Ten Open Problems in Computational Immunogenomics

Yana Safonova, Data Science Postdoc, UCSD Information Theory and Applications Center


Date: 2017-06-14
Time: 11:00am
Location: Room 5417, CSE Building, UC San Diego

Guest Speaker: Yana Safonova, Postdoctoral Researcher, ITA

Host: ECE Prof. Alon Orlitsky, Director, ITA


The Information Theory and Applications Center (ITA) in the Qualcomm Institute is organizing this seminar featuring Dr. Yana Safonova, currently a Data Science Postdoctoral Fellow in a program co-sponsored by CSE, ECE and QI. Safonova is looking for new collaborators, and welcomes interest from faculty and graduate students..

Rapid development of DNA sequencing technologies opened new avenues for analyzing adaptive immune systems through deep interrogation of antibody repertoires. I will describe some unanticipated features of the immune system revealed by these studies and will discuss new computational problems that have emerged. In particular, I will also discuss how these immunoinformatics challenges relate to information theory, clustering, evolutionary tree reconstruction, analysis of variations in the immune system across human population, and building adequate statistical models for antibody generation.

This is a joint work with Sergey Bankevich (Center for Algorithmic Biology (CAB) at Saint Petersburg State University), Stefano Bonissone (Digital Proteomics), Andrey Bzikadze (CAB), Dmitry Chudakov (Moscow Institute for Bioorganic Chemistry), Klaus Ley (La Jolla Institute for Allergy and Immunology), Jennie Lill (Genentech), Pavel Pevzner (UCSD), Timofey Prodanov (CAB), Wendy Sandoval (Genentech), Alexander Shlemov (CAB), Andrey Slabodkin (CAB), and Sonia Timberlake (Juno Therapeutics).


Yana Safonova holds an M.S. in Computer Science (2012) from Nizhny Novgorod State University and a Ph.D. in Bioinformatics (2017) from Saint Petersburg State University. She is now a Postdoctoral Fellow in the Center for Information Theory and Applications at UC San Diego. She is an author of many tools for analysis of antibody repertoire, including IgRepertoireConstructor, an algorithm for constructing antibody repertoires and AntEvolo, an algorithm for evolutionary reconstruction of antibody repertoires.