Imperial College London

DrPeterDiMaggio

Faculty of EngineeringDepartment of Chemical Engineering

Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 5589p.dimaggio Website

 
 
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Location

 

218ACE ExtensionSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

45 results found

Chen PB, Ding S, Zanghi G, Soulard V, DiMaggio PA, Fuchter MJ, Mecheri S, Mazier D, Scherf A, Malmquist NAet 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

JOURNAL ARTICLE

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.

CONFERENCE PAPER

Brownstein NC, Guan X, Mao Y, Zhang Q, DiMaggio PA, Xia Q, Zhang L, Marshall AG, Young NLet 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

JOURNAL ARTICLE

Dattani R, Gibson KF, Few S, Borg AJ, DiMaggio PA, Nelson J, Kazarian SG, Cabral JTet 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

JOURNAL ARTICLE

Horejs C-M, Serio A, Purvis A, Gormley AJ, Bertazzo S, Poliniewicz A, Wang AJ, DiMaggio P, Hohenester E, Stevens MMet 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

JOURNAL ARTICLE

O'Connor CM, DiMaggio PA, Shenk T, Garcia BAet 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

JOURNAL ARTICLE

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

JOURNAL ARTICLE

Cherblanc FL, Chapman KL, Reid J, Borg AJ, Sundriyal S, Alcazar-Fuoli L, Bignell E, Demetriades M, Schofield CJ, DiMaggio PA, Brown R, Fuchter MJet al., 2013, On the Histone Lysine Methyltransferase Activity of Fungal Metabolite Chaetocin, JOURNAL OF MEDICINAL CHEMISTRY, Vol: 56, Pages: 8616-8625, ISSN: 0022-2623

JOURNAL ARTICLE

Evertts AG, Zee BM, DiMaggio PA, Gonzales-Cope M, Coller HA, Garcia BAet 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

JOURNAL ARTICLE

LeRoy G, DiMaggio PA, Chan EY, Zee BM, Blanco MA, Bryant B, Flaniken IZ, Liu S, Kang Y, Trojer P, Garcia BAet al., 2013, A quantitative atlas of histone modification signatures from human cancer cells, EPIGENETICS & CHROMATIN, Vol: 6, ISSN: 1756-8935

JOURNAL ARTICLE

Wu Y, DiMaggio PA, Perlman DH, Zakian VA, Garcia BAet 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

JOURNAL ARTICLE

Baliban RC, DiMaggio PA, Plazas-Mayorca MD, Garcia BA, Floudas CAet 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

JOURNAL ARTICLE

Baliban RC, Sakellari D, Li Z, DiMaggio PA, Garcia BA, Floudas CAet 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

JOURNAL ARTICLE

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.

JOURNAL ARTICLE

LeRoy G, Chepelev I, DiMaggio PA, Blanco MA, Zee BM, Zhao K, Garcia BAet al., 2012, Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins, GENOME BIOLOGY, Vol: 13, ISSN: 1474-760X

JOURNAL ARTICLE

Yu Y, Song C, Zhang Q, DiMaggio PA, Garcia BA, York A, Carey MF, Grunstein Met 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

JOURNAL ARTICLE

Vedadi M, Barsyte-Lovejoy D, Liu F, Rival-Gervier S, Allali-Hassani A, Labrie V, Wigle TJ, DiMaggio PA, Wasney GA, Siarheyeva A, Dong A, Tempel W, Wang S-C, Chen X, Chau I, Mangano TJ, Huang X-P, Simpson CD, Pattenden SG, Norris JL, Kireev DB, Tripathy A, Edwards A, Roth BL, Janzen WP, Garcia BA, Petronis A, Ellis J, Brown PJ, Frye SV, Arrowsmith CH, Jin Jet 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

JOURNAL ARTICLE

Baliban RC, DiMaggio PA, Plazas-Mayorca MD, Young NL, Garcia BA, Floudas CAet 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

JOURNAL ARTICLE

DiMaggio PA, Garcia BA, 2010, Mass Spectrometry Based Proteomics for Interrogating the Histone Code, CURRENT PROTEOMICS, Vol: 7, Pages: 177-187, ISSN: 1570-1646

JOURNAL ARTICLE

DiMaggio PA, McAllister SR, Floudas CA, Feng X-J, Li G, Rabinowitz JD, Rabitz HAet 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

JOURNAL ARTICLE

DiMaggio PA, McAllister SR, Floudas CA, Feng X-J, Rabinowitz JD, Rabitz HAet 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

CONFERENCE PAPER

DiMaggio PA, Subramani A, Judson RS, Floudas CAet 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

JOURNAL ARTICLE

Plazas-Mayorca MD, Bloom JS, Zeissler U, Leroy G, Young NL, DiMaggio PA, Krugylak L, Schneider R, Garcia BAet 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

JOURNAL ARTICLE

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

JOURNAL ARTICLE

Young NL, Plazas-Mayorca MD, DiMaggio PA, Flaniken IZ, Beltran AJ, Mishra N, LeRoy G, Floudas CA, Garcia BAet 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

JOURNAL ARTICLE

Zee BM, Levin RS, DiMaggio PA, Garcia BAet al., 2010, Global turnover of histone post-translational modifications and variants in human cells, EPIGENETICS & CHROMATIN, Vol: 3, ISSN: 1756-8935

JOURNAL ARTICLE

McAllister SR, DiMaggio PA, Floudas CA, 2009, Mathematical modeling and efficient optimization methods for the distance-dependent rearrangement clustering problem, Workshop on Global Optimization, Publisher: SPRINGER, Pages: 111-129, ISSN: 0925-5001

CONFERENCE PAPER

Subramani A, DiMaggio PA, Floudas CA, 2009, Selecting High Quality Protein Structures from Diverse Conformational Ensembles, BIOPHYSICAL JOURNAL, Vol: 97, Pages: 1728-1736, ISSN: 0006-3495

JOURNAL ARTICLE

Young NL, DiMaggio PA, Plazas-Mayorca MD, Baliban RC, Floudas CA, Garcia BAet al., 2009, High Throughput Characterization of Combinatorial Histone Codes, MOLECULAR & CELLULAR PROTEOMICS, Vol: 8, Pages: 2266-2284, ISSN: 1535-9476

JOURNAL ARTICLE

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