Genetic network inference: from co-expression clustering to reverse engineering. - Patrik D'haeseleer; Shoudan Liang; Roland Somogyi (Bioinform., 2000)

cWINNOWER Algorithm for Finding Fuzzy DNA Motifs. - Shoudan Liang (CSB, 2003)

fREDUCE: Detection of degenerate regulatory elements using correlation with expression. - Randy Z. Wu; Christina Chaivorapol; Jiashun Zheng; Hao Li; Shoudan Liang (BMC Bioinform., 2007)

Genome-Wide Analysis of Epigenetic Modifications. - Shoudan Liang (J. Comput. Sci. Technol., 2009)

A Bayesian model for SNP discovery based on next-generation sequencing data. - Yanxun Xu; Xiaofeng Zheng; Yuan Yuan 003; Marcos R. Estecio; Jean-Pierre Issa; Yuan Ji; Shoudan Liang (GENSiPS, 2012)

Accuracy of RNA-Seq and its dependence on sequencing depth. - Guoshuai Cai; Hua Li; Yue Lu; Xuelin Huang; Juhee Lee; Peter Müller 003; Yuan Ji; Shoudan Liang (BMC Bioinform., 2012)

BM-BC: a Bayesian method of base calling for Solexa sequence data. - Yuan Ji; Riten Mitra; Fernando Quintana; Alejandro Jara; Peter Müller 003; Ping Liu; Yue Lu; Shoudan Liang (BMC Bioinform., 2012)

dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes. - Hua Li; Xiao Su; Juan J. Gallegos; Yue Lu; Yuan Ji; Jeffrey J. Molldrem; Shoudan Liang (BMC Bioinform., 2012)

BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data. - Yanxun Xu; Xiaofeng Zheng; Yuan Yuan 003; Marcos R. Estecio; Jean-Pierre Issa; Peng Qiu; Yuan Ji; Shoudan Liang (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Local sequence and sequencing depth dependent accuracy of RNA-seq reads. - Guoshuai Cai; Shoudan Liang; Xiaofeng Zheng; Feifei Xiao (BMC Bioinform., 2017)