TopicNet: a framework for measuring transcriptional regulatory network change. - Shaoke Lou; Tianxiao Li; 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)

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)

Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization. - Shaoke Lou; Tianxiao Li; Jason Liu 003; 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)