About

I am an AI and Machine Learning specialist holding a Ph.D. in Computer Science from the Technion, co-advised by Prof. Yonatan Belinkov (Technion) and Prof. Tal Pupko (Tel Aviv University). My background combines rigorous academic research in sequence modeling, tokenization, and deep learning architectures with hands-on industry experience at Corephotonics (acquired by Samsung).

Expertise & Skills

My core technical capabilities encompass machine learning, deep learning, natural language processing (NLP), and generative modeling. I specialize in bridging classical algorithms with deep neural networks, bringing end-to-end expertise across the entire model lifecycle—from large-scale pre-training to domain-specific fine-tuning.

Education

• Ph.D. in Computer Science, Technion (2023 – 2026)
• M.Sc. in Bioinformatics (Magna cum laude), Tel Aviv University (2021 – 2022)
• B.Sc. in Computer Science, The Open University (2018 – 2020)

Publications

• [9] Dotan, E., Lyubman, I., Bacharach, E., Pupko, T., and Belinkov, Y. (2026). BetaDescribe: Providing Rich Descriptions for Protein Sequences. Proceedings of the National Academy of Sciences (PNAS). [Code]
• [8] Wygoda, E., Moshe, A., Serok, N., Dotan, E., Ecker, N., Jabareen, N., Israeli, O., Peer, I., and Pupko, T. (2025). Efficient algorithms for simulating sequences along a phylogenetic tree. Bioinformatics.
• [7] Shimony, Y., Dotan, E., Wygoda, E., Wagner, N., Lyubman, I., Ecker, N., Durante, G., Mishan, G., Chang, J., Avram, O., and Pupko, T. (2025). M1CR0B1AL1Z3R 2.0 – An enhanced web server for comparative analysis of bacterial genomes at scale. Nucleic Acids Research. [Website]
• [6] Dotan, E., Wygoda, E., Ecker, N., Alburquerque, M., Avram, O., Belinkov, Y., and Pupko, T. (2025). BetaAlign: a deep learning approach for multiple sequence alignment. Bioinformatics.
• [5] Ben-Ruby, D., Atias-Varon, D., Kagan, M., Chowers, G., Shlomovitz, O., Slabodnik-Kaner, K., Mano, N., Avihu, S., Atsmony, Y., Levin, D., Dotan, E., Calderon-Margalit, R., Schneider, E., Haviv, Y., Birk, O., Hadar, N., Anikster, Y., Berar Yanai, N., Chernin, G., Kruzel-Davila, E., Beckerman, P., Rozen-Zvi, B., Doctor, G., Stanescu, H., Shemer, R., Reznik-Wolf, H., Hashahar Nahoum, A., Dominissini, D., Skorecki, K., and Vivante, A. (2024). Multiethnic prevalence of the APOL1 G1 and G2 variants among the Israeli Dialysis population. Clinical Kidney Journal.
• [4] Dotan, E., Jaschek, G., Pupko, T., and Belinkov, Y. (2024). Effect of Tokenization on Transformers for Biological Sequences. Bioinformatics. [Code]
• [3] Dotan, E.*, Alburquerque, M.*, Wygoda, E.*, Huchon, D., and Pupko, T. (2023). GenomeFLTR: Filtering Reads Made Easy. Nucleic Acids Research. [Website]
• [2] Dotan, E., Belinkov, Y., Avram, O., Wygoda, E., Ecker, N., Alburquerque, M., Keren, O., Loewenthal, G., and Pupko, T. (2023). Multiple sequence alignment as a sequence-to-sequence learning problem. International Conference on Learning Representations (ICLR 2023).
• [1] Wagner, N., Alburquerque, M., Ecker, N., Dotan, E., Pena, M.M., Potnis, N., and Pupko, T. (2022). Natural language processing approach to model the secretion signal of type III effectors. Frontiers in Plant Science.

Preprints

• [3] Dotan, E., Schers, A., Wygoda, E., Pupko, T., and Belinkov, Y. (2026). Phylogenetic tree inference using generative models. Submitted. [Code]
• [2] Dotan, E., Wygoda, E., Schers, A., Lyubman, I., Belinkov, Y., and Pupko, T. (2026). Ancestral sequence reconstruction using generative models. Submitted. [Code]
• [1] Stern, A., Fleishon, S., Kustin, T., Dotan, E., Mandelboim, M., Erster, O., Mendelson, E., Mor, O., and Zuckerman, N. (2021). The unique evolutionary dynamics of the SARS-CoV-2 Delta variant. medRxiv.