Traditional disease diagnostics test for virus presence, but an alternate strategy could examine the body’s host response against the virus. Using multi-cohort analysis with public transcriptional data, the Khatri group identified an 11-gene host transcriptional signature1, or Influenza Meta Signature (IMS), that distinguishes individuals with influenza from those with bacterial or respiratory viral infections. Detecting IMS transcripts in blood with a sensitive tool could be a rapid diagnostic for predicting influenza infection. PCR is normally used to quantify transcript levels, but is limited in multiplexing. We propose a gene expression analysis assay to measure IMS transcripts using a giant magnetoresistive (GMR) biosensor array, which has previously been used for DNA detection in biological samples, and allows multiplexed transcript quantification through magnetic detection. Advantages of magnetic sensing compared to optical detection include a lower limit of detection and lower background in biological samples. By measuring IMS expression using GMR sensors, we accurately distinguished influenza patients from human rhinovirus patients and symptomatic but negative patients (p<0.0001, n=54) with an AUC of 0.92.