Super-resolution microscopy; Single-particle tracking; Single-cell biology; Gene regulation; 3D genome structure

2009-2015                                                  Ph.D. in Computational Biology and Bioinformatics

                                                                   Duke University, North Carolina, USA

2005-2009                                                  M.S. in Biology

                                                                   Tsinghua University, Beijing, China

2001-2005                                                  B.E. in Automatic Control

                                                                   Tsinghua University, Beijing, China

2015-2022         Postdocal researcher, Howard Hughes Medical Institute/Janelia Research Campus

·       Develop super-resolution labelling and imaging methods to investigate 3D genome structure in single nucleus

·       Develop single-molecule imaging platform for quantitative understanding of transcriptional regulation in stem cells

·       Apply multiple imaging approaches to investigate phase-separation mechanisms underlying gene regulation.

2010-2015         Graduate student, Computational Biology and Bioinformatics Program, Duke University

·       Developed an integrated platform (including fluorescence biosensor, microfluidic device for live cell imaging and procedures/codes for image processing) for the measurement of E2F transcriptional dynamics at the single-cell level

·       Established quantitative relationship between E2F dynamics and cell cycle entry

·       Elucidated the design principle of Myc/Rb/E2F network and proposed a revised model for the control of cell cycle entry

2006-2009         Graduate student, Medical Systems Biology Research Center, School of Medicine, Tsinghua University

·       Identified miR-133b as an oncogene through miRNA expression profiling

·       Discovered tumorigenic and metastatic function of miR-133b in vitro and in vivo

·       Explored signaling pathways that contributed to the tumorigenic function of miR-133b

