{"id":95,"date":"2017-06-03T23:52:00","date_gmt":"2017-06-03T23:52:00","guid":{"rendered":"http:\/\/labs.icahn.mssm.edu\/pei-wang-lab\/?page_id=95"},"modified":"2026-09-15T14:39:38","modified_gmt":"2026-09-15T14:39:38","slug":"publications","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/pei-wang-lab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
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Recent Publications<\/strong><\/h2>\n

Google Scholar<\/a><\/p>\n

2026<\/u><\/em><\/strong><\/p>\n

F. Petralia, A. Krek, A. P. Calinawan, D. Charytonowicz, R. Sebra, S. Feng, S. Gosline, P. Pugliese, A. G. Paulovich, J. J. Kennedy, M. Ceccarelli, P. Wang<\/strong>\u00a0\u201cBayesDeBulk: A Flexible Bayesian Algorithm for the Deconvolution of Bulk Tumor Data\u201d, JASA<\/u><\/em> 2026 (under 2nd<\/sup> revision)<\/p>\n

J. Gong, F. Petralia, M. V. Ruiz Cuevas, N. Tigno, R. Jain, M. A. Gritsenko, \u2026\u2026, M. P. Cieslik, T. Liu, P. Wang<\/strong>, Clinical Proteomic Tumor Analysis Consortium, \u201c<\/strong>A comprehensive proteogenomic, immunopeptidomic, and metabolomic atlas decodes immunogenicity in cutaneous melanoma\u201d, Cancer Discovery<\/u><\/em> 2026 (under revision)<\/p>\n

S. Chowdhury, K. Abdollahi, F. Petralia, J. J. Kennedy, J. Gong, W. Ma, \u2026\u2026, T. Liu, M. P. Cieslik, P. Wang<\/strong>, D. Davar, and A. G. Paulovich \u201c<\/strong>Identification of Proteomic Subtypes with Differential Responses to Immune Checkpoint Inhibition in Melanoma\u201d, Cancer Clinical Research<\/u><\/em> 2026 (under revision)<\/p>\n

J. R Bloom, N. Tignor; T. Van Vleck, D. P. Mendoza, S. Caroline Tavolacci, O. Fankuchen, \u2026\u2026, R. M. Samstein. P. Wang<\/strong>, R. R. Veluswamy, \u201cNatural Language Processing-Based Model to Predict Radiation Pneumonitis in Patients with Locally Advanced Non-Small Cell Lung Cancer Undergoing Chemoradiotherapy\u201d eClinicalMedicine<\/u> <\/em>2026 (imprint)<\/p>\n

Chu SA et.al., \u201cIntegrated proteogenomic and metabolomic profiling of acute myeloid leukemias to identify molecular subtypes and associated therapy targets.\u201d Nat Cancer<\/u><\/em>. 2026 Jun;7(6):993-1015. doi: 10.1038\/s43018-026-01175-6. Epub 2026 Jun 12. PMID: 42286338; PMCID: PMC13309276. (CPTAC consortium author)<\/p>\n

A.N. Lund, B.H. Kopell, N. Golestani, E. Vornholt,\u2026, P. Wang<\/strong>,\u2026, E. Schadt, A. W. Charney, N. D. Beckmann, \u201cEstablishing the relationship between brain cellular senescence and brain structure.\u201d Cell.<\/u><\/em> 2026, 189, 511-527.e17.<\/p>\n

Wang Y et. al. Clinical Proteomic Tumor Analysis Consortium. \u201cA 15-layer multi-omics analysis of gastric cancer ecotypes provides therapeutic insights\u201d. Cell Report Medicine<\/u><\/em>. 2026 Apr 20:102756. doi: 10.1016\/j.xcrm.2026.102756. Epub ahead of print. PMID: 42013851.<\/p>\n

