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 Professional Organizations

American Statistical Association   International Biometric Society (East-North American Region) (West-North American Region) (East-Mediterranean Region)   International Society for Bayesian Analysis   Institute of Mathematical Statistics   American Association for the Advancement of Science

 

Statistical/Bioinformatics Publications

2008+

Find links to papers on my Bepress Works Website

 

Supplementary Simulation tables for Robust Functional Mixed Models paper

 

 

2007

1. Morris JS, Brown PJ, Herrick RC, Baggerly KA, and Coombes KR (2007): Bayesian Analysis of Mass Spectrometry Data using Wavelet Based Functional Mixed Models.  Biometrics, to appear.       Supplementary Material

2. Song JJ, Lee HJ, Morris JS, and Kang S: Clustering of time-course gene expression data using functional data analysis. Computational Biology and Chemistry, 31(4), 265-274, 2007.

3. Coombes KR, Baggerly KA, and Morris JS (2007): Pre-Processing Mass Spectrometry Data.  Fundamentals of Data Mining in Genomics and Proteomics, W Dubitzky, M Granzow, and D Berrar, eds. Kluwer, Boston, 79-99.

4. Morris JS, Baggerly KA, Gutstein HB, and Coombes KR (2007): Statistical contributions to proteomic research.  The Urine Proteome, Humana, to be published 2007.

 

2006

1. Morris JS, Arroyo C, Coull B, Ryan LM, Herrick R, and Gortmaker SL (2006). Using Wavelet-Based Functional Mixed Models to characterize Population Heterogeneity in Accelerometer Profiles: A Case Study. Journal of the American Statistical Association, 101(476): 1352-1364.  Supplementary Material

2. Morris JS and Carroll RJ (2006). Wavelet-Based Functional Mixed Models. Journal of the Royal Statistical Society, Series B, 68(2): 179-199.                                       Supplementary Material and code

3. Herrick RC and Morris JS (2006). Wavelet-Based Functional Mixed Model Analysis: Computational Considerations.  Proceedings, Joint Statistical Meetings, ASA Section on Statistical Computing,  2051-2053.

4.  Morris JS, Brown PJ, Baggerly KA, and Coombes KR (2006). Analysis of Mass Spectrometry Data Using Bayesian Wavelet-Based Functional Mixed Models.  Bayesian Inference for Gene Expression and Proteomics, KA Do, P Mueller, and M Vannucci, eds., Cambridge University Press, 269-292.

5. Morris JS, Baggerly KA, and Coombes KR (2006). Shrinkage Estimation for SAGE Data using a Mixture Dirichlet Prior. Bayesian Inference for Gene Expression and Proteomics, KA Do, P Mueller, and M Vannucci, eds., Cambridge University Press, 254-268.

6. Karpievitch YV, Hill EG, Morris JS, Coombes KR, Baggerly KA and Almeida JS: PrepMs.  Bioinformatics, Advance Access published November 22, 2006.                                                Click here for PrepMS software (preprocessing MS)

7. Mayo MS, Gajewski BJ, and Morris JS (2006). Some Statistical Issues in Microarray Gene Expression Data.  Radiation Research, 165(6): 745-748.

8. Baggerly KA, Coombes KR, and Morris JS (2006). An Introduction to High-Throughput Bioinformatics Data.  Bayesian Inference for Gene Expression and Proteomics, KA Do, P Mueller, and M Vannucci, eds., Cambridge University Press, 1-39.

9. Guindani M, Do KA, Muller P, and Morris JS (2006).  Bayesian Mixture Models for Gene Expression and Protein Profiles.  Bayesian Inference for Gene Expression and Proteomics, KA Do, P Mueller, and M Vannucci, eds., Cambridge University Press, 238-253.

10. Morris JS, Wu C, Coombes KR, Baggerly KA, Wang J, and Zhang L  (2006).  Alternative Probeset Definitions for Combining Microarray Data Across Studies Using Different Versions of Affymetrix Oligonucleotide Arrays. To appear in Meta-Analysis in Genetics, edited by Rudy Guerra and David Allison,Chapman-Hall.    

2005

1. Coombes KR, Morris JS, Hu J, Edmondson SR, and Baggerly KA   (2005). Serum Proteomics Profiling: A Young Technology Begins to Mature. Nature Biotechnology, 23(3): 291-292.

2.  Morris JS, Coombes KR, Kooman J, Baggerly KA, and Kobayashi R (2005). Feature Extraction and Quantification for Mass Spectrometry Data in Biomedical Applications Using the Mean Spectrum. Bioinformatics, 21(9): 1764-1775.                 Supplementary material and code  

3.  Coombes KR, Tsavachidis S, Morris JS, Baggerly KA, and Kuerer HM (2005). 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. Proteomics, 5, 4107-4117.  "Cromwell" code

4. Hu J, Coombes KR, Morris JS, and Baggerly KA (2005). The Importance of Experimental Design in Proteomic Mass Spectrometry Experiments: Some Cautionary Tales. Briefings in Genomics and Proteomics, 3(4), 322-331.

