A research article co-authored by CDS researchers Ghanshyam Chandra and Chirag Jain has been featured on the cover of Genome Research, one of the leading journals in genomics and computational biology. This was a collaborative effort with researchers at the University of Texas Dallas and Heinrich Heine University.
Link to full article: Chandra, G., Hossen, M.H., Scholz, S., Dilthey, A.T., Gibney, D. and Jain, C., 2025. Pangenome-based genome inference using integer programming. Genome Research. https://doi.org/10.1101/gr.280567.125
Summary: Genotyping (the process of identifying which genetic variants an individual carries) remains challenging in highly variable and repetitive regions of the human genome. To address this, Chandra et al. leveraged pangenome references and formulated genotyping as a graph-based optimization problem. By leveraging integer programming techniques, the proposed algorithm offers optimality guarantees and delivers superior accuracy compared to previous approaches.
