References Cited
1. Chung, C.H., E.H. Seeley, J. Grigorieva, W.G. Yarbrough, J. Gilbert, B.A. Murphy, A. Argiris, R. Caprioli, D.P. Carbone, and E.E. Cohen, Mass Spectrometry Profile as a Predictor of Overall Survival Benefit after Treatment with Epidermal Growth Factor Receptor Inhibitors in Head and Neck Squamous Cell Carcinoma. Journal of Clinical Oncology, 2009. 27(15).
2. Ellsworth, R.E., E.H. Seeley, D.L. Ellsworth, B. Deyarmin, J.A. Hooke, M. Sanders, R. Caprioli, C.D. Shriver, and M. Henry, Proteomic Discrimination of Well- from Poorly-Differentiated Breast Carcinomas.Cancer Research, 2009. 69(24): p. 865s-865s.
3. Mazur, M.T., H.L. Cardasis, D.S. Spellman, A. Liaw, N.A. Yates, and R.C. Hendrickson, Quantitative Analysis of Intact Apolipoproteins in Human HDL by Top-Down Differential Mass Spectrometry.Proceedings of the National Academy of Sciences of the United States of America, 2010. 107(17): p.7728-7733.
4. Tran, J.C., L. Zamdborg, D.R. Ahlf, J.E. Lee, A.D. Catherman, K.R. Durbin, J.D. Tipton, A. Vellaichamy, J.F. Kellie, M. Li, C. Wu, S.M.M. Sweet, B.P. Early, N. Siuti, R.D. LeDuc, P.D. Compton, P.M. Thomas, and N.L. Kelleher, Mapping Intact Protein Isoforms in Discovery Mode Useing Top-Down Proteomics. Nature, 2011. 480: p. 254-258. PMCID: PMC3237778.
5. Kreeger, P.K., J.W. Deck, T.K. Woodruff, and L.D. Shea, The in vitro Regulation of Ovarian Follicle Development Using Alginate-Extracellular Matrix Gels. Biomaterials, 2006. 27(5): p. 714-723.
6. Pangas, S.A., H. Saudye, L.D. Shea, and T.K. Woodruff, Novel Approach for the Three-Dimensional Culture of Granulosa Cell-Oocyte Complexes. Tissue Engineering, 2003. 9(5): p. 1013-1021.
7. Xu, M., A. Banc, T.K. Woodruff, and L.D. Shea, Secondary Follicle Growth and Oocyte Maturation by Culture in Alginate Hydrogel Following Cryopreservation of the Ovary or Individual Follicles. Biotechnology and Bioengineering, 2009. 103(2): p. 378-386.
8. Xu, M., P.K. Kreeger, L.D. Shea, and T.K. Woodruff, Tissue-Engineered Follicles Produce Live, FertileOffspring. Tissue Engineering, 2006. 12(10): p. 2739-2746.
9. Hollstein, M., D. Sidransky, B. Vogelstein, and C.C. Harris, p53 Mutations in Human Cancers. Science, 1991. 253(5015): p. 49-53.
10. Green, D.R. and G. Kroemer, Cytoplasmic Functions of the Tumour Suppressor p53. Nature, 2009. 458(7242): p. 1127-1130. PMCID: PMC2814168.
11. Murray-Zmijewski, F., E.A. Slee, and X. Lu, A Complex Barcode Underlies the Heterogeneous Response of P53 to Stress. Nat Rev Mol Cell Biol, 2008. 9(9): p. 702-712.
12. Horn, H.F. and K.H. Vousden, Coping with Stress: Multiple Ways to Activate p53. Oncogene, 2007. 26(9): p. 1306-1316.
13. Moll, U.M., S. Wolff, D. Speidel, and W. Deppert, Transcription-Independent Pro-Apoptotic Functions of P53. Curr Opin Cell Biol, 2005. 17(6): p. 631-636.
14. Brooks, C.L. and W. Gu, Ubiquitination, Phosphorylation and Acetylation: The Molecular Basis for P53 Regulation. Curr Opin Cell Biol, 2003. 15(2): p. 164-171.
15. Gu, B. and W.G. Zhu, Surf the Post-Translational Modification Network of p53 Regulation. Int J Biol Sci, 2012. 8(5): p. 672-684. PMCID: PMC3354625.
16. Kruse, J.P. and W. Gu, Modes of p53 Regulation. Cell, 2009. 137(4): p. 609-622. PMCID: PMC3737742.
17. Chi, P., C.D. Allis, and G.G. Wang, Covalent Histone Modifications–Miswritten, Misinterpreted and Mis-Erased in Human Cancers. Nature Reviews Cancer, 2010. 10(7): p. 457-469. PMCID: PMC3262678.
