Selected Publications

Each of the publications was in part or in full supported by the Statistical Informatics for Cancer Research PO1 grant.

Project 1

Chen JT, Coull BA, Waterman PD, Schwartz J, Krieger N. 2008. Methodological implications of social inequalities for analyzing health disparities in large spatiotemporal datasets: an example using breast cancer incidence data (Northern and Southern California, 1988-2002). Statistics in Medicine 27:3957-3983. Publication.
Guha S, Ryan L, and Morara M. 2009. Gauss–Seidel Estimation of Generalized Linear Mixed Models With Application to Poisson Modeling of Spatially Varying Disease Rates. Journal of Computational and Graphical Statistics 18(4):818–837. Publication.
Janes J, Dominici F, and Zeger S. 2010. On quantifying the magnitude of confounding. Biostatistics 11:572-582. Publication.
Paciorek CJ. 2010. The importance of scale for spatial-confounding bias and precision of spatial regression estimators. Statistical Science 25(1): 107-125. Publication.
Philip L. 2010. Impact of model misspecification in conditional and marginalized zero-altered Poisson models. Dissertation.
Rava M, White R, and Dominici F. 2010. Does Attainment Status For The PM10 National Air Ambient Quality Standard Change the Trend in Ambient Levels of Particulate Matter? Air Quality, Atmosphere and Health. Air Quality, Atmosphere, & Health 4(2):133-143. Publication.
Philip L. 2010. Bayesian marginalized models for zero-inflated spatio-temporal count data. Dissertation.
Zhou Y, Dominici F, and Louis T. 2010. Racial Disparities in Mortality Rates in a Sample of the U.S. Medicare Population. Journal of the Royal Statistical Society, Series C 59(2):319-339. Publication.
Zhou Y, Dominici F, and Louis T. 2010. A Smoothing Approach for Data Masking. Annals of Applied Statistics. To appear. Article from imstat.org.
Chang H, Peng R, and Dominici F. 2011. Model Approach for Estimating the Acute Health Effects of Coarse Particulate Matter Accounting for Exposure Measurement Error. Biostatistics. In press. Publication.
Feder J, Dominici F, and Peng R. 2011. A Bayesian Model Averaging Approach for Estimating the Relative Risk of Mortality Associated with Heat Waves in 105 U.S. Cities. Biometrics. In press. Publication.
Wang C, Parmigiani G, and Dominici F. 2011. Bayesian effect estimation accounting for adjustment uncertainty. Biometrics. In press
Greven S, Dominici F, and Zeger SL. 2011. An Approach to the Estimation of Chronic Air Pollution Effects Using Spatio-Temporal Information. Journal of American Statistical Association 106(494):396-406. Publication.
Bliznyuk N, Ruppert D, and Shoemaker C. 2011. Bayesian inference using efficient interpolation of computationally expensive densities with variable parameter costs. JCGS. To appear.
Chang H, Peng R, and Dominici F. Bayesian Model Averaging For Clustered Data. Biometrics. In press.
Barr CD, Diez DM, Wang Y, Samet JM, and Dominici F. Comprehensive smoking bans and acute myocardial infarction among Medicare enrollees in 387 U.S. counties: 1999 to 2008. Submitted.
Bliznyuk N, Paciorek C, and Coull B. Nonlinear Latent Process Models for Integrating Spatio-Temporal Exposure Data from Multiple Sources. Submitted.
Hund L, Chen J, Melly SJ, and Coull BA. A geostatistical approach to disease mapping for aggregated space-time count data. Submitted.
Philip L, Tchetgen EJ, Wellenius GA, and Coull BA. Marginalized zero-altered Poisson models for count data with excessive zeros. Submitted.