Fu Z, Song Y, Liu F, Chen L, Cai S, Cui P, Wang G, Xie W, Zhang S, Ding L, Wang P,<\/strong> Zhang B, Rodriguez H, Feng F, Zhang X, Gong W, Gao Q, Gao D, Zhou H, Fan J. \u201cIntegrative proteogenomic analysis provides molecular insights and clinical significance in gallbladder cancer.\u201d Cancer Cell<\/u><\/em>. 2026 Feb 9;44(2):405-423.e13. doi: 10.1016\/j.ccell.2025.12.014. Epub 2026 Jan 8. PMID: 41512870.<\/p>\n

N. L. Tignor, M. Koptyra, S. Chowdhury, F. Petralia, M. A. Gritsenko, W. Ma, \u2026\u2026, A. Resnick, B. R. Rood, P. Wang<\/strong>,<\/strong> PC4C, CBTN and CPTAC \u201c<\/strong>Proteogenomic Analysis of Pediatric and AYA High-Grade Glioma Reveals Age- and Sex-Dependent Biology and Candidate Kinase Targets\u201d, Cell Report Medicine<\/u><\/em> 2026 (imprint)<\/p>\n<\/div>\n

2025<\/u><\/em><\/strong><\/p>\n

Geng Z, Wafula E, Corbett RJ, Zhang Y, Jin R, Gaonkar KS, Shukla S, \u2026\u2026, Wang P<\/strong>, Taylor D, Rokita JL. The Open Pediatric Cancer Project. Gigascience<\/u><\/em>. 2025 Jan 6;14:giaf093. doi: 10.1093\/gigascience\/giaf093. PMID: 40891528; PMCID: PMC12402770.<\/p>\n

Song X, Chavez-Fuentes JC, Ma W, Fu W, Shin SC, Wang P<\/strong>, Yuan GC. \u201csCCIgen: a high-fidelity spatially resolved transcriptomics data simulator for cell-cell interaction studies.\u201d Genome Biol.<\/u><\/em> 2025 Oct 15;26(1):354. doi: 10.1186\/s13059-025-03762-9. PMID: 41094512; PMCID: PMC12522593.<\/p>\n

M. Rodrigues et.al. \u201cPrecision proteogenomics reveals pan-cancer impact of germline variants\u201d, Cell<\/u><\/em>. 2025 May 1;188(9):2312-2335.e26. doi: 10.1016\/j.cell.2025.03.026. PMID: 40233739. (CPTAC consortium author)\u00a0<\/strong><\/p>\n

X. Song, Y. Shang, M. E. Ehrlich, P. Roussos, GC Yuan, P. Wang<\/strong>, \u201cQuadST identifies cell-cell interaction-changed genes in spatially resolved transcriptomics data\u201d, Genome Research<\/u><\/em>, 2025, 2025 Jun 23:gr.279859.124. doi: 10.1101\/gr.279859.124. PMID: 40550690.<\/p>\n

S. Satpathy, N. M. Clark, Y. Chen, N. Hosseini, Y. Chang, Y. Hsiao, J. T. Lei, F. Petralia, \u2026, P. Wang<\/strong>, \u2026, Y. Chen, M. A. Gillette, Taiwan Cancer Moonshot Program, Clinical Proteomic Tumor Analysis Consortium, \u201cIntegrative Analysis of Lung Adenocarcinoma Across Diverse Ethnicities and Exposures\u201d, Caner Cell<\/u><\/em>, 2025, April (Imprint)<\/p>\n

I. K.-Guglas, R. L.S. Sim\u00f5es, E. S. Santos, E. G. Demicco, \u2026, P. Wang<\/strong>, \u2026, T. M. Malta, M. Wiznerowicz, \u201cProteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets\u201d, Cell Genomics<\/u><\/em>, 2025, Feb<\/p>\n

A. Nandy, F. Petralia, C. Porter, S. Elledge,\u2026, P. Wang<\/strong>,\u2026, J. F. Colombel, S. B. Snapper, Epstein-Barr Virus (EBV) Exposure Precedes Crohn`s Disease Development, Gastroenterology<\/u><\/em>, 2025, Jan<\/p>\n

