48 results found
Kostrzewski T, Borg AJ, Meng Y, et al., 2018, Multiple Levels of Control Determine How E4bp4/Nfil3 Regulates NK Cell Development, JOURNAL OF IMMUNOLOGY, Vol: 200, Pages: 1370-1381, ISSN: 0022-1767
Lucia A, DiMaggio PA, Alonso-Martinez D, 2018, Metabolic pathway analysis using a nash equilibrium approach, Journal of Global Optimization, Pages: 1-14, ISSN: 0925-5001
© 2018 Springer Science+Business Media, LLC, part of Springer Nature A novel approach to metabolic network analysis using a Nash Equilibrium (NE) formulation is proposed in which enzymes are considered players in a multi-player game. Each player has its own payoff function with the objective of minimizing the Gibbs free energy associated with the biochemical reaction(s) it catalyzes subject to elemental mass balances while the network objective is to find the best solution to the sum of the player payoff functions. Consequently, any NE solution may not be best solution for all players. Key advantages of the NE approach include the ability to account for (1) aqueous electrolyte behavior, (2) the consumption/production of co-factors, and (3) charge balancing. However, the proposed Nash equilibrium formulation results in a set of nonlinear programming sub-problems that are more demanding to solve than conventional flux balance analysis (FBA) formulations which rely on linear programming. A direct substitution solution methodology for pathways with feedback is described. The Krebs cycle is used to demonstrate the efficacy of the NE approach while comparisons with both FBA and experimental data are used to show that it represents a paradigm shift in metabolic network analysis.
Lucia A, Thomas E, DiMaggio PA, 2018, On the explicit use of enzyme-substrate reactions in metabolic pathway analysis, Pages: 88-99, ISSN: 0302-9743
© Springer International Publishing AG 2018. Flux balance (or constraint-based) analysis has been the mainstay for understanding metabolic networks for many years. However, recently Lucia and DiMaggio  have argued that metabolic networks are more correctly modeled using game theory, specifically Nash Equilibrium, because it (1) captures the natural competition between enzymes, (2) includes rigorous chemical reaction equilibrium thermodynamics, (3) incorporates element mass balance constraints, and therefore charge balancing, in a natural way, and (4) allows regulatory constraints to be included as additional constraints. The novel aspects of this work center on the explicit inclusion of enzyme-substrate reactions at the cellular length scale and molecular length scale protein docking information in metabolic network modeling. This multi-scale information offers the advantages of directly (1) computing cellular enzyme concentrations and activities, (2) incorporating genetic modification of enzymes, and (3) encoding the effects of age-related changes in enzymatic behavior (e.g., protein misfolding) within any pathway. Molecular length scale binding histograms are computed using protein-ligand docking and directly up-scaled to the cellular level. A small, proof-of-concept example from the Krebs cycle is presented to illustrate key ideas. Numerical results show that the proposed approach provides a wealth of quantitative enzyme information.
Chen PB, Ding S, Zanghi G, et al., 2016, Plasmodium falciparum PfSET7: enzymatic characterization and cellular localization of a novel protein methyltransferase in sporozoite, liver and erythrocytic stage parasites, SCIENTIFIC REPORTS, Vol: 6, ISSN: 2045-2322
Lucia A, Dimaggio PA, 2016, A Nash Equilibrium approach to metabolic network analysis, Pages: 45-58, ISSN: 0302-9743
© Springer International Publishing AG 2016. A novel approach to metabolic network analysis using a Nash Equilibrium formulation is proposed. Enzymes are considered to be players in a multi-player game in which each player attempts to minimize the dimensionless Gibbs free energy associated with the biochemical reaction(s) it catalyzes subject to elemental mass balances. Mathematical formulation of the metabolic network as a set of nonlinear programming (NLP) sub-problems and appropriate solution methodologies are described. A small example representing part of the production cycle for acetyl-CoA is used to demonstrate the efficacy of the proposed Nash Equilibrium framework and show that it represents a paradigm shift in metabolic network analysis.
