I work across two things I care about equally: protein structure and molecular simulation, and data science and deep learning. Antibody–antigen complex prediction and MD on one side; CNNs, single-cell analysis and GPU-accelerated pipelines on the other. My repositories run across both.
MSc in Molecular Biology — Bioinformatics track, University of Padova (2026). Thesis carried out at the Zuse Institute Berlin, applying structure prediction to molecular mimicry, where a pathogen epitope resembles a host one closely enough to matter:
In Silico Investigation of Molecular Mimicry in Antibody–Antigen Complexes — A Structural Prediction Pipeline for Targets Lacking Experimental Structures
- 🎯 Currently looking for my next role — research, PhD or industry
- 🔬 Previously Research Intern at Zuse Institute Berlin — antibody–antigen structural analysis & explainable AI
- 📄 Paper accepted at xAI-2026 — Stop Throwing Away Your Decoder
- 🧠 Interests: protein structure & molecular dynamics · deep learning & computer vision · single-cell genomics
- ⚙️ I care about Snakemake, Docker, Slurm and tests as much as the science
- 💬 Ask me about AlphaFold on clusters, epitope–paratope mapping, or why your MD run crashed
- 📫 ateferos77@gmail.com
Stop Throwing Away Your Decoder: Extracting the Learnt Local Coordinate System Using Latent-XAI
Sunkara V., Rostami A., von Tycowicz C., Schütte C. — 4th World Conference on Explainable AI (xAI-2026)
Identification of Key Genes Involved in Heat Stress Response in Brassica napus
Makvandi et al. — Iranian Journal of Genetics and Plant Breeding, 11(1), 71–86 (2022)
🏆 2nd Place — RahNeshan National Research Competition, Iran National Elite Foundation (2020–2021)
| When | What | Where |
|---|---|---|
| Aug 2025 – May 2026 | Research Intern — Ab–Ag Structural Analysis & Explainable AI | Zuse Institute Berlin |
| 2024 · 3 months | Research Intern — Computational Drug Discovery | Zuse Institute Berlin |
| 2024 | Single-Cell RNA-seq Analysis — Martello Lab | University of Padova |
| 2019 – 2021 | Molecular Lab Assistant Consultant | Topazgene, Iran |
| 🎓 2023 – 2026 | MSc Molecular Biology — Bioinformatics Track | University of Padova |
| 🎓 2018 – 2022 | BSc Cellular and Molecular Biology | Zanjan University |
