A hitchhiker's guide to expressed sequence tag (EST) analysis. - Shivashankar H. Nagaraj; Robin B. Gasser; Shoba Ranganathan (Briefings Bioinform., 2007)

ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform. - Shivashankar H. Nagaraj; Nandan Deshpande; Robin B. Gasser; Shoba Ranganathan (Nucleic Acids Res., 2007)

In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches. - Shivashankar H. Nagaraj; Robin B. Gasser; Alasdair J. Nisbet; Shoba Ranganathan (BMC Bioinform., 2008)

Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data. - Antonio Reverter; Nicholas J. Hudson 001; Shivashankar H. Nagaraj; Miguel Pérez-Enciso; Brian P. Dalrymple (Bioinform., 2010)

A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer. - Shivashankar H. Nagaraj; Antonio Reverter (BMC Syst. Biol., 2011)

Functional Enrichment Analysis. - Srikanth Manda; Daliah Michael; Sudhir Jadhao; Shivashankar H. Nagaraj (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Exome Sequencing Data Analysis. - Anita Sathyanarayanan; Srikanth Manda; Mukta Poojary; Shivashankar H. Nagaraj (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping. - Anita Sathyanarayanan; Rohit Gupta; Erik W. Thompson; Dale R. Nyholt; Denis C. Bauer; Shivashankar H. Nagaraj (Briefings Bioinform., 2020)

Identification of Small Open Reading Frame-encoded Proteins in the Human Genome. - Hitesh Kore; Satomi Okano; Keshava K. Datta; Jackson Thorp; Parthiban Periasamy; Mayur Divate; Upekha Liyanage; Gunter Hartel; Shivashankar H. Nagaraj; Harsha Gowda (Genom. Proteom. Bioinform., 2025)