Project 2

Cook AJ and Li Y. 2008. Notes on Permutation Tests for Spatial Cluster Detection with Censored Outcome Data (Rejoiner to "Asymptotic Distribution of Score Statistics for Spatial Cluster Detection with Censored Data"). Biometrics 64:1289-1292.
Guha S. 2008. Posterior Simulation in the Generalized Linear Mixed Model with Semiparametric Random Effects. Journal of Computational and Graphical Statistics 17:410-425. Publication. Software.
Guha S, Li Y, and Neuberg D. 2008. Bayesian Hidden Markov Modeling of Array CGH Data. Journal of the American Statistical Association 103:485-497. Publication. Matlab package demo.
Li Y and Tiwari R. 2008. Comparing Trends in Cancer Rates Across Overlapping Regions. Biometrics 64:1280-1286. Publication.
Li Y, Tiwari R, and Zou Z. 2008. An Age-Stratified Poisson Model for Comparing Trends in Cancer Rates Across Overlapping Regions. Biometrical Journal 50(4):608-619. Publication.
Cook AJ, Gold DR, Li Y. 2009. Spatial Cluster detection for Repeatedly Measured Outcomes while Accounting for Residential History. Biometrical Journal 51(5):801-18. Publication. Software.
Engler D and Li Y. 2009. Survival Analysis with High-Dimensional Covariates: An Application in Microarray Studies. Statistical Applications in Genetics and Molecular Biology 8(1):Article 14. Publication.
Othus M, Li Y, and Tiwari R. 2009. A Class of Semiparametric Mixture Cure Survival Models with Dependent Censoring. Journal of the American Statistical Association 104(487):1241-1250. Publication.
Park PJ, Manjourides J, Bonetti M, Pagano M. 2009. A permutation test for determining significance of clusters with applications to spatial and gene expression data. Computational Statistics and Data Analysis 53:4290-4300. Publication.
Cook AJ, Li Y, Arterburn D, Tiwari RC. 2010. Spatial cluster detection for weighted outcomes using cumulative geographic residuals. Biometrics 66(3): 783-792. Publication. Software.
Guha S. 2010. Bayesian Hidden Markov Modeling of Array CGH Data. Bayesian Modeling in Bioinformatics (eds. Dey DK, Ghosh S and Mallick B), Chapman & Hall/CRC, to appear.
Guha S. 2010. Posterior Simulation in Countable Mixture Models for Large Datasets. Journal of the American Statistical Association 105(490):775-786. Publication.
Manjourides J and Pagano M. 2011. Improving the power of chronic disease surveillance by incorporating residential history. Statistics in Medicine 30(18):2222–2233. Publication.
Walters KA, Li Y, Tiwari RC, and Zou Z. 2010. A Weighted-Least-Squares Estimation Approach to Comparing Trends in Age-Adjusted Cancer Rates Across Overlapping Regions. Journal of Data Science 8(4):645-664. Publication.
Tiwari RC, Li Y, and Zou Z. 2010. Interval Estimation for Ratios of Correlated Age-Adjusted Rates. Journal of Data Science 8(3):483-493. Publication
MacEachern SN and Guha S. 2011. Parametric and Semiparametric Hypotheses in the Linear Model. The Canadian Journal of Statistics 39(1):165-180. Publication.
Martin N and Li Y. 2011. A New Class of Minimum Power Divergence Estimators with Applications to Cancer Surveillance. Journal of Multivariate Analysis 102:1175-1193. Publication.
Goodman M, Li Y, and Tiwari R. 2011. Detecting Multiple Change Points in Piecewise Constant Hazard Functions. Journal of Applied Statistics. In press. Publication.
Martin N and Li Y. 2011. Multiple Comparison of Change Trends in Cancer Mortality/Incidence Rates Taking with Overlapping Regions and Time-Periods. Understanding Complex Systems (Springer Series). 485-494. Publication.
Manjourides J, Lin H, Shin S, Jeffery C, Contreras C, Santa Cruz J, Jave HC, Yagui M, Asencios L, Cohen T. 2012. Identifying multidrug resistant tuberculosis transmission hotspots using routinely collected data, Tuberculosis. In press.
Zhu J, Sharma DB, Gray SW, Chen AB, Weeks JC, Schrag D. 2012. Association between Treatment with Carboplatin and Paclitaxel with and without Bevacizumab and Survival among Patients 65 Years and Older with Advancer Non-Small Cell Lung Cancer. Journal of the American Medical Association. In press.
Cook AJ, Gold DR, and Li Y. Spatial Cluster Detection for Longitudinal Outcomes using Administrative Regions. Communications in Statistics - Theory and Methods. Submitted.
Guha S and Li Y. Semiparametric Bayesian Analysis of High-Dimensional Censored Outcome Data: Discovering Spatial Variation in Breast Cancer Mortality from the SEER Database. Submitted.
Zhao D and Li Y. Principled sure independence screening for Cox models with ultra-high-dimensional covariate. Submitted. (Won 2010 IBM Student Paper Award and 2010 ICSA Student Paper Award.)
Guha S, Li Y, Melly S. Breast Cancer Mortality Rates in New Mexico: Semiparametric Bayesian Analysis of a Large Survival Dataset. Submitted.
Guha S and Ryan L. Spatio-temporal Analysis of Areal Data and Discovery of Neighborhood Relationships in Conditionally Autoregressive Models. Submitted.
Marino M and Li Y. Random matrix theory with applications in the study of cancer mortality change trends. Submitted.
Othus M, Li Y, and Tiwari R. Estimating the change-point effect of age of diagnosis among prostate cancer patients. Submitted.

