Publications, manuscripts and supplementary information

2008

• Hwang T, Sicotte H, Tian Z, Wu B, Kocher J, Wigle D, Kumar V and Kuang R (2008). Robust and efficient identication of biomarkers by classifying features on graphs. Bioinformatics, 24(18):2023-2029.
• Chen W, Kumar A, Hudson W, Li Q, Wu B, Staggs R, Lund E, Sam T and Kersey J (2008). Malignant transformation initiated by Mll-AF9: Gene dosage and critical target cells. Cancer Cell, 13: 432-440.
• Liu J, Yu W, Wu B and Zhao H (2008). Bayesian mass spectra peak alignment from Mass charge ratios. Cancer Informatics, 4: 217-241.
• Guan Z, Wu B and Zhao H (2008). Application of Bernstein polynomial in the estimation of false-discovery-rate. Statistica Sinica, 18: 905-923.
• Fu S, Kodl M, Joseph A, Hatsukami D, Johnson E, Breslau N, Wu B, Bierut L (2008). Racial/Ethnic Disparities in the Use of Nicotine Replacement Therapy and Quit Ratios in Lifetime Smokers Aged 25-44. Cancer Epidemiology, Biomarkers & Prevention, 17: 1640-1647.
• John C, Bangirana P, Byarugaba J, Opika-Opoka R, Idro R, Jurek A, Wu B, Boivin M (2008). Cerebral Malaria in Children Is Associated With Long-term Cognitive Impairment. Pediatrics, 122: e92-e99.
• Wu B (2008). Flexible prediction analysis of microarrays. Statistical applications in genetics and molecular biology, accepted.
• Whitson B, D'Cunha J, Hoang C, Wu B, Ikramuddin S, Buchwald H, Panoskaltsis-Mortari A, Kratzke R, Miller J and Maddaus M (2008). Minimally invasive versus open roux-en-y gastric bypass: impact on immune eector cells. Surgery for Obesity and Related Diseases, in press. doi:10.1016/j.soard.2008.08.019.
• Whitson B, D'Cunha J, Andrade R, Kelly R, Groth S, Wu B, Miller J, Kratzke R and Maddaus M (2008). Thoracoscopic versus thoracotomy approaches to lobectomy: differential impairment of cellular immunity. Annals of Thoracic Surgery, 86: 1735-1744.

2007

• Li N, Wu B, Wei P, Xie B, Xie Y, Xiao G and Pan W (2007). Functional group based linkage analysis of gene expression trait loci. BMC Proceedings 2007, 1(Suppl1):S117.
• Wu B (2007). Cancer outlier differential gene expression detection. Biostatistics, 8: 566-575.
• Liu F and Wu B (2007). Multi-group cancer outlier differential gene expression detection. Computational Biology and Chemistry, 31: 65-71.

2006

• Wu B (2006). Differential gene expression detection and sample classification using penalized linear regression models. Bioinformatics, 22: 472-476.
• Wu B, Guan Z and Zhao H (2006). Parametric and nonparametric FDR estimation revisited. Biometrics, 62:735-744.
• Wu B, Liu N and Zhao H (2006). PSMIX: an R package for population structure inference via maximum likelihood method. BMC Bioinformatics, 7:317.
• Wu B, Abbott T, Fishman D, McMurray W, Mor G, Stone K, Ward D, Williams K, Zhao H (2006). Ovarian cancer classification based on mass spectrometry analysis of sera. Cancer Informatics, 2: 123-132.
• Yu W, Wu B, Lin N, Stone K, Williams K, Zhao H (2006). Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Computational Biology and Chemistry, 30: 27-38.
• Yu W, Wu B, Liu J, Li X, Williams K, Zhao H (2006). MALDI-MS Data Analysis for Disease Biomarker Discovery. Methods in Molecular Biology, 328: 199-216.
• Yu W, Wu B, Huang T, Li X, Williams K, Zhao H (2006). Statistical methods in proteomics. In Pham H(ed). Springer Handbook of Engineering Statistics, Springer-Verlag, London, UK.
• Yu W, Li X, Liu J, Wu B, Williams K, Zhao H (2006). Multiple peak alignment in sequential data analysis: A scale-space based approach. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3: 208-219.

2005

• Wu B (2005). Boosting nearest shrunken centroid classifier for microarray data. Division of Biostatistics report 2005-029 (pdf)
• Wu B (2005). Predictive model building for microarray data using generalized partial least squares model. Division of Biostatistics report 2005-023 (pdf)
• Huang T, Wu B, Lizardi P, Zhao H (2005). Detection of DNA Copy Number Alterations Using Penalized Least Squares Regression. Bioinformatics, 21: 3811-3817.
• Wu B (2005). Regularized singular value decomposition: a sparse dimension reduction technique. Division of Biostatistics report 2005-002 (pdf)
• Wu B (2005). Differential gene expression detection using penalized linear regression model: the improved SAM statistics. Bioinformatics, 21: 1565-1571.
• Carriero N, Osier M, Cheung K, Miller P, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M (2005). A 'High Productivity/Low Maintenance' Approach to High Performance Computation for Biomedicine: Four Case Studies. Journal of American Medical Informatics Association, 12: 90-98.
• Gulcicek E, Colangelo C, McMurray W, Stone K, Wu B, Wu T, Spratt H, Kurosky A, Zhao H, Williams K (2005). Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein-Profiling Technologies. In Davison D, Page R, Petsko G, Stormo G, and Stein L(ed). Current Protocols in Bioinformatics, John Wiley and Sons, Indianapolis, IN.

2004

• Wu B, Guan Z, Lai Y and Zhao H (2004). Assessing false positives in detecting differentially expressed genes.
• Guan Z, Wu B and Zhao H (2004). Model-based approach to FDR estimation. Division of Biostatistics report 2004-016 (pdf)
• Lai Y, Wu B, Chen L, and Zhao H (2004). Statistical method for identifying differential gene-gene coexpression patterns. Bioinformatics, 20: 3146-3155.
• Lin N, Wu B, Jansen R, Gerstein M and Zhao H (2004). Information assessment on predicting protein-protein interactions. BMC Bioinformatics, 5: 154.

2003

• Wu B, Abbott T, Fishman D, McMurray W, Mor G, Stone K, Ward D, Williams K, Zhao H (2003). Comparison of statistical methods for classification of ovarian cancer using a proteomics dataset. Bioinformatics, 19: 1636-1643.
• Zhao H, Wu B, Sun N (2003). DNA-protein binding and gene expression patterns. In Goldstein DR(ed). Science and Statistics: A Festschrift for Terry Speed. IMS Lecture Notes-Monograph Series, Vol. 40, 259-274.
• Goh C, Lan N, Douglas S, Wu B, Bertone P, Echols N, Milburn D, Montelione G, Zhao H, Gerstein M (2003). Mining the Structural Genomics Pipeline: Identification and Analysis of Protein Properties that Affect High-Throughput Experimental Analysis. Journal of Molecular Biology, 336: 115-30.