Development of Decision Tree Software and Protein Profiling using Surface Enhanced laser Desorption/lonization - Time of Flight - Mass Spectrometry (SELDI-TOF-MS) in Papillary Thyroid Cancer |
Yoon, Joon-Kee
(Department of Nuclear Medicine & Molecular Imaging, Ajou University School of Medicine)
Lee, Jun (Department of Computer Engineering, Konkuk University) An, Young-Sil (Department of Nuclear Medicine & Molecular Imaging, Ajou University School of Medicine) Park, Bok-Nam (Department of Nuclear Medicine & Molecular Imaging, Ajou University School of Medicine) Yoon, Seok-Nam (Department of Nuclear Medicine & Molecular Imaging, Ajou University School of Medicine) |
1 | Zhang Z, Bast RC, Jr., Yu Y, Li J, Sokoll LJ, Rai AJ, et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res 2004;64: 5882-90 DOI ScienceOn |
2 | Ringel MD, Ladenson PW. Controversies in the follow-up and management of well-differentiated thyroid cancer. Endocr Relat Cancer 2004;11:97-116 DOI ScienceOn |
3 | Engwegen JY, Gast MC, Schellens JH, Beijnen JH. Clinical proteomics: searching for better tumour markers with SELDI-TOF mass spectrometry. Trends Pharmacol Sci 2006;27:251-9 DOI ScienceOn |
4 | Smolle J, Kahofer P. Automated detection of connective tissue by tissue counter analysis and classification and regression trees. Anal Cell Pathol 2001;23:153-8 |
5 | Grizzle WE, Adam BL, Bigbee WL, Conrads TP, Carroll C, Feng Z, et al. Serum protein expression profiling for cancer detection: validation of a SELDI-based approach for prostate cancer. Dis Markers 2003;19:185-95 |
6 | Salzberg SL. Book Review: C4.5: Programs for Machine Learning by J. Ross Quinlan. Morgan Kaufmann Publishers, Inc.,1993. Machine Learning 1994;16:235-40 |
7 | Chang LY, Wang HW. Analysis of traffic injury severity: an application of non-parametric classification tree techniques. Accid Anal Prev 2006;38:1019-27 DOI ScienceOn |
8 | Won Y, Song HJ, Kang TW, Kim JJ, Han BD, Lee SW. Pattern analysis of serum proteome distinguishes renal cell carcinoma from other urologic diseases and healthy persons. Proteomics 2003;3:2310-6 DOI ScienceOn |
9 | Vlahou A, Laronga C, Wilson L, Gregory B, Fournier K, McGaughey D, et al. A novel approach toward development of a rapid blood test for breast cancer. Clin Breast Cancer 2003;4: 203-9 DOI |
10 | Baggerly KA, Morris JS, Coombes KR. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics 2004;20:777-85 DOI ScienceOn |
11 | Bons JAP, Wodzig WKWH, De Boer D, Drent M, Van Dieijen-Visser MP. Application of SELDI-TOF-MS in protein profiling: promises and Pitfalls. Jugoslov Med Biohem 2006;25: 201-10 DOI |
12 | Suzuyama K, Shiraishi T, Oishi T, Ueda S, Okamoto H, Furuta M, et al. Combined proteomic approach with SELDI-TOF-MS and peptide mass fingerprinting identified the rapid increase of monomeric transthyretin in rat cerebrospinal fluid after transient focal cerebral ischemia. Brain Res Mol Brain Res 2004;129:44-53 DOI ScienceOn |
13 | Jr GW, Cazares LH, Leung SM, Nasim S, Adam BL, Yip TT, et al. Proteinchip(R) surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate Cancer Prostatic Dis 1999;2:264-76 DOI ScienceOn |
14 | Xiao Z, Prieto D, Conrads TP, Veenstra TD, Issaq HJ. Proteomic patterns: their potential for disease diagnosis. Mol Cell Endocrinol 2005;230:95-106 DOI ScienceOn |
15 | Haberkorn U, Altmann A, Eisenhut M. Functional genomics and proteomics-the role of nuclear medicine. Eur J Nucl Med Mol Imaging 2002;29:115-32 DOI ScienceOn |
16 | Spurgeon SE, Hsieh YC, Rivadinera A, Beer TM, Mori M, Garzotto M. Classification and regression tree analysis for the prediction of aggressive prostate cancer on biopsy. J Urol 2006; 175:918-22 DOI ScienceOn |
