kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets. - Christopher Fletez-Brant; Dongwon Lee 005; Andrew S. McCallion; Michael A. Beer (Nucleic Acids Res., 2013)

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features. - Mahmoud Ghandi; Dongwon Lee 005; Morteza Mohammad Noori; Michael A. Beer (PLoS Comput. Biol., 2014)

gkmSVM: an R package for gapped-kmer SVM. - Mahmoud Ghandi; Morteza Mohammad Noori; Narges Ghareghani; Dongwon Lee 005; Levi A. Garraway; Michael A. Beer (Bioinform., 2016)

Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy. - Wang Xi; Michael A. Beer (PLoS Comput. Biol., 2018)

Non-local modeling of enhancer-promoter interactions, a correspondence on "LOCO-EPI: Leave-one-chromosome-out (LOCO) as a benchmarking paradigm for deep learning based prediction of enhancer-promoter interactions". - Michael A. Beer (Appl. Intell., 2025)