S. Ji, L. Cao, J. Gao, Y. Du, Z. Ye, X. Lou, F. Liu, Y. Zhang,\u2026, P. Wang<\/strong>, \u2026, D. Gao, G. Jin, H. Zhou, J. Wu, and X. Yu, Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors unravels clinically relevant subgroups, Cancer Cell<\/u><\/em>, 2025, Jan (Imprint)<\/p>\n

\u00a0<\/strong>S. Chowdhury, S. Ferri-Borgogno, P. Yang, W. Wang, J. Peng, S. C Mok, and P. Wang, <\/strong>Learning directed acyclic graphs for ligands and receptors based on spatially resolved transcriptomic analysis of ovarian cancer, Briefing Bioinformatics<\/u><\/em>. 2025 Mar 4;26(2):bbaf085. doi: 10.1093\/bib\/bbaf085. PMID: 40062614; PMCID: PMC11891659.<\/p>\n

2024<\/u><\/em><\/strong><\/p>\n

Naru J, Othus M, Lin C, Biernacki MA, Bleakley M, Chauncey TR, \u2026, Wang P<\/strong>, Whiteaker JR, Willman CL, Wu F, Paulovich AG, Stirewalt DL. Proteogenomic characterization of highly enriched viable leukemic blasts in acute myeloid leukemia: A SWOG report. EJHaem<\/u><\/em>. 2024 Oct 25;5(6):1243-1251. doi: 10.1002\/jha2.1041. PMID: 39691254; PMCID: PMC11647701.<\/p>\n

Deng EZ, Marino GB, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P<\/strong>, Ma’ayan A. Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics. Cell Rep Methods<\/u><\/em>. 2024 Aug 19;4(8):100839. doi: 10.1016\/j.crmeth.2024.100839. Epub 2024 Aug 9. PMID: 39127042; PMCID: PMC11384097.<\/p>\n

Liu J, Cao S, Imbach KJ, Gritsenko MA, Lih TM, Kyle JE, Yaron-Barir TM, Binder ZA, Li Y, Strunilin I, Wang YT, Tsai CF, Ma W, Chen L, \u2026 Wang P<\/strong>, \u2026, Ding L; Philadelphia Coalition for a Cure; Clinical Proteomic Tumor Analysis Consortium. Multi-scale signaling and tumor evolution in high-grade gliomas. Cancer Cell<\/u><\/em>. 2024 Jul 8;42(7):1217-1238.e19. doi: 10.1016\/j.ccell.2024.06.004. PMID: 38981438; PMCID: PMC11337243.<\/p>\n

C. Lin, R. M. Schoenherr, U. J. Voytovich, R. G. Ivey, J. J. Kennedy, J. R. Whiteaker, P. Wang<\/strong>, A. G. Paulovich, \u201cRNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage\u201d, Scientific Data<\/u><\/em>, (2024), 10.1038\/s41597-023-02829-1. PMID: 38177134<\/p>\n

F. Petralia, W. Ma, T. M. Yaron, F. Pia Caruso, N. Tignor, J. M. Wang, D. Charytonowicz, J. L. Johnson, E. M. Huntsman, A. Calinawan, \u2026\u2026, L. C. Cantley, A. Ma’ayan, A. J. Lazar, M. Ceccarelli, P. Wang<\/strong> and Clinical Proteomic Tumor Analysis Consortium. \u201cProteogenomics Characterization of Cancer Immunity\u201d, Cell<\/u><\/em>. (2024). Feb 12:S0092-8674(24)00064-3. doi: 10.1016\/j.cell.2024.01.027. PMID: 38359819.<\/p>\n

Feng S, Calinawan A, Pugliese P, Wang P<\/strong>, Ceccarelli M, Petralia F, Gosline SJC. Decomprolute is a benchmarking platform designed for multiomics-based tumor deconvolution. Cell Rep Methods<\/u><\/em>. 2024 Feb 26;4(2):100708. doi: 10.1016\/j.crmeth.2024.100708. PMID: 38412834; PMCID: PMC10921018.<\/p>\n

