Grant Number:	5R01CA107304-03 Interpret this number
Primary Investigator:	Morris, Jeffrey
Organization:	University Of Tx Md Anderson Can Ctr
Project Title:	Adaptive Methodology for Functional Biomedical Data
Fiscal Year:	2006

DESCRIPTION (provided by applicant): An ever-increasing number of biomedical studies yield functional data, in which the ideal units of observation are curves. The goal of this research program is to develop new Bayesian methodology that provides a unifying framework for performing nonparametric estimation and inference for samples of curves. These methods will be flexible enough to model functions obtained from a variety of experimental designs, provide answers to a broad range of research questions, and will be sufficiently adaptive to apply to functional data from a wide range of applications. We will apply these methods to model functional data from a series of cancer-related biomedical studies that have motivated our methodological thinking. The methods we propose are appropriate for functional data characterized by numerous local features like peaks since we employ adaptive regularization procedures which denoise the functions with minimal attenuation of the dominant local features. The specific aims of this research are: 1. Introduce a unified functional mixed model framework for modeling samples of curves. Develop a wavelet-based method to fit this model and obtain adaptively regularized nonparametric estimates and Bayesian inference for fixed and random effect functions as well as covariance parameters. 2. Develop methodology to perform formal Bayesian inference and model selection in functional mixed models. Applications of this method include testing functional hypotheses on fixed/random effects, comparing models with different covariance structures, determining the number of basis functions, testing for correlation among different functional responses, and identifying appropriate piecewise constant compartment models. 3. Develop methods to perform wavelet-regularized functional principal component analysis. Extend our wavelet-based functional mixed model methods developed in Specific Aims 1 and 2 to other basis functions, including wavelet-regularized eigen functions and splines. 4. Apply the methods we develop in Specific Aims 1, 2, and 3 to a series of biomedical applications involving functional data, including colon carcinogenesis studies, a Planet Health children's activity study, an animal study investigating acute renal failure, and medical studies involving proteomics. 5. Produce publicly available statistical software for implementing the methods developed in this proposal.




The Relationship Between Scleral Strain Change and Differential Cumulative Intraocular Pressure Exposure in the Nonhuman Primate Chronic Ocular Hypertension Model.
Authors: Fazio M.A. , Girard M.J.A. , Lee W. , Morris J.S. , Burgoyne C.F. , Downs J.C. .
Source: Investigative Ophthalmology & Visual Science, 2019-10-01 00:00:00.0; 60(13), p. 4141-4150.
PMID: 31598625
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A Unified Analysis of Structured Sonar-terrain Data using Bayesian Functional Mixed Models.
Authors: Zhu H. , Caspers P. , Morris J.S. , Wu X. , Müller R. .
Source: Technometrics : A Journal Of Statistics For The Physical, Chemical, And Engineering Sciences, 2018; 60(1), p. 112-123.
EPub date: 2017-05-25 00:00:00.0.
PMID: 29749977
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Multivariate functional response regression, with application to fluorescence spectroscopy in a cervical pre-cancer study.
Authors: Zhu H. , Morris J.S. , Wei F. , Cox D.D. .
Source: Computational Statistics & Data Analysis, 2017 Jul; 111, p. 88-101.
EPub date: 2017-02-15 00:00:00.0.
PMID: 29051679
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Comparison and Contrast of Two General Functional Regression Modeling Frameworks.
Authors: Morris J.S. .
Source: Statistical Modelling, 2017 Feb; 17(1-2), p. 59-85.
EPub date: 2017-02-16 00:00:00.0.
PMID: 28736502
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Identification of differentially methylated loci using wavelet-based functional mixed models.
Authors: Lee W. , Morris J.S. .
Source: Bioinformatics (oxford, England), 2016-03-01 00:00:00.0; 32(5), p. 664-72.
EPub date: 2016-03-01 00:00:00.0.
PMID: 26559505
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Detection and Quantification of Protein Spots by Pinnacle.
Authors: Morris J.S. , Gutstein H.B. .
Source: Methods In Molecular Biology (clifton, N.j.), 2016; 1384, p. 185-201.
PMID: 26611416
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Functional Car Models For Large Spatially Correlated Functional Datasets
Authors: Zhang L. , Baladandayuthapani V. , Zhu H. , Baggerly K.A. , Majewski T. , Czerniak B.A. , Morris J.S. .
