You are cordially invited to attend the seminar organized by the Department of Molecular Biology and Genetics
Title: “RNAtranslator, Modeling protein-conditional RNA design as sequence-to-sequence natural language translation”
Speaker: Assoc. Prof. Dr. Ercüment Çiçek
Date: September 24, 2025
Time: 15:30
Place: SB-Z14
” RNAtranslator, Modeling protein-conditional RNA design as sequence-to-sequence natural language translation ”
Assoc. Prof. Dr. Ercüment Çiçek
Bilkent University
Computer Engineering Department
Abstract: Protein-RNA interactions are essential in gene regulation, splicing, RNA stability, and translation, making RNA a promising therapeutic agent for targeting proteins, including those considered undruggable. However, designing RNA sequences that selectively bind to proteins remains a significant challenge due to the vast sequence space and limitations of current experimental and computational methods. Traditional approaches rely on in vitro selection techniques or computational models that require post-generation optimization, restricting their applicability to well-characterized proteins.
In this seminar, I will talk about RNAtranslator, a generative language model that formulates protein-conditional RNA design as a sequence-to-sequence natural language translation problem for the first time. By learning a joint representation of RNA and protein interactions from large-scale datasets, RNAtranslator directly generates binding RNA sequences for any given protein target without the need for additional optimization. Our results demonstrate that RNAtranslator produces RNA sequences with natural-like properties, high novelty, and enhanced binding affinity compared to existing methods. This approach enables efficient RNA design for a wide range of proteins and even proteins with no RNA-interaction data available, paving the way for new RNA-based therapeutics and synthetic biology applications. The model and the code are released at github.com/ciceklab/RNAtranslator.
Bio: Ercüment Çiçek is an Associate Professor at Bilkent University Computer Engineering Department. He has obtained his BS and MS degrees in Computer Science and Engineering Department from Sabanci University and his Ph.D. degree in Computer Science from Case Western Reserve University in 2013. In addition, he worked on gene discovery algorithms for Autism Spectrum Disorder in Cold Spring Harbor Laboratory during his PhD. He was a Lane Fellow in Computational Biology at Carnegie Mellon University before joining Bilkent University Computer Engineering Department as a faculty member in 2015. He is also an adjunct faculty member in the Computational Biology Department of Carnegie Mellon University.
Date: September 24, 2025
Time: 15:30
Place: SB-Z14
Host: Associate Prof. Dr. Ozlen Konu
All interested are cordially invited.