PAGER: constructing PAGs and new PAG-PAG relationships for network biology. - Zongliang Yue; Madhura M. Kshirsagar; Thanh Nguyen 005; Chayaporn Suphavilai; Michael T. Neylon; Liugen Zhu; Timothy Ratliff; Jake Yue Chen (Bioinform., 2015)

Towards constructing "Super Gene Sets" regulatory networks. - Jake Y. Chen; Zongliang Yue; Michael T. Neylon; Thanh Nguyen 005; Nafisa Bulsara; Itika Arora; Timothy Ratliff (BIBM, 2016)

Phenotyping Immune Cells in Tumor and Healthy Tissue Using Flow Cytometry Data. - Ye Chen; Ryan D. Calvert; Ariful Azad; Bartek Rajwa; James Fleet; Timothy Ratliff; Alex Pothen (BCB, 2018)

"Super Gene Set" Causal Relationship Discovery from Functional Genomics Data. - Zongliang Yue; Michael T. Neylon; Thanh Nguyen 005; Timothy Ratliff; Jake Y. Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)