Source: Journal Of The American Statistical Association, 2016; 111(514), p. 772-786.
PMID: 28018013
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Bayesian function-on-function regression for multilevel functional data.
Authors: Meyer M.J. , Coull B.A. , Versace F. , Cinciripini P. , Morris J.S. .
Source: Biometrics, 2015 Sep; 71(3), p. 563-74.
PMID: 25787146
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Automatic Quantitative Analysis Of Ultrasound Tongue Contours Via Wavelet-based Functional Mixed Models
Authors: Lancia L. , Rausch P. , Morris J.S. .
Source: The Journal Of The Acoustical Society Of America, 2015 Feb; 137(2), p. EL178-83.
PMID: 25698047
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Human Scleral Structural Stiffness Increases More Rapidly With Age In Donors Of African Descent Compared To Donors Of European Descent
Authors: Fazio M.A. , Grytz R. , Morris J.S. , Bruno L. , Girkin C.A. , Downs J.C. .
Source: Investigative Ophthalmology & Visual Science, 2014 Nov; 55(11), p. 7189-98.
PMID: 25237162
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Age-related Changes In Human Peripapillary Scleral Strain
Authors: Fazio M.A. , Grytz R. , Morris J.S. , Bruno L. , Gardiner S.K. , Girkin C.A. , Downs J.C. .
Source: Biomechanics And Modeling In Mechanobiology, 2014 Jun; 13(3), p. 551-63.
PMID: 23896936
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A Study Of Mexican Free-tailed Bat Chirp Syllables: Bayesian Functional Mixed Models For Nonstationary Acoustic Time Series
Authors: Martinez J.G. , Bohn K.M. , Carroll R.J. , Morris J.S. .
Source: Journal Of The American Statistical Association, 2013-06-01 00:00:00.0; 108(502), p. 514-526.
PMID: 23997376
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Ibag: Integrative Bayesian Analysis Of High-dimensional Multiplatform Genomics Data
Authors: Wang W. , Baladandayuthapani V. , Morris J.S. , Broom B.M. , Manyam G. , Do K.A. .
Source: Bioinformatics (oxford, England), 2013-01-15 00:00:00.0; 29(2), p. 149-59.
PMID: 23142963
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Robust Classification Of Functional And Quantitative Image Data Using Functional Mixed Models
Authors: Zhu H. , Brown P.J. , Morris J.S. .
Source: Biometrics, 2012 Dec; 68(4), p. 1260-8.
PMID: 22670567
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Statistical Methods For Proteomic Biomarker Discovery Based On Feature Extraction Or Functional Modeling Approaches
Authors: Morris J.S. .
Source: Statistics And Its Interface, 2012-01-01 00:00:00.0; 5(1), p. 117-135.
PMID: 23814640
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Robust, Adaptive Functional Regression In Functional Mixed Model Framework
Authors: Zhu H. , Brown P.J. , Morris J.S. .
Source: Journal Of The American Statistical Association, 2011-09-01 00:00:00.0; 106(495), p. 1167-1179.
PMID: 22308015
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Reproducibility Of Seldi Spectra Across Time And Laboratories
Authors: Diao,L. , Clarke,C.H. , Coombes,K.R. , Hamilton,S.R. , Roth,J. , Mao,L. , Czerniak,B. , Baggerly,K.A. , Morris,J.S. , Fung,E.T. , et al. .
Source: Cancer Informatics, 2011; 10, p. 45-64.
PMID: 21552492
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Automated Analysis Of Quantitative Image Data Using Isomorphic Functional Mixed Models, With Application To Proteomics Data
Authors: Morris J.S. , Baladandayuthapani V. , Herrick R.C. , Sanna P. , Gutstein H. .
Source: The Annals Of Applied Statistics, 2011-01-01 00:00:00.0; 5(2A), p. 894-923.
PMID: 22408711
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Image Analysis Tools And Emerging Algorithms For Expression Proteomics
Authors: Dowsey,A.W. , English,J.A. , Lisacek,F. , Morris,J.S. , Yang,G.Z. , Dunn,M.J. .
Source: Proteomics, 2010 Dec; 10(23), p. 4226-57.
PMID: 21046614
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Bayesian Random Segmentation Models to Identify Shared Copy Number Aberrations for Array CGH Data.
