2024

Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1

Cheng Xu, Holly Kleinschmidt, Jianyu Yang, Erik M. Leith, Jenna Johnson, Song Tan, Shaun Mahony, Lu Bai
Molecular Cell, 84(15), 2838–2855.e10 (2024)
10.1016/j.molcel.2024.06.022

SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes

Jianyu Yang, Kuangyu Yen, Shaun Mahony
In: Research in Computational Molecular Biology – RECOMB 2024 Proceedings, pp. 320–323 (2024)
10.1007/978-1-0716-3989-4_21

2023

Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin

Sonny Arora, Jianyu Yang, Tomohiko Akiyama, Daniela Q. James, Alexis Morrissey, Thomas R. Blanda, Nitika Badjatia, William K.M. Lai, Minoru S.H. Ko, B. Franklin Pugh, Shaun Mahony
bioRxiv (2023)
10.1101/2023.10.06.561228

2021

Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification

Houyu Zhang, Ting Lu, Shan Liu, Jianyu Yang, Guohuan Sun, Tao Cheng, Jin Xu, Fangyao Chen, Kuangyu Yen
NAR Genomics and Bioinformatics, 3(4), lqab094 (2021)
10.1093/nargab/lqab094

RUNX1 upregulates CENPE to promote leukemic cell proliferation

Shan Liu, Jianyu Yang, Guohuan Sun, Yawen Zhang, Cong Cheng, Jin Xu, Kuangyu Yen, Ting Lu
Frontiers in Molecular Biosciences, 8, 692880 (2021)
10.3389/fmolb.2021.692880