5. Coombes KR, Koomen, JM, Baggerly KA, Morris JS, and Kobayashi R (2005). Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Informatics, 1(1): April 14, 2005.     Click here for simulation engine software

6. Baggerly KA, Coombes KR, and Morris JS (2005). Are the NCI/FDA Ovarian Proteomic Data Biased? A Reply to Producers and Consumers. Cancer Informatics, 1(1): April 14, 2005.

7. Baggerly KA, Morris JS, Edmonson S, and Coombes KR (2005). Signal in Noise: Evaluating Reported Reproducibility of Serum Proteomic Tests for Ovarian Cancer. Journal of the National Cancer Institute, 97: 307-309 (with commentary).

8. Morris JS, Yin G, Baggerly KA, Wu C, and Zhang L (2005).  Pooling Information Across Different Studies and Oligonucleotide Microarray Chip Types to Identify Prognostic Genes for Lung Cancer. Methods of Microarray Data Analysis IV, eds. JS Shoemaker and SM Lin, pp. 51-66, New York: Springer-Verlag (Won best presentation at CAMDA 2003 meetings).

9. Hu, J, Yin G, Morris JS, Zhang L, and Wright FA (2005). Entropy and Survival-based Weights to Combine Affymetrix Array Types in the Analysis of Differential Expression and Survival. Methods of Microarray Data Analysis IV, eds. JS Shoemaker and SM Lin pp. 95-108, New York: Springer-Verlag.

2004

1. Baggerly KA, Deng L, Morris JS, and Aldez CM (2004). Overdispersed Logistic Regression for SAGE: Modeling Multiple Groups and Covariates. BMC Bioinformatics, 5:144.

2. Baggerly, KA, Morris JS, and Coombes KR (2004). Reproducibility of SELDI Mass Spectrometry Patterns in Serum: Comparing Proteomic Data Sets from Different Experiments. Bioinformatics, 20(5): 777-785, 2004. (Identified by Thomson-ISI as “one of the most cited recent papers in the field of computer science”,see http://www.esi-topics.com/nhp/2005/july-05-KeithBaggerly.html)

3. Baggerly KA, Edmonson S, Morris JS, and Coombes KR (2004). High-Resolution Serum Proteomic Patterns for Ovarian Cancer Detection. Endocrine-Related Cancers, 11(4): 583-584.

2003

1. Morris JS, Vannucci M, Brown PJ and Carroll RJ (2003). Wavelet-Based Nonparametric Modeling of Hierarchical Functions in Colon Carcinogenesis. Journal of the American Statistical Association. 98: 573-583, 2003 (Won Mitchell Prize and was 2003 JASA-ACS Invited Paper).

2. Morris JS, Vannucci M, Brown PJ and Carroll RJ (2003). Rejoinder to “Wavelet-Based Nonparametric Modeling of Hierarchical Functions in Colon Carcinogenesis.” Journal of the American Statistical Association. 98: 591--597.

3. Morris JS, Baggerly K, and Coombes K: Bayesian Shrinkage Estimators of the Relative Abundance of mRNA Transcripts using SAGE. Biometrics 59: 476-486.

4. Coombes KR, Fritsche HA Jr., Clarke C, Cheng JN, Baggerly KA,  Morris JS, Xiao LC, Hung MC, and Kuerer HM (2003). Quality Control and Peak Finding for Proteomics Data Collected from Nipple Aspirate Fluid Using Surface Enhanced Laser Desorption and Ionization. Clinical Chemistry. 49(10): 1615-1623.

5. Morris JS, Wang N, Lupton JR, Chapkin RS, Turner ND, Hong MY, and Carroll RJ (2003). Understanding the Relationship between Carcinogen-induced DNA Adduct Levels in Distal and Proximal Regions of the Colon. Advances in Experimental Medicine and Biology, 537: 105-116.

6. Baggerly K, Morris JS, Wang J, Gold D, Xiao LC and Coombes K (2003). A comprehensive approach to the analysis of MALDI-TOF proteomics spectra from serum samples. Proteomics 3: 1667- 1672, (Won Best Presentation at 2002 Duke University Proteomics Data Mining Competition).

7. Baggerly K, Deng L, Morris JS, Aldez CM (2003). Differential expression in SAGE: Accounting for normal between-library variation. Bioinformatics 19(12): 1477-1483.

2002
 

1. Morris JS, Wang N, Lupton JR, Chapkin RS, Turner ND, Hong MY and Carroll RJ (2002). A Bayesian Analysis Involving Colonic Crypt Structure and Coordinated Response to Carcinogens Incorporating Missing Crypts, Biostatistics 3: 529--546.

2. Morris JS (2002).  The BLUPs Are Not “Best” When It Comes To Bootstrapping. Statistics and Probability Letters 56: 425-430.

2001

1. Morris JS, Wang N, Lupton JR, Chapkin RS, Turner ND, Hong MY and Carroll RJ (2001). Parametric and Nonparametric Methods for Understanding the Relationship Between Carcinogen-Induced DNA Adduct Levels in Distal and Proximal Regions of the Colon. Journal of the American Statistical Association 96: 816-826.