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IIDR Trainee Publishes “How To” Guide for Bioinformatics

Feb. 7, 2014 – Fiona Whelan, a graduate student in IIDR member Mike Surette’s lab, has published a review article called “A guide to bioinformatics for immunologists” in Frontiers Immunology.

“The idea of this article spawned from research that I conducted in the Bowdish lab on the elucidation of the evolutionary history and relationships between the members of the class A scavenger receptors, proteins required for host defense and homeostasis,” says Whelan.

Whelan worked collaboratively in Dawn Bowdish’s lab in 2013 and at the time used multiple bioinformatic techniques and tools to form hypotheses as to the function of one under-annotated member of the family, SCARA3.

“Even though most of these tools are easy-to-use and require little computational knowledge, I discovered through interactions with Dr. Bowdish and other immunologists that these tools are being under utilized.” She decided to write a review on how bioinformatic techniques can help the average immunologist in their quest for knowledge about the structure of their protein of interest, how to find SNPs that may correlate with disease phenotype, and how to conduct sequence alignments in order to find areas that are conserved across various genes.

The review article is written as a case study that follows Whelan’s research into SCARA3 that begins with obtaining the NCBI Reference FASTA sequence of the protein, predicting post-translational modifications, identifying conserved motifs, hypothesizing as to the structure of the protein, examining SCARA3’s transcriptomic profile in different immunological cell types, and analyzing any potential SNPs within the DNA sequence of SCARA3 that may correlate with disease. “The article is written with the immunologist in mind,” she says, “and includes the use of only “point and click” tools that require no computational background.”

To view the Open Access paper visit http://www.frontiersin.org/Journal/10.3389/fimmu.2013.00416/abstract