Project 3

Harezlak J, Wu MC, Wang M, Schwartzman A, Christiani DC, and Lin X. 2008. Biomarker discovery for arsenic exposure using functional data analysis and feature learning of mass spectrometry proteomic data. Journal of Proteome Research 7: 217-224. Publication.
Houseman EA, Christensen BC, Yeh RF, Marsit CJ, Karagas MR, Wrensch M, Nelson HH, Wiemels J, Zheng S, Wiencke JK, and Kelsey KT. Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions. BMC Bioinformatics 9:365. Publication.
Kwee L, Liu D, Lin X, Ghosh D, and Epstein M. 2008. A powerful and flexible multilocus association test for quantitative traits. American Journal of Human Genetics 82: 386-397. Publication.
Liu D, Ghosh D, and Lin X. 2008. Estimation and Testing for the Effect of a Genetic Pathway on a Disease Outcome Using Logistic Kernel Machine Regression via Logistic Mixed Models. BMC Bioinformatics 9: 292. Publication.
Basu P, Rudoy D, and Wolfe PJ. 2009. A nonparametric test for stationarity based on local Fourier analysis. Proc. IEEE Intl. Conf. Acoust. Speech Signal Process: 3005-3008. Proceedings.
Belabbas MA and Wolfe PJ. 2009. On landmark selection and sampling in high-dimensional data analysis. Philos Transact A Math Phys Eng Sci. 367(1906): 4295-4312. Publication.
DeSantis SM, Houseman EA, Coull BA, Louis DN, Mohapatra G, Betensky RA. 2009. A Latent Class Model with Hidden Markov Dependence for Array CGH Data. Biometrics 65:1296-1305. Publication.
Epstein MP, Hunter JE, Allen EG, Sherman SL, Lin X, and Boehnke M. 2009. A variance-component framework for pedigree analysis of continuous and categorical outcomes. Statistics in Biosciences 2: 181-198. Publication.
Huang YT, Chirieac LR, Lin X, Heist R, Skaug V, Haugen A, Wu M, Wang Z, Su L, Asomaning K, and Christiani D. 2009. Genome Wide Analysis of Survival in Early-Stage Non-Small Cell Lung Cancer. Journal of Clinical Oncology 27: 2660-2667. Publication.
Wu M and Lin X. 2009. Prior biological knowledge based approaches for the analysis of genome-wide expression proles using gene sets and pathways. Statistical Methods in Medical Research 18: 577-593.
Wu MC, Zhang L, Wang Z, Christiani DC, Lin X. 2009. Sparse linear discriminant analysis for simultaneous gene set/pathway significance test and gene selection. Bioinformatics 25(9):1145-1151. Publication.
Dicker L, Lin X, Ivanov A. 2010. Increased Power for the Analysis of Label-Free LC-MS/MS Proteomic Data by Combining Spectral Counts and Peptide Peak Attributes. Molecular and Cellular Proteomics 9:2704-2718. Publication
Koestler DC, Marsit CJ, Christensen BC, Karagas MR, Bueno R, Sugarbaker DJ, Kelsey KT, Houseman EA. 2010. Semi-supervised recursively partitioned mixture models for identifying cancer subtypes. Bioinformatics 26:2578-2585. Publication.
