Compression-based Network Interpretability Schemes
J Warrell, H Mohsen, M Gerstein (2020). bioRxiv.

Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements
HE Pratt, G Andrews, N Shedd, N Phalke, T Li, A Pampari, M Jensen, C Wen, P Consortium, MJ Gandal, DH Geschwind, M Gerstein, J Moore, A Kundaje, A Colubri, Z Weng (2024). Sci Adv 10: eadj4452.

scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding
Z Duan, S Xu, S Sai Srinivasan, A Hwang, CY Lee, F Yue, M Gerstein, Y Luan, M Girgenti, J Zhang (2024). Brief Bioinform 25.

SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments.
Z Chen, J Zhang, J Liu, Z Zhang, J Zhu, D Lee, M Xu, M Gerstein (2021). Bioinformatics 37: 1756-1758.

Quantum computing at the frontiers of biological sciences
PS Emani, J Warrell, A Anticevic, S Bekiranov, M Gandal, MJ McConnell, G Sapiro, A Aspuru-Guzik, JT Baker, M Bastiani, JD Murray, SN Sotiropoulos, J Taylor, G Senthil, T Lehner, MB Gerstein, AW Harrow (2021). Nat Methods 18: 701-709.

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