Publications

Recent Publications


2018

M. Wang, N. D. Beckmann, P. R., E. Wang, X. Zhou, Q. Wang, C. Ming, R. Neff, W. Ma, J. F. Fullard, M. E. Hauberg, J. Bendl, M. A. Peters, B. Logsdon, P. Wang, and et.al., Eric Schadt & Bin Zhang “The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease” Scientific Data 5, Article number: 180185 (2018)

E. Boja, Z. Tezak, B. Zhang, P. Wang, E. Johanson, D. Hinton, H. Rodriguez,“Right data for right patient – a precisionFDA NCI-CPTAC Multi-omics Mislabeling Challenge”, Nature Medicine 2018, 24, pages1301–1302.

K. J. Brunst, N. Tignor, A. Just, Z. Liu, X. Lin, M. Hacker, M. B. Enlow, R. Wright,  P. Wang, Baccarelli, R. J. Wright, “Cumulative lifetime maternal stress and genome-wide placental DNA methylation: the PRISM cohort”, Epigenetics2018 Aug 15:1-17. doi: 10.1080/15592294

C.J. Conley, U. Ozbek, P. Wang and J. Peng, Characterizing major functional consequences of DNA copy number alterations in breast and ovarian tumors through spaceMap, J. of Genetics and Genomics2018 Jul 20;45(7):361-371.

J. Wang, P. Wang, D. Hedeker, L. S. Chen, “A multivariate mixed-effects selection model framework for batch-processed proteomics data with non-ignorable missingness”, Biostatistics (imprint)

L. Mak, M. Li, C. Cao, P. Gordon, C. Bousman, P. Wang and Quan Long, “SimPERD: Simulation-based Power Estimation for design of Rare Disease sequencing studies”, Genetic Epidemiology(imprint)

F. Petralia, L. Wang, J. Peng, A. Yan, J. Zhu and P. Wang&, “A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity”, Bioinformatics 2018 Jul 1;34(13):i528-i536.

Whiteaker, JR, Zhao, L, Saul, R, Kaczmarczyk, JA, Schoenherr, RM, Moore, HD, Jones-Weinert, C, Ivey, RG, Lin, C, Hiltke, T, Reding, KW, Whiteley, G, Wang, P, Paulovich, AG. “A multiplexed mass spectrometry-based assay for robust quantification of phospho-signaling in response to DNA damage”, Radiation Research2018 May;189(5):505-518.

Y. Yvonne Chan, B. M. Bot, M. Zweig, N. Tignor, W. Ma, C. Suver, R. Cedeno, E. Schadt, P. Wang&, “The Asthma Mobile Health Study, Smartphone Data Collected Using Research Kit”, Scientific Data 5, Article number: 180096 (2018)

2017

Petralia, V. N. Aushev, K. Gopalakrishnan, M. Kappil, N. W. Khin, J. Chen, S. L. Teitelbaum, P. Wang&, iJRF to Study the Effect of Environmental Exposures on miRNA-mRNA interactions in Mammary Transcript, Bioinformatics, 2017, DOI10.1093/bioinformatics/btx256F. Felix, B.R. Joubert, A. A. Baccarelli, G.C. Sharp, I.Annesi-Maesano… (P. Wang)…S.J.London, “Cohort Profile: Pregnancy and childhood epigenetics (PACE) Consortium”, International Journal of Epidemiology, 2017, Imprint

Chen, J. Wang, X. Wang, P. Wang&, “A mixed-effects model for incomplete data with Experiment-level Abundance-Dependent Missing-data Mechanism”, Annals Of Applied Statistics 2017, Vol. 11, No. 1, 114-138.

Yu-Feng Yvonne Chan, Pei Wang, Linda Rogers, Nicole Tignor, Nicholas Genes, Steven G. Hershman, Eric R. Scott, Micol Zweig, Marcus Badgeley, Samantha Violante, Eric Krock, Ron Edgar, Rosalind Wright, Charles Powell, Joel Dudley, Eric E. Schadt, “The Asthma Mobile Health Study, a Large Scale Clinical Study Using ResearchKit”, Nature Biotechnology, 2017 doi:10.1038/nbt.382

Zhou, P. Wang, X. Wang, J. Zhu, and P. Song “Sparse multivariate factor analysis regression models and its applications to integrative genomics analysis”, Genetic Epidemiology.2017, Jan;41(1):70-80

2016

Tignor, P. Wang&, N. Genes, L. Rogers, S. G. Hershman, E. R. Scott, M Zweig, Y. Chan, Eric Schadt, “Methods for clustering time series data acquired from mobile health apps ”, Pac Symp Biocomputing 2016; 22:300-311.

