Three essays on analytical models to improve early detection of cancer

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[1]  J. Potter,et al.  A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection. , 2003, Biostatistics.

[2]  B. Morson.  The Polyp-Cancer Sequence in the Large Bowel , 1974, Proceedings of the Royal Society of Medicine.

[3]  Gregory Piatetsky-Shapiro,et al.  Microarray data mining: facing the challenges , 2003, SKDD.

[4]  F. Carey,et al.  The colorectal adenoma–carcinoma sequence , 2002, The British journal of surgery.

[5]  D. Black.  Mechanisms of alternative pre-messenger RNA splicing. , 2003, Annual review of biochemistry.

[6]  Peicheng Du,et al.  Data reduction of isotope-resolved LC-MS spectra , 2007, Bioinform..

[7]  L. Schuman,et al.  The earlier detection of colorectal cancers. A preliminary report of the results of the occult blood study , 1980, Cancer.

[8]  J. Mitchell,et al.  A DECISION MODEL AND COST-EFFECTIVENESS ANALYSIS OF COLORECTAL CANCER SCREENING AND SURVEILLANCE GUIDELINES FOR AVERAGE-RISK ADULTS , 2000, International Journal of Technology Assessment in Health Care.

[9]  H. Burke.  Proteomics: Analysis of Spectral Data , 2007, Cancer informatics.

[10]  H. Gendelman,et al.  Multidimensional protein fractionation using ProteomeLab PF 2D™ for profiling amyotrophic lateral sclerosis immunity: A preliminary report , 2008, Proteome Science.

[11]  Hongyu Zhao,et al.  Multiple Peak Alignment in Sequential Data Analysis: A Scale-Space-Based Approach , 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[12]  Ralf J. O. Torgrip,et al.  Peak alignment using reduced set mapping , 2003 .

[13]  Jeffrey S. Morris,et al.  Improved peak detection and quantification of mass spectrometry data acquired from surface‐enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform , 2005, Proteomics.

[14]  A. Neugut,et al.  Epidemiology of colorectal adenomatous polyps. , 1993, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[15]  Pan Du,et al.  Bioinformatics Original Paper Improved Peak Detection in Mass Spectrum by Incorporating Continuous Wavelet Transform-based Pattern Matching , 2022 .

[16]  Young-Ki Paik,et al.  Application of a peptide‐based PF2D platform for quantitative proteomics in disease biomarker discovery , 2008, Proteomics.

[17]  T. Joos,et al.  The proteomics bottleneck: strategies for preliminary validation of potential biomarkers and drug targets. , 2004, Trends in biotechnology.

[18]  Jeffrey S. Morris,et al.  Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum , 2005, Bioinform..

[19]  H. Brenner,et al.  Risk of progression of advanced adenomas to colorectal cancer by age and sex: estimates based on 840 149 screening colonoscopies , 2007, Gut.

[20]  A. Venetsanopoulos,et al.  A multichannel order-statistic technique for cDNA microarray image processing , 2004, IEEE Transactions on NanoBioscience.

[21]  Lijun Wang,et al.  Development of a simulation model of colorectal cancer , 2007, TOMC.

[22]  Thomas P Conrads,et al.  The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. , 2002, Biochemical and biophysical research communications.

[23]  S. Duffy,et al.  Progression Rates of Colorectal Cancer by Dukes' Stage in a High‐Risk Group: Analysis of Selective Colorectal Cancer Screening , 2004, Cancer journal.

[24]  Thomas A Neubert,et al.  Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry , 2006, Journal of Chromatography A.

[25]  Matej Oresic,et al.  MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data , 2006, Bioinform..

[26]  M Daszykowski,et al.  A comparison of three algorithms for chromatograms alignment. , 2006, Journal of chromatography. A.

[27]  T. Sapatinas,et al.  Wavelet Analysis and its Statistical Applications , 2000 .

[28]  Kit S Lam,et al.  Profiling of glycans in serum for the discovery of potential biomarkers for ovarian cancer. , 2006, Journal of proteome research.

[29]  R. Hayward,et al.  Which colon cancer screening test? A comparison of costs, effectiveness, and compliance. , 2001, The American journal of medicine.

[30]  L M Schuman,et al.  Reducing mortality from colorectal cancer by screening for fecal occult blood. Minnesota Colon Cancer Control Study. , 1993, The New England journal of medicine.

[31]  N. Kingsbury.  Complex Wavelets for Shift Invariant Analysis and Filtering of Signals , 2001 .

[32]  Albert Sickmann,et al.  Challenges in mass spectrometry‐based proteomics , 2004, Proteomics.

[33]  R.S.H. Istepanian,et al.  Microarray image enhancement by denoising using stationary wavelet transform , 2003, IEEE Transactions on NanoBioscience.

[34]  R. Dutton,et al.  Biological shot-noise and quantum-limited signal-to-noise ratio in affinity-based biosensors , 2005 .

[35]  Stefano Toppo,et al.  MPA: A multiple peak alignment algorithm to perform multiple comparisons of liquid‐phase proteomic profiles , 2008, Proteomics.

[36]  Yu-Kyong Shin,et al.  Proteomic analysis of mammalian basic proteins by liquid‐based two‐dimensional column chromatography , 2006, Proteomics.

[37]  J D Habbema,et al.  Endoscopic colorectal cancer screening: a cost-saving analysis. , 2000, Journal of the National Cancer Institute.

[38]  M. Leshno,et al.  Cost-Effectiveness of Colorectal Cancer Screening in the Average Risk Population , 2003, Health care management science.

