Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter. - Boian S. Alexandrov; Vladimir Gelev; Sang Wook Yoo; Alan R. Bishop; Kim Ø. Rasmussen; Anny Usheva (PLoS Comput. Biol., 2009)

Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites. - Miriam R. Kantorovitz; Zoi Rapti; Vladimir Gelev; Anny Usheva (BMC Bioinform., 2010)

Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics. - Kristy Nowak-Lovato; Ludmil B. Alexandrov; Afsheen Banisadr; Amy L. Bauer; Alan R. Bishop; Anny Usheva; Fangping Mu; Elizabeth Hong-Geller; Kim Ø. Rasmussen; William S. Hlavacek; Boian S. Alexandrov (PLoS Comput. Biol., 2013)

Examining DNA breathing with pyDNA-EPBD. - Anowarul Kabir; Manish Bhattarai; Kim Ø. Rasmussen; Amarda Shehu; Anny Usheva; Alan R. Bishop; Boian S. Alexandrov (Bioinform., 2023)