Vadim Karnaukhov

Research advisor: Professor Dmitrii Chudakov

Program entry year: 2019

Graduated from MSU, Faculty of Chemistry in 2019

Research project: Structural basis for T-cell receptor specificity and cross-reactivity prediction

Research interests:  systems immunology, structural bioinformatics, immuno-oncology, application of machine learning to immunology, prediction of neoepitope immunogenicity, TCR-based immunotherapeutics, single-cell transcriptomics

Publications:

Predicting TCR-peptide recognition based on residue-level pairwise statistical potential. Karnaukhov V., Shcherbinin D., Chugunov A., Chudakov D., Efremov R., Zvyagin I., Shugay M. 2022. Preprint: https://www.biorxiv.org/content/10.1101/2022.02.15.480516v1

HLA binding of self-peptides is biased towards proteins with specific molecular functions. V. Karnaukhov, W. Paes, I. Woodhouse,  T. Partridge, A. Nicastri,  S. Brackenridge, D. Scherbinin, D. Chudakov, I. Zvyagin,  N. Ternette,  H. Koohy,  P. Borrow,  M. Shugay.  2021. Preprint: https://www.biorxiv.org/content/10.1101/2021.02.16.431395v1

Pinpointing the tumor-specific T-cells via TCR clusters. Goncharov M., Bryushkova E., Sharaev N., Skatova V., Baryshnikova A., Sharonov G., Karnaukhov V., Vakhitova M., Samoylenko I., Demidov L., Lukyanov S., Chudakov D., Serebrovskaya E. Elife. 2022 Apr 4;11:e77274.

Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones. Minervina A.A., Pogorelyy M.V., Komech E.A., Karnaukhov V.K., Bacher P., Rosati E., Franke A., Chudakov D.M., Mamedov I.Z., Lebedev Y.B., Mora T., Walczak A.M. Elife, 2020 9: e53704

Conference presentations:

TCRen: a statistical potential for residue interaction that accurately predicts TCR:peptide recognition. Karnaukhov V., Shcherbinin D., Chugunov A., Chudakov D., Efremov R., Zvyagin I., Shugay M.  ISMB/ECCB 2021 (3D-SIG: Structural Bioinformatics and Computational Biophysics). Oral presentation

HLA binding preferences of self-peptides are biased towards proteins with specific molecular functions. Karnaukhov V., Paes W., Woodhouse I., Partridge T., Nicastri A., Brackenridge S., Scherbinin D., Chudakov D., Zvyagin, Ternette N., Koohy H., Borrow P., Shugay M. Moscow Conference on Computational Molecular Biology 2021. Oral presentation

HLA variants differ in binding preferences of self-peptides from proteins with specific molecular functions. Karnaukhov V., Paes W., Woodhouse I., Partridge T., Nicastri A., Brackenridge S., Scherbinin D., Chudakov D., Zvyagin, Ternette N., Koohy H., Borrow P., Shugay M. European Congress of Immunology 2021. Poster presentation

Computational approach to predict epitopes for ankylosing spondylitis-related TCR. V.K. Karnaukhov, E.A. Komech, A.A. Myasoutova, A.I. Mikelov, D.S. Shcherbinin, M. Shugay, I.V. Zvyagin. 2nd Meeting on Stochasticity and Control in Adaptive Immune Repertoires, Paris, France (October 28-31, 2018). Poster presentation

Computational approach for prediction of autoimmune disease-associated T-cell receptor epitopes. V.K. Karnaukhov, E.A. Komech, A.A. Novikova, A.I. Mikelov, M. Shugay, A.O. Chugunov, I.V. Zvyagin. Moscow Conference on Computational Molecular Biology (MCCMB), Moscow (July 27-30, 2019). Poster presentation