Brownstein NC, Guan X, Mao Y, et al., 2015, Paired single residue-transposed Lys-N and Lys-C digestions for label-free identification of N-terminal and C-terminal MS/MS peptide product ions: ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry for peptide de novo sequencing, RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Vol: 29, Pages: 659-666, ISSN: 0951-4198
Dattani R, Gibson KF, Few S, et al., 2015, Fullerene oxidation and clustering in solution induced by light, JOURNAL OF COLLOID AND INTERFACE SCIENCE, Vol: 446, Pages: 24-30, ISSN: 0021-9797
Horejs C-M, Serio A, Purvis A, et al., 2014, Biologically-active laminin-111 fragment that modulates the epithelial-to-mesenchymal transition in embryonic stem cells, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 111, Pages: 5908-5913, ISSN: 0027-8424
O'Connor CM, DiMaggio PA, Shenk T, et al., 2014, Quantitative Proteomic Discovery of Dynamic Epigenome Changes that Control Human Cytomegalovirus (HCMV) Infection, MOLECULAR & CELLULAR PROTEOMICS, Vol: 13, Pages: 2399-2410, ISSN: 1535-9476
Bartke T, Borgel J, DiMaggio PA, 2013, Proteomics in epigenetics: new perspectives for cancer research, BRIEFINGS IN FUNCTIONAL GENOMICS, Vol: 12, Pages: 205-218, ISSN: 2041-2649
Cherblanc FL, Chapman KL, Reid J, et al., 2013, On the Histone Lysine Methyltransferase Activity of Fungal Metabolite Chaetocin, JOURNAL OF MEDICINAL CHEMISTRY, Vol: 56, Pages: 8616-8625, ISSN: 0022-2623
Evertts AG, Zee BM, DiMaggio PA, et al., 2013, Quantitative Dynamics of the Link between Cellular Metabolism and Histone Acetylation, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 288, Pages: 12142-12151, ISSN: 0021-9258
LeRoy G, DiMaggio PA, Chan EY, et al., 2013, A quantitative atlas of histone modification signatures from human cancer cells, EPIGENETICS & CHROMATIN, Vol: 6, ISSN: 1756-8935
Wu Y, DiMaggio PA, Perlman DH, et al., 2013, Novel Phosphorylation Sites in the S. cerevisiae Cdc13 Protein Reveal New Targets for Telomere Length Regulation, JOURNAL OF PROTEOME RESEARCH, Vol: 12, Pages: 316-327, ISSN: 1535-3893
Baliban RC, DiMaggio PA, Plazas-Mayorca MD, et al., 2012, PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization, JOURNAL OF PROTEOME RESEARCH, Vol: 11, Pages: 4615-4629, ISSN: 1535-3893
Baliban RC, Sakellari D, Li Z, et al., 2012, Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples, JOURNAL OF CLINICAL PERIODONTOLOGY, Vol: 39, Pages: 203-212, ISSN: 0303-6979
DiMaggio PA, Subramani A, Floudas CA, 2012, Novel biclustering methods for re-ordering data matrices, Fields Institute Communications, Vol: 63, Pages: 1-39, ISSN: 1069-5265
Clustering of large-scale data sets is an important technique that is used for analysis in a variety of fields. However, a number of these methods are based on heuristics for the identification of the best arrangement of data points. In this chapter, we present rigorous clustering methods based on the iterative optimal re-ordering of data matrices. Distinct Mixed-integer linear programming (MILP) models have been implemented to carry out clustering of dense data matrices (such as gene expression data) and sparse data matrices (such as drug discovery and toxicology).We present the capability of the optimal re-orderingmethods on a wide array of data sets from systems biology, molecular discovery and toxicology. © Springer Science+Business Media New York 2012.
LeRoy G, Chepelev I, DiMaggio PA, et al., 2012, Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins, GENOME BIOLOGY, Vol: 13, ISSN: 1474-760X
Yu Y, Song C, Zhang Q, et al., 2012, Histone H3 Lysine 56 Methylation Regulates DNA Replication through Its Interaction with PCNA, MOLECULAR CELL, Vol: 46, Pages: 7-17, ISSN: 1097-2765
Vedadi M, Barsyte-Lovejoy D, Liu F, et al., 2011, A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells, NATURE CHEMICAL BIOLOGY, Vol: 7, Pages: 566-574, ISSN: 1552-4450
Baliban RC, DiMaggio PA, Plazas-Mayorca MD, et al., 2010, A Novel Approach for Untargeted Post-translational Modification Identification Using Integer Linear Optimization and Tandem Mass Spectrometry, MOLECULAR & CELLULAR PROTEOMICS, Vol: 9, Pages: 764-779, ISSN: 1535-9476
DiMaggio PA, Garcia BA, 2010, Mass Spectrometry Based Proteomics for Interrogating the Histone Code, CURRENT PROTEOMICS, Vol: 7, Pages: 177-187, ISSN: 1570-1646
DiMaggio PA, McAllister SR, Floudas CA, et al., 2010, Enhancing Molecular Discovery Using Descriptor-Free Rearrangement Clustering Techniques for Sparse Data Sets, AICHE JOURNAL, Vol: 56, Pages: 405-418, ISSN: 0001-1541
DiMaggio PA, McAllister SR, Floudas CA, et al., 2010, A network flow model for biclustering via optimal re-ordering of data matrices, 2nd International Conference on Complementarity, Duality and Global Optimization in Science and Engineering, Publisher: SPRINGER, Pages: 343-354, ISSN: 0925-5001
DiMaggio PA, Subramani A, Judson RS, et al., 2010, A Novel Framework for Predicting In Vivo Toxicities from In Vitro Data Using Optimal Methods for Dense and Sparse Matrix Reordering and Logistic Regression, TOXICOLOGICAL SCIENCES, Vol: 118, Pages: 251-265, ISSN: 1096-6080
Plazas-Mayorca MD, Bloom JS, Zeissler U, et al., 2010, Quantitative proteomics reveals direct and indirect alterations in the histone code following methyltransferase knockdown, MOLECULAR BIOSYSTEMS, Vol: 6, Pages: 1719-1729, ISSN: 1742-206X
Young NL, DiMaggio PA, Garcia BA, 2010, The significance, development and progress of high-throughput combinatorial histone code analysis, CELLULAR AND MOLECULAR LIFE SCIENCES, Vol: 67, Pages: 3983-4000, ISSN: 1420-682X
Young NL, Plazas-Mayorca MD, DiMaggio PA, et al., 2010, Collective Mass Spectrometry Approaches Reveal Broad and Combinatorial Modification of High Mobility Group Protein A1a, JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, Vol: 21, Pages: 960-970, ISSN: 1044-0305
Zee BM, Levin RS, DiMaggio PA, et al., 2010, Global turnover of histone post-translational modifications and variants in human cells, EPIGENETICS & CHROMATIN, Vol: 3, ISSN: 1756-8935
DiMaggio PA, Young NL, Baliban RC, et al., 2009, A Mixed Integer Linear Optimization Framework for the Identification and Quantification of Targeted Post-translational Modifications of Highly Modified Proteins Using Multiplexed Electron Transfer Dissociation Tandem Mass Spectrometry, MOLECULAR & CELLULAR PROTEOMICS, Vol: 8, Pages: 2527-2543, ISSN: 1535-9476
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