课题组在生物信息学方法、网络模型构建、衰老和代谢的调控机制研究取得了一系列进展：1）开发了共表达网络分析新方法，能够揭示网络的拓扑结构，生成精细的基因模块；2）构建了50种人体组织的衰老调控网络，解析了衰老基因的功能模块和关键的细胞类型；3）阐明了衰老的代谢机制，鉴定了胰岛素抵抗的分子网络及驱动基因。研究成果发表在国际顶尖杂志，包括 Cell、Nature Medicine、 Nature Aging、 Nature Cell Biology 和 Nature Cancer 等。其中以第一/通讯作者发表于Cell  Systems、Aging Cell、Molecular Neurodegeneration、Genome Research和Bioinformatics等知名期刊。参与 NIH R01 科研项目等 4项， 参与国际大型群体队列 AAGMEx、 GTEx、 Mount Sinai Brain Bank（MSBB）和 TCGA 的数据分析，论文引用数为 1287， H-index 为 15。

代表性论文：

1、Xu, P. , Kong, Y.,Palmer, N., Ng, M., Zhang, B., and Das, S.K. (2024). Integrated Multi-OmicAnalyses Uncover the Effects of Aging on Cell-Type Regulation inGlucose-Responsive Tissues. Aging Cell, 23(8): e14199. (一作兼通讯)

2、Xu,P. andB. Zhang (2023). Multiscale network modeling reveals the gene regulatorylandscape driving cancer prognosis in 32 cancer types. Genome Research33(10): 1806-1817. (一作兼通讯, 封面文章)

3、Xu, P. +, Wang, M.+, Sharma, N.K. +, Comeau, M.E., Wabitsch, M., Langefeld,C.D., Civelek, M., Zhang, B., and Das, S.K. (2023). Multi-omic integration reveals cell-type-specific regulatory networksof insulin resistance in distinct ancestry populations. Cell Systems 14, 41-57.e48. 

4、Xu, P., Wang, M., Song, W.M.,Wang, Q., Yuan, G.C., Sudmant, P.H., Zare, H., Tu, Z., Orr, M.E., and Zhang, B.(2022). The landscape of human tissue andcell type specific expression and co-regulation of senescence genes. Molecular Neurodegeneration 17, 5. 

5、Wang,M. +, Song, W.M. +, Ming, C. +, Wang, Q.+, Zhou, X. +, Xu, P.+, Krek, A., Yoon, Y., Ho, L., Orr, M.E., et al. (2022). Guidelines for Bioinformatics of Single-CellSequencing Data Analysis in Alzheimer’s Disease: Review, Recommendation,Implementation and Application. MolecularNeurodegeneration 17, 17. (共同一作)

6、Xu, P., Chen, Y., Gao, M.,Chong, Z. (2021). ClipSV: Improvingstructural variation detection by read extension, spliced alignment, andtree-based decision rules. NAR GenomBioinform 3, lqab003. 

7、Xu, P., Kennell Jr, T., Gao,M., Consortium, H.G.S.V., Kimberly, R.P., and Chong, Z. (2020). MRLR: unraveling high-resolution meioticrecombination by linked reads. Bioinformatics36, 10-16. 

8、Kong,Y.+, Xu, P.+,Jing, X., Chen, L., Li, L., and Li, X. (2017). Decipher the ancestry of the plant-specific LBD gene family. BMC Genomics 18, 1-10. (共同一作)

9、Xu, P. +, Kong, Y. +,Song, D., Huang, C., Li, X., and Li, L. (2014). Conservation and functional influence of alternative splicing in woodformation of Populus and Eucalyptus. BMCGenomics 15, 1-12. 

10、Xu,P.,Kong, Y., Li, X., and Li, L. (2013). Identificationof molecular processes needed for vascular formation through transcriptomeanalysis of different vascular systems. BMC Genomics 14, 1-11. 

其它论文：

1、Wang, E.,  K. Yu,  J. Cao, M. Wang,  P. Katsel,  W. M. Song,  Z. Wang, Y. Li,  X. Wang, Q. Wang,  P. Xu,  G. Yu,  L. Zhu,  J. Geng,  P. Habibi,  L. Qian, T. Tuck,  A. Li,  J. Tcw,  P. Roussos,  K. J. Brennand,  V. Haroutunian,  E. C. B. Johnson,  N. T. Seyfried,  A. I. Levey,  D. A. Bennett,  J. Peng,  D. Cai and B. Zhang (2025).  "Multiscale proteomic modeling reveals protein networks driving Alzheimer's disease pathogenesis." Cell.

2、Huang,F., Xu, P., Yue, Z., Song, Y., Hu, K., Zhao, X., Gao, M., & Chong,Z. (2024). Body Weight Correlates with Molecular Variances in Patients with Cancer. Cancer Research, 84(5), 757-770.

3、Gonzales,M. M., Garbarino, V. R., Kautz, T. F., Palavicini, J. P., Lopez-Cruzan, M.,Dehkordi, S. K., Mathews, J. J., Zare, H., Xu, P., Zhang, B., Franklin,C., Habes, M., Craft, S., Petersen, R. C., Tchkonia, T., Kirkland, J. L.,Salardini, A., Seshadri, S., Musi, N., & Orr, M. E. (2023). Senolytictherapy in mild Alzheimer's disease: a phase 1 feasibility trial. Nature Medicine, 29(10), 2481-2488.

4、Choi,I., Wang, M., Yoo, S., Xu, P., Seegobin, S. P., Li, X., Han, X., Wang,Q., Peng, J., Zhang, B., & Yue, Z. (2023). Autophagy enables microgliato engage amyloid plaques and prevents microglial senescence. Nature Cell Biology, 25(7), 963-974.

5、Song,W. M., Elmas, A., Farias, R., Xu, P., Zhou, X., Hopkins, B., Huang, K.L., & Zhang, B. (2023). Multiscale protein networks systematicallyidentify aberrant protein interactions and oncogenic regulators in seven cancertypes. Journal of Hematology & Oncology, 16(1), 120.

6、Forst,C. V., Zeng, L., Wang, Q., Zhou, X., Vatansever, S., Xu, P., Song, W.M., Tu, Z., & Zhang, B. (2023). Multiscale network analysis identifiespotential receptors for SARS‐CoV‐2 and reveals their tissue‐specific andage‐dependent expression. FEBS Letters, 597(10), 1384-1402.

7、Zhang,Z., Luo, L., Xing, C., Chen, Y., Xu, P.,Li, M., Zeng, L., Li, C., Ghosh, S., Della Manna, D., et al. (2021). RNF2 ablation reprograms the tumor-immunemicroenvironment and stimulates durable NK and CD4+ T-cell-dependent antitumorimmunity. Nature Cancer 2,1018-1038.

8、Dehkordi,S. K., Walker, J., Sah, E., Bennett, E., Atrian, F., Frost, B., Woost, B.,Bennett, R. E., Orr, T. C., Zhou, Y., Andhey, P. S., Colonna, M., Sudmant, P.H., Xu, P., Wang, M., Zhang, B., Zare, H., & Orr, M. E. (2021). Profilingsenescent cells in human brains reveals neurons with CDKN2D/p19 and tauneuropathology. Nature Aging, 1(12), 1107-1116.