- Maria Luisa Amaral, Sainath Mamde, Michael Miller, Xiaomeng Hou, Jessica Arzavala, Julia Osteen, Nicholas D Johnson, Elizabeth Walker Smoot, Qian Yang, Emily Eisner, Qiurui Zeng, Cindy Tatiana Báez-Becerra, Jacqueline Olness, Joseph Colin Kern, Jonathan Rink, Ariana Barcoma, Silvia Cho, Stella Cao, Nora Emerson, Jasper Lee, Jackson Willier, Timothy Loe, Henry Jiao, Songpeng Zu, Quan Zhu, Sebastian Preissl, Allen Wang, Joseph R Ecker, Maria Margarita Behrens, Bing Ren. Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging. bioRxiv (2025)
- Songpeng Zu*, Yang Eric Li*, Kangli Wang*, Ethan J Armand, Sainath Mamde, Maria Luisa Amaral, Yuelai Wang, Andre Chu, Yang Xie, Michael Miller, Jie Xu, Zhaoning Wang, Kai Zhang, Bojing Jia, Xiaomeng Hou, Lin Lin, Qian Yang, Seoyeon Lee, Bin Li, Samantha Kuan, Hanqing Liu, Jingtian Zhou, Antonio Pinto-Duarte, Jacinta Lucero, Julia Osteen, Michael Nunn, Kimberly A Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Zihan Wang, Jingbo Shang, M Margarita Behrens, Joseph R Ecker, Allen Wang, Sebastian Preissl, Bing Ren. Single-cell analysis of chromatin accessibility in the adult mouse brain. Nature (2023)
- Hanqing Liu, Qiurui Zeng, Jingtian Zhou, Anna Bartlett, Bang-An Wang, Peter Berube, Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R Nery, Huaming Chen, Rosa G Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K Osteen, Antonio Pinto-Duarte, Jasper Lee, Jon Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O’Connor, Zhanghao Wu, Ion Stoica, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Chongyuan Luo, Jesse R Dixon, Hongkui Zeng, Bing Ren, M Margarita Behrens, Joseph R Ecker. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature (2023)
- Zhirui Hu*, Songpeng Zu*, Jun S Liu. SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation. NAR genomics and bioinformatics (2020)
- Qingyang Ding, Siyu Hou, Songpeng Zu, Yonghui Zhang, Shao Li. VISAR: an interactive tool for dissecting chemical features learned by deep neural network QSAR models. Bioinformatics (2020)
- Zijian Ding, Songpeng Zu, Jin Gu. Evaluating the molecule-based prediction of clinical drug responses in cancer. Bioinformatics (2016)
- Songpeng Zu, Ting Chen, Shao Li. Global optimization-based inference of chemogenomic features from drug–target interactions. Bioinformatics (2015)
(*: co-first author)