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)

Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes. - Dhwani K. Desai; Harald Schunck; Johannes W. Löser; Julie LaRoche (Bioinform., 2013)

Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study. - Swati Sinha; Andrew M. Lynn; Dhwani K. Desai (BMC Bioinform., 2020)