Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors. - Andrew Wight; Doo Yang; Ilya Ioshikhes; Andrew P. Makrigiannis (PLoS Comput. Biol., 2016)

Drosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns. - Doo Yang; Ilya Ioshikhes (J. Comput. Biol., 2017)

Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules. - A. K. M. Firoj Mahmud; Doo Yang; Per Stenberg; Ilya Ioshikhes; Soumyadeep Nandi (J. Comput. Biol., 2020)