Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes. - Michael F. Lin; Ameya N. Deoras; Matthew D. Rasmussen; Manolis Kellis (PLoS Comput. Biol., 2008)

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. - Michael F. Lin; Irwin Jungreis; Manolis Kellis (Bioinform., 2011)

Identifying protein-coding genes and synonymous constraint elements using phylogenetic codon models. - Michael F. Lin (2012)

Sparse Project VCF: efficient encoding of population genotype matrices. - Michael F. Lin; Xiaodong Bai; William J. Salerno; Jeffrey G. Reid (Bioinform., 2021)

Accurate, scalable cohort variant calls using DeepVariant and GLnexus. - Taedong Yun; Helen Li; Pi-Chuan Chang; Michael F. Lin; Andrew Carroll; Cory Y. McLean (Bioinform., 2021)