ExPrimer: to design primers from exon-exon junctions. - Kuljeet S. Sandhu; Kshitish K. Acharya (Bioinform., 2005)

Systematic comparison of the protein-protein interaction databases from a user's perspective. - Akhilesh Kumar Bajpai; Sravanthi Davuluri; Kriti Tiwary; Sithalechumi Narayanan; Sailaja Oguru; Kavyashree Basavaraju; Deena Dayalan; Kavitha Thirumurugan; Kshitish K. Acharya (J. Biomed. Informatics, 2020)

Computational analysis of promoter features associated with contrasting expression patterns of human genes under normal and disease conditions. - Vasumathi Manivelan; Bindu Sadanandan; Sravanti Vaidya; Kshitish K. Acharya (Comput. Biol. Medicine, 2025)