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)

Rational Mutational Analysis of a Multidrug MFS Transporter CaMdr1p of Candida albicans by Employing a Membrane Environment Based Computational Approach. - Khyati Kapoor; Mohd Rehan; Ajeeta Kaushiki; Ritu Pasrija; Andrew M. Lynn; Rajendra Prasad (PLoS Comput. Biol., 2009)

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)

MetaNET - a web-accessible interactive platform for biological metabolic network analysis. - Pankaj Narang; Shawez Khan; Anmol Hemrom; Andrew M. Lynn (BMC Syst. Biol., 2014)

g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations. - Rashmi Kumari; Rajendra Kumar 003; Andrew M. Lynn (J. Chem. Inf. Model., 2014)

GCAC: galaxy workflow system for predictive model building for virtual screening. - Deepak R. Bharti; Anmol Hemrom; Andrew M. Lynn (BMC Bioinform., 2019)

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)

Cytochrome P450 2C9 polymorphism: Effect of amino acid substitutions on protein flexibility in the presence of tamoxifen. - Manish Manish; Andrew M. Lynn; Smriti Mishra (Comput. Biol. Chem., 2020)

Identifying the natural polyphenol catechin as a multi-targeted agent against SARS-CoV-2 for the plausible therapy of COVID-19: an integrated computational approach. - Chandra Bhushan Mishra; Preeti Pandey; Ravi Datta Sharma; Md. Zubbair Malik; Raj Kumar Mongre; Andrew M. Lynn; Rajendra Prasad; Raok Jeon; Amresh Prakash (Briefings Bioinform., 2021)

Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review. - Trishala Das; Harbinder Kaur; Pratibha Gour; Kartikay Prasad; Andrew M. Lynn; Amresh Prakash; Vijay Kumar (Briefings Bioinform., 2022)

In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes. - Siddharth Yadav; Swati Rana; Manish Manish; Sohini Singh; Andrew M. Lynn; Puniti Mathur (J. Comput. Aided Mol. Des., 2025)