Publications

For the most complete and up-to-date list, see Google Scholar.

* represents co-first authorship, # represents co-corresponding authorship

Computational MethodsClinical ApplicationEpiFluidLab

Genome-wide variation in cell-free DNA end motif entropy predicts immunotherapy response in head and neck cancer

Ravi Bandaru, Hailu Fu, Haizi Zheng, Jocelyn Liang, Li Wang, Shuchi Gulati, Benjamin H. Hinrichs, Mingxiang Teng, Bin Zhang, Masha Kocherginsky, De-Chen Lin, David A. Hildeman, Francis P. Worden, Matthew O. Old, Neal E. Dunlap, John M. Kaczmar, Maura L. Gillison, Dalia El-Gamal, Trisha Wise Draper^#, Yaping Liu^#

Journal of Clinical Investigation · 2026 · DOI: 10.1172/JCI196284 · Source Code

Computational MethodsToolsEpiFluidLab

FinaleToolkit: accelerating cell-free DNA fragmentation analysis with a high-speed computational toolkit

James Wenhan Li^*, Ravi Bandaru^*, Kundan Baliga, Yaping Liu

Bioinformatics Advances · 2025 · DOI: 10.1093/bioadv/vbaf236 · FinaleToolkit Source Code

Computational MethodsClinical ApplicationEpiFluidLab

Circulating cell-free DNA methylation profiles as noninvasive multiple sclerosis biomarkers: A proof-of-concept study

Hailu Fu, Kevin Huang, Wen Zhu, Lili Zhang, Ravi Bandaru, Shruthi Venkatesh, Elizabeth Walker, Li Wang, Yaping Liu^#, Zongqi Xia^#

medRxiv (preprint) · 2025 · DOI: 10.1101/2025.02.14.25322180 · Source Code

Computational MethodsEpiFluidLab

FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA

Yaping Liu^#, Sarah C. Reed, Christopher Lo, Atish D. Choudhury, Heather A. Parsons, Daniel G. Stover, Gavin Ha, Gregory Gydush, Justin Rhoades, Denisse Rotem, Samuel Freeman, David W. Katz, Ravi Bandaru, Haizi Zheng, Hailu Fu, Viktor A. Adalsteinsson^#, Manolis Kellis^#

Nature Communications · 2024 · DOI: 10.1038/s41467-024-47196-6 · FinaleMe Source Code

Collaboration

Downstream-of-gene (DoG) transcripts contribute to an imbalance in the cancer cell transcriptome

Kouki Abe, Brian Maunze, Pedro Avila Lopez, Jessica Xu, Nefertiti Muhammad, Guang-Yu Yang, David W. Katz, Yaping Liu^#, Shannon M. Lauberth^#

Science Advances · 2024 · DOI: 10.1126/sciadv.adh9613

Journal of the American Society of Nephrology

Collaboration

Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer–Promoter Interactions in the Transgene

Alison J. Perl, Han Liu, Matthew Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan

Journal of the American Society of Nephrology · 2024 · DOI: 10.1681/ASN.0000000000000324

Collaboration

Tet-mediated DNA methylation dynamics affect chromosome organization

Hao Tian, Pengfei Luan, Yaping Liu, Guoqiang Li

Nucleic Acids Research · 2024 · DOI: 10.1093/nar/gkae054

Multi-omics TechnologyEpiFluidLab

NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

Hailu Fu, Haizi Zheng, Xiaoting Chen, Matthew T. Weirauch, Louis J. Muglia, Li Wang^#, Yaping Liu^#

Genome Biology · 2023 · DOI: 10.1186/s13059-023-02889-x

Collaboration

Human fetal cerebellar cell atlas informs medulloblastoma origin and oncogenesis

Zaili Luo, Mingyang Xia, Wei Shi, Chuntao Zhao, Jiajia Wang, Dazhuan Xin, Xinran Dong, Yu Xiong, Feng Zhang, Kalen Berry, Sean Ogurek, Xuezhao Liu, Rohit Rao, Rui Xing, Lai Man Natalie Wu, Siying Cui, Lingli Xu, Yifeng Lin, Wenkun Ma, Shuaiwei Tian, Qi Xie, Li Zhang, Mei Xin, Xiaotao Wang, Feng Yue, Haizi Zheng, Yaping Liu, Charles B. Stevenson, Peter de Blank, John P. Perentesis, Richard J. Gilbertson, Hao Li, Jie Ma, Wenhao Zhou, Michael D. Taylor, Q. Richard Lu

Nature · 2022 · DOI: 10.1038/s41586-022-05487-2