Papers from 2009

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Comparison of Pinnacle and SameSpots for Spot Quantification and Differential Expression in 2-Dimensional Gel Electrophoresis Studies, Jeffrey S. Morris, Brittan N. Clark, Wei Wei, and Howard B. Gutstein, UT MD Anderson Cancer Center Department of Biostatistics Working Paper Series (2009)

Papers from 2008

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Microproteomics: Analysis of protein diversity in small samples, Howard B. Gutstein, Jeffrey S. Morris, Suresh P. Annangudi, and Jonathan V. Sweedler, Mass Spectrometry Reviews (2008)

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Pinnacle: A Fast, Automatic Method for Detecting and Quantifying Protein Spots in 2-Dimensional Gel Electrophoresis Data, Jeffrey S. Morris, Brittain C. Walla, and Howard B. Gutstein, Bioinformatics (2008)

Papers from 2007

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Statistical Issues in Proteomic Research, Jeffrey S. Morris, Bulletin of the International Society for Bayesian Analysis (2007)

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Statistical contributions to proteomic research, Jeffrey S. Morris, Keith A. Baggerly, Howard B. Gutstein, and Kevin R. Coombes, The Urine Proteome (2007)

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Bayesian Analysis of Mass Spectrometry Proteomics Data using Wavelet Based Functional Mixed Models, Jeffrey S. Morris, Philip J. Brown, Richard C. Herrick, Keith A. Baggerly, and Kevin R. Coombes, Biometrics (2007)

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Pre-Processing Mass Spectrometry Data, Kevin R. Coombes, Keith A. Baggerly, and Jeffrey S. Morris, Fundamentals of Data Mining in Genomics and Proteomics (2007)

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Laser capture sampling and analytical issues in proteomics, Howard Gutstein and Jeffrey S. Morris, Expert Reviews in Proteomics (2007)

Papers from 2006

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Wavelet-Based Functional Mixed Models to characterize Population Heterogeneity in Accelerometer Profiles: A Case Study. , Jeffrey S. Morris, Cassandra Arroyo, Brent A. Coull, Louise M. Ryan, and Steven L. Gortmaker, Journal of the American Statstical Association (2006)

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Alternative Probeset Definitions for Combining Microarray Data Across Studies Using Different Versions of Affymetrix Oligonucleotide Arrays, Jeffrey S. Morris, Chunlei Wu, Kevin R. Coombes, Keith A. Baggerly, Jing Wang, and Li Zhang, Meta-Analysis in Genetics (2006)

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PrepMS: TOF MS Data Graphical Preprocessing Tool, Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, and Jonas S. Almeida, Bioinformatics (2006)

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Wavelet-based functional mixed model analysis: Computational considerations, Richard C. Herrick and Jeffrey S. Morris, Proceedings, Joint Statistical Meetings, ASA Section on Statistical Computing (2006)

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Some Statistical Issues in Microarray Gene Expression Data, Matthew S. Mayo, Byron J. Gajewski, and Jeffrey S. Morris, Radiation Research (2006)

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Wavelet-Based Functional Mixed Models, Jeffrey S. Morris and Raymond J. Carroll, Journal of the Royal Statistical Society, Series B (2006)

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Analysis of Mass Spectrometry Data Using Bayesian Wavelet-Based Functional Mixed Models, Jeffrey S. Morris, Philip J. Brown, Keith A. Baggerly, and Kevin R. Coombes, Bayesian Inference for Gene Expression and Proteomics (2006)

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Shrinkage Estimation for SAGE Data using a Mixture Dirichlet Prior, Jeffrey S. Morris, Keith A. Baggerly, and Kevin R. Coombes, Bayesian Inferene for Gene Expression and Proteomics (2006)

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An Introduction to High-Throughput Bioinformatics Data, Keith A. Baggerly, Kevin R. Coombes, and Jeffrey S. Morris, Bayesian Inference in Gene Expression and Proteomics (2006)

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Bayesian Mixture Models for Gene Expression and Protein Profiles, Michele Guindani, Kim-Anh Do, Peter Mueller, and Jeffrey S. Morris, Bayesian Inference for Gene Expression and Proteomics (2006)

Papers from 2005

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Pooling Information Across Different Studies and Oligonucleotide Microarray Chip Types to Identify Prognostic Genes for Lung Cancer., Jeffrey S. Morris, Guosheng Yin, Keith A. Baggerly, Chunlei Wu, and Li Zhang, Methods of Microarray Data Analysis IV (2005)

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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, Kevin R. Coombes, Spiros Tsavachidis, Jeffrey S. Morris, Keith A. Baggerly, and Henry M. Kuerer, Proteomics (2005)

