# Publications Research contributions and academic publications > **Dmitry Bagaev, PhD** — Senior Software Engineer & Scientist, based in Eindhoven, the Netherlands. > [bvdmitri@gmail.com](mailto:bvdmitri@gmail.com) · [GitHub](https://github.com/bvdmitri) · [LinkedIn](https://linkedin.com/in/bvdmitri) · [Google Scholar](https://scholar.google.com/citations?user=zjfAwAEAAAAJ&hl=en) > > This page is one section of my auto-generated personal site. See the [overview](/index.md) for a full summary and links to the other sections. ## Citation Metrics - **h-index:** 13 - **i10-index:** 14 - **Total citations:** 2713+ - **Citations since 2021:** 2143+ - **Google Scholar:** https://scholar.google.com/citations?user=0460230115345 - **TU/e research portal:** https://research.tue.nl/en/persons/dmitry-bagaev/ - **ORCID:** https://orcid.org/0000-0001-9655-7986 --- ## PhD Dissertation **Reactive Probabilistic Programming for Scalable Bayesian Inference** *Dmitry V. Bagaev • Eindhoven University of Technology • 2023* Bayesian inference realizes optimal information processing through a full commitment to reasoning by probability theory. The Bayesian framework is a crucial technology at the core of modern AI with applications such as speech and image recognition and generation, biomedical analysis, robot navigation, and more. This dissertation focuses on the realization of efficient Bayesian inference in large-scale probabilistic models, targeting real-time signal processing and control applications under real-world conditions. We present a practical architecture based on reactive message passing-based inference in a factor graph representation of the probabilistic model under study. - Read: https://research.tue.nl/en/publications/reactive-probabilistic-programming-for-scalable-bayesian-inferenc - Source code: https://github.com/bvdmitri/phdthesis --- ## Nature Publication **VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2** *M Goncharov, D Bagaev, D Shcherbinin, I Zvyagin, D Bolotin, PG Thomas, ...* Nature methods 19 (9), 1017-1019 • 2022 • 242+ citations Read: https://www.nature.com/articles/s41592-022-01578-0 --- ## Other Publications Note: this list might be outdated. Check Google Scholar for the most recent updates. ### VDJtools: unifying post-analysis of T cell receptor repertoires *M Shugay, DV Bagaev, MA Turchaninova, DA Bolotin, OV Britanova, ...* PLoS computational biology 11 (11), e1004503 • 2015 • 703+ citations --- ### VDJdb: a curated database of T-cell receptor sequences with known antigen specificity *M Shugay, DV Bagaev, IV Zvyagin, RM Vroomans, JC Crawford, G Dolton, ...* Nucleic acids research 46 (D1), D419-D427 • 2018 • 676+ citations --- ### VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium *DV Bagaev, RMA Vroomans, J Samir, U Stervbo, C Rius, G Dolton, ...* Nucleic acids research 48 (D1), D1057-D1062 • 2020 • 467+ citations --- ### SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T cell receptors *AS Shomuradova, MS Vagida, SA Sheetikov, KV Zornikova, D Kiryukhin, ...* Immunity 53 (6), 1245-1257. e5 • 2020 • 294+ citations --- ### MAGERI: Computational pipeline for molecular-barcoded targeted resequencing *M Shugay, AR Zaretsky, DA Shagin, IA Shagina, IA Volchenkov, ...* PLoS computational biology 13 (5), e1005480 • 2017 • 63+ citations --- ### Exploring the pre-immune landscape of antigen-specific T cells *MV Pogorelyy, AD Fedorova, JE McLaren, K Ladell, DV Bagaev, ...* Genome medicine 10 (1), 1-14 • 2018 • 51+ citations --- ### VDJviz: a versatile browser for immunogenomics data *DV Bagaev, IV Zvyagin, EV Putintseva, M Izraelson, OV Britanova, ...* BMC genomics 17 (1), 453 • 2016 • 49+ citations --- ### Variational message passing and local constraint manipulation in factor graphs *İ Şenöz, T van de Laar, D Bagaev, B de Vries* Entropy 23 (7), 807 • 2021 • 40+ citations --- ### RxInfer: A Julia package for reactive real-time Bayesian inference *D Bagaev, A Podusenko, B De Vries* Journal of Open Source Software 8 (84), 5161 • 2023 • 33+ citations --- ### Improving parallel efficiency of a complex hydrogeological problem simulation in GeRa *D Bagaev, F Grigoriev, I Kapyrin, I Konshin, V Kramarenko, A Plenkin* Russian Supercomputing Days, 265-277 • 2019 • 16+ citations --- ### Reactive message passing for scalable Bayesian inference *D Bagaev, B de Vries* Scientific Programming 2023 (1), 6601690 • 2023 • 15+ citations --- ### Dynamic optimization of linear solver parameters in mathematical modelling of unsteady processes *D Bagaev, I Konshin, K Nikitin* Russian supercomputing days, 54-66 • 2017 • 10+ citations --- ### Multi-agent trajectory planning with NUV priors *B van Erp, D Bagaev, A Podusenko, İ Şenöz, B de Vries* 2024 American Control Conference (ACC), 2766-2771 • 2024 • 6+ citations --- ### ReactiveMP.jl: A Julia package for reactive variational Bayesian inference *D Bagaev, B van Erp, A Podusenko, B de Vries* Software Impacts 12, 100299 • 2022 • 6+ citations --- ### Message passing-based inference in the Gamma mixture model *A Podusenko, B van Erp, D Bagaev, İ Şenöz, B de Vries* 2021 IEEE 31st International Workshop on Machine Learning for Signal Processing • 2021 • 6+ citations --- ### Expected free energy-based planning as variational inference *B de Vries, W Nuijten, T van de Laar, W Kouw, S Adamiat, T Nisslbeck, ...* arXiv preprint • 2025 • 3+ citations --- --- ## Other pages - **Overview:** / — or /index.md for markdown format - **Experience:** /experience — or /experience.md for markdown format - **Education:** /education — or /education.md for markdown format - **Software:** /software — or /software.md for markdown format - **Presentations:** /presentations — or /presentations.md for markdown format - **Hobbies:** /hobbies — or /hobbies.md for markdown format