Peter A. DiMaggio, Ph.D. - Publications

Affiliations: 
Princeton University, Princeton, NJ 

42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Chen PB, Ding S, Zanghì G, Soulard V, DiMaggio PA, Fuchter MJ, Mecheri S, Mazier D, Scherf A, Malmquist NA. Plasmodium falciparum PfSET7: enzymatic characterization and cellular localization of a novel protein methyltransferase in sporozoite, liver and erythrocytic stage parasites. Scientific Reports. 6: 21802. PMID 26902486 DOI: 10.1038/srep21802  1
2015 Brownstein NC, Guan X, Mao Y, Zhang Q, DiMaggio PA, Xia Q, Zhang L, Marshall AG, Young NL. 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 : Rcm. 29: 659-66. PMID 26212284 DOI: 10.1002/rcm.7137  1
2015 Dattani R, Gibson KF, Few S, Borg AJ, DiMaggio PA, Nelson J, Kazarian SG, Cabral JT. Fullerene oxidation and clustering in solution induced by light. Journal of Colloid and Interface Science. 446: 24-30. PMID 25646787 DOI: 10.1016/j.jcis.2015.01.005  1
2014 O'Connor CM, DiMaggio PA, Shenk T, Garcia BA. Quantitative proteomic discovery of dynamic epigenome changes that control human cytomegalovirus (HCMV) infection. Molecular & Cellular Proteomics : McP. 13: 2399-410. PMID 24987098 DOI: 10.1074/mcp.M114.039792  1
2014 Horejs CM, Serio A, Purvis A, Gormley AJ, Bertazzo S, Poliniewicz A, Wang AJ, DiMaggio P, Hohenester E, Stevens MM. 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. 111: 5908-13. PMID 24706882 DOI: 10.1073/pnas.1403139111  1
2013 Cherblanc FL, Chapman KL, Reid J, Borg AJ, Sundriyal S, Alcazar-Fuoli L, Bignell E, Demetriades M, Schofield CJ, DiMaggio PA, Brown R, Fuchter MJ. On the histone lysine methyltransferase activity of fungal metabolite chaetocin. Journal of Medicinal Chemistry. 56: 8616-25. PMID 24099080 DOI: 10.1021/jm401063r  1
2013 Leroy G, Dimaggio PA, Chan EY, Zee BM, Blanco MA, Bryant B, Flaniken IZ, Liu S, Kang Y, Trojer P, Garcia BA. A quantitative atlas of histone modification signatures from human cancer cells. Epigenetics & Chromatin. 6: 20. PMID 23826629 DOI: 10.1186/1756-8935-6-20  1
2013 Evertts AG, Zee BM, Dimaggio PA, Gonzales-Cope M, Coller HA, Garcia BA. Quantitative dynamics of the link between cellular metabolism and histone acetylation. The Journal of Biological Chemistry. 288: 12142-51. PMID 23482559 DOI: 10.1074/jbc.M112.428318  1
2013 Bartke T, Borgel J, DiMaggio PA. Proteomics in epigenetics: new perspectives for cancer research. Briefings in Functional Genomics. 12: 205-18. PMID 23401080 DOI: 10.1093/bfgp/elt002  1
2013 Wu Y, DiMaggio PA, Perlman DH, Zakian VA, Garcia BA. Novel phosphorylation sites in the S. cerevisiae Cdc13 protein reveal new targets for telomere length regulation. Journal of Proteome Research. 12: 316-27. PMID 23181431 DOI: 10.1021/pr300408v  1
2012 LeRoy G, Chepelev I, DiMaggio PA, Blanco MA, Zee BM, Zhao K, Garcia BA. Proteo-Genomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins Genome Biology. R68. PMID 22897906 DOI: 10.1186/gb-2012-13-8-r68  1
2012 Baliban RC, Dimaggio PA, Plazas-Mayorca MD, Garcia BA, Floudas CA. PILOT_PROTEIN: identification of unmodified and modified proteins via high-resolution mass spectrometry and mixed-integer linear optimization. Journal of Proteome Research. 11: 4615-29. PMID 22788846 DOI: 10.1021/pr300418j  1
