Harry J. Whitwell; Peter A. DiMaggio Jr. (Bioinform., 2020)