Authors: Baladandayuthapani V. , Ji Y. , Talluri R. , Nieto-Barajas L.E. , Morris J.S. .
Source: Journal Of The American Statistical Association, 2010 Dec; 105(492), p. 1358-1375.
PMID: 21512611
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Wavelet-based Functional Linear Mixed Models: An Application To Measurement Error-corrected Distributed Lag Models
Authors: Malloy,E.J. , Morris,J.S. , Adar,S.D. , Suh,H. , Gold,D.R. , Coull,B.A. .
Source: Biostatistics (oxford, England), 2010 Jul; 11(3), p. 432-52.
PMID: 20156988
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Evaluating The Performance Of New Approaches To Spot Quantification And Differential Expression In 2-dimensional Gel Electrophoresis Studies
Authors: Morris,J.S. , Clark,B.N. , Wei,W. , Gutstein,H.B. .
Source: Journal Of Proteome Research, 2010 Jan; 9(1), p. 595-604.
PMID: 19919108
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Informatics And Statistics For Analyzing 2-d Gel Electrophoresis Images
Authors: Dowsey,A.W. , Morris,J.S. , Gutstein,H.B. , Yang,G.Z. .
Source: Methods In Molecular Biology (clifton, N.j.), 2010; 604, p. 239-55.
PMID: 20013375
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Statistical Contributions To Proteomic Research
Authors: Morris,J.S. , Baggerly,K.A. , Gutstein,H.B. , Coombes,K.R. .
Source: Methods In Molecular Biology (clifton, N.j.), 2010; 641, p. 143-66.
PMID: 20407946
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Youth Destinations Associated With Objective Measures Of Physical Activity In Adolescents
Authors: Cradock,A.L. , Melly,S.J. , Allen,J.G. , Morris,J.S. , Gortmaker,S.L. .
Source: The Journal Of Adolescent Health : Official Publication Of The Society For Adolescent Medicine, 2009 Sep; 45(3 Suppl), p. S91-8.
PMID: 19699443
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Microproteomics: Analysis Of Protein Diversity In Small Samples
Authors: Gutstein,H.B. , Morris,J.S. , Annangudi,S.P. , Sweedler,J.V. .
Source: Mass Spectrometry Reviews, 2008 Jul-Aug; 27(4), p. 316-30.
PMID: 18271009
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Bayesian Analysis Of Mass Spectrometry Proteomic Data Using Wavelet-based Functional Mixed Models
Authors: Morris,J.S. , Brown,P.J. , Herrick,R.C. , Baggerly,K.A. , Coombes,K.R. .
Source: Biometrics, 2008 Jun; 64(2), p. 479-89.
PMID: 17888041
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Pinnacle: A Fast, Automatic And Accurate Method For Detecting And Quantifying Protein Spots In 2-dimensional Gel Electrophoresis Data
Authors: Morris,J.S. , Clark,B.N. , Gutstein,H.B. .
Source: Bioinformatics (oxford, England), 2008-02-15 00:00:00.0; 24(4), p. 529-36.
PMID: 18194961
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Laser Capture Sampling And Analytical Issues In Proteomics
Authors: Gutstein,H.B. , Morris,J.S. .
Source: Expert Review Of Proteomics, 2007 Oct; 4(5), p. 627-37.
PMID: 17941818
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Clustering Of Time-course Gene Expression Data Using Functional Data Analysis
Authors: Song,J.J. , Lee,H.J. , Morris,J.S. , Kang,S. .
Source: Computational Biology And Chemistry, 2007 Aug; 31(4), p. 265-74.
PMID: 17631419
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Characteristics Of School Campuses And Physical Activity Among Youth
Authors: Cradock,A.L. , Melly,S.J. , Allen,J.G. , Morris,J.S. , Gortmaker,S.L. .
Source: American Journal Of Preventive Medicine, 2007 Aug; 33(2), p. 106-113.
PMID: 17673097
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Prepms: Tof Ms Data Graphical Preprocessing Tool
Authors: Karpievitch,Y.V. , Hill,E.G. , Smolka,A.J. , Morris,J.S. , Coombes,K.R. , Baggerly,K.A. , Almeida,J.S. .
Source: Bioinformatics (oxford, England), 2007-01-15 00:00:00.0; 23(2), p. 264-5.