[39]  Zoltan Szallasi,et al.  Increased measurement accuracy for sequence-verified microarray probes. , 2004, Physiological genomics.

[40]  Babak Hassibi,et al.  A statistical model for microarrays, optimal estimation algorithms, and limits of performance , 2006, IEEE Transactions on Signal Processing.

[41]  Chao Yang,et al.  Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis , 2009, BMC Bioinformatics.

[42]  S. Woolf,et al.  Colorectal cancer screening and surveillance: clinical guidelines and rationale-Update based on new evidence. , 2003, Gastroenterology.

[43]  Levent Sendur,et al.  A bivariate shrinkage function for wavelet-based denoising , 2002, 2002 IEEE International Conference on Acoustics, Speech, and Signal Processing.

[44]  N. Kingsbury.  Image processing with complex wavelets , 1999, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[45]  Dante Mantini,et al.  LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise , 2007, BMC Bioinformatics.

[46]  Walter Park,et al.  Prevalence of nonpolypoid (flat and depressed) colorectal neoplasms in asymptomatic and symptomatic adults. , 2008, JAMA.

[47]  Hugh M. Cartwright,et al.  SpecAlign - processing and alignment of mass spectra datasets , 2005, Bioinform..

[48]  Georgios B. Giannakis,et al.  Identifying differentially expressed genes in microarray experiments with model-based variance estimation , 2006, IEEE Transactions on Signal Processing.

[49]  A. Eggert,et al.  Proteomics: techniques and applications in cancer research. , 2003, Klinische Padiatrie.

[50]  K. Markides,et al.  Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography-mass spectrometry data. , 2002, Journal of chromatography. A.

[51]  C. Mulrow,et al.  Colorectal cancer screening: clinical guidelines and rationale. , 1997, Gastroenterology.

[52]  Justin K. Romberg,et al.  Bayesian tree-structured image modeling using wavelet-domain hidden Markov models , 2001, IEEE Trans. Image Process..

[53]  Ron O. Dror,et al.  Noise Models in Gene Array Analysis , 2001 .

[54]  Nasreen S Jessani,et al.  The development and application of methods for activity-based protein profiling. , 2004, Current opinion in chemical biology.

[55]  Pei Wang,et al.  Bioinformatics Original Paper a Suite of Algorithms for the Comprehensive Analysis of Complex Protein Mixtures Using High-resolution Lc-ms , 2022 .

[56]  J. Carstensen,et al.  Aligning of single and multiple wavelength chromatographic profiles for chemometric data analysis using correlation optimised warping , 1998 .

[57]  Ann G Zauber,et al.  National Polyp Study data: Evidence for regression of adenomas , 2004, International journal of cancer.

[58]  Deborah Schrag,et al.  How much can current interventions reduce colorectal cancer mortality in the U.S.? , 2006, Cancer.

[59]  I. Selesnick,et al.  Bivariate shrinkage with local variance estimation , 2002, IEEE Signal Processing Letters.

[60]  T. Church,et al.  Colorectal cancer mortality: effectiveness of biennial screening for fecal occult blood. , 1999, Journal of the National Cancer Institute.

[61]  Christopher J. Lacke,et al.  Analysis of Colorectal Cancer Screening Regimens , 2001, Health Care Management Science.

[62]  C. Dukes.  The classification of cancer of the rectum , 1980 .

[63]  Maureen Kachman,et al.  Validated MALDI-TOF/TOF mass spectra for protein standards , 2007, Journal of the American Society for Mass Spectrometry.

[64]  Y. Tu,et al.  Quantitative noise analysis for gene expression microarray experiments , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[65]  J. Gohagan,et al.  Results of repeat sigmoidoscopy 3 years after a negative examination. , 2003, JAMA.

[66]  Rob Boer,et al.  The MISCAN-COLON Simulation Model for the Evaluation of Colorectal Cancer Screening , 1999, Comput. Biomed. Res..

[67]  A. Geller,et al.  Increased cancer risk for individuals with a family history of prostate cancer, colorectal cancer, and melanoma and their associated screening recommendations and practices , 2008, Cancer Causes & Control.

[68]  Marina Vannucci,et al.  Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data , 2008, Bioinform..

[69]  Rebecca Sutphen,et al.  Lysophospholipids are potential biomarkers of ovarian cancer. , 2004, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[70]  Knut Reinert,et al.  High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques , 2005, Pacific Symposium on Biocomputing.

[71]  P. Harper,et al.  Mathematical Models for the Early Detection and Treatment of Colorectal Cancer , 2005, Health care management science.

[72]  R. Gentleman,et al.  SELDI-TOF Mass Spectrometry Protein Data , 2005 .

[73]  Jeffrey S. Morris,et al.  PrepMS: TOF MS data graphical preprocessing tool , 2007, Bioinform..

[74]  Michael Recce,et al.  Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer , 2004, BMC Bioinformatics.

[75]  Stéphane Mallat,et al.  A Theory for Multiresolution Signal Decomposition: The Wavelet Representation , 1989, IEEE Trans. Pattern Anal. Mach. Intell..

[76]  R. Abagyan,et al.  XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. , 2006, Analytical chemistry.

[77]  Roy D. Wallen,et al.  The Illustrated Wavelet Transform Handbook , 2004 .

[78]  D. Ward,et al.  Identification of serum biomarkers for colon cancer by proteomic analysis , 2006, British Journal of Cancer.

[79]  Tapas K. Das,et al.  Wavelet-based multiscale statistical process monitoring: A literature review , 2004 .

[80]  R Levine,et al.  Prevention and early detection of colorectal cancer. , 1992, American family physician.