1. Wang, Y., Yang, J., Zhuang, X., Ling, Y., Cao, R., Xu, Q., Wang, P. #, Xu, P. # and Zhang, G. # (2022) Linking genomic and epidemiologic information to advance the study of COVID-19. Scientific Data, 9, 121.
  2. Wang, W., Yuan, T., Ma, L., Zhu, Y., Bao, J., Zhao, X., Zhao, Y., Zong, Y., Zhang, Y., Yang, S., Qiu X., Shen, S., Wu R., Wu, T., Wang, H. #, Gao, D. #, Wang, P. #, Chen, L. # Hepatobiliary Tumor Organoids Reveal HLA Class I Neoantigen Landscape and Antitumoral Activity of Neoantigen Peptide Enhanced with Immune Checkpoint Inhibitors. Advanced Science (Weinh)(2022):e2105810.
  3. Liu, Y.W., Xue, M.Z., Cao, Y., Qin, H., Wang, Y., Miao, H., Wang, P. #, Hu, X. #, Shen, J.K. #, Xiong, B.# (2021) Multi-omics characterization of WNT pathway reactivation to ameliorate BET inhibitor resistance in liver cancer cells, Genomics, 113, 1057.
  4. Lang, G.T., Jiang, Y.Z., Shi, X., Yang, F., Li, G., Pei, C., Zhang, H., Ma, D., Xiao, Y., Hu, C., Wang, H., Yang, S., Guo, W., Lu, X., Xue, Z., Wang, P, Cao, Y., Ling, H., Wang, H., Yu, D., Di, H., Li, D.Q., Wang, J., Yu, Y., Shi, M., Hu, X. #, Huang, W. #, Shao Z.M.# (2020) Characterization of the genomic landscape and actionable mutations in Chinese breast cancers by clinical sequencing, Nature communications., 11, 1-13
  5. Wang, P., and Chen, L. # (2020) Critical transitions and tipping points in EMT, Quantitative Biology, 1-8.
  6. Wang, L., Lang, G.T., Xue, M.Z., Yang, L., Chen, L., Yao, L., Li, X.G., Wang, P. #, Hu, X. # and Shao, Z.M. # (2020) Dissecting the heterogeneity of the alternative polyadenylation profiles in triple-negative breast cancers. Theranostics, 2020, 10: 10531-10547
  7. Jiang, Z., Lu, L., Liu, Y., Zhang, S., Li, S., Wang, G. #, Wang, P. #, and Chen, L. # (2020) SMAD7 and SERPINE1 as novel dynamic network biomarkers to detect and regulate the tipping point of TGF-beta induced EMT. Science Bulletin., 65: 842-853
  8. Xiao, Y., Ma, D., Zhao, S., Suo, C., Shi, J., Xue, M. Z., Ruan, M., Wang, H., Zhao, J., Li, Q., Wang, P., Shi, L., Yang, W. T., Huang, W., Hu, X., Yu, K., Huang, S., Bertucci, F., Jiang, Y. Z., and Shao, Z. M#. (2019) Multi-omics profiling reveals distinct microenvironment characterization and suggests immune escape mechanisms of triple-negative breast cancer, Clinical Cancer Research.
  9. Wang, L., Hu, X., Wang, P. #, and Shao, Z. M#. (2019) Integrative 3′ Untranslated Region-Based Model to Identify Patients with Low Risk of Axillary Lymph Node Metastasis in Operable Triple-Negative Breast Cancer, Oncologist 24, 22-30.
  10. Liu, Y., Xue, M., Du, S., Feng, W., Zhang, K., Zhang, L., Liu, H., Jia, G., Wu, L., Hu, X. #, Chen, L. #, and Wang, P. # (2019) Competitive endogenous RNA is an intrinsic component of EMT regulatory circuits and modulates EMT, Nature Communications 10, 1637.
  11. Jiang, Y. Z., Ma, D., Suo, C., Shi, J., Xue, M., Hu, X., Xiao, Y., Yu, K. D., Liu, Y. R., Yu, Y., Zheng, Y., Li, X., Zhang, C., Hu, P., Zhang, J., Hua, Q., Zhang, J., Hou, W., Ren, L., Bao, D., Li, B., Yang, J., Yao, L., Zuo, W. J., Zhao, S., Gong, Y., Ren, Y. X., Zhao, Y. X., Yang, Y. S., Niu, Z., Cao, Z. G., Stover, D. G., Verschraegen, C., Kaklamani, V., Daemen, A., Benson, J. R., Takabe, K., Bai, F., Li, D. Q., Wang, P. #, Shi, L. #, Huang, W. #, and Shao, Z. M. # (2019) Genomic and Transcriptomic Landscape of Triple-Negative Breast Cancers: Subtypes and Treatment Strategies, Cancer Cell 35, 428-440 e425.
  12. Zheng, Y. Z., Xue, M. Z., Shen, H. J., Li, X. G., Ma, D., Gong, Y., Liu, Y. R., Qiao, F., Xie, H. Y., Lian, B., Sun, W. L., Zhao, H. Y., Yao, L., Zuo, W. J., Li, D. Q., Wang, P., Hu, X. , and Shao, Z. M. # (2018) PHF5A Epigenetically Inhibits Apoptosis to Promote Breast Cancer Progression, Cancer Research 78, 3190-3206.