18. Jenuwein, T. and C.D. Allis, Translating the Histone Code. Science, 2001. 293(5532): p. 1074-1080.
19. Barnidge, D.R., S. Dasari, C.M. Botz, D.H. Murray, M.R. Snyder, J.A. Katzmann, A. Dispenzieri, and D.L. Murray, Using Mass Spectrometry to Monitor Monoclonal Immunoglobulins in Patients with a Monoclonal Gammopathy. Journal of Proteome Research, 2014. 13(3): p. 1419-1427.
20. Pascual, M., T. Theruvath, T. Kawai, N. Tolkoff-Rubin, and A.B. Cosimi, Medical Progress – Strategies to Improve Long-Term Outcomes after Renal Transplantation. New England Journal of Medicine, 2002. 346(8): p. 580-590.
21. Rogier, E., A. Durrbach, L. Abecassis, S. Ferlicot, R. Snanoudj, S. Baudreuil, N. Arzouk, A. Vazquez, B. Charpentier, and M.F. Bourgeade, A Novel Biological Assay to Detect the Active Form of Tgf-Beta in Urine to Monitor Renal Allograft Rejection. Kidney International, 2005. 68(4): p. 1875-1883.
22. Binet, J.L., M. Lepoprier, G. Dighiero, D. Charron, P. D’Athis, G. Vaugier, H.M. Beral, J.C. Natali, M. Raphael, B. Nizet, and J.Y. Follezou, A Clinical Staging System for Chronic Lymphocytic Leukemia: Prognostic Significance. Cancer, 1977. 40(2): p. 855-864.
23. Rai, K.R., A. Sawitsky, E.P. Cronkite, A.D. Chanana, R.N. Levy, and B.S. Pasternack, Clinical Staging of Chronic Lymphocytic Leukemia. Blood, 1975. 46(2): p. 219-234.
24. Chiorazzi, N., K.R. Rai, and M. Ferrarini, Mechanisms of Disease: Chronic Lymphocytic Leukemia. New England Journal of Medicine, 2005. 352(8): p. 804-815.
25. Oscier, D.G., A.C. Gardiner, S.J. Mould, S. Glide, Z.A. Davis, R.E. Ibbotson, M.M. Corcoran, R.M. Chapman, P.W. Thomas, J.A. Copplestone, J.A. Orchard, and T.J. Hamblin, Multivariate Analysis of Prognostic Factors in CLL: Clinical Stage, IgVH Gene Mutational Status, and Loss or Mutation of the p53 Gene Are Independent Prognostic Factors. Blood, 2002. 100(4): p. 1177-1184.
26. Byrd, J.C., R.R. Furman, S.E. Coutre, I.W. Flinn, J.A. Burger, K.A. Blum, B. Grant, J.P. Sharman, M. Coleman, W.G. Wierda, J.A. Jones, W. Zhao, N.A. Heerema, A.J. Johnson, J. Sukbuntherng, B.Y. Chang, F. Clow, E. Hedrick, J.J. Buggy, D.F. James, and S. O’Brien, Targeting Btk with Ibrutinib in Relapsed Chronic Lymphocytic Leukemia. N Engl J Med, 2013. 369(1): p. 32-42. PMCID:PMC3772525.
28. Paulsson, A.K., S. Franklin, S.A. Mitchell-Jordan, S.X. Ren, Y.B. Wang, and T.M. Vondriska, Post-Translational Regulation of Calsarcin-1 During Pressure Overload-Induced Cardiac Hypertrophy. Journal of Molecular and Cellular Cardiology, 2010. 48(6): p. 1206-1214.
29. Berger, M.F., M.S. Lawrence, F. Demichelis, Y. Drier, K. Cibulskis, A.Y. Sivachenko, A. Sboner, R. Esgueva, D. Pflueger, C. Sougnez, R. Onofrio, S.L. Carter, K. Park, L. Habegger, L. Ambrogio, T. Fennell, M. Parkin, G. Saksena, D. Voet, A.H. Ramos, T.J. Pugh, J. Wilkinson, S. Fisher, W. Winckler, S. Mahan, K. Ardlie, J. Baldwin, J.W. Simons, N. Kitabayashi, T.Y. MacDonald, P.W. Kantoff, L. Chin, S.B. Gabriel, M.B. Gerstein, T.R. Golub, M. Meyerson, A. Tewari, E.S. Lander, G. Getz, M.A. Rubin, and L.A. Garraway, The Genomic Complexity of Primary Human Prostate Cancer. Nature, 2011. 470(7333): p. 214-220. PMCID: PMC3075885.