2012 Yu Y, Song C, Zhang Q, DiMaggio PA, Garcia BA, York A, Carey MF, Grunstein M. Histone H3 lysine 56 methylation regulates DNA replication through its interaction with PCNA. Molecular Cell. 46: 7-17. PMID 22387026 DOI: 10.1016/j.molcel.2012.01.019  1
2012 Baliban RC, Sakellari D, Li Z, DiMaggio PA, Garcia BA, Floudas CA. Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples. Journal of Clinical Periodontology. 39: 203-12. PMID 22092770 DOI: 10.1111/j.1600-051X.2011.01805.x  1
2012 DiMaggio PA, Subramani A, Floudas CA. Novel biclustering methods for re-ordering data matrices Fields Institute Communications. 63: 1-39. DOI: 10.1007/978-1-4614-4133-5_1  1
2011 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 SC, Chen X, Chau I, et al. A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells. Nature Chemical Biology. 7: 566-74. PMID 21743462 DOI: 10.1038/nchembio.599  1
2010 Zee BM, Levin RS, Dimaggio PA, Garcia BA. Global turnover of histone post-translational modifications and variants in human cells. Epigenetics & Chromatin. 3: 22. PMID 21134274 DOI: 10.1186/1756-8935-3-22  1
2010 DiMaggio PA, Subramani A, Judson RS, Floudas CA. 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 : An Official Journal of the Society of Toxicology. 118: 251-65. PMID 20702588 DOI: 10.1093/toxsci/kfq233  1
2010 Young NL, Dimaggio PA, Garcia BA. The significance, development and progress of high-throughput combinatorial histone code analysis. Cellular and Molecular Life Sciences : Cmls. 67: 3983-4000. PMID 20683756 DOI: 10.1007/s00018-010-0475-7  1
2010 Plazas-Mayorca MD, Bloom JS, Zeissler U, Leroy G, Young NL, DiMaggio PA, Krugylak L, Schneider R, Garcia BA. Quantitative proteomics reveals direct and indirect alterations in the histone code following methyltransferase knockdown. Molecular Biosystems. 6: 1719-29. PMID 20577673 DOI: 10.1039/c003307c  1
2010 Young NL, Plazas-Mayorca MD, DiMaggio PA, Flaniken IZ, Beltran AJ, Mishra N, LeRoy G, Floudas CA, Garcia BA. Collective mass spectrometry approaches reveal broad and combinatorial modification of high mobility group protein A1a. Journal of the American Society For Mass Spectrometry. 21: 960-70. PMID 20202861 DOI: 10.1016/j.jasms.2010.01.020  1
2010 Baliban RC, DiMaggio PA, Plazas-Mayorca MD, Young NL, Garcia BA, Floudas CA. A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry. Molecular & Cellular Proteomics : McP. 9: 764-79. PMID 20103568 DOI: 10.1074/mcp.M900487-MCP200  1
2010 DiMaggio PA, Garcia BA. Mass spectrometry based proteomics for interrogating the histone code Current Proteomics. 7: 177-187. DOI: 10.2174/157016410792928189  1
2010 Dimaggio PA, McAllister SR, Floudas CA, Feng XJ, Rabinowitz JD, Rabitz HA. A network flow model for biclustering via optimal re-ordering of data matrices Journal of Global Optimization. 47: 343-354. DOI: 10.1007/s10898-008-9349-z  1
2010 DiMaggio PA, McAllister SR, Floudas CA, Feng XJ, Li G, Rabinowitz JD, Rabitz HA. Enhancing molecular discovery using descriptor-free rearrangement clustering techniques for sparse data sets Aiche Journal. 56: 405-418. DOI: 10.1002/aic.11986  1
2009 Subramani A, DiMaggio PA, Floudas CA. Selecting high quality protein structures from diverse conformational ensembles. Biophysical Journal. 97: 1728-36. PMID 19751678 DOI: 10.1016/j.bpj.2009.06.046  1
