TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites. - Tsu-Pei Chiu; Beibei Xin; Nicholas Markarian; Yingfei Wang; Remo Rohs (Nucleic Acids Res., 2020)

DNAproDB: an expanded database and web-based tool for structural analysis of DNA?protein complexes. - Jared M. Sagendorf; Nicholas Markarian; Helen M. Berman; Remo Rohs (Nucleic Acids Res., 2020)

Enrichment on steps, not genes, improves inference of differentially expressed pathways. - Nicholas Markarian; Kimberly M. Van Auken; Dustin Ebert; Paul W. Sternberg (PLoS Comput. Biol., 2024)