HMM-ModE - Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences. - Prashant K. Srivastava; Dhwani K. Desai; Soumyadeep Nandi; Andrew M. Lynn (BMC Bioinform., 2007)

ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities. - Dhwani K. Desai; Soumyadeep Nandi; Prashant K. Srivastava; Andrew M. Lynn (Adv. Bioinformatics, 2011)

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)

ProkSeq for complete analysis of RNA-Seq data from prokaryotes. - A. K. M. Firoj Mahmud; Nicolas Delhomme; Soumyadeep Nandi; Maria Fällman (Bioinform., 2021)