2009 DiMaggio PA, Young NL, Baliban RC, Garcia BA, Floudas CA. 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 : McP. 8: 2527-43. PMID 19666874 DOI: 10.1074/mcp.M900144-MCP200  1
2009 Young NL, DiMaggio PA, Plazas-Mayorca MD, Baliban RC, Floudas CA, Garcia BA. High throughput characterization of combinatorial histone codes. Molecular & Cellular Proteomics : McP. 8: 2266-84. PMID 19654425 DOI: 10.1074/mcp.M900238-MCP200  1
2009 McAllister SR, Dimaggio PA, Floudas CA. Mathematical modeling and efficient optimization methods for the distance-dependent rearrangement clustering problem Journal of Global Optimization. 45: 111-129. DOI: 10.1007/s10898-008-9393-8  1
2008 DiMaggio PA, McAllister SR, Floudas CA, Feng XJ, Rabinowitz JD, Rabitz HA. Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. Bmc Bioinformatics. 9: 458. PMID 18954459 DOI: 10.1186/1471-2105-9-458  1
2008 McAllister SR, Feng XJ, DiMaggio PA, Floudas CA, Rabinowitz JD, Rabitz H. Descriptor-free molecular discovery in large libraries by adaptive substituent reordering. Bioorganic & Medicinal Chemistry Letters. 18: 5967-70. PMID 18851908 DOI: 10.1016/j.bmcl.2008.09.068  1
2008 DiMaggio PA, Floudas CA, Lu B, Yates JR. A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry. Journal of Proteome Research. 7: 1584-93. PMID 18324765 DOI: 10.1021/pr700577z  1
2008 DiMaggio PA, McAllister SR, Floudas CA, Feng XJ, Rabinowitz JD, Rabitz HA. Biclustering of data matrices in systems biology via optimal re-ordering Computer Aided Chemical Engineering. 25: 569-574. DOI: 10.1016/S1570-7946(08)80100-9  1
2008 Dimaggio PA, Baliban R, Garcia BA, Floudas CA. A novel mixed-integer linear optimization framework for the identification of post-translationally modified proteins using ETD/ECD tandem mass spectrometry Aiche Annual Meeting, Conference Proceedings 1
2008 Dimaggio PA, Floudas CA, Salinas KA, Hemmer MJ, Serrano JA, Walker CC. De novo identification of biomarker proteins using tandem mass spectrometry Aiche Annual Meeting, Conference Proceedings 1
2008 Dimaggio PA, Mcallister SR, Floudas CA, Feng XJ, Rabinowitz JD, Rabitz HA. Optimal methods for re-ordering data matrices in systems biology and drug discovery applications Biophysical Reviews and Letters. 3: 19-42.  1
2007 Dimaggio PA, Floudas CA. A Mixed-Integer Optimization Framework for De Novo Peptide Identification. Aiche Journal. American Institute of Chemical Engineers. 53: 160-173. PMID 19412358 DOI: 10.1002/aic.11061  1
2007 DiMaggio PA, Floudas CA. De novo peptide identification via tandem mass spectrometry and integer linear optimization. Analytical Chemistry. 79: 1433-46. PMID 17297942 DOI: 10.1021/ac0618425  1
2005 Lucia A, Dimaggio PA, Bellows ML, Octavio LM. The phase behavior of n-alkane systems Computers and Chemical Engineering. 29: 2363-2379. DOI: 10.1016/j.compchemeng.2005.05.016  1
2004 Lucia A, Dimaggio PA, Depa P. A Geometric terrain methodology for global optimization Journal of Global Optimization. 29: 297-314. DOI: 10.1023/B:JOGO.0000044771.25100.2d  1
2004 Lucia A, DiMaggio PA. Multi-scale optimization Computer Aided Chemical Engineering. 18: 1093-1098. DOI: 10.1016/S1570-7946(04)80248-7  1
2004 Lucia A, DiMaggio PA, Depa P. Funneling algorithms multiscale optimization on rugged terrains Industrial and Engineering Chemistry Research. 43: 3770-3781.  1
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