Selection of antisense oligonucleotides based on multiple predicted target mRNA structures. - Xiaochen Bo; Shaoke Lou; Daochun Sun; Wenjie Shu; Jing Yang; Shengqi Wang (BMC Bioinform., 2006)

AOBase: a database for antisense oligonucleotides selection and design. - Xiaochen Bo; Shaoke Lou; Daochun Sun; Jing Yang; Shengqi Wang (Nucleic Acids Res., 2006)

Regulators Associated with Clinical Outcomes Revealed by DNA Methylation Data in Breast Cancer. - Matthew H. Ung; Frederick S. Varn; Shaoke Lou; Chao Cheng (PLoS Comput. Biol., 2015)

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions. - Koon-Kiu Yan; Shaoke Lou; Mark Gerstein (PLoS Comput. Biol., 2017)

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)

Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients. - Shaoke Lou; Tianxiao Li; Daniel Spakowicz; Xiting Yan; Geoffrey Lowell Chupp; Mark Gerstein (BMC 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)

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)

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)

Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes. - Shaoke Lou; Mingjun Yang; Tianxiao Li; Weihao Zhao; Hannah Cevasco; Yucheng T. Yang; Mark Gerstein (PLoS Comput. Biol., 2023)