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Peter A. DiMaggio, Ph.D. - Publications

Affiliations: 
Princeton University, Princeton, NJ 
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41/55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
2024 Lukauskas S, Tvardovskiy A, Nguyen NV, Stadler M, Faull P, Ravnsborg T, Özdemir Aygenli B, Dornauer S, Flynn H, Lindeboom RGH, Barth TK, Brockers K, Hauck SM, Vermeulen M, Snijders AP, ... ... DiMaggio PA, et al. Decoding chromatin states by proteomic profiling of nucleosome readers. Nature. PMID 38448585 DOI: 10.1038/s41586-024-07141-5  0.37
2020 Whitwell HJ, DiMaggio P. HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs. Bioinformatics (Oxford, England). 36: 938-939. PMID 31424526 DOI: 10.1093/Bioinformatics/Btz654  0.388
2019 Kalesh K, Lukauskas S, Borg AJ, Snijders AP, Ayyappan V, Leung AKL, Haskard DO, DiMaggio PA. An Integrated Chemical Proteomics Approach for Quantitative Profiling of Intracellular ADP-Ribosylation. Scientific Reports. 9: 6655. PMID 31040352 DOI: 10.1038/S41598-019-43154-1  0.438
2018 Chavas TEJ, Fuchter MJ, DiMaggio PA. Unbiased Mass Spectrometry Elucidation of the Targets and Mechanisms of Activity-Based Probes: A Case Study involving Sulfonyl Fluorides. Acs Chemical Biology. PMID 30192509 DOI: 10.1021/Acschembio.8B00530  0.408
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  0.416
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  0.603
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  0.554
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  0.455
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  0.792
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  0.782
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  0.504
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  0.512
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  0.811
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  0.756
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  0.562
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  0.783
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  0.633
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  0.539
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  0.792
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  0.677
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  0.698
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  0.773
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  0.792
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  0.774
2010 DiMaggio PA, Garcia BA. Mass spectrometry based proteomics for interrogating the histone code Current Proteomics. 7: 177-187. DOI: 10.2174/157016410792928189  0.385
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  0.481
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  0.497
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  0.679
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  0.814
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  0.784
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  0.484
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  0.499
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  0.475
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  0.573
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. DOI: 10.1142/S1793048008000605  0.492
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  0.492
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.  0.761
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.  0.523
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  0.569
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  0.574
2007 DiMaggio PA, Floudas CA. De novo peptide identification via mixed-integer linear optimization and tandem mass spectrometry Computer-Aided Chemical Engineering. 24: 989-994. DOI: 10.1016/S1570-7946(07)80189-1  0.581
Low-probability matches (unlikely to be authored by this person)
2024 Lukauskas S, Tvardovskiy A, Nguyen NV, Stadler M, Faull P, Ravnsborg T, Özdemir Aygenli B, Dornauer S, Flynn H, Lindeboom RGH, Barth TK, Brockers K, Hauck SM, Vermeulen M, Snijders AP, ... ... DiMaggio PA, et al. Publisher Correction: Decoding chromatin states by proteomic profiling of nucleosome readers. Nature. PMID 38594341 DOI: 10.1038/s41586-024-07392-2  0.3
2018 Kostrzewski T, Borg AJ, Meng Y, Filipovic I, Male V, Wack A, DiMaggio PA, Brady HJM. Multiple Levels of Control Determine How E4bp4/Nfil3 Regulates NK Cell Development. Journal of Immunology (Baltimore, Md. : 1950). PMID 29311361 DOI: 10.4049/Jimmunol.1700981  0.294
2004 Lucia A, DiMaggio PA, Depa P. Funneling Algorithms for Multiscale Optimization on Rugged Terrains Industrial & Engineering Chemistry Research. 43: 3770-3781. DOI: 10.1021/Ie030636+  0.264
2018 Lucia A, DiMaggio PA, Alonso-Martinez D. Metabolic pathway analysis using a nash equilibrium approach Journal of Global Optimization. 71: 537-550. DOI: 10.1007/S10898-018-0605-6  0.26
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 S, Chen X, Chau I, et al. Erratum: A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells Nature Chemical Biology. 7: 648-648. DOI: 10.1038/Nchembio0911-648C  0.241
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  0.224
2020 Xie M, Inguva P, Chen W, Prasetya N, Macey A, DiMaggio P, Shah UV, Brechtelsbauer C. Accelerating Students’ Learning of Chromatography with an Experiential Module on Process Development and Scaleup Journal of Chemical Education. 97: 1001-1007. DOI: 10.1021/Acs.Jchemed.9B01076  0.216
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  0.2
2004 Lucia A, DiMaggio PA. Multi-scale optimization Computer Aided Chemical Engineering. 18: 1093-1098. DOI: 10.1016/S1570-7946(04)80248-7  0.15
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  0.143
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  0.11
2004 Lucia A, DiMaggio PA, Depa P. Funneling algorithms multiscale optimization on rugged terrains Industrial and Engineering Chemistry Research. 43: 3770-3781.  0.105
2011 DiMaggio P. Extending Jefferson’s Vision Civil Engineering Magazine Archive. 81: 64-81. DOI: 10.1061/ciegag.0000346  0.032
2004 Rittenhouse T, DiMaggio P, Ettouney M. Behavior of steel structures subjected to blast loading Structures - a Structural Engineering Odyssey, Structures 2001 - Proceedings of the 2001 Structures Congress and Exposition. 109. DOI: 10.1061/40558(2001)76  0.017
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