Publications

Below are selected publications. See my Google Scholar for the complete list.

In-progress Publications

2026

Barazandeh, S., Gün Kaynar, Arth Banka, Joshua Kangas, Carl Kingsford, Jose Lugo-Martinez. simPCL: An Open-Framework Simulator and Benchmark Generator for Programmable Cloud Laboratories. Manuscript in preparation.

[Project]

Peer-Reviewed Publications

2026

Ozden, F., Barazandeh, S., Akboga, D., Tabrizi, S.S., Seker, U.O.S., Cicek, A.E. (2026). RNAGEN: A generative adversarial network-based model to generate synthetic RNA sequences to target proteins. ChemBioChem, 27(13): e202500445.
[Paper] [Preprint] [Code]

2025

Barazandeh, S., Ozden, F., Hincer, A., Seker, U.O.S., Cicek, A.E. (2025). UTRGAN: Learning to generate 5’ UTR sequences for optimized translation efficiency and gene expression. Bioinformatics Advances, 5(1): vbaf134.
[Paper] [bioRxiv] [Code]

Tabrizi, S.S., Barazandeh, S., Aghdam, H.H., Cicek, A.E. (2025). RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation. PLOS Computational Biology, 21(10): e1013541.
[Paper] [bioRxiv] [Code] [Model]

Other Publications

2018

Asali, E., Negahbani, F., Tafazzol, S., Maghareh, M.S., Bahmeie, S., Barazandeh, S., Mirian, S., Moshkelgosha, M. (2018). Namira Soccer 2D Simulation Team Description Paper 2018. RoboCup 2018, Montreal, Canada.