Selected publications. For complete list, please refer to [Google Scholar].

3D Genome Organization & Gene Regulation

•  Wang P, Wang J, Wang Q, et al., Fan R^#, Yue F^#. Spatial chromatin architecture and accessibility co-profiling of mammalian tissues . Nature Methods (2026).

•  Dekker J^#, Akgol Oksuz B, Zhang Y, et al., Wang X^#, Nicodemi M^#, Ren B^#, Zhong S^#, Phillips-Cremins JE^#, Gilbert DM^#, Pollard KS^#, Alber F^#, Ma J^#, Noble WS^#, Yue F^#. An integrated view of the structure and function of the human 4D nucleome . Nature 649(8097):759-776 (2026).

•  Wang K, Wang J, Feng R, et al., Yue F^#, Xu J^#. Silencing of BCL11A by disrupting enhancer-dependent epigenetic insulation . Blood 147(13):1470-1484 (2026).

•  Xu J, Song F, Lyu H, et al., Zheng H^#, Yue F^#. Subtype-specific 3D genome alteration in acute myeloid leukaemia . Nature 611(7935):387-398 (2022).

•  Yang H, Zhang H, Luan Y, et al., Yue F^#, Yang JJ^#. Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation . Nature Genetics 54(2):170-179 (2022).

•  Yang H, Luan Y, Liu T, et al., Yue F. A map of cis-regulatory elements and 3D genome structures in zebrafish . Nature 588(7837):337-343 (2020).

•  Yue F^*, Cheng Y^*, Breschi A^*, Vierstra J^*, Wu W^*, Ryba T^*, Sandstrom R^*, Ma Z^*, Davis C^*, Pope BD^*, Shen Y^*, et al. A comparative encyclopedia of DNA elements in the mouse genome . Nature 515(7527):355-364 (2014).

Cancer Genomics & Epigenomics

•  Wang Q, Wang J, Mathur R, et al., Costello JF^#, Yue F^#. Spatial 3D genome organization reveals intratumor heterogeneity in primary glioblastoma samples . Science Advances 11(11):eadn2830 (2025).

•  Lyu H, Chen X, Cheng Y, Zhang T, Wang P, Wong JHY, Wang J, Stasiak L, Sun L, Yang G, Wang L, Yue F. Pioneer factor GATA6 promotes colorectal cancer through 3D genome regulation . Science Advances 11(6):eads4985 (2025).

•  Mathur R, Wang Q, Schupp PG, et al., Yue F^#, Costello JF^#. Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective . Cell 187(2):446-463.e16 (2024).

•  Liu T, Wang J, Yang H, et al., Pollock R^#, Yue F^#. Enhancer Coamplification and Hijacking Promote Oncogene Expression in Liposarcoma . Cancer Research 83(9):1517-1530 (2023).

•  Wang J, Huang TY, Hou Y, Bartom E, Lu X, Shilatifard A, Yue F^#, Saratsis A^#. Epigenomic landscape and 3D genome structure in pediatric high-grade glioma . Science Advances 7(23):eabg4126 (2021).

•  Iyyanki T, Zhang B, Wang Q, et al., DeGraff DJ^#, Yue F^#. Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer . Genome Biology 22(1):105 (2021).

•  Zhang J, Lee D, Dhiman V, et al., Yue F^#, Liu XS^#, White KP^#, Gerstein M^#. An integrative ENCODE resource for cancer genomics . Nature Communications 11(1):3696 (2020).

•  Dixon JR, Xu J, Dileep V, et al., Ay F^#, Noble WS^#, Dekker J^#, Gilbert DM^#, Yue F^#. Integrative detection and analysis of structural variation in cancer genomes . Nature Genetics 50(10):1388-1398 (2018).

Computational Genomics & AI/ML Methods

•  Yu S, Fu Y, Wong JHY, Wang J, Zhao H, Zhao J, Yue F. The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D genome architecture . Nucleic Acids Research 54(D1):D48-D54 (2026).

•  Li L, Hong C, Xu J, et al., Yue F^#, Yip KY^#. Accurate identification of structural variations from cancer samples . Briefings in Bioinformatics 25(1):bbad520 (2024).

•  Wang X, Yue F. HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies . Bioinformatics 39(6):btad389 (2023).

•  Wang X, Luan Y, Yue F. EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps . Science Advances 8(24):eabn9215 (2022).

•  Wang X, Xu J, Zhang B, Hou Y, Song F, Lyu H, Yue F. Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes . Nature Methods 18(6):661-668 (2021).

•  Salameh TJ, Wang X, Song F, Zhang B, Wright SM, Khunsriraksakul C, Ruan Y, Yue F. A supervised learning framework for chromatin loop detection in genome-wide contact maps . Nature Communications 11(1):3428 (2020).

•  Wang Y, Song F, Zhang B, et al., Wang T^#, Yue F^#. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions . Genome Biology 19(1):151 (2018).

•  Zhang Y, An L, Xu J, Zhang B, Zheng WJ, Hu M, Tang J, Yue F. Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus . Nature Communications 9(1):750 (2018).

•  Yang T, Zhang F, Yardımcı GG, Song F, Hardison RC, Noble WS, Yue F^#, Li Q^#. HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient . Genome Research 27(11):1939-1949 (2017).