Publications

Recent Publications


2021

D. Huang, S. Chowdhury, H. Wang, S. R. Savage, R. G. Ivey, J. J. Kennedy, Jeffrey R. Whiteaker, Chenwei Lin, Xiaonan Hou, Ann L. Oberg, Melissa C. Larson, Najmeh Eskandari, Davide A. Delisi, Saverio Gentile, Catherine J. Huntoon, Uliana J. Voytovich, Zahra J. Shire, Qing Yu, Steven P. Gygi, Andrew N. Hoofnagle, Zachary T. Herbert, Travis D. Lorentzen, Anna Calinawan, Larry M Karnitz, S. John Weroha, Scott H. Kaufmann, Bing Zhang,Pei Wang&, Michael J. Birrer&, Amanda G. Paulovich&, “Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory high grade serous ovarian cancer”, Cell Medicine Report 2021 imprint

D. Huang, S. R. Savage, A. P. Calinawan, C. Lin, B. Zhang, P. Wang, T K. Starr, M. J. Birrer, A. G. Paulovich, “A highly annotated database of genes associated with platinum resistance in cancer”, Oncogene 2021 imprint

Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG., “Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues”.Clin Chem. 2021 Jun 17 doi: 10.1093/clinchem/hvab047. PMID: 34136904.

S. Tuminello, F. Petralia, R. Veluswamy, P. Wang, R. Flores, E. Taioli, “Prognostic Value of the Tumor Immune Microenvironment for Early-Stage, Non-small Cell Lung Cancer”, Am J Clin Oncol. 2021 May 19. doi: 10.1097/COC.0000000000000832.

S. Yoo, Z. Shi, B. Wen, S. Kho, R. Pan, H. Feng, H. Chen, A. Carlsson, P. Edén, W. Ma, M. Raymer, E. J. Maier, Z. Tezak, E. Johanson, D. Hinton, H. Rodriguez, J. Zhu, E. Boja, P. Wang, B Zhang, “A Community Effort to Identify and Correct Mislabeled Samples in Proteogenomic Studies”, Patterns 2021, Volume 2, Issue 5.

S. Satpath, P. M. Jean Beltran, S. R. Savage, K. Krug, F. Petralia, C. Kumar-Sinha, Y. Dou, B. Reva, S. V. Vascaikar, M. H. Kane, …… Pei Wang, Steve A. Carr, B. Zhang, D.R. Mani, M. A. Gillette, CPTAC, “Systems-wide analysis of proteogenomic variation in lung squamous cell carcinoma”, Cell 2021, DOI:https://doi.org/10.1016/j.cell.2021.07.016

Xiaoyu Song, Jiayi Ji, Boris Reva, Himanshu Joshi, Anna Pamela Calinawan, Madhu Mazumdar, Juan P. Wisnivesky, Emanuela Taioli, Pei Wang, Rajwanth R. Veluswamy, “Post-Anticoagulant D-dimer is a Highly Prognostic Biomarker of COVID-19 Mortality”, ERJ Open Research 2021, DOI: 10.1183/23120541.00018-2021

L. Wang, Alla Karpova, Marina A. Gritsenko, Jennifer E. Kyle, Song Cao, Yize Li, Dmitry Rykunov, Antonio Colaprico, Joseph H. Rothstein, Runyu Hong, Vasileios Stathias, MacIntosh Cornwell, Francesca Petralia,… Pei Wang…, T. Liu, L. Ding, CPTAC “Proteogenomic and metabolomics characterization of human glioblastoma”, Cancer Cell 2021, Apr 12;39(4):509-528.e20

D. Yan, Y. Xu and Pei Wang,“Estimating the Number of Infected Cases in COVID-19 2 Pandemic”, Journal of Data Science 2021 Imprint; https://arxiv.org/abs/2005.12993

Chen Huang, Lijun Chen, Sara R. Savage, Rodrigo Vargas Eguez, Yongchao Dou, Yize Li, Felipe da Veiga Leprevost, Eric J. Jaehnig, Jonathan T. Lei, Bo Wen, Michael Schnaubelt, Karsten Krug, Xiaoyu Song, … , Pei Wang,…, H. Zhang, B. Zhang, CPTAC, “Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma”, Cancer Cell 2021, Mar 8;39(3):361-379.e16.