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Feature Extraction and Quantification for Mass Spectrometry Data in Biomedical Applications Using the Mean Spectrum., Jeffrey S. Morris, Kevin R. Coombes, John Koomen, Keith A. Baggerly, and Ryuji Kobayashi, Bioinformatics (2005)

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Understanding the Characteristics of Mass Spectrometry Data Through the Use of Simulation, Kevin R. Coombes, John Koomen, Keith A. Baggerly, Jeffrey S. Morris, and Ryuji Kobayashi, Cancer Informatics (2005)

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Bias, Randomization, and Ovarian Proteomic Data: A Reply to "Producers and Consumers", Keith A. Baggerly, Kevin R. Coombes, and Jeffrey S. Morris, Cancer Informatics (2005)

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The Importance of Experimental Design in Proteomic Mass Spectrometry Experiments: Some Cautionary Tales, Jeffrey S. Morris, Jianhua Hu, Kevin R. Coombes, and Keith A. Baggerly, Briefings in Genomics and Proteomics (2005)

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Serum Proteomics Profiling: A Young Technology Begins to Mature, Kevin R. Coombes, Jeffrey S. Morris, Jianhua Hu, Sarah R. Edmondson, and Keith A. Baggerly, Nature Biotechnology (2005)

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Signal in Noise: Evaluating Reported Reproducibility of Serum Proteomic Tests for Ovarian Cancer, Keith A. Baggerly, Jeffrey S. Morris, Sarah R. Edmonson, and Kevin R. Coombes, Journal of the National Cancer Institute (2005)

Papers from 2004

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High-resolution serum proteomic patterns for ovarian cancer detection, Keith A. Baggerly, Sarah R. Edmonson, Jeffrey S. Morris, and Kevin R. Coombes, Endocrine-Related Cancer (2004)

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Overdispersed logistic regression for SAGE: Modelling multiple groups and covariates, Keith A. Baggerly, Li Deng, Jeffrey S. Morris, and C. Marcelo Aldaz, BMC Bioninformatics (2004)

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Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments, Keith A. Baggerly, Jeffrey S. Morris, and Kevin R. Coombes, Bioinformatics (2004)

Papers from 2003

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Differential Expression in SAGE: accounting for normal between-library variation, Keith A. Baggerly, Li Deng, Jeffrey S. Morris, and C. Marcelo Aldez, Bioinformatics (2003)

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Rejoinder to "“Wavelet-Based Nonparametric Modeling of Hierarchical Functions in Colon Carcinogenesis.”, Jeffrey S. Morris, Marina Vannucci, Philip J. Brown, and Raymond J. Carroll, Journal oftthe American Statistical Association (2003)

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Quality Control and Peak Finding for Proteomics Data Collected from Nipple Aspirate Fluid Using Surface Enhanced Laser Desorption and Ionization., Jeffrey S. Morris, Kevin R. Coombes, Herbert A. Fritsche, Charlotte Clarke, Jeng-Neng Chen, Keith A. Baggerly, Lian-Chun Xiao, Mien-Chie Hung, and Henry M. Kuerer, Clinical Chemistry (2003)

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Wavelet-Based Nonparametric Modeling of Hierarchical Functions in Colon Carcinogenesis., Jeffrey S. Morris, Marina Vannucci, Philip J. Brown, and Raymond J. Carroll, Journal of the American Statistical Association (2003)

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A comprehensive approach to the analysis of MALDI-TOF proteomics spectra from serum samples., Keith A. Baggerly, Jeffrey S. Morris, Jing Wang, David Gold, Lian-Chun Xiao, and Kevin R. Coombes, Proteomics (2003)

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Bayesian Shrinkage Estimation of the Relative Abundance of mRNA Transcripts using SAGE, Jeffrey S. Morris, Keith A. Baggerly, and Kevin R. Coombes, Biometrics (2003)

Papers from 2002

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A Bayesian Analysis Involving Colonic Crypt Structure and Coordinated Response to Carcinogens Incorporating Missing Crypts, Jeffrey S. Morris, Naisyin Wang, Joanne R. Lupton, Robert S. Chapkin, Nancy D. Turner, Mee-Young Hong, and Raymond J. Carroll, Biostatistics (2002)

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The BLUPs Are Not “Best” When It Comes To Bootstrapping, Jeffrey S. Morris, Statistics and Probability Letters (2002)

Papers from 2001

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Parametric and Nonparametric Methods for Understanding the Relationship Between Carcinogen-Induced DNA Adduct Levels in Distal and Proximal Regions of the Colon., Jeffrey S. Morris, Naisyin Wang, Joanne R. Lupton, Robert S. Chapkin, Nancy D. Turner, Mee-Young Hong, and Raymond J. Carroll, Journal of the American Statistical Association (2001)