2026

TPCAV: Interpreting deep learning genomics models via concept attribution

Jianyu Yang, Shaun Mahony
bioRxiv, 2026.01. 20.700723
10.64898/2026.01.20.700723

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

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