Zhang, T. Liu, Z. Zhang, S. H. Payne, B. Zhang, J. E. McDermott, …, & the NCI CPTAC investigators (P. Wang), “Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer”, Cell, 2016 Jul 28;166(3):755-65

Fu, P. Wang&, A. Taguchi, CH Wong, Q. Zhang, A. Gazdar, S.M. Hanash, Q. Zhou, Z. Feng, “A statistical method for detecting differentially expressed SNVs based on next-generation RNA-seq data”, Biometrics, 2016 Jun 8. doi: 10.1111/biom.12548, PMCID:PMC5151178

Petralia, W. Song, Z. Tu, P. Wang&, “New Method for Joint Network Analysis Reveals Common and Different Coexpression Patterns among Genes and Proteins in Breast Cancer”, Journal of Proteomics Research 2016 Mar 4;15(3):743-54, ACS Editors’ Choice Article Selection, PMC4782177

Mertins, D. R. Mani, K. V. Ruggles, M. A. Gillette, K. R. Clauser, P. Wang, et. al., Steven A. Carr & the NCI CPTAC, “Proteogenomic connects somatic mutations to signaling in breast cancer”, Nature 2016 May 25;534(7605):55-62

2015

Chen C, Zhang Y, Loomis MM, Upton MP, Lohavanichbutr P, Houck JR, Doody DR, Mendez E, Futran N, Schwartz SM, Wang P. “Genome-wide loss of heterozygosity and DNA copy number aberration in HPV-negative oral squamous cell carcinoma and their associations with oral cancer-specific survival”. PLOS One. 2015, August, DOI: 10.1371.

Petralia, P. Wang, J. Yang, Z. Tu, “A General Framework of Integrative Random Forest for Gene Regulatory Network Inference”, Bioinformatics 2015, Jun; 15;31(12), i197-205. PMCID: PMC4542785

Bhatti, Y. Zhang, X. Song, K. Makar, C. Sather, K. Kelsey, A. Houseman, P. Wang, “Response to ‘Civil time ≠ biological time: Recent options for empirically testing possible effects of chronodisruption’”, Chronobiology International 2015 Jun; 32(5):699-700.

K. Teixeira, X. Wang, Y. Li, S. Ekholm-Reed, X. Wu, P. Wang, S.I Reed, “Cyclin E Deregulation Promotes Loss of Specific Genomic Regions”, Current Biology. 2015, 18; 25(10): 1327-33, PMID:25959964

Danaher, D. Paul, P. Wang, “Covariance-based analyses of biological pathways”, Biometrika, 2015 Sep 1; 102(3): 533–544. PMCID: PMC4581526

Auerbach J, Agne M, Fan R, Lo A, Lo S, Zheng T, and Wang P, “Identifying Regions of Disease Related Variants in Admixed Populations with the Summation Partition Approach”, BMC Proc.(GAW19), 2015, 9 Suppl 8: S12

Bhatti, Y. Zhang, X. Song, K. Makar, C. Sather, K. Kelsey, A. Houseman, P. Wang, “Nightshift Work and Genome-wide DNA Methylation”, Chronobiology International 2015 Feb;32(1):103-12.

Wang, Q. Li, H. Zhang, Y. Zhang, L. Hsu, P. Wang&, “A regularized multivariate regression approach for eQTL analysis”, Statistics in Biosciences.2015, 7 (1), 129-146; PMC4465818

2014

Cheng, E. Levina, P. Wang and J. Zhu, “Sparse Ising Models with Covariates”, Biometrics. (2014) 70(4): 943-53 : PMCID:PMC4425428

L.S. Chen, R. Prentice, P. Wang&, “A penalized EM algorithm for multivariate Gaussian parameter estimation with non-ignorable missing data”. Biometrics (2014), 70(2):312-22 PMID:24471933, NIHMSID: 560470

Hu, S. Wang, P. Wang&, “Testing Gene-gene interactions in genome wide association studies”, Genetic Epidemiology (2014), Vol 38 (2), 123-34.

Danaher, P. Wang&, D. Witten, “The joint graphical lasso for inverse covariance estimation across multiple classes”. Journal of the Royal Statistical Society, Series B (2014), Vol 76(2), 373-397, PMCID: PMC4012833

J. Kennedy, S. E. Abbatiello, K. Kim, P. Yan, J. R. Whiteaker, C. Lin, J. Kim, Y. Zhang, X. Wang, R. G. Ivey, L. Zhao, H. Min, Y. Lee, E. G. Yang, C. Lee, P. Wang, M.-H. Yu, H. Rodriguez, Y. Kim, S. A. Carr, A. G. Paulovich, “Demonstration of the feasibility of an international effort to develop and distribute analytically validated Multiple Reaction Monitoring (MRM)-based assays to large suites of human proteins”, Nature Methods(2014) Feb;11(2):149-55. PMCID: PMC3922286.