·       Confirmed the pathological relevance of miR-133b in clinical samples

* [Co-first author]；# [Co-coresponding author]
1. Dong, P. #, Zhang, S., Gandin, V., Xie, L., Wang, L., Lemire, L. L., L. W., Otsuna, H., Kawase, T., Lander, A.D., Chang, H. Y. & Liu, Z. # Cohesin prevents cross-domain gene co-activation. Nat Genet 56, 1654–1664 (2024).
2. Van, H. T., Xie, G., Dong, P., Liu, Z. & Ge, K. KMT2 Family of H3K4 Methyltransferases: Enzymatic Activity-dependent and -independent Functions. J Mol Biol 436, 168453 (2024).
3. Grimm, J. B., Tkachuk, A. N., Patel, R., Hennigan, S. T., Gutu, A., Dong, P., Gandin, V., Osowski, A. M., Holland, K. L., Liu, Z. J., Brown, T. A. & Lavis, L. D. Optimized Red-Absorbing Dyes for Imaging and Sensing. J Am Chem Soc 145, 23000-23013 (2023).
4. Xie, L., Dong, P. *, Qi, Y., Hsieh, T. S., English, B. P., Jung, S., Chen, X., De Marzio, M., Casellas, R., Chang, H. Y., Zhang, B., Tjian, R. & Liu, Z. BRD2 compartmentalizes the accessible genome. Nat Genet 54, 481-491 (2022).
5. Xie, L., Dong, P. *, Chen, X., Hsieh, T. S., Banala, S., De Marzio, M., English, B. P., Qi, Y., Jung, S. K., Kieffer-Kwon, K. R., Legant, W. R., Hansen, A. S., Schulmann, A., Casellas, R., Zhang, B., Betzig, E., Lavis, L. D., Chang, H. Y., Tjian, R. & Liu, Z. 3D ATAC-PALM: super-resolution imaging of the accessible genome. Nat Methods 17, 430-436 (2020).
6. Mathey-Prevot, B., Parker, B. T., Im, C., Hong, C., Dong, P., Yao, G. & You, L. Quantifying E2F1 protein dynamics in single cells. Quant Biol 8, 20-30 (2020).
7. Yu, H., Yang, F., Dong, P., Liao, S., Liu, W. R., Zhao, G., Qin, B., Dou, Z., Liu, Z., Liu, W., Zang, J., Lippincott-Schwartz, J., Liu, X. & Yao, X. NDP52 tunes cortical actin interaction with astral microtubules for accurate spindle orientation. Cell Res 29, 666-679 (2019).
8. Piccolo, F. M., Liu, Z., Dong, P., Hsu, C. L., Stoyanova, E. I., Rao, A., Tjian, R. & Heintz, N. MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions. Elife 8 (2019).
9. Cai, D., Feliciano, D., Dong, P., Flores, E., Gruebele, M., Porat-Shliom, N., Sukenik, S., Liu, Z. & Lippincott-Schwartz, J. Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression. Nat Cell Biol 21, 1578-1589 (2019).
10. Liu, H., Dong, P., Ioannou, M. S., Li, L., Shea, J., Pasolli, H. A., Grimm, J. B., Rivlin, P. K., Lavis, L. D., Koyama, M. & Liu, Z. Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling. Proc Natl Acad Sci U S A 115, 343-348 (2018).
11. Dong, P., Zhang, C., Parker, B. T., You, L. & Mathey-Prevot, B. Cyclin D/CDK4/6 activity controls G1 length in mammalian cells. PLoS One 13, e0185637 (2018).
12. Chong, S., Dugast-Darzacq, C., Liu, Z., Dong, P., Dailey, G. M., Cattoglio, C., Heckert, A., Banala, S., Lavis, L., Darzacq, X. & Tjian, R. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science 361 (2018).
13. Xie, L., Torigoe, S. E., Xiao, J., Mai, D. H., Li, L., Davis, F. P., Dong, P., Marie-Nelly, H., Grimm, J., Lavis, L., Darzacq, X., Cattoglio, C., Liu, Z. & Tjian, R. A dynamic interplay of enhancer elements regulates Klf4 expression in naive pluripotency. Genes Dev 31, 1795-1808 (2017).
14. Kieffer-Kwon, K. R., Nimura, K., Rao, S. S. P., Xu, J., Jung, S., Pekowska, A., Dose, M., Stevens, E., Mathe, E., Dong, P., Huang, S. C., Ricci, M. A., Baranello, L., Zheng, Y., Tomassoni Ardori, F., Resch, W., Stavreva, D., Nelson, S., McAndrew, M., Casellas, A., Finn, E., Gregory, C., St Hilaire, B. G., Johnson, S. M., Dubois, W., Cosma, M. P., Batchelor, E., Levens, D., Phair, R. D., Misteli, T., Tessarollo, L., Hager, G., Lakadamyali, M., Liu, Z., Floer, M., Shroff, H., Aiden, E. L. & Casellas, R. Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Mol Cell 67, 566-578 e510 (2017).
15. Dong, P. # & Liu, Z. Shaping development by stochasticity and dynamics in gene regulation. Open Biol 7 (2017).
16. Li, L., Liu, H., Dong, P., Li, D., Legant, W. R., Grimm, J. B., Lavis, L. D., Betzig, E., Tjian, R. & Liu, Z. Real-time imaging of Huntingtin aggregates diverting target search and gene transcription. Elife 5 (2016).
17. Grimm, J. B., English, B. P., Choi, H., Muthusamy, A. K., Mehl, B. P., Dong, P., Brown, T. A., Lippincott-Schwartz, J., Liu, Z., Lionnet, T. & Lavis, L. D. Bright photoactivatable fluorophores for single-molecule imaging. Nat Methods 13, 985-988 (2016).
18. Dong, P., Maddali, M. V., Srimani, J. K., Thelot, F., Nevins, J. R., Mathey-Prevot, B. & You, L. Division of labour between Myc and G1 cyclins in cell cycle commitment and pace control. Nat Commun 5, 4750 (2014).
19. Qin, W., Dong, P., Ma, C., Mitchelson, K., Deng, T., Zhang, L., Sun, Y., Feng, X., Ding, Y., Lu, X., He, J., Wen, H. & Cheng, J. MicroRNA-133b is a key promoter of cervical carcinoma development through the activation of the ERK and AKT1 pathways. Oncogene 31, 4067-4075 (2012).
20. Wong, J. V., Dong, P., Nevins, J. R., Mathey-Prevot, B. & You, L. Network calisthenics: control of E2F dynamics in cell cycle entry. Cell Cycle 10, 3086-3094 (2011).

1. Qin W, Dong P, Deng T et al. United States Patent No. US8957039B2. Methods and compositions for the diagnosis and prognosis of cervical intraepithelial neoplasia and cervical cancer.
2. Qin W, Dong P, Deng T et al. European Patent No. EP2463381A4. Methods and compositions for the diagnosis and prognosis of cervical intraepithelial neoplasia and cervical cancer.
3. ​Qin W, Dong P, Deng T et al. World Intellectual Property Organization Patent No. WO2011014980A1. Methods and compositions diagnosing cervical cancer and cervical dysplasia, guidding subsequent treatment, determining prognosis, and improving patient survival.