For a full list of publications, please see google scholar page.
Selected Publications
1. Yang H*, Zhang H*, Luan Y*, Liu T, Yang W, Roberts KG, Qian M-x, Zhang B, Yang W, Perez-Andreu V, Xu J, Iyyanki S, Kuang D, Stasiak LA, Reshmi SC, Gastier-Foster J, Smith C, Pui C-H, Evans WE, Hunger SP, Platanias LC, Relling MV, Mullighan CG, Loh ML, Yue F, Yang JJ. Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation. Nature Genetics.(2022)
2. Yang H*, Luan Y*, Liu T*, Lee HJ, Fang L, Wang Y, Wang X, Zhang B, Jin Q, Ang KC, Xing X, Wang J, Xu J, Song F, Sriranga I, Khunsriraksakul C, Salameh T, Li D, Choudhary MNK, Topczewski J, Wang K, Gerhard GS, Hardison RC, Wang T, Cheng KC, Yue F. A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature. (2020).
3. Duan Z, Xu S, Sai Srinivasan S, Hwang A, Lee CY, Yue F, Gerstein M, Luan Y, Girgenti M, Zhang J. scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Briefings in Bioinformatics. (2024)
4. Liu T, Wang J, Yang H, Jin Q, Wang X, Fu Y, Luan Y, Wang Q, Youngblood MW, Lu X, Casadei L, Pollock R, Yue F. Enhancer Coamplification and Hijacking Promote Oncogene Expression in Liposarcoma. Cancer Res. (2023)
5. Xu J, Song F, Lyu H, Kobayashi M, Zhang B, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wong JH-y, Wang Q, Jin Q, Jin Q, Fu Y, Yang H, Hardison RC, Dovat S, Platanias LC, Diao Y, Yang Y, Yamada T, Viny AD, Levine RL, Claxton D, Broach JR, Zheng H, Yue F. Subtype-specific 3D genome alteration in acute myeloid leukaemia. Nature. (2022)
6. Wang, X., Luan, Y. and Yue, F. EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps. Science advances (2022)
7. Sun F, Ou J, Shoffner AR, Luan Y, Yang H, Song L, Safi A, Cao J, Yue F, Crawford GE, Poss KD. Enhancer selection dictates gene expression responses in remote organs during tissue regeneration. Nature Cell Biology. (2022)
8. Zhao Y, Hou Y, Xu Y, Luan Y, Zhou H, Qi X, Hu M, Wang D, Wang Z, Fu Y, Li J, Zhang S, Chen J, Han J, Li X, Zhao S. A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. Nature Communications. (2021);
9. Iyyanki T, Zhang B, Wang Q, Hou Y, Jin Q, Xu J, Yang H, Liu T, Wang X, Song F, Luan Y, Yamashita H, Chien R, Lyu H, Zhang L, Wang L, Warrick J, Raman JD, Meeks JJ, DeGraff DJ, Yue F. Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer. Genome Biology.(2021)
10. Luan Y, Zhang L, Hu M, Xu Y, Hou Y, Li X, Zhao S, Zhao Y, Li C. Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver. Genes. (2019)
11. Shi, Q., Aryal, S., Jin, Q., Zhou, X., He, C., Yang, H., Lu, R#. and Luan, Y#., 2025. Acute depletion of HOXA9 reveals its direct role in cis-elements regulation and 3D genome organization during Acute Myeloid Leukemia. Blood, 146, p.1461.
12. Sui P, Li Y, Hong J, Delma CR, Chen S, Wang J, Zhang P, Han S, Noor A, Yang H, Pang Y, Luan Y, Xu M, Lee J, Yang F-C. Oncogenic activation of EVC/EVC2 defines a therapeutically targetable subset of acute myeloid leukemia. Leukemia. 2026;40(1):166-77. doi: 10.1038/s41375-025-02803-3.
13. Xu, Y., Nipper, M.H., Dominguez, A.A., He, C., Sharkey, F.E., Khan, S., Xu, H., Zhou, D., Zheng, L., Luan, Y. Liu, J and Pei Wang. NF2 loss malignantly transforms human pancreatic acinar cells and enhances cell fitness under environmental stress. JCI, 2026.
14. IGVF Consortium. Deciphering the impact of genomic variation on function. Nature. 2024;633(8028):47-57. doi: 10.1038/s41586-024-07510-0.
15. Wang Q, Wang J, Mathur R, Youngblood MW, Jin Q, Hou Y, Stasiak LA, Luan Y, Zhao H, Hilz S, Hong C, Chang SM, Lupo JM, Phillips JJ, Costello JF, Yue F. Spatial 3D genome organization reveals intratumor heterogeneity in primary glioblastoma samples. Science Advances. 2025;11(11):eadn2830. doi: doi:10.1126/sciadv.adn2830.
16. Li J, Bai J, Pham VT, Hashimoto M, Sezaki M, Shi Q, Jin Q, He C, Armstrong A, Li T, Pan M, Liu S, Luan Y, Zeng H, Andreassen PR, Huang G. Loss of Cpt1a results in elevated glucose-fueled mitochondrial oxidative phosphorylation and defective hematopoietic stem cells. J Clin Invest. 2025. Epub 20250109. doi: 10.1172/JCI184069. PubMed PMID: 39786963.
17. Gould A*, Luan Y, Hou Y, Korobova FV, Chen L, Arrieta VA, Amidei C, Ward R, Gomez C, Castro B, Habashy K, Zhang D, Youngblood M, Dmello C, Bebawy J, Bouchoux G, Stupp R, Canney M, Yue F, Iruela-Arispe ML, Sonabend AM. Endothelial Response to Blood-Brain Barrier Disruption in the Human Brain. JCI Insight. 2024. Epub 20241226. doi: 10.1172/jci.insight.187328. PubMed PMID: 39724015
18. Duan Z, Xu S, Sai Srinivasan S, Hwang A, Lee CY, Yue F, Gerstein M, Luan Y, Girgenti M#, Zhang J#. scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Briefings in Bioinformatics. 2024;25(2):bbae096.
19. Zhang L, Zhou X, Aryal S, Veasey V, Zhang P, Li FJ, Luan Y, Bhatia R, Zhou Y, Lu R. CRISPR screen of venetoclax response-associated genes identifies transcription factor ZNF740 as a key functional regulator. Cell Death & Disease. 2024;15(8):627. doi: 10.1038/s41419-024-06995-x
20. Wu Y, Qin K, Xu Y, Rajhans S, Vo T, Lopez KM, Liu J, Nipper MH, Deng J, Yin X, Ramjit LR, Ye Z, Luan Y, Arda HE, Wang P. Hippo pathway-mediated YAP1/TAZ inhibition is essential for proper pancreatic endocrine specification and differentiation. eLife. 2024;13:e84532. doi: 10.7554/eLife.84532.