| Year |
Citation |
Score |
| 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 |
0.555 |
|
| 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 |
0.513 |
|
| 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 |
0.54 |
|
| 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 |
0.491 |
|
| 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 |
|
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