  13. Xue, M., Liu, H., Zhang, L., Chang, H., Liu, Y., Du, S., Yang, Y., and Wang, P. # (2017) Computational identification of mutually exclusive transcriptional drivers dysregulating metastatic microRNAs in prostate cancer, Nature Communications 8, 14917.
  14. Wang, L., Hu, X. #, Wang, P. #, and Shao, Z. M. # (2016) The 3’UTR signature defines a highly metastatic subgroup of triple-negative breast cancer, Oncotarget 7, 59834-59844.
  15. Chang, H., Liu, Y., Xue, M., Liu, H., Du, S., Zhang, L., and Wang, P. # (2016) Synergistic action of master transcription factors controls epithelial-to-mesenchymal transition, Nucleic Acids Research 44, 2514-2527.
  16. Wang, L., Yao, L., Zheng, Y. Z., Xu, Q., Liu, X. P., Hu, X. #, Wang, P. #, and Shao, Z. M. # (2015) Expression of autophagy-related proteins ATG5 and FIP200 predicts favorable disease-free survival in patients with breast cancer, Biochemical and Biophysical Research Communications 458, 816-822.
  17. Li, L., Wang, D., Xue, M., Mi, X., Liang, Y., and Wang, P. # (2014) 3’UTR shortening identifies high-risk cancers with targeted dysregulation of the ceRNA network, Scientific Reports 4, 5406.
  18. Mucida, D., Husain, M. M., Muroi, S., van Wijk, F., Shinnakasu, R., Naoe, Y., Reis, B. S., Huang, Y., Lambolez, F., Docherty, M., Attinger, A., Shui, J. W., Kim, G., Lena, C. J., Sakaguchi, S., Miyamoto, C., Wang, P., Atarashi, K., Park, Y., Nakayama, T., Honda, K., Ellmeier, W., Kronenberg, M., Taniuchi, I., and Cheroutre, H. (2013) Transcriptional reprogramming of mature CD4(+) helper T cells generates distinct MHC class II-restricted cytotoxic T lymphocytes, Nature Immunology 14, 281-289.
  19. Kim, Y., Ponomarenko, J., Zhu, Z., Tamang, D., Wang, P., Greenbaum, J., Lundegaard, C., Sette, A., Lund, O., Bourne, P. E., Nielsen, M., and Peters, B. (2012) Immune epitope database analysis resource, Nucleic Acids Research 40, W525-530.
  20. Wang, P., Sidney, J., Sette, A., and Peters, B. (2011) A computational pipeline to generate MHC binding motifs, Immunome Research 7.
  21. Chen, C., Dow, C., Wang, P., Sidney, J., Read, A., Harmsen, A., Samuel, J. E., and Peters, B. (2011) Identification of CD4+ T cell epitopes in C. burnetii antigens targeted by antibody responses, PLoS One 6, e17712.
  22. Wang, P., Sidney, J., Kim, Y., Sette, A., Lund, O., Nielsen, M., and Peters, B. (2010) Peptide binding predictions for HLA DR, DP and DQ molecules, BMC Bioinformatics 11, 568.
  23. Zhang, Q., Wang, P., Kim, Y., Haste-Andersen, P., Beaver, J., Bourne, P. E., Bui, H. H., Buus, S., Frankild, S., Greenbaum, J., Lund, O., Lundegaard, C., Nielsen, M., Ponomarenko, J., Sette, A., Zhu, Z., and Peters, B. (2008) Immune epitope database analysis resource (IEDB-AR), Nucleic Acids Research 36, W513-518.
  24. Wang, P., Sidney, J., Dow, C., Mothe, B., Sette, A., and Peters, B. (2008) A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach, PLoS Computational Biology 4, e1000048.
  25. Arens, R., Wang, P., Sidney, J., Loewendorf, A., Sette, A., Schoenberger, S. P., Peters, B., and Benedict, C. A. (2008) Cutting edge: murine cytomegalovirus induces a polyfunctional CD4 T cell response, Journal of Immunology 180, 6472-6476.
  26. Wang, P., Morgan, A. A., Zhang, Q., Sette, A., and Peters, B. (2007) Automating document classification for the Immune Epitope Database, BMC Bioinformatics 8, 269.
  27. Yan, B., Zhou, T., Wang, P., Liu, Z., Emanuele, V. A., 2nd, Olman, V., and Xu, Y. (2006) A point-process model for rapid identification of post-translational modifications, Pacific Symposium on Biocomputing, 327-338.
  28. Olman, V., Hicks, C., Wang, P. and Xu, Y. (2006) Gene expression data analysis in subtypes of ovarian cancer using covariance analysis. Journal of Bioinformatics and Computational Biology 4, 999-1014.
  29. Wang, P., Yan, B., Guo, J. T., Hicks, C., and Xu, Y. (2005) Structural genomics analysis of alternative splicing and application to isoform structure modeling, The Proceedings of the National Academy of Sciences 102, 18920-18925.
  30. Liu, Z., Mao, F., Guo, J. T., Yan, B., Wang, P., Qu, Y., and Xu, Y. (2005) Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential, Nucleic Acids Research 33, 546-558.
  31. Wang, P. and Malkovsky, M. (2000) Different roles of the CD2 and LFA-1 T-cell co-receptors for regulating cytotoxic, proliferative, and cytokine responses of human V gamma 9/V delta 2 T cells. Molecular Medicine, 6, 196-207.