Oscad: An open source EDA tool for circuit design, simulation, analysis and PCB design. - Yogesh Dilip Save; Rajalekshmi Rakhi; N. D. Shambhulingayya; Ambikeshwar Srivastava; Manas Ranjan Das; Saket Choudhary; Kannan M. Moudgalya (ICECS, 2013)

Reaction Decoder Tool (RDT): extracting features from chemical reactions. - Syed Asad Rahman; Gilliean Torrance; Lorenzo Baldacci; Sergio Martínez Cuesta; Franz Fenninger; Nimish Gopal; Saket Choudhary; John W. May; Gemma L. Holliday; Christoph Steinbeck; Janet M. Thornton (Bioinform., 2016)

pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. - Saket Choudhary (F1000Research, 2019)

Accurate detection of short and long active ORFs using Ribo-seq data. - Saket Choudhary; Wenzheng Li; Andrew D. Smith (Bioinform., 2020)