publications
XIE LAB PUBLICATIONS
(* equal contribution, # co-corresponding authors, Xie lab members are highlighted in bold)
40. M.D. Gibbons, V. Nganga, A. Lee, M.A. Hossain, E.M. Gunn, A. Adolphson, L. Perez, L. Li, N. Linzer, Y. Fang, X. Huang, J. Lu, J.E. Payton, E. Oltz, M. Xie, G. Hudalla and J. Bungert. Disrupting the MYB-TAL1 oncogenic axis in T-ALL via direct delivery of synthetic high-affinity zinc finger DNA-binding proteins. accepted in Nucleic Acids Research
39. C.M. Traugot, J. Effinger-Morris, T. Li, N.M. Hiers, L. Li and M. Xie, Examine RNA abundance and molecular weight using high sensitivity northern blots. accepted in Methods in Molecular Biology
38. L. Li, Q. Yang, L. Li, H. Zhao, J. Xu, M. Xie and R. Yin. GIN-CRC-Pareto: A graph-based areto-optimal multi-task learning framework to identify miRNA-target interactions in colorectal cancer. Journal of Biomedical Informatics (2026)
37. L. Li, P. Sheng, N.M. Hiers, T. Li, A.L. Grimme, Y. Wang, C.M. Traugot, O.M. D’Agati and M. Xie. CLASHub is an integrated database and analytical platform for microRNA-target interactions. Nature Communications, 17 (1): 6204 (2026).
36. Y. Li, Y. Zhou, Q. Li, J. Arrington, M.F.A. Siadahmed, Y. Wang, J. Ren, Y. Cheng, M. Xie, W.A. Tao, S. Kuang and F. Yue. A myocyte-enriched long non-coding RNA NRMLncR enhances myogenesis in mouse. the FASEB Journal,40 (13):e72109 (2026).
35. J. Liang, Q. Wang, S. Guo, W. Zhang, M. Xie and Q. Song. scDeepAPA: A deep learning framework for single-cell alternative polyadenylation identification. Briefings in Bioinformatics, 27 (3):bbag301 (2026).
34. J. Liang, Y. Wang, M. Xie and Q. Song. VIRSE: A Variational Bayesian Framework for RNA Structural Ensemble Inference. Briefings in Bioinformatics, 27 (3):bbag301 (2026).
33. J. Liang, M. Zhou, M. Xie and Q. Song. ShapeRNA: An integrated web server for RNA secondary structure, ensemble, and functional analysis. Nucleic Acids Research, gkag387 (2026).
32. M. Huang, Y. Chen, C. Liang, O.P. Narayan, C. Stallings, M. Yu, C.M. Traugot, L. Li, K. Li, Q. Vo, H. Wang, Y.-T. Chou, L. Cech, D. Parra, L. Garzon, D. Parsons, E. Diaz, C. Zhang, C. Mackey, H. Sussman, I. Zmirska, M. Chung, C. Zhou, G. Glynatsis, D.W. Siemann, J.D. Licht, C. Li, F.J. Kaye, M. Xie, Y. Tan, L. Wu, T.G. Bivona, J. Guan and X. Tang. Drug resistant cancer cells show increased nuclear mechanotransduction and mechanically targetable YAP-regulated vulnerability. Biomaterials, 329, 123920 (2026).
31. A.L. Grimme*, L. Li*, A. Scholl, B.F. Donnelly, N. Channamraju, K.F. Vieux, L. Zhou, G. Seydoux, M. Xie and K. McJunkin. A lncRNA drives developmentally-timed decay of all members of an essential microRNA family. Genes & Development, 40 (9-10):737-755 (2026).
30. X. Huang, M. Zhang, A.D. Pearce, M. Gibbons, D. Jin, L. Li, D. Hu, R. Liu, Y. Mu, M. Tan, J. Chang, J. Dong, M. Xie, W. Zhang, L. Wu, C.T. Flores, J. Bungert, T. Brusko and J. Lu. Epithelial-mesenchymal transition activates YAP to drive malignant progression and immune evasion. Cancers, 17 (17), 2767 (2025).
29. N.M. Hiers, L. Li, T. Li, P. Sheng, Y. Wang, C.M. Traugot, M. Yao and M. Xie, An endogenous cluster of target-directed microRNA degradation sites induces decay of distinct microRNA families. Cell Reports, 44 (9), 116162 (2025).
28. A. Nguyễn*, T. Li*, C.M. Traugot*, K. Paulsen, M. Xie# and Z. Ma#, Essential function of the Integrator complex in Kapok’s sarcoma-associated herpesvirus lytic replication. Journal of Virology, e0026625 (2025).