30. Cancer Genome Atlas Research, N., Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia. N Engl J Med, 2013. 368(22): p. 2059-2074. PMCID: PMC3767041.
31. Chinnaiyan, A.M. and N. Palanisamy, Chromosomal Aberrations in Solid Tumors. Prog Mol Biol Transl Sci, 2010. 95: p. 55-94.
32. Figueroa, M.E., O. Abdel-Wahab, C. Lu, P.S. Ward, J. Patel, A. Shih, Y. Li, N. Bhagwat, A. Vasanthakumar, H.F. Fernandez, M.S. Tallman, Z. Sun, K. Wolniak, J.K. Peeters, W. Liu, S.E. Choe, V.R. Fantin, E. Paietta, B. Lowenberg, J.D. Licht, L.A. Godley, R. Delwel, P.J. Valk, C.B. Thompson, R.L. Levine, and A. Melnick, Leukemic Idh1 and Idh2 Mutations Result in a Hypermethylation Phenotype, Disrupt Tet2 Function, and Impair Hematopoietic Differentiation. Cancer Cell, 2010. 18(6):p. 553-567.
33. Figueroa, M.E., S. Lugthart, Y. Li, C. Erpelinck-Verschueren, X. Deng, P.J. Christos, E. Schifano, J. Booth, W. van Putten, L. Skrabanek, F. Campagne, M. Mazumdar, J.M. Greally, P.J. Valk, B. Lowenberg, R. Delwel, and A. Melnick, DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia. Cancer Cell, 2010. 17(1): p. 13-27. PMCID: PMC3008568.
35. Lawrence, M.S., P. Stojanov, P. Polak, G.V. Kryukov, K. Cibulskis, A. Sivachenko, S.L. Carter, C. Stewart, C.H. Mermel, S.A. Roberts, A. Kiezun, P.S. Hammerman, A. McKenna, Y. Drier, L. Zou, A.H. Ramos, T.J. Pugh, N. Stransky, E. Helman, J. Kim, C. Sougnez, L. Ambrogio, E. Nickerson, E. Shefler, M.L. Cortes, D. Auclair, G. Saksena, D. Voet, M. Noble, D. DiCara, P. Lin, L. Lichtenstein, D.I. Heiman, T. Fennell, M. Imielinski, B. Hernandez, E. Hodis, S. Baca, A.M. Dulak, J. Lohr, D.A. Landau, C.J. Wu, J. Melendez-Zajgla, A. Hidalgo-Miranda, A. Koren, S.A. McCarroll, J. Mora, R.S. Lee, B. Crompton, R. Onofrio, M. Parkin, W. Winckler, K. Ardlie, S.B. Gabriel, C.W. Roberts, J.A. Biegel, K. Stegmaier, A.J. Bass, L.A. Garraway, M. Meyerson, T.R. Golub, D.A. Gordenin, S. Sunyaev, E.S. Lander, and G. Getz, Mutational Heterogeneity in Cancer and the Search for New Cancer-Associated Genes. Nature, 2013.499(7457): p. 214-218. PMCID: PMC3919509.
36. Tran, J.C. and A.A. Doucette, Gel-Eluted Liquid Fraction Entrapment Electrophoresis: An Electrophoretic Method for Broad Molecular Weight Range Proteome Separation. Analytical Chemistry, 2008. 80(5): p. 1568-1573.
37. Michalski, A., E. Damoc, J.P. Hauschild, O. Lange, A. Wieghaus, A. Makarov, N. Nagaraj, J. Cox, M. Mann, and S. Horning, Mass Spectrometry-Based Proteomics Using Q Exactive, a High-Performance Benchtop Quadrupole Orbitrap Mass Spectrometer. Molecular & Cellular Proteomics, 2011. 10(9).
38. Compton, P.D., L. Zamdborg, P.M. Thomas, and N.L. Kelleher, On the Scalability and Requirements of Whole Protein Mass Spectrometry. Analytical Chemistry, 2011. 83(17): p. 6868-6874. PMCID: PMC3165072.
39. Anderson, N.L. and N.G. Anderson, The Human Plasma Proteome – History, Character, and Diagnostic Prospects. Molecular & Cellular Proteomics, 2002. 1(11): p. 845-867.
40. Mann, M. and N.L. Kelleher, Precision Proteomics: The Case for High Resolution and High Mass Accuracy. Proceedings of the National Academy of Sciences of the United States of America, 2008. 105(47): p. 18132-18138. PMCID: PMC2587563.
