VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. - Duo Xu; Yousef Jaber; Pavlos Pavlidis; Omer Gokcumen (BMC Bioinform., 2017)

Gene communities in co-expression networks across different tissues. - Madison Russell; Alber Aqil; Marie Saitou; Omer Gokcumen; Naoki Masuda (PLoS Comput. Biol., 2023)