27. T. Li, L. Li, N.M. Hiers, P. Sheng, Y. Wang, C.M. Traugot, J.F. Effinger-Morris, P. Akaphan, Y. Liu, J. Bian, K. Fujii and M. Xie, Translation suppresses exogenous target RNA-mediated microRNA degradation. Nature Communications, 16 (1), 5257 (2025).
26. W. Meng, R. Inampudi, X. Zhang, J. Xu, Y. Huang, M. Xie, J. Bian and R. Yin. An interpretable population graph network to identify rapid progression of Alzheimer’s Disease using UK Biobank. AMIA Annu. Symp. Proc., 2024: 808-817 (2025).
25. Y. Sheng, A. Abreu, Z. Markovich, P. Enea, L. Davis, E. Park, P. Sheng, M. Xie, S.M. Han and R. Xiao. A mitochondrial unfolded protein response (mitoUPR)-independent role of DVE-1 in longevity regulation. Cell Reports, 43 (11), 114889 (2024).
24. R. Yin#, H. Zhao, L. Li, Q. Yang, M. Zeng, C. Yang, J. Bian and M. Xie#, Gra-CRC-miRTar: The pre-trained nucleotide-to-graph neural networks to identify potential miRNA targets in colorectal cancer. Computational and Structural Biotech. J., 23, 3020-3029 (2024).
23. Y. Zhou*, P. Sheng*, J. Li, Y. Li, M. Xie#and A.A. Green#. Conditional RNA interference in mammalian cells via RNA transactivation. Nature Communications, 15, 6855 (2024).
22. N.M. Hiers, T. Li, C.M. Traugot and M. Xie. Target-directed microRNA degradation: Mechanisms, significance, and functional implications. WIREs RNA, 15 (2):e1832 (2024).
21. Y. Wang, C.M. Traugot, J. Bubenik, T. Li, P. Sheng, N.M. Hiers, L. Li, P. Fernandez, J. Bian, M.S. Swanson and M. Xie. N6-methyladenosine in 7SK small nuclear RNA underlies RNA Polymerase II transcription regulation. Molecular Cell, 83 (21), 3818-3834 (2023).
20. M. Huang, H. Wang, C. Mackey, M.C. Chung, J. Guan, G. Zheng, A. Roy, M. Xie, C. Vulpe and X. Tang, YAP at the Crossroads of Biomechanics and Drug Resistance in Human Cancer. International Journal of Molecular Sciences, 24 (15), 12491 (2023).
19. C. Liang, M. Huang, M. Tanaka, S. Lightsey, M. Temples, S.E. Lepler, P. Sheng, W.P. Mann, A.E. Widener, D.W. Siemann, B. Sharma, M. Xie, Y. Dai, E. Phelps E, B. Zeng# and X. Tang#. Functional Interrogation of Ca2+ Signals in Human Cancer Cells In Vitro and Ex Vivo by Fluorescent Microscopy and Molecular Tools. Methods in Molecular Biology, 2679, 95-125 (2023).
18. T. Li, W. Zhang and M. Xie, Fluorescent in situ detection of RNA-Protein interactions in intact cells by RNA-PLA. Methods in Molecular Biology, 2666, 165-175 (2023).
17. P. Sheng*, L. Li*#, T. Li, Y. Wang, N.M. Hiers, J.S. Mejia, J.S. Sanchez, L. Zhou# and M. Xie#, Screening of Drosophila microRNA-degradation sequences reveals Argonaute1 mRNA’s role in regulating miR-999. Nature Communications, 14, 2108 (2023).
16. C. Gobin, S. Inkabi, C.C. Lattimore, T. Gu, J.N. Menefee, M. Rodriguez, H. Kates, C.J. Fields, T. Bian, N. Silver, C. Xing, C. Yates, R. Renne, M. Xie and K.M. Fredenburg, Investigating miR-9 as a mediator in laryngeal cancer health disparities. Frontiers in Oncology, 13: 1096882, (2023).
15. M.D. Gibbons, Y. Fang, A.P. Spicola, N. Linzer, S.M. Jones, B.R. Johnson, L. Li, M. Xie and J. Bungert, Enhancer mediated formation of nuclear transcription initiation domains. International Journal of Molecular Sciences, 23 (16), 9290 (2022).
14. Y. Qi*, L. Ding*, M. Xie# and P. Du#, RDR1-mediated broad antitumor response: a novel strategy manipulating miRNAs as a powerful weapon. Life Medicine, lnac007 (2022).
