MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods. - Michael Stevens; Jeffrey B. Cheng; Mingchao Xie; Joseph F. Costello; Ting Wang (RECOMB, 2013)

ALEA: a toolbox for allele-specific epigenomics analysis. - Hamid Younesy; Torsten Möller; Alireza Heravi Moussavi; Jeffrey B. Cheng; Joseph F. Costello; Matthew C. Lorincz; Mohammad M. Karimi; Steven J. M. Jones (Bioinform., 2014)

Spectral clustering of single-cell multi-omics data on multilayer graphs. - Shuyi Zhang; Jacob R. Leistico; Raymond J. Cho; Jeffrey B. Cheng; Jun S. Song (Bioinform., 2022)