Open problems of computational immunogenomics

Yana Safonova, University of California, San Diego
Host: Ben Langmead

Twelve years ago, biologists developed the repertoire sequencing technology (Rep-seq) that samples millions out of a billion constantly changing antibodies (or immunoglobulins) circulating in each of us. Repertoire sequencing represented a paradigm shift as compared to the previous “one-antibody-at-a-time” approaches, raised novel algorithmic, statistical, information theory, and machine learning challenges, and led to the emergence of computational immunogenomics.

I will describe our recent work on reconstructing the evolution of antibody repertoires, inferring novel diversity (D) genes in the immunoglobulin loci, and solving the three-decade-old puzzle of explaining the mechanism for generating biomedically important ultralong antibodies via tandem D-D fusions. I will also describe several collaborative projects in the emerging fields of personalized immunogenomics (analyzing how mutations in the immunoglobulin loci affect our ability to develop antibodies that neutralize flu and HIV) and agricultural immunogenomics (analyzing cow antibody repertoires to assist in breeding efforts).

Speaker Biography

Yana Safonova received the B.Sc. (2010) and M.Sc. (2012) degrees in Computer Science from the Nizhny Novgorod State University, Russia, and the Ph.D. degree (2017) in Bioinformatics from the Saint Petersburg State University, Russia. Since 2017, she has been a Postdoctoral Scholar at the Computer Science and Engineering Department at University of California, San Diego (UCSD), USA. Since 2019, she has also been affiliated with the Department of Biochemistry and Molecular Genetics at the University of Louisville School of Medicine, USA.

Her research interests cover open problems in immunogenomics and computational immunology that include applications of the recently emerged repertoire sequencing technologies to design of antibody drugs, prediction of vaccine efficacy, and population analysis of the immune loci. Dr. Safonova was selected as a recipient of the Data Science Postdoctoral Fellowship (2017) by UCSD and the Intersect Fellowship for Computational Scientists and Immunologists (2019) by the American Associations of Immunologists. She is a member of the The Adaptive Immune Receptor Repertoire (AIRR) Community of The Antibody Society and an author of a graduate Immunogenomics course.