13. C. Liang*, M. Huang*, T. Li*, L. Li*, H. Sussaman, Y. Dai, D. Siemann, M. Xie# and X. Tang#, Towards an Integrative Understanding of Cancer Mechanobiology: Calcium, YAP, and microRNA under Biophysical Forces. Soft Matter, 18 (6), 1112-1148 (2022).
12. C.J. Fields, L. Li, N.M. Hiers, T. Li, P. Sheng, T. Huda, J. Shan, L. Gay, T. Gu, J. Bian, M.S. Kilberg, R. Renne and M. Xie, Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a. PLOS Genetics, 17 (12), e1009934 (2021).
11. T. Gu, M. Xie, W.B. Barbazuk and J.-H. Lee, Biological features between miRNAs and their targets are unveiled from deep learning models. Scientific Reports, 11 (1), 23825 (2021).
10. L. Li*, P. Sheng*, T. Li, C.J. Fields, N.M. Hiers, Y. Wang, J. Li, C.M. Guardia, J.D. Licht and M. Xie, Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins. Genes & Development, 35 (23-24), 1595-1609 (2021).
9. M. Xie and J. Bungert, When Pol II sees red. Blood, 138 (18), 1648-1649 (2021).
8. D. Stribling*, Y. Lei*, C.M. Guardia*, L. Li, C.J. Fields, P. Nowialis, R. Opavsky, R. Renne# and M. Xie#, A non-canonical microRNA derived from the snaR-A non-coding RNA targets a metastasis inhibitor. RNA, 27 (6), 694-709 (2021).
7. A. Gurumurthy, D. Yu, J.R. Stees, P. Chamales, E. Gavrilova, P. Wassel, L. Li, D. Stribling, J. Chen, M. Brackett, A. Ishov, M. Xie and J. Bungert, Super-enhancer mediated regulation of adult β-globin gene expression: the role of eRNA and Integrator. Nucleic Acids Research, 49 (3), 1383-1396 (2021).
6. M. Xie and M.S. Swanson, UTteR control through miRs: fine-tuning ATXN1 levels to prevent ataxia. Genes & Development, 34 (17-18), 1107-1109 (2020).
5. P. Sheng, K.A. Flood and M. Xie, Short hairpin RNAs for strand-specific small interfering RNA production. Frontiers in Bioengineering & Biotechnology, 8, 940 (2020).
4. P. Nowialis*, K. Lopusna*, J. Opavska, S.L. Haney, A. Abraham, P. Sheng, A. Riva, A. Natarajan, O. Guryanova, M.Simpson, R. Hlady, M. Xie and R. Opavsky, Catalytically inactive Dnmt3b rescues mouse embryonic development by accessory and repressive functions. Nature Communications, 10, 4374 (2019).
3. C.J. Fields, P. Sheng, B.R. Miller, T. Wei and M. Xie, Northern blot with IR fluorescent probes: Strategies for probe preparation. Bio-protocol, 9 (8), e3219 (2019).
2. B.R. Miller*, T. Wei*, C.J. Fields, P. Sheng and M. Xie, Near-infrared fluorescent northern blot. RNA, 24 (12), 1871-1877 (2018).
1. P. Sheng, C.J. Fields, K. Aadland, T. Wei, O. Kolaczkowski, T. Gu, B. Kolaczkowski# and M. Xie#, Dicer cleaves 5′-extended microRNA precursors originating from RNA Polymerase II transcription start sites. Nucleic Acids Research, 46 (11), 5737-5752 (2018).
Ming’s Postdoc Work
9. K.E. Hayes, J.A. Barr, M. Xie, J.A. Steitz and I. Martinez, Immunoprecipitation of Tri-methylated Capped RNA. Bio-protocol, 8 (3): e2717 (2018).
8. I. Martinez, K. Hayes, J. Barr, A. Harold, M. Xie, S.I.A. Bukhari, S. Vasudevan, J.A. Steitz and D. DiMaio, An Exportin-1-dependent microRNA biogenesis pathway during human cell quiescence. Proc. Natl. Acad. Sci. U.S.A. 114 (25), 4961-4970 (2017).
7. W. Zhang*, M. Xie*, M. Shu, J.A. Steitz and D. DiMaio, A proximity-dependent assay for specific RNA-protein interactions in intact cells. RNA, 22 (11), 1785-1792 (2016).
6. M. Xie, W. Zhang, M. Shu, A. Xu, D. Lenis, D. DiMaio and J.A. Steitz, The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3′ ends. Genes & Development, 29 (14), 1552-1564 (2015).