G.X. Li, L. Chen, Y. Hsiao, R. Mannan, Y. Zhang, J. Luo, F. Petralia, H. Cho, \u2026\u2026 P. Wang<\/strong>, \u2026 S. M. Dhanasekaran, H. Zhang, A. I. Nesvizhskii, Clinical Proteomic Tumor Analysis Consortium, Comprehensive Proteogenomic Characterization of Rare Kidney Tumors, Cell Report Medicine<\/u><\/em>, (2024), May 21;5(5):101547. doi: 10.1016\/j.xcrm.2024.101547. Epub 2024 May 3. PMID: 38703764; PMCID: PMC11148773.<\/p>\n

W. Ma, X. Song, G.C. Yuan, P. Wang<\/strong>, <\/strong>RECCIPE: a new framework assessing localized cell-cell interaction on gene expression in multicellular ST data, Frontiers in Genetics<\/u><\/em>, (2024), Jan 24;15:1322886. doi: 10.3389\/fgene.2024.1322886. PMID: 38327830; PMCID: PMC10847567.<\/p>\n

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2023<\/em><\/strong><\/span><\/p>\n<\/div>\n

Habel LA, Alexeeff SE, Achacoso N, Arasu VA, Gastounioti A, \u2026\u2026, Wang P<\/strong>, Kontos D, Sieh W. Examination of fully automated mammographic density measures using LIBRA and breast cancer risk in a cohort of 21,000 non-Hispanic white women. Breast Cancer Res<\/u><\/em>. 2023 Aug 6;25(1):92. doi: 10.1186\/s13058-023-01685-6. PMID: 37544983; PMCID: PMC10405373.<\/p>\n

Zhu H, Lin Y, Lu D, Wang S, Liu Y, Dong L, Meng Q, Gao J, Wang Y, Song N, Suo Y, Ding L, Wang P<\/strong>, Zhang B, Gao D, Fan J, Gao Q, Zhou H. Proteomics of adjacent-to-tumor samples uncovers clinically relevant biological events in hepatocellular carcinoma. Natl Sci Rev<\/u><\/em>. 2023 Jun 2;10(8):nwad167. PMID: 37575948; PMCID: PMC10416816.<\/p>\n

Ren Y, Hao L, Liu J, Wang P<\/strong>, Ding Q, Chen C, Song Y. Alterations in the Gut Microbiota in Pregnant Women with Pregestational Type 2 Diabetes Mellitus. mSystems<\/u><\/em>. 2023 Apr 27;8(2):e0114622. doi: 10.1128\/msystems.01146-22. Epub 2023 Feb 28. PMID: 36853013; PMCID: PMC10134876.<\/p>\n

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Lundeen RA, Kennedy JJ, Murillo OD\u2026\u2026,Wang P<\/strong>, Whiteaker JR, Paulovich AG. \u201cMonitoring 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.\u201d Mol Cell Proteomics<\/u><\/em>. 2023 Jul 19:100621. Epub ahead of print. PMID: 37478973.<\/p>\n

Y. Li, Y. Dou, F. D. Leprevost, Y. Geffen, A. Calinawan, F. Aguet, Y. Akiyama, S. Anand, C. Birger, S. Cao\u2026\u2026, P. Wang<\/strong>, A. I. Robles, B. Zhang, S. H. Payne, Clinical Proteomic Tumor Analysis Consortium \u201c<\/strong>Proteogenomic Data and Resources for Pan-Cancer Analysis\u201d, Cancer Cell<\/u><\/em>. 2023 Imprint<\/p>\n

S. Chowdhury, J. J. Kennedy, R. G. Ivey, O. D. Murillo, N. Hosseini, X. Song, F. Petralia, A. Calinawan, S. R. Savage\u2026\u2026S. C. Mok, S. H. Kaufmann, C. Drescher, M. Cieslik, P. Wang<\/strong>, M. J. Birrer, Amanda G. Paulovich, and Clinical Proteomic Tumor Analysis Consortium (CPTAC) Coaborators, \u201cProteogenomic analysis of chemo-refractory high grade serous ovarian cancer\u201d, Cell<\/u><\/em>. 2023 Imprint<\/p>\n