2020

Petralia, N. Tignor, B. Reva, M. Koptyra, S. Chowdhury, D. Rykunov, A. Krek, W. Ma, J. Ji, X. Song, P. Raman, Y. Zhu, J. R. Whiteaker, A. Colaprico, A. Calinawan, S. Kalayci, Z. H. Gümüş … A. C Resnick&, Phillip B. Storm&, Brian R. Rood&, Pei Wang&, Children’s Brain Tumor Tissue Consortium and Clinical Proteomic Tumor Analysis Consortium, “Integrated Proteogenomic Characterization across Major Histological types of Pediatric Brain Cancer”, Cell 2020 Dec 20;S0092-8674(20)31451-3. doi: 10.1016/j.cell.2020.10.044.

Li, A. Aue, D. Paul, J. Peng, P. Wang, “An adaptable generatlization of Hotelling’s T^2 test in high dimension”, Annual of Statistics Volume 48, Number 3 (2020), 1815-1847.

D. Beckmann*, W-J Lin*, M. Wang*, A. T. Cohain, P. Wang, W. Ma, Y.-C. Wang, C. Jiang, S. Hariharan, G. M. Belbin, A. Levey, N. Seyfried, E. Dammer, D. Duong, J. Lah, M. Audrain, J.-Vianney Haure-Mirande, B. Shackleton, A. W. Charney, E. Kenny, J. Zhu, V. Haroutunian, S. Gandy, Z. Tu, M. Ehrlich, B. Zhang, S. R. Salton, E. E. Schadt, “Multiscale causal network models identify VGF as an Alzheimers disease gene”. Nature Communication. 2020 Aug 7;11(1):3942. doi: 10.1038/s41467-020-17405-z.

M. Yang, F. Petralia, Z. Li, X. Song, S. Kim., H. Li, H. Yu, B. Lee, S. Park, E. Heo, J. Kaczmarczyk, P. Stępniak, M. Warchoł, T. Yu, NCI-CPTAC-DREAM Consortium, P Boutros, Y. Guan, J. Kang, H. Rodriguez, G. Stolovitzky, P. Wang, D. Fenyo, J. Saez-Rodriguez, “Community Assessment of the predictability of cancer protein and phosphoprotein levels from Genomics and Transcriptomics”, Cell Systems 2020 Aug 26; 11, 186–195.  

A. P. Calinawan, X. Song, J. Ji, S M. Dhanasekaran, F. Petralia, P. Wang&, Boris Reva&, “ProTrack: An Interactive Multi-Omics Data Browser for Proteogenomic Studies”, Proteomics 2020 Jun 8;e1900359. doi: 10.1002/pmic.201900359.

S. Kalayci, F. Petralia, P. Wang and Z. H. Gümüş,*ProNetView-ccRCC: A web-based portal to interactively explore clear cell renal cell carcinoma proteogenomics networks”, Proteomics 2020 May 2;e2000043. doi: 10.1002/pmic.202000043.

M.A. Gillette, S. Satpathy, S. Cao, S. M. Dhanasekaran, S. Vasaikar, K. Krug, F. Petralia, …, P. Wang, A. Nesvizhskii, L. Ding, D.R. Mani, S. A. Carr, and Cancer Proteogenomic Tumor Analysis Consortium, “Proteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma”, Cell 2020 Jul 9;182(1):200-225.e35. doi: 10.1016/j.cell.2020.06.013.

J. Torres, F. Petralia, T. Sato, P. Wang, S. Telesco, R. S. Choung, R. Strauss, X. Li, R. M. Laird, R. Gutierrez, C. K. Porter, S. Plevy, F. Princen, J. A. Murray, M. S. Riddle, J.-F. Colombel, “Serum Biomarkers Identify Patients Who Will Develop Inflammatory Bowel Diseases Up to 5 y Before Diagnosis”, Gastroenterology 2020 Mar 9; S0016-5085 (20) 30327-9. doi: 10.1053/j.gastro.2020.03.007.

