SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. - Guorong Xu; Nan Deng; Zhiyu Zhao; Thair Judeh; Erik K. Flemington; Dongxiao Zhu (Source Code Biol. Medicine, 2011)

QSEA for fuzzy subgraph querying of KEGG pathways. - Thair Judeh; Tin Chi Nguyen; Dongxiao Zhu (BCB, 2012)

Optimal structural inference of signaling pathways from unordered and overlapping gene sets. - Lipi R. Acharya; Thair Judeh; Guangdi Wang; Dongxiao Zhu (Bioinform., 2012)

GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets. - Lipi R. Acharya; Thair Judeh; Zhansheng Duan; Michael G. Rabbat; Dongxiao Zhu (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Gene Set Cultural Algorithm: A Cultural Algorithm Approach to Reconstruct Networks from Gene Sets. - Thair Judeh; Thaer Jayyousi; Lipi R. Acharya; Robert G. Reynolds; Dongxiao Zhu (BCB, 2013)

GSCA: Reconstructing biological pathway topologies using a cultural algorithms approach. - Thair Judeh; Thaer Jayyousi; Lipi R. Acharya; Robert G. Reynolds; Dongxiao Zhu (IEEE Congress on Evolutionary Computation, 2014)