Y. Dou, Lizabeth Katsnelson, Marina A. Gritsenko*<\/sup>, Yingwei Hu, Boris Reva, Runyu Hong, Yi-Ting Wang, Iga Kolodziejczak, Rita Jui-Hsien Lu, Chia-Feng Tsai,, \u2026\u2026, Wang P<\/strong>,\u2026\u2026, Matthew L. Anderson, Karin D. Rodland, Bing Zhang, Tao Liu, David Feny\u00f6, Clinical Proteomic Tumor Analysis Consortium. Proteogenomic insights suggest druggable pathways in endometrial carcinoma. Cancer Cell<\/u><\/em>. 2023 June Imprint.<\/p>\n

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<\/strong>, and W. Sieh, \u201cMiXcan: a Framework for Cell-Type-Aware Transcriptome-Wide Association Studies with an Application to Breast Cancer\u201d, Nature Communication<\/u><\/em>. 14, 377 (2023). 2023 Jan 23;14(1):377. doi: 10.1038\/s41467-023-35888-4. PMID: 36690614; PMCID: PMC9871010.<\/p>\n

L Lih TM, Dhanasekaran SM, Mannan R, Chen L, Cieslik M, Wu Y, Lu RJ, Clark DJ, Ko\u0142odziejczak I, Hong R, Chen S, \u2026\u2026, Wang P<\/strong>,\u2026\u2026,Zhang H, Ding L; Clinical Proteomic Tumor Analysis Consortium. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness. Cancer Cell<\/u><\/em>. 2023 Jan 9;41(1):139-163.e17. PMID: 36563681; PMCID: PMC9839644.<\/p>\n

J. R. Whiteaker, L. Zhao, R. M. Schoenherr, D. Huang, R. A. Lundeen, U. Voytovich, J. J. Kennedy, R. G. Ivey, \u2026, P. Wang<\/strong> and A. G. Paulovich; \u201cA multiplexed assay for quantifying immunomodulatory proteins supports correlative studies in immunotherapy clinical trials.\u201d Frontiers in Oncology<\/u><\/em>. 2023 May 2;13:1168710. doi: 10.3389\/fonc.2023.1168710. PMID: 37205196; PMCID: PMC10185886.<\/p>\n

2022<\/em><\/strong><\/span><\/p>\n

Chen H, Fan S, Stone J, Thompson DJ, Douglas J, Li S, Scott C, Bolla MK, Wang Q, Dennis J, Michailidou K, Li C, \u2026, Wang P<\/strong>, \u2026, Tamimi RM, Vachon CM, Lindstr\u00f6m S. \u201cGenome-wide and transcriptome-wide association studies of mammographic density phenotypes reveal novel loci.\u201d Breast Cancer Res<\/u><\/em>. 2022 Apr 12;24(1):27. doi: 10.1186\/s13058-022-01524-0. PMID: 35414113; PMCID: PMC9006574.<\/p>\n

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<\/strong>, Lewis MT, Paulovich AG. \u201cInternal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma.\u201d Anal Chem<\/u><\/em>. (2022) Jul 12;94(27):9540-9547. PMID: 35767427.<\/p>\n

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<\/strong>, \u201cDAGBagM: Learning directed acyclic graphs of mixed variables with an application to identify prognostic protein biomarkers in ovarian cancer\u201d, BMC Bioinformatics, (2022) Aug 5;23(1):321. doi: 10.1186\/s12859-022-04864-y. PMID: 35931981; PMCID: PMC9354326.<\/p>\n

Lee, N. Tignor, W. Cowell, E. Colicino, A. Bozack, A. Baccarelli, P. Wang<\/strong>\u2666<\/sup><\/em><\/strong>, R. Wright, \u201cAssociations between antenatal maternal asthma status and placental DNA methylation\u201d, Placenta<\/u><\/em> (2022) Aug;126:184-195. doi: 10.1016\/j.placenta.2022.06.008. Epub 2022 Jul 3. PMID: 35858526; PMCID: PMC9679966.<\/p>\n