Y. Dou, E. A. Kawaler, D. Cui Zhou, M. A. Gritsenko, C. Huang, L. Blumenberg, A. Karpova, V. A. Petyuk, S. R. Savage, S. Satpathy, W. Liu, Y. Wu, …, Pei Wang, …, K. D. Rodland, L. Ding, B. Zhang, T. Liu, D. Fenyö, and Cancer Proteogenomic Tumor Analysis Consortium. “Proteogenomic Characterization of Endometrial Carcinoma”, Cell 2020 Feb 20;180(4):729-748, PMID: 32059776

2019

S. J. Hectors, M. Cherny, K. K. Yadav, A. T. Beksaç, H. Thulasidass, S. Lewis, E. Davicioni, P. Wang, A. K. Tewari, B. Taouli, “Radiomics Features Measured with Multiparametric Magnetic Resonance Imaging Predict Prostate Cancer Aggressiveness” J Urol. 2019 Sep;202(3):498-505.

Chen C, Lohavanichbutr P, Zhang Y, Houck JR, Upton MP, Abedi-Ardekani B, Agudo A, Ahrens W, Alemany L, Anantharaman D, Conway DI, Futran ND, Holcatova I, Günther K, Hansen BT, Healy CM, Itani D, Kjaerheim K, Monroe MM, Thomson PJ, Witt BL, Nakoneshny S, Peterson LA, Schwartz SM, Zarins KR, Hashibe M, Brennan P, Rozek LS, Wolf G, Dort JC, Wang P.  “Prediction of survival of HPV16-negative, p16-negative oral cavity cancer patients using a 13-gene signature: A multicenter study using FFPE samples.” Oral Oncology, 2019,10; 100:104487

D. J. Clark, S. M. Dhanasekaran, F. Petralia, J. Pan, X. Song, Y. Hu, F. Veiga Leprevost, B. Reva, T.-S. M. Lih,…, M. Cieslik&, D. W. Chan&, A. I. Nesvizhskii&, P. Wang&, H. Zhang&, and the NCI CPTAC Investigators. “Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma”, Cell 2019 Oct 31;179(4):964-983.e31.

Q. Gao, H. Zhu, L. Dong, W. Shi, R Chen, Z. Song, C. Huang, J. Li, X. Dong, Y. Zhou, Q. Liu, L. Ma, X. Wang, J. Zhou, Y. Liu, E. Boja, A. I. Robles, W. Ma, P. Wang, Y. Li, L. Ding, B. Wen, B. Zhang, H. Rodriguez, D. Gao, H. Zhou, J. Fan, “Integrated Proteogenomic Characterization of HBV-related Hepatocellular Carcinoma”, Cell 2019 Oct 3; 179 (2): 561-577

X. Song, J. Ji, K. J. Gleason, J. A. Martignetti, L. Chen, P. Wang&, “Insights into impact of DNA copy number alterations and methylations on proteogenomics landscape in human ovarian cancer via a multi-omics integrative analysis” Molecular & Cellular Proteomics, 2019, 18 (8 suppl 1) S52-S65

W. Ma, L.S. Chen, S. W. Han, C. Lin, A. Paulovich, H. Zhong, P. Wang&, “Integrative Proteo-genomic Analysis to Construct CNA-protein Regulatory Map in Breast and Ovarian Tumors”, Molecular & Cellular Proteomics 2019, 18 (8 suppl 1) S66-S81

Han SW, Park S, Zhong H, Ryu E, Wang P, Jung S, Lim J, Yoon J and Kim S (2019). “Estimation of joint directed acyclic graphs with lasso family for gene networks.” Communications in Statistics – Simulation and Computation 2019, 1(15). https://doi.org/10.1080/03610918.2019.1618869

S. Tuminello, R. Veluswamy, W. Lieberman-Cribbin, S. Gnjatic, F. Petralia, P. Wang, R. Flores, E. Taioli, “Prognostic value of immune cells in the tumor microenvironment of early-stage lung cancer: a meta-analysis”, Oncotarget 2019; 10:7142-7155.


2018

Lohavanichbutr, Y. Zhang, P. Wang, H. Gu, G. Nagana Gowda, D. Djukovic, M. F. Buas, D. Raftery, C. Chen, “Salivary metabolomics profiling distinguishes patients with oral cavity squamous cell carcinoma from normal controls”, PLoS One, 2018,13(9)

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 precision FDA 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”, Epigenetics 2018 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 Genomics 2018 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 2019 Oct; 20(4): 648–665

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 Epidemiology2018 Jul;42(5):480-487.

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 Research 2018 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