41. Poste, G., Bring on the Biomarkers. Nature, 2011. 469(7329): p. 156-157.
42. Martinez-Garcia, E., R. Popovic, D.J. Min, S.M.M. Sweet, P.M. Thomas, L. Zamdborg, A. Heffner, C. Will, L. Lamy, L.M. Staudt, D.L. Levens, N.L. Kelleher, and J.D. Licht, The Mmset Histone Methyl Transferase Switches Global Histone Methylation and Alters Gene Expression in T(4;14) Multiple Myeloma Cells. Blood, 2011. 117(1): p. 211-220. PMCID: PMC3037745.
43. Zheng, Y., J.D. Tipton, P.M. Thomas, N.L. Kelleher, and S.M. Sweet, Site-Specific Human Histone H3 Methylation Stability: Fast K4me3 Turnover. Proteomics, 2014.
44. Ye, H., R. Mandal, A. Catherman, P.M. Thomas, N.L. Kelleher, C. Ikonomidou, and L. Li, Top-Down Proteomics with Mass Spectrometry Imaging: A Pilot Study Towards Discovery of Biomarkers for Neurodevelopmental Disorders. PLoS One, 2014. 9(4): p. e92831. PMCID: PMC3978070.
45. Southey, B.R., J.E. Lee, L. Zamdborg, N. Atkins, Jr., J.W. Mitchell, M. Li, M.U. Gillette, N.L. Kelleher, and J.V. Sweedler, Comparing Label-Free Quantitative Peptidomics Approaches to Characterize Diurnal Variation of Peptides in the Rat Suprachiasmatic Nucleus. Analytical Chemistry, 2014. 86(1): p.443-452. PMCID: PMC3886391.
47. Oyer, J.A., X. Huang, Y. Zheng, J. Shim, T. Ezponda, Z. Carpenter, M. Allegretta, C.I. Okot-Kotber, J.P. Patel, A. Melnick, R.L. Levine, A. Ferrando, A.D. Mackerell, Jr., N.L. Kelleher, J.D. Licht, and R. Popovic, Point Mutation E1099k in MMSET/Nsd2 Enhances Its Methyltranferase Activity and Leads to Altered Global Chromatin Methylation in Lymphoid Malignancies. Leukemia, 2014. 28(1): p. 198-201. PMCID: PMC3888226.
48. Ntai, I., K. Kim, R.T. Fellers, O.S. Skinner, A.D.t. Smith, B.P. Early, J.P. Savaryn, R.D. Leduc, P.M. Thomas, and N.L. Kelleher, Applying Label-Free Quantitation to Top Down Proteomics. Analytical Chemistry, 2014. PMCID: PMC in process.
49. Li, Y., P.D. Compton, J.C. Tran, I. Ntai, and N.L. Kelleher, Optimizing Capillary Electrophoresis for Top-Down Proteomics of 30-80 Kda Proteins. Proteomics, 2014. 14(10): p. 1158-1164.
50. LeDuc, R.D., R.T. Fellers, B.P. Early, J.B. Greer, P.M. Thomas, and N.L. Kelleher, The C-Score: A Bayesian Framework to Sharply Improve Proteoform Scoring in High-Throughput Top Down Proteomics. Journal of Proteome Research, 2014. in press.
51. Hong, S.H., I. Ntai, A.D. Haimovich, N.L. Kelleher, F.J. Isaacs, and M.C. Jewett, Cell-Free Protein Synthesis from a Release Factor 1 Deficient Escherichia Coli Activates Efficient and Multiple Site-Specific Nonstandard Amino Acid Incorporation. ACS Synth Biol, 2014.
52. Durbin, K.R., R.T. Fellers, I. Ntai, N.L. Kelleher, and P.D. Compton, Autopilot: An Online Data Acquisition Control System for the Enhanced High-Throughput Characterization of Intact Proteins. Analytical Chemistry, 2014. 86(3): p. 1485-1492. PMCID: PMC3958137.
53. Dang, X., J. Scotcher, S. Wu, R.K. Chu, N. Tolic, I. Ntai, P.M. Thomas, R.T. Fellers, B.P. Early, Y. Zheng, K.R. Durbin, R.D. Leduc, J.J. Wolff, C.J. Thompson, J. Pan, J. Han, J.B. Shaw, J.P. Salisbury, M. Easterling, C.H. Borchers, J.S. Brodbelt, J.N. Agar, L. Pasa-Tolic, N.L. Kelleher, and N.L. Young, The First Pilot Project of the Consortium for Top-Down Proteomics: A Status Report. Proteomics, 2014. 14(10): p. 1130-1140.
54. Catherman, A.D., O.S. Skinner, and N.L. Kelleher, Top Down Proteomics: Facts and Perspectives. Biochem Biophys Res Commun, 2014. 445(4): p. 683-693.