Song X, Ji J, Wang P<\/strong>, \u201ciProMix: A mixture model for studying the function of ACE2 based on bulk proteogenomic data\u201d, Journal of the American Statistical Association<\/u><\/em> (2022), PMCID:\u00a0PMC9871010<\/a><\/p>\n

Li, S., Wang, Z., Vieira, L.A\u2026, Wang P<\/strong>, \u2026, E. E. Schadt, L Li, \u201cImproving preeclampsia risk prediction by modeling pregnancy trajectories from routinely collected electronic medical record data.\u201d\u00a0NPJ Digit. Med<\/u><\/em>.\u00a05,\u00a068 (2022). https:\/\/doi.org\/10.1038\/s41746-022-00612-x<\/p>\n

2021<\/em><\/strong><\/span><\/p>\n

Leader AM, Grout JA, Maier BB, Nabet BY, Park MD, Tabachnikova A, Chang C, \u2026, Flores R, Wang P<\/strong>, M\u00fcller S, Mellman I, Beasley MB, Salmon H, Rahman AH, Marron TU, Kenigsberg E, Merad M. \u201cSingle-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification.\u201d Cancer Cell<\/u><\/em>. 2021 Dec 13;39(12):1594-1609.e12. doi: 10.1016\/j.ccell.2021.10.009. PMID: 34767762; PMCID: PMC8728963.<\/p>\n

Livanos AE, Jha D, Cossarini F, Gonzalez-Reiche AS, Tokuyama M, Aydillo T, Parigi TL, Ladinsky MS, Ramos I, Dunleavy K, Lee B, \u2026Wang P<\/strong>, \u2026 Petralia F, van Bakel H, Garcia-Sastre A, Mehandru S. \u201cIntestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms.\u201d Gastroenterology<\/u><\/em>. 2021 Jun;160(7):2435-2450.e34. doi: 10.1053\/j.gastro.2021.02.056. Epub 2021 Mar 4. PMID: 33676971; PMCID: PMC7931673.<\/p>\n

Lewis S, Cedillo MA, Lee KM, Bane O, Hectors S, Ma W, Wang P<\/strong>, Stocker D, Morris DV, Pinato D, Sung M, Marron T, Schwartz M, Taouli B. \u201cComparative assessment of standard and immune response criteria for evaluation of response to PD-1 monotherapy in unresectable HCC\u201d, Abdom Radiol (NY)<\/u><\/em>. 2021 Dec 29. doi: 10.1007\/s00261-021-03386-0. Epub ahead of print. PMID: 34964909.<\/p>\n

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<\/strong>, Michael J. Birrer, Amanda G. Paulovich, \u201cMultiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory high grade serous ovarian cancer\u201d, Cell Medicine Report<\/span> 2021 Dec 21;2(12):100471. doi: 10.1016\/j.xcrm.2021.100471. <\/em><\/p>\n

D. Huang, S. R. Savage, A. P. Calinawan, C. Lin, B. Zhang, P. Wang<\/strong>, T K. Starr, M. J. Birrer, A. G. Paulovich, \u201cA highly annotated database of genes associated with platinum resistance in cancer\u201d, Oncogene<\/span> 2021 Nov;40(46):6395-6405. doi: 10.1038\/s41388-021-02055-2. Epub 2021 Oct 13. PMID: 34645978; PMCID: PMC8602037.<\/em><\/p>\n

Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P<\/strong>, Hoofnagle AN, Baird GS, Paulovich AG., \u201cQuantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues\u201d.Clin Chem. <\/span> 2021 Jun 17 doi: 10.1093\/clinchem\/hvab047. PMID: 34136904.<\/em><\/p>\n

S. Tuminello, F. Petralia, R. Veluswamy, P. Wang<\/strong>, R. Flores, E. Taioli, \u201cPrognostic Value of the Tumor Immune Microenvironment for Early-Stage, Non-small Cell Lung Cancer\u201d, Am J Clin Oncol.<\/span> 2021 May 19. doi: 10.1097\/COC.0000000000000832.<\/em><\/p>\n

