Recent Publications

2023

Lundeen RA, Kennedy JJ, Murillo OD……,Wang P, Whiteaker JR, Paulovich AG. “Monitoring both extended and tryptic forms of stable isotope-labeled standard peptides provides an internal quality control of proteolytic digestion in targeted mass spectrometry-based assays.” Mol Cell Proteomics. 2023 Jul 19:100621. Epub ahead of print. PMID: 37478973.

Y. Li, Y. Dou, F. D. Leprevost, Y. Geffen, A. Calinawan, F. Aguet, Y. Akiyama, S. Anand, C. Birger, S. Cao……, P. Wang, A. I. Robles, B. Zhang, S. H. Payne, Clinical Proteomic Tumor Analysis Consortium “Proteogenomic Data and Resources for Pan-Cancer Analysis”, Cancer Cell. 2023 Imprint

S. Chowdhury, J. J. Kennedy, R. G. Ivey, O. D. Murillo, N. Hosseini, X. Song, F. Petralia, A. Calinawan, S. R. Savage……S. C. Mok, S. H. Kaufmann, C. Drescher, M. Cieslik, P. Wang^&, M. J. Birrer^&, Amanda G. Paulovich^&, and Clinical Proteomic Tumor Analysis Consortium (CPTAC) Coaborators, “Proteogenomic analysis of chemo-refractory high grade serous ovarian cancer”, Cell. 2023 Imprint

Y. Dou, Lizabeth Katsnelson, Marina A. Gritsenko^*, Yingwei Hu, Boris Reva, Runyu Hong, Yi-Ting Wang, Iga Kolodziejczak, Rita Jui-Hsien Lu, Chia-Feng Tsai,, ……, Wang P,……, Matthew L. Anderson, Karin D. Rodland, Bing Zhang, Tao Liu, David Fenyö, Clinical Proteomic Tumor Analysis Consortium. Proteogenomic insights suggest druggable pathways in endometrial carcinoma. Cancer Cell. 2023 June Imprint.

X. Song, J. Ji, J. H. Rothstein, S. E. Alexeeff, L. C. Sakoda, A. Sistig, N. Achacoso, E. Jorgenson, A. S. Whittemore, R. J. Klein, L. A. Habel, P. Wang^&, and W. Sieh^&, “MiXcan: a Framework for Cell-Type-Aware Transcriptome-Wide Association Studies with an Application to Breast Cancer”, Nature Communication. 14, 377 (2023). 2023 Jan 23;14(1):377. doi: 10.1038/s41467-023-35888-4. PMID: 36690614; PMCID: PMC9871010.

L Lih TM, Dhanasekaran SM, Mannan R, Chen L, Cieslik M, Wu Y, Lu RJ, Clark DJ, Kołodziejczak I, Hong R, Chen S, ……, Wang P,……,Zhang H, Ding L; Clinical Proteomic Tumor Analysis Consortium. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness. Cancer Cell. 2023 Jan 9;41(1):139-163.e17. PMID: 36563681; PMCID: PMC9839644.

J. R. Whiteaker, L. Zhao, R. M. Schoenherr, D. Huang, R. A. Lundeen, U. Voytovich, J. J. Kennedy, R. G. Ivey, …, P. Wang and A. G. Paulovich; “A multiplexed assay for quantifying immunomodulatory proteins supports correlative studies in immunotherapy clinical trials.” Frontiers in Oncology. 2023 May 2;13:1168710. doi: 10.3389/fonc.2023.1168710. PMID: 37205196; PMCID: PMC10185886.

2022

Chen H, Fan S, Stone J, Thompson DJ, Douglas J, Li S, Scott C, Bolla MK, Wang Q, Dennis J, Michailidou K, Li C, …, Wang P, …, Tamimi RM, Vachon CM, Lindström S. “Genome-wide and transcriptome-wide association studies of mammographic density phenotypes reveal novel loci.” Breast Cancer Res. 2022 Apr 12;24(1):27. doi: 10.1186/s13058-022-01524-0. PMID: 35414113; PMCID: PMC9006574.