55. Cannon, J.R., M.B. Cammarata, S.A. Robotham, V.C. Cotham, J.B. Shaw, R.T. Fellers, B.P. Early, P.M. Thomas, N.L. Kelleher, and J.S. Brodbelt, Ultraviolet Photodissociation for Characterization of Whole Proteins on a Chromatographic Time Scale. Analytical Chemistry, 2014. 86(4): p. 2185-2192. PMCID: PMC3958131.
56. Zheng, Y., P.M. Thomas, and N.L. Kelleher, Measurement of Acetylation Turnover at Distinct Lysines in Human Histones Identifies Long-Lived Acetylation Sites. Nat Commun, 2013. 4: p. 2203. PMCID: PMC3929392.
57. Yates, J.R., 3rd and N.L. Kelleher, Top Down Proteomics. Analytical Chemistry, 2013. 85(13): p. 6151.
58. Wu, X., A. Vellaichamy, D. Wang, L. Zamdborg, N.L. Kelleher, S.C. Huber, and Y. Zhao, Differential Lysine Acetylation Profiles of Erwinia Amylovora Strains Revealed by Proteomics. J Proteomics, 2013. 79: p. 60-71.
59. Smith, L.M., N.L. Kelleher, and Consortium for Top Down, Proteoform: A Single Term Describing Protein Complexity. Nat Methods, 2013. 10(3): p. 186-187.
61. Savaryn, J.P., A.D. Catherman, P.M. Thomas, M.M. Abecassis, and N.L. Kelleher, The Emergence of Top-Down Proteomics in Clinical Research. Genome Med, 2013. 5(6): p. 53. PMCID: PMC3707033.
63. Lee, J.E., L. Zamdborg, B.R. Southey, N. Atkins, Jr., J.W. Mitchell, M. Li, M.U. Gillette, N.L. Kelleher, and J.V. Sweedler, Quantitative Peptidomics for Discovery of Circadian-Related Peptides from the Rat Suprachiasmatic Nucleus. J Proteome Res, 2013. 12(2): p. 585-593. PMCID: PMC3562399.
64. Kelleher, N.L. and L. Pasa-Tolic, 25th ASMS Sanibel Conference on Top Down Mass Spectrometry. J Am Soc Mass Spectrom, 2013. 24(7): p. 983-985.
66. Ezponda, T., R. Popovic, M.Y. Shah, E. Martinez-Garcia, Y. Zheng, D.J. Min, C. Will, A. Neri, N.L. Kelleher, J. Yu, and J.D. Licht, The Histone Methyltransferase MMSET/Whsc1 Activates Twist1 to Promote an Epithelial-Mesenchymal Transition and Invasive Properties of Prostate Cancer. Oncogene, 2013. 32(23): p. 2882-2890. PMCID: PMC3495247.
67. Catherman, A.D., M. Li, J.C. Tran, K.R. Durbin, P.D. Compton, B.P. Early, P.M. Thomas, and N.L. Kelleher, Top Down Proteomics of Human Membrane Proteins from Enriched Mitochondrial Fractions. Analytical Chemistry, 2013. 85(3): p. 1880-1888. PMCID: PMC3565750.
68. Catherman, A.D., K.R. Durbin, D.R. Ahlf, B.P. Early, R.T. Fellers, J.C. Tran, P.M. Thomas, and N.L. Kelleher, Large-Scale Top-Down Proteomics of the Human Proteome: Membrane Proteins, Mitochondria, and Senescence. Molecular & Cellular Proteomics, 2013. 12(12): p. 3465-3473. PMCID: PMC3861700.
69. Belov, M.E., E. Damoc, E. Denisov, P.D. Compton, S. Horning, A.A. Makarov, and N.L. Kelleher, From Protein Complexes to Subunit Backbone Fragments: A Multi-Stage Approach to Native Mass Spectrometry. Analytical Chemistry, 2013. 85(23): p. 11163-11173. PMCID: PMC in process.
70. Ahlf, D.R., P.M. Thomas, and N.L. Kelleher, Developing Top Down Proteomics to Maximize Proteome and Sequence Coverage from Cells and Tissues. Curr Opin Chem Biol, 2013. 17(5): p. 787-794. PMCID: PMC3878305
71. Group, P.R. PRG 2011 Proteomics Survey. in ABRF Annual Meeting. 2011. San Antonio, TX.
73. Meehan, T.F., A.M. Masci, A. Abdulla, L.G. Cowell, J.A. Blake, C.J. Mungall, and A.D. Diehl, Logical Development of the Cell Ontology. BMC Bioinformatics, 2011. 12: p. 6.
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