 

D Liebler, B. Zhang, J. Wang, X. Wang, J. Zhu, Q.liu, Z.Shi, M.C. Chambers, …, P. Wang,… NCI CPTAC Network, “Proteogenomic characterization of human colon and rectal cancer”, Nature (2014) 513(7518): 382-387

2013

Li, L. Hsu, J. Peng and P. Wang&, “Bootstrap inference for network construction”. Annals of Applied Statistics 2013, 7(1), 391-417. PMCID:PMC3930359

Xu, P. Wang, Y. Liu, Y. Zhang, W. Fan, M. P. Upton, P. Lohavanichbutr, J. D. Houck, D. R. Doody, N. D. Futran, L. Zhao, S. M. Schwartz, C. Chen, E. Méndez, “Integrative genomics in combination with RNA interference identifies prognostic and functionally relevant gene targets associated with metastatic oral squamous cell carcinoma”. PLoS Genetics 2013, 9 (1), doi: 10.1371

Lohavanichbutr, E. Méndez, F. C. Holsinger,T. C. Rue, Y. Zhang, J. Houck, M. P. Upton, N. Futran, S. M. Schwartz, P. Wang, C. Chen, “A 13-gene signature prognostic of HPV-negative oral cavity cancer: discovery and external validation in a two-institution study”, Clinical Cancer Research, 2013, 19:1197.

2012

I. Milac, T. W. Randolph, P. Wang, “Analyzing LC-MS/MS data by spectral count and ion abundance: two case studies”. Statistics and Its Interface (Special issue on proteomics) 2012, 5 (1), 75-87. PMCID: PMC3806317

Whiteaker JR, Zhao L, Lin C, Yan P, Wang P, Paulovich AG., “Sequential multiplexed analyte quantification using peptide immunoaffinity enrichment coupled to mass spectrometry” Mol Cell Proteomics, 2012, 11(6):M111.015347.

Lohavanichbutr, J. Houck, D. R. Doody, P. Wang, E. Mendez, N. Futran, M. P. Upton, C. Holsinger, S. M. Schwartz, C. Chen, “Gene expression in uninvolved oral mucosa of OSCC patients facilitates identification of markers predictive of OSCC outcomes”. PLoS One. 2012; 7(9).

A. Serrano, C. Xu, Y. Liu, P. Wang, W. Fan, M. P. Upton, J. R Houck, P. Lohavanichbutr, L. P. Zhao, M. Kao and E. Méndez, “Integrative analysis in OSCC reveals three DNA copy number-driven miRNAs dysregulating target genes”. Academy of Otolaryngology — Head and Neck Surgery 2012 Sep; 147(3):501-8.

L. Thu, E. A. Vucic, R. Chari, W. Zhang, W. W. Lockwood, J.C. English, R. Fu, P. Wang, Z. Feng, C.E. MacAulay, A. F. Gazdar, S. Lam, W.L. Lam, “Lung adenocarcinoma of never smokers and smokers harbor differential regions of genetic alteration and exhibit different levels of genomic instability”. PLOS One 2012, 7(3):e33003.doi:10.1371.

Huang and P. Wang&, “Network based prediction models for genomics data”. Statistics in Biosciences (Special issue on network) 2012, 4(1), 47-65, PMCID: PMC3859188

Yan, P. Wang, M. Linden, B. S. Knudsen and T. Randolph, “Statistical Methods for Analyzing Tissue microarray Images — Algorithmic Scoring and Co-training”. Annals of Applied Statistics 2012, 6(3), 1280-1305, PMCID: PMC3441061

2011

Schoenherr RM, Kelly-Spratt KS, Lin C, Whiteaker JR, Liu T, Holzman T, Coleman I, Feng LC, Lorentzen TD, Krasnoselsky AL, Wang P, Liu Y, Gurley KE, Amon LM, Schepmoes AA, Moore RJ, Camp DG 2nd, Chodosh LA, Smith RD, Nelson PS, McIntosh MW, Kemp CJ, Paulovich AG. “Proteome and transcriptome profiles of a Her2/Neu-driven mouse model of breast cancer”, Proteomics Clin Appl, 2011, 5(3-4):179:88.

Wang, J. Peng, P. Wang, “SNP set analysis for detecting disease association using exon sequence data”. BMC Proceedings, 2011, 5(Suppl 9):S91. GAW17

L.S. Chen, R. Prentice, D. Paul, P. Wang&, “A Regularized Hotelling’s T2 test for pathway analysis in proteomics studies”. Journal of the American Statistics Association 2011, 106(496), 1345-1360, PMCID: PMC3755504

J.R. Whiteaker, C. Lin., J. Kennedy, L. Hou, M. Trute, I. Sokal, P. Yan, R. M. Schoenherr, L. Zhao, U. J. Voytovich, K.S. Kelly-Spratt, A. Krasnoselsky, P. Gafken, J. Hogan, L. Jones., P. Wang, L. Amon, M. W. Mcintosh, C. J. Kemp, and A. G. Paulovich, “A targeted proteomics-based pipeline for verification of biomarkers in plasma”, Nature Biotechnology 2011, 29, 625-634.