Rudoy P, Basu P, and Wolfe PJ. 2010. Superposition frames for adaptive time-frequency analysis and fast reconstruction. IEEE Transactions on Signal Processing 58:2581-2596. Publication.
Wu MC, Kraft P, Epstein MP, Taylor DM, Chanock SJ, Hunter DJ, and Lin X. 2010. Powerful SNP Set Analysis for Case-Control GenomeWide Association Studies. American Journal of Human Genetics 86:929-942. Publication.
Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Maruyama R, Bessarabova M, Nikolskaya T, Sukumar S, Schwartzman A, Liu JS, Polyak K, Liu XS. 2010. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Research 20:1730-1739. Publication.
Cai T, Tonini G, and Lin X. 2011. Kernel machine approach to testing the significance of multiple genetic markers for risk prediction. Biometrics 67:975-986. Publication.
Schwartzman A and Lin X. 2011. The effect of correlation in false discovery rate estimation. Biometrika 98(1):199-214. Publication.
Hirakawa K and Wolfe PJ. 2011. "Rewiring" filterbanks for local Fourier analysis: Theory and practice. IEEE Transactions on Information Theory 57(8):5360-5374. Publication.
Huang YT, Lin X, Liu Y, Chirieac LR, McGovern R, Wain J, Heist R, Skaug V, Zienolddiny S, Haugen A, Su L, Fox EA, Wong KK, Christiani DC. 2011. Cigarette smoking increases copy number alterations in nonsmall-cell lung cancer. Proceedings Nat Acad Sci USA 108:16345-16350. Publication.
Lin X, Cai T, Wu MC, Zhou Q, Liu G, Christiani DC, and Lin X. 2011. Kernel Machine SNP-set Analysis for Censored Survival Outcomes in Genome-wide Association Studies. Genetic Epidemiology (online). Publication.
Dicker L, Huang B, and Lin X. 2011. Variable selection and estimation with the seamless-L0 penalty. Statistica Sinica. In press.
Hirakawa K and Wolfe PJ. 2011. Skellam shrinkage: Wavelet based intensity estimation for inhomogeneous Poisson data. IEEE Transactions on Information Theory. In press.
Maity A and Lin X. 2011. Powerful tests for detecting a gene effect in the presence of possible gene-gene interactions using garrote kernel machines. Biometrics. In press. Publication.
Wu M, Lee S, Cai T, Li Y, Boehnke M, and Lin X. 2011. Rare Variant Association Testing for Sequencing Data Using the Sequence Kernel Association Test (SKAT). American Journal of Human Genetics 89(1):82-93. Publication.
Dicker L and Lin X. Variable selection using the Dantzig Selector: Asymptotic theory and extensions. Submitted.
Schwartzman A, Jaffe A, Gavrilov Y, and Meyer CE. Multiple Testing of Local Maxima for Detection of Peaks in ChIP-Seq Data. Submitted.
Liu CY, Maity A, Lin X, Wright RO, and Christiani DC. Design and Analysis Issues in Genes and Environment Studies. Submitted.
Schwartzman A, Gavrilov Y, and Adler R. Multiple Testing of Local Maxima for Detection of Peaks in 1D. Submitted.