This study shows that endogenous retroelements promote tolerance to dietary antigens by regulating regulatory T cell function and dendritic cell activity through innate sensing pathways.

bioRxiv · Sep 9, 2025 · PreprintImmunology

ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data

Michael K.B. Ford, Ananth Hari, Oscar L. Rodriguez, Junyan Xu, Justin Lack, Cihan Oguz, Yu Zhang, Andrew J. Oler, Ottavia M. Delmonte, Sarah E. Weber, Mary Magliocco, Jason Barnett, Sandhya Xirasagar, Smilee Samuel, Luisa Imberti, , S. Cenk Şahinalp

ImmunoTyper-SR genotypes IGHV alleles from short read data and identifies associations between IGHV alleles and anti-type I IFN autoantibodies in COVID-19 patients.

Cell Systems · Oct 1, 2022Peer-reviewedBioinformatics

Machine learning identifies SNPs predictive of advanced coronary artery calcium in ClinSeq(R) and Framingham Heart Study cohorts

Cihan Oguz, Shurjo Kumar Sen, Adam R. Davis, Yi‐Ping Fu, Christopher J. O’Donnell, Gary H. Gibbons

The paper uses machine learning to identify SNPs predictive of advanced coronary artery calcium in two cohorts, finding that SNPs from extreme cases outperform those from prior GWAS.

BMC Systems Biology · Oct 26, 2017Peer-reviewedGenomics