G. Ivey, H. D. Moore, U. J Voytovich, C. P. Thienes, T. D. Lorentzen, E. Pogosova-Agadjanyan, S. Frayo, V. K Izaguirre, S. J Lundberg, L. Hedin, K. Ray Badiozamani, A. N. Hoofnagle, D. L. Stirewalt, P. Wang, G. E. Georges, A. K. Gopal, and A. G. Paulovich. “Blood-based detection of radiation exposure in humans based on novel phospho-Smc1 ELISA assays”. Radiation Research 2011, 175(3):266-81

Wang, D. Chao, L. Hsu, “Learning oncogenic pathways from binary genomic instability data”, Biometrics 2011, 67(1) 164-173

2010

L. Prentice, S. Paczesny, A. Aragaki, L. M. Amon, L. Chen, S. J. Pitteri, M.McIntosh, P. Wang, J. Hsia, R. D. Jackson, J. E. Rossouw, J. E. Manson, K. Johnson, C. Eaton, S. M. Hanash, “Novel Proteins Associated with Risk for Coronary Heart Disease or Stroke among Postmenopausal Women Identified by In-Depth Plasma Proteome Profiling”. Genome Medicine 2010, 2:48

Xu, Y. Liu, P. Wang, W. Fan, M. P. Upton, P. Lohavanichbutr, J. R. Houck, D. R. Doody, N. D. Futran, L. P. Zhao, S. M. Schwartz, C. Chen, E. Méndez, “Integrative analysis of DNA copy number and gene expression in metastatic oral squamous cell carcinoma identifies genes associated with poor survival”. Molecular Cancer, 2010, 9:143

Jin, J. Peng, P. Wang, “A Generalized Fourier Approach to Estimating the null parameters and Proportion of non-null Effects in Large-Scale Multiple Testing”, J. of Statistical Research (special issue in honor of Prof. Efron) 2010, 44(1). NIHMS551871; PMCID:PMC3928715

H. Kim, K.A. Kwei, L. Girard, K. Salari, J. Kao, M. P. Gengelbach, P. Wang, T. H. Boussard, A. F. Gazdar, I. Petersen, J. D. Minna, and J. R. Pollack, “Genomic and functional analysis identifies CRKL as an oncogene amplified in lung cancer” Oncogene 2010, 11;29(10), 1421-30

G. Paulovich, D. D. Billheimer*, A. L. Ham*, L. V. Montoto*, P. A. Rudnick*, D. L. Tabb*, P. Wang*, and the NCI Clinical Proteomic Technology Assessment for Cancer (CPTAC) Unbiased Discovery Working Group,Inter-laboratory study characterizing a yeast performance standard for benchmarking LC-MS Platform Performance”, Mollecular and Cellular Proteomics2010, 9:242-254

A. Rudnick, K. R. Clauser, L. E. Kilpatrick, D. V. Tchekhovskoi, P. Neta, D. D. Billheimer, R. K. Blackman, D. M. Bunk, H. L. Cardasis, S. A. Carr, A. L. Ham, C. R. Kinsinger, T. A. Neubert, A. G. Paulovich, B. Schilling, C. Spiegelman, D. L. Tabb, T. J. Tegler, M. Wang, P. Wang, J. R. Whiteaker, L. J. Zimmerman, D. C. Liebler, S. E. Stein and the CPTAC Network, “Performance Metrics for Evaluating Liquid Chromatography-Tandem Mass Spectrometry Systems in Shotgun Proteomics”, Mollecular and Cellular Proteomics2010 9:225-241.

Tabb DL, Vega-Montoto L, Rudnick P, Variyath A, Ham AJ, Bunk DM, Kilpatrick L, Billheimer D, Blackman R, Cardasis HL, Carr SA, Clauser KR, Jaffe JD, Kowalski K, Neubert TA, Regnier F, Schilling B, Tegeler T, Wang M, Wang P, Whiteaker JR, Zimmerman L, Fisher SJ, Gibson BW, Kinsinger CR, Mesri M, Rodriguez H, Stein SE, Tempst P, Paulovich A, Liebler DC, Spiegelman C.,“Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography-Tandem Mass Spectrometry.J Proteome Res. 2010 Feb 5;9(2): 761-76

Peng, J. Zhu, A. Bergamaschi, W. Han, D.-Y. Noh, J. R. Pollack, P. Wang&, “Regularized Multivariate Regression for Identifying Master Predictors with Application to Integrative Genomics Study of Breast Cancer”, Annals of Applied Statistics, 2010, 4 (1), 53-77, PMCID: PMC3905690