17 | Merchant M, Weinberger SR. Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis 2000;21:1164-77 DOI ScienceOn |
18 | Qu Y, Adam BL, Yasui Y, Ward MD, Cazares LH, Schellhammer PF, et al. Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. Clin Chem 2002;48: 1835-43 |
19 | Mansi L, Moncayo R, Cuccurullo V, Dottorini ME, Rambaldi PF. Nuclear medicine in diagnosis, staging and follow-up of thyroid cancer. Q J Nucl Med Mol Imaging 2004;48:82-95 |
20 | Twa MD, Parthasarathy S, Roberts C, Mahmoud AM, Raasch TW, Bullimore MA. Automated decision tree classification of corneal shape. Optom Vis Sci 2005;82:1038-46 DOI ScienceOn |
21 | Streckfus CF, Bigler LR, Zwick M. The use of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry to detect putative breast cancer markers in saliva: a feasibility study. J Oral Pathol Med 2006;35:292-300 DOI ScienceOn |
22 | Paweletz CP, Trock B, Pennanen M, Tsangaris T, Magnant C, Liotta LA, et al. Proteomic patterns of nipple aspirate fluids obtained by SELDI-TOF: potential for new biomarkers to aid in the diagnosis of breast cancer. Dis Markers 2001;17:301-7 DOI |
23 | Quinlan JR. Improved use of continuous attributes in C4.5. J Artif Intell Res 1996;5:139-61 |
24 | Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002;359:572-7 DOI ScienceOn |
25 | Webster AP, Goodacre S, Walker D, Burke D. How do clinical features help identify paediatric patients with fractures following blunt wrist trauma? Emerg Med J 2006;23:354-7 DOI ScienceOn |
26 | Li J, Zhang Z, Rosenzweig J, Wang YY, Chan DW. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002;48:1296-304 |
27 | Issaq HJ, Veenstra TD, Conrads TP, Felschow D. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem Biophys Res Commun 2002;292:587-92 DOI ScienceOn |
28 | Lehmann G, Schmitt C, Kehl V, Schmieder S, Schomig A. Electrocardiographic algorithm for assignment of occluded vessel in acute myocardial infarction. Int J Cardiol 2003;89:79-85 DOI ScienceOn |
29 | Chan AL, Chen JX, Wang HY. Application of data mining to predict the dosage of vancomycin as an outcome variable in a teaching hospital population. Int J Clin Pharmacol Ther 2006; 44:533-8 DOI |
30 | Wulfkuhle JD, McLean KC, Paweletz CP, Sgroi DC, Trock BJ, Steeg PS, et al. New approaches to proteomic analysis of breast cancer. Proteomics 2001;1:1205-15 DOI ScienceOn |
31 | Takahashi O, Cook EF, Nakamura T, Saito J, Ikawa F, Fukui T. Risk stratification for in-hospital mortality in spontaneous intracerebral haemorrhage: a Classification and Regression Tree analysis. Qjm 2006;99:743-50 DOI ScienceOn |
32 | Quinlan JR. Learning logical definitions from relations. Machine Learning 1990;5:239-66 |
33 | Isbister GK, Sibbritt D. Developing a decision tree algorithm for the diagnosis of suspected spider bites. Emerg Med Australas 2004;16:161-6 DOI |
34 | Langlois RG, Trebes JE, Dalmasso EA, Ying Y, Davies RW, Curzi MP, et al. Serum protein profile alterations in hemodialysis patients. Am J Nephrol 2004;24:268-74 DOI ScienceOn |
35 | Masic N, Gagro A, Rabatic S, Sabioncello A, Dasic G, Jaksic B, et al. Decision-tree approach to the immunophenotype-based prognosis of the B-cell chronic lymphocytic leukemia. Am J Hematol 1998;59:143-8 DOI ScienceOn |
36 | Esquerda A, Trujillano J, Lopez UI, Bielsa S, Madronero AB, Porcel JM. Classification tree analysis for the discrimination of pleural exudates and transudates. Clin Chem Lab Med 2007;45: 82-7 DOI ScienceOn |
37 | van Gerven MA, Jurgelenaite R, Taal BG, Heskes T, Lucas PJ. Predicting carcinoid heart disease with the noisy-threshold classifier. Artif Intell Med 2006 (epub) |