Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation. - Joti Giordano; Yongchao Ge; Yevgeniy Gelfand; György Abrusán; Gary Benson; Peter E. Warburton (PLoS Comput. Biol., 2007)

Methyl-Analyzer - whole genome DNA methylation profiling. - Yurong Xin; Yongchao Ge; Fatemeh G. Haghighi (Bioinform., 2011)

flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding. - Yongchao Ge; Stuart C. Sealfon (Bioinform., 2012)

MethylomeDB: a database of DNA methylation profiles of the brain. - Yurong Xin; Benjamin Chanrion; Anne H. O'Donnell; Maria Milekic; Ramiro Costa; Yongchao Ge; Fatemeh G. Haghighi (Nucleic Acids Res., 2012)