PMID: 17121773
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Using Wavelet-based Functional Mixed Models To Characterize Population Heterogeneity In Accelerometer Profiles: A Case Study
Authors: Morris J.S. , Arroyo C. , Coull B.A. , Ryan L.M. , Herrick R. , Gortmaker S.L. .
Source: Journal Of The American Statistical Association, 2006-12-01 00:00:00.0; 101(476), p. 1352-1364.
PMID: 19169424
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Wavelet-based Functional Mixed Models
Authors: Morris J.S. , Carroll R.J. .
Source: Journal Of The Royal Statistical Society. Series B, Statistical Methodology, 2006-04-01 00:00:00.0; 68(2), p. 179-199.
PMID: 19759841
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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
Authors: Coombes,K.R. , Tsavachidis,S. , Morris,J.S. , Baggerly,K.A. , Hung,M.C. , Kuerer,H.M. .
Source: Proteomics, 2005 Nov; 5(16), p. 4107-17.
PMID: 16254928
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Feature Extraction And Quantification For Mass Spectrometry In Biomedical Applications Using The Mean Spectrum
Authors: Morris,J.S. , Coombes,K.R. , Koomen,J. , Baggerly,K.A. , Kobayashi,R. .
Source: Bioinformatics (oxford, England), 2005-05-01 00:00:00.0; 21(9), p. 1764-75.
PMID: 15673564
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Serum Proteomics Profiling--a Young Technology Begins To Mature
Authors: Coombes,K.R. , Morris,J.S. , Hu,J. , Edmonson,S.R. , Baggerly,K.A. .
Source: Nature Biotechnology, 2005 Mar; 23(3), p. 291-2.
PMID: 15765078
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Signal In Noise: Evaluating Reported Reproducibility Of Serum Proteomic Tests For Ovarian Cancer
Authors: Baggerly,K.A. , Morris,J.S. , Edmonson,S.R. , Coombes,K.R. .
Source: Journal Of The National Cancer Institute, 2005-02-16 00:00:00.0; 97(4), p. 307-9.
PMID: 15713966
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The Importance Of Experimental Design In Proteomic Mass Spectrometry Experiments: Some Cautionary Tales
Authors: Hu,J. , Coombes,K.R. , Morris,J.S. , Baggerly,K.A. .
Source: Briefings In Functional Genomics & Proteomics, 2005 Feb; 3(4), p. 322-31.
PMID: 15814023
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Bias, Randomization, And Ovarian Proteomic Data: A Reply To "producers And Consumers"
Authors: Baggerly,K.A. , Coombes,K.R. , Morris,J.S. .
Source: Cancer Informatics, 2005; 1, p. 9-14.
PMID: 19305627
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Understanding The Characteristics Of Mass Spectrometry Data Through The Use Of Simulation
Authors: Coombes,K.R. , Koomen,J.M. , Baggerly,K.A. , Morris,J.S. , Kobayashi,R. .
Source: Cancer Informatics, 2005; 1, p. 41-52.
PMID: 19305631
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Cutaneous Angiosarcoma Of The Scalp: A Multidisciplinary Approach
Authors: Pawlik,T.M. , Paulino,A.F. , McGinn,C.J. , Baker,L.H. , Cohen,D.S. , Morris,J.S. , Rees,R. , Sondak,V.K. .
Source: Cancer, 2003-10-15 00:00:00.0; 98(8), p. 1716-26.
PMID: 14534889
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Quality Control And Peak Finding For Proteomics Data Collected From Nipple Aspirate Fluid By Surface-enhanced Laser Desorption And Ionization
Authors: Coombes,K.R. , Fritsche,H.A. , Clarke,C. , Chen,J.N. , Baggerly,K.A. , Morris,J.S. , Xiao,L.C. , Hung,M.C. , Kuerer,H.M. .
Source: Clinical Chemistry, 2003 Oct; 49(10), p. 1615-23.
PMID: 14500586
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A Comprehensive Approach To The Analysis Of Matrix-assisted Laser Desorption/ionization-time Of Flight Proteomics Spectra From Serum Samples
Authors: Baggerly,K.A. , Morris,J.S. , Wang,J. , Gold,D. , Xiao,L.C. , Coombes,K.R. .
Source: Proteomics, 2003 Sep; 3(9), p. 1667-72.
PMID: 12973722
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