S. Yoo, Z. Shi, B. Wen, S. Kho, R. Pan, H. Feng, H. Chen, A. Carlsson, P. Ed\u00e9n, W. Ma, M. Raymer, E. J. Maier, Z. Tezak, E. Johanson, D. Hinton, H. Rodriguez, J. Zhu, E. Boja, P. Wang<\/strong>, B Zhang, \u201cA Community Effort to Identify and Correct Mislabeled Samples in Proteogenomic Studies\u201d, Patterns<\/span> 2021, Volume 2, Issue 5.<\/em><\/p>\n

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, \u2026\u2026 Pei Wang<\/strong>, Steve A. Carr, B. Zhang, D.R. Mani, M. A. Gillette, CPTAC, \u201cSystems-wide analysis of proteogenomic variation in lung squamous cell carcinoma\u201d, Cell<\/span> 2021, DOI:https:\/\/doi.org\/10.1016\/j.cell.2021.07.016 <\/em><\/p>\n

Xiaoyu Song, Jiayi Ji, Boris Reva, Himanshu Joshi, Anna Pamela Calinawan, Madhu Mazumdar, Juan P. Wisnivesky, Emanuela Taioli, Pei Wang<\/strong>, Rajwanth R. Veluswamy, \u201cPost-Anticoagulant D-dimer is a Highly Prognostic Biomarker of COVID-19 Mortality\u201d, ERJ Open Research <\/span> 2021, DOI: 10.1183\/23120541.00018-2021<\/em><\/p>\n

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,\u2026 Pei Wang<\/strong>\u2026, T. Liu, L. Ding, CPTAC \u201cProteogenomic and metabolomics characterization of human glioblastoma\u201d, Cancer Cell<\/span> 2021, Apr 12;39(4):509-528.e20<\/em><\/p>\n

D. Yan, Y. Xu and Pei Wang<\/strong>,\u201cEstimating the Number of Infected Cases in COVID-19 2 Pandemic\u201d, Journal of Data Science <\/span> 2021 Imprint; https:\/\/arxiv.org\/abs\/2005.12993<\/em><\/p>\n

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, \u2026 , Pei Wang<\/strong>,\u2026, H. Zhang, B. Zhang, CPTAC, \u201cProteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma\u201d, Cancer Cell<\/span> 2021, Mar 8;39(3):361-379.e16.<\/em><\/p>\n

2020<\/em><\/strong><\/span><\/p>\n

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. G\u00fcm\u00fc\u015f \u2026 A. C Resnick, Phillip B. Storm, Brian R. Rood, Pei Wang,<\/strong>\u00a0Children\u2019s Brain Tumor Tissue Consortium and Clinical Proteomic Tumor Analysis Consortium, \u201cIntegrated Proteogenomic Characterization across Major Histological types of Pediatric Brain Cancer\u201d, Cell<\/span> 2020 Dec 20;S0092-8674(20)31451-3. doi: 10.1016\/j.cell.2020.10.044.<\/em><\/p>\n

Li, A. Aue, D. Paul, J. Peng, P. Wang<\/strong>, \u201cAn adaptable generatlization of Hotelling\u2019s T^2 test in high dimension\u201d, Annual of Statistics<\/em><\/span> Volume 48, Number 3 (2020), 1815-1847.<\/p>\n

D. Beckmann*, W-J Lin*, M. Wang*, A. T. Cohain, P. Wang<\/strong>, 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, \u201cMultiscale causal network models identify VGF as an Alzheimers disease gene\u201d. Nature Communication<\/span>.\u00a02020 Aug 7;11(1):3942. doi: 10.1038\/s41467-020-17405-z.<\/em><\/p>\n

