PAR-3D: a server to predict protein active site residues. - Kshama Goyal; Debasisa Mohanty; Shekhar C. Mande (Nucleic Acids Res., 2007)

Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data. - Shubhada R. Hegde; Palanisamy Manimaran; Shekhar C. Mande (PLoS Comput. Biol., 2008)

Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions. - Shubhada R. Hegde; Khushbu Pal; Shekhar C. Mande (BMC Syst. Biol., 2014)

Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. - Gaurang Mahajan; Shekhar C. Mande (BMC Bioinform., 2017)