Kennedy JJ, Whiteaker JR, Ivey RG, Burian A, Chowdhury S, Tsai CF, Liu T, Lin C, Murillo OD, Lundeen RA, Jones LA, Gafken PR, Longton G, Rodland KD, Skates SJ, Landua J, Wang P, Lewis MT, Paulovich AG. “Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma.” Anal Chem. (2022) Jul 12;94(27):9540-9547. PMID: 35767427.

S. Chowdhury, R. Wang, Q. Yu, C. J. Huntoon, L. M. Karnitz, S. H. Kaufmann, S. P. Gygi, Michael J. Birrer, Amanda G. Paulovich, J Peng^&, P. Wang^&, “DAGBagM: Learning directed acyclic graphs of mixed variables with an application to identify prognostic protein biomarkers in ovarian cancer”, BMC Bioinformatics, (2022) Aug 5;23(1):321. doi: 10.1186/s12859-022-04864-y. PMID: 35931981; PMCID: PMC9354326.

Lee, N. Tignor, W. Cowell, E. Colicino, A. Bozack, A. Baccarelli, P. Wang^♦, R. Wright, “Associations between antenatal maternal asthma status and placental DNA methylation”, Placenta (2022) Aug;126:184-195. doi: 10.1016/j.placenta.2022.06.008. Epub 2022 Jul 3. PMID: 35858526; PMCID: PMC9679966.

Song X, Ji J, Wang P^&, “iProMix: A mixture model for studying the function of ACE2 based on bulk proteogenomic data”, Journal of the American Statistical Association (2022), PMCID: PMC9871010

Li, S., Wang, Z., Vieira, L.A…, Wang P, …, E. E. Schadt, L Li, “Improving preeclampsia risk prediction by modeling pregnancy trajectories from routinely collected electronic medical record data.” NPJ Digit. Med. 5, 68 (2022). https://doi.org/10.1038/s41746-022-00612-x

2021

Leader AM, Grout JA, Maier BB, Nabet BY, Park MD, Tabachnikova A, Chang C, …, Flores R, Wang P, Müller S, Mellman I, Beasley MB, Salmon H, Rahman AH, Marron TU, Kenigsberg E, Merad M. “Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification.” Cancer Cell. 2021 Dec 13;39(12):1594-1609.e12. doi: 10.1016/j.ccell.2021.10.009. PMID: 34767762; PMCID: PMC8728963.

Livanos AE, Jha D, Cossarini F, Gonzalez-Reiche AS, Tokuyama M, Aydillo T, Parigi TL, Ladinsky MS, Ramos I, Dunleavy K, Lee B, …Wang P, … Petralia F, van Bakel H, Garcia-Sastre A, Mehandru S. “Intestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms.” Gastroenterology. 2021 Jun;160(7):2435-2450.e34. doi: 10.1053/j.gastro.2021.02.056. Epub 2021 Mar 4. PMID: 33676971; PMCID: PMC7931673.

Lewis S, Cedillo MA, Lee KM, Bane O, Hectors S, Ma W, Wang P, Stocker D, Morris DV, Pinato D, Sung M, Marron T, Schwartz M, Taouli B. “Comparative assessment of standard and immune response criteria for evaluation of response to PD-1 monotherapy in unresectable HCC”, Abdom Radiol (NY). 2021 Dec 29. doi: 10.1007/s00261-021-03386-0. Epub ahead of print. PMID: 34964909.

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 Dec 21;2(12):100471. doi: 10.1016/j.xcrm.2021.100471.

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 Nov;40(46):6395-6405. doi: 10.1038/s41388-021-02055-2. Epub 2021 Oct 13. PMID: 34645978; PMCID: PMC8602037.

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.  

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-S81Han 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 Epidemiology, 2018 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)

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