TopicNet: a framework for measuring transcriptional regulatory network change. - Shaoke Lou; Tianxiao Li 001; Xiangmeng Kong; Jing Zhang 062; Jason Liu 003; Donghoon Lee 006; Mark Gerstein (Bioinform., 2020)

DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring. - Jing Zhang 062; Jason Liu 003; Donghoon Lee 006; Shaoke Lou; Zhanlin Chen; Gamze Gürsoy; Mark Gerstein (BMC Bioinform., 2020)

NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis. - Jing Zhang 062; Jason Liu 003; Patrick D. McGillivray; Caroline Yi; Lucas Lochovsky; Donghoon Lee 006; Mark Gerstein (BMC Bioinform., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Epigenome-based splicing prediction using a recurrent neural network. - Donghoon Lee 006; Jing Zhang 062; Jason Liu 003; Mark Gerstein (PLoS Comput. Biol., 2020)

DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays. - Zhanlin Chen; Jing Zhang 062; Jason Liu 003; Yi Dai; Donghoon Lee 006; Martin Renqiang Min; Min Xu 009; Mark Gerstein (Bioinform., 2021)

Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions. - Jason Liu 003; Daniel J. Spakowicz; Garrett I. Ash; Rebecca Hoyd; Rohan Ahluwalia; Andrew Zhang; Shaoke Lou; Donghoon Lee 006; Jing Zhang 062; Carolyn Presley; Ann Greene; Matthew Stults-Kolehmainen; et al. (PLoS Comput. Biol., 2021)