M. Yang, F. Petralia, Z. Li, X. Song, S. Kim., H. Li, H. Yu, B. Lee, S. Park, E. Heo, J. Kaczmarczyk, P. St\u0119pniak, M. Warcho\u0142, T. Yu, NCI-CPTAC-DREAM Consortium, P Boutros, Y. Guan, J. Kang, H. Rodriguez, G. Stolovitzky, P. Wang<\/strong>, D. Fenyo, J. Saez-Rodriguez, \u201cCommunity Assessment of the predictability of cancer protein and phosphoprotein levels from Genomics and Transcriptomics\u201d, Cell Systems<\/span> 2020 Aug 26; 11, 186\u2013195. \u00a0<\/em><\/p>\n<\/div>\n

A. P. Calinawan, X. Song, J. Ji, S M. Dhanasekaran, F. Petralia, P. Wang<\/strong>, Boris Reva, \u201cProTrack: An Interactive Multi-Omics Data Browser for Proteogenomic Studies\u201d, Proteomics<\/span> 2020 Jun 8;e1900359. doi: 10.1002\/pmic.201900359.<\/em><\/p>\n

S. Kalayci, F. Petralia, P. Wang<\/strong> and Z. H. G\u00fcm\u00fc\u015f,*ProNetView-ccRCC: A web-based portal to interactively explore clear cell renal cell carcinoma proteogenomics networks\u201d, Proteomics<\/span> 2020 May 2;e2000043. doi: 10.1002\/pmic.202000043.<\/em><\/p>\n

M.A. Gillette, S. Satpathy, S. Cao, S. M. Dhanasekaran, S. Vasaikar, K. Krug, F. Petralia, \u2026, P. Wang<\/strong>, A. Nesvizhskii, L. Ding, D.R. Mani, S. A. Carr, and Cancer Proteogenomic Tumor Analysis Consortium, \u201cProteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma\u201d, Cell<\/span> 2020 Jul 9;182(1):200-225.e35. doi: 10.1016\/j.cell.2020.06.013.<\/em><\/p>\n

J. Torres, F. Petralia, T. Sato, P. Wang<\/strong>, 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, \u201cSerum Biomarkers Identify Patients Who Will Develop Inflammatory Bowel Diseases Up to 5 y Before Diagnosis\u201d, Gastroenterology<\/span> 2020 Mar 9; S0016-5085 (20) 30327-9. doi: 10.1053\/j.gastro.2020.03.007.<\/em><\/p>\n

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, \u2026, Pei Wang<\/strong>, \u2026, K. D. Rodland, L. Ding, B. Zhang, T. Liu, D. Feny\u00f6, and Cancer Proteogenomic Tumor Analysis Consortium. \u201cProteogenomic Characterization of Endometrial Carcinoma\u201d, Cell<\/span> 2020 Feb 20;180(4):729-748, PMID: 32059776<\/em><\/p>\n

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 <\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

Recent Publications Google Scholar 2026 F. Petralia, A. Krek, A. P. Calinawan, D. Charytonowicz, R. Sebra, S. Feng, S. Gosline, P. Pugliese, A. G. Paulovich, J. J. Kennedy, M. Ceccarelli, P. Wang\u00a0\u201cBayesDeBulk: A Flexible Bayesian Algorithm for the Deconvolution of Bulk Tumor Data\u201d, JASA 2026 (under 2nd revision) J. Gong, F. Petralia, M. V. Ruiz […]<\/p>\n","protected":false},"author":233,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-95","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/pei-wang-lab\/wp-json\/wp\/v2\/pages\/95","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/pei-wang-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/pei-wang-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/pei-wang-lab\/wp-json\/wp\/v2\/users\/233"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/pei-wang-lab\/wp-json\/wp\/v2\/comments?post=95"}],"version-history":[{"count":18,"href":"https:\/\/labs.icahn.mssm.edu\/pei-wang-lab\/wp-json\/wp\/v2\/pages\/95\/revisions"}],"predecessor-version":[{"id":499,"href":"https:\/\/labs.icahn.mssm.edu\/pei-wang-lab\/wp-json\/wp\/v2\/pages\/95\/revisions\/499"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/pei-wang-lab\/wp-json\/wp\/v2\/media?parent=95"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}