5. K.T. Tycowski*, Y.E. Guo*, N. Lee*, W.N. Moss*, T.K. Vallery*, M. Xie* and J.A. Steitz, Viral noncoding RNAs: more surprises. Genes & Development, 29 (6), 567-584 (2015).
4. M. Xie# and J.A. Steitz, Versatile microRNA biogenesis in animals and their viruses. RNA biology, 11 (6), 673-681 (2014).
3. M. Xie, M. Li, A.Vilborg, N. Lee, M. Shu, V. Yartseva, N. Sestan and J.A. Steitz, Mammalian 5′-capped microRNA precursors that generate a single microRNA. Cell, 155 (7), 1568-1580 (2013).
2. C. Qiao, J. Ma, J. Xu, M. Xie, W. Ma and Y. Huang, Drosha mediates destabilization of Lin28 mRNA targets. Cell Cycle, 11 (19), 3590-3598 (2012).
1. D. Cazalla, M. Xie and J.A. Steitz, A primate Herpesvirus uses the Integrator complex to generate viral microRNAs. Molecular Cell, 43 (6), 982-992 (2011).
MING’S GRADUATE WORK
8. A.F. Brown, J.D. Podlevsky, X. Qi, Y. Chen, M. Xie and J.J.-L. Chen, A self-regulating template in human telomerase. Proc. Natl. Acad. Sci. U.S.A. 111 (31), 11311-11316 (2014).
7. X. Qi*, M. Xie*, A.F. Brown*, C.J. Bley, J.D. Podlevsky and J.J.-L. Chen, RNA/DNA hybrid binding affinity determines telomerase template translocation efficiency. EMBO Journal, 31 (1), 150-161 (2012).
6. M. Xie, J.D. Podlevsky, X. Qi, C.J. Bley and J.J.-L. Chen, A novel motif in telomerase reverse transcriptase regulates telomere repeat addition rate and processivity. Nucleic Acids Research, 38 (6), 1982-1996 (2010).
5. M. Xie, A. Mosig, X. Qi, Y. Li, P.F. Stadler and J.J.-L. Chen, Structure and function of the smallest vertebrate telomerase RNA from teleost fish. Journal of Biological Chemistry, 283 (4), 2049-2059 (2008).
4. J.K. Alder, J.J.-L. Chen, L. Lancaster, S. Danoff, S.C. Su, M. Prince, I. Vulto, M. Xie, X. Qi, R.M. Tuder, J.A. Phillips, P.M. Lansdorp, J.E. Loyd, and M.Y. Armanios, Short telomeres are a risk factor for idiopathic pulmonary fibrosis. Proc. Natl. Acad. Sci. U.S.A. 105 (35), 13051-13056 (2008).
3. Y. Xiang, M. Xie, R. Bash, J.J.-L. Chen, and J. Wang, Ultrasensitive label-free aptamer-based electronic detection. Angew. Chem. Int. Ed., 46 (47), 9054-9056(2007).
2. M. Armanios, J.J.-L. Chen, W.E. Lawson, J.K. Alder, R.G. Ingersoll, C. Markin, M. Xie, J. Cogan, J.A. Philips III, P.M. Lansdorp, C.W. Greider and J.E. Loyd, Telomerase mutations in families with idiopathic pulmonary fibrosis. New England Journal of Medicine, 356 (13), 1317-1326 (2007).
1. C. Lin, M. Xie, J.J.-L. Chen, Y. Liu, and H. Yan, Rolling-circle amplification of a DNA nanojunction. Angew. Chem. Int. Ed., 45 (45), 7537-7539(2006).
MING’S UNDERGRADUATE WORK
3. X. Zhu, Z. Li, M. Xie, A. Song, and Y. Liu. [Effect of illumination through simulated forest gap on the germination of seed bank in Hexi subtropical rainforest in Nanjing, China. in Chinese] Journal of Xiamen University (Natural Sci.), 45,125-130 (2006).
2. J. Zheng, Y. Gao, Q. Wei, J. Ouyang, C. Tang and M. Xie, Optimization of cultivation technique for Ca-enriched Spirulina maxima. Journal of Jimei University (Natural Sci.), 9, 205-209(2004).
1. J. Zheng, Y. Gao, Q. Wei, J. Ouyang, C. Tang and M. Xie, [Distribution of calcium and changes of the major biochemical components in Spiraling maxima after the addition of CaCO3. in Chinese] Chinese Fishery Sciences, 11, 462-466(2004).