Saez-Rodriguez Group

Systems Biomedicine

Ahmet Sureyya Rifaioglu

I obtained my B.Sc. degree from the Computer Engineering Department of İstanbul Doğuş University in 2010. After working in a software company for a short period as a software engineer, I joined the Middle East Technical University (METU), Ankara as a teaching/research assistant and a master student. I also joined the Cancer Systems Laboratory at METU and started doing research in the bioinformatics field where I worked on computational protein function prediction.

After I got my master degree in 2015, I continued my PhD in the same department and started working on a project called “Comprehensive Resource of Biomedical Relations with Deep Learning and Network Representations” (CROssBAR). This was a joint project between Middle East Technical University and EMBL-EBI where I have spent about one year during my PhD studies. My main aim was to develop deep learning-based methods for computational drug discovery and work with the EMBL-EBI team to create the CROssBAR database. In 2020 I obtained my PhD degree and became a faculty member at İskenderun Technical University, Hatay, Turkey.

In July 2021, I joined the Saez-Rodriguez group as a postdoctoral researcher. In this position, I will mainly work on the application of deep learning algorithms to single-cell data in cancer.

Research Interests

Understanding the inner mechanisms of living beings from the molecular level to the organism level is one of the most challenging and important research areas of our era. With the advance of technology, a massive amount of experimental data has accumulated in public and private databases. I believe that the availability of these data will help us understand our complex biological system using the correct usage of data and machine learning algorithms. My main research interest is to extract hidden knowledge from these complex and big data using machine learning algorithms. Specifically, I am highly interested in computational drug discovery and developing machine learning methods for understanding molecular mechanisms of diseases such as cancer.

My current goal is to propose new methods and develop machine learning algorithms on single-cell data. Specifically, I will be working on applications of deep learning methods using large-scale single-cell data focusing on cancer within the framework of the  “DeepSC2 – Deep learning for single-cell genomics in cancer”, a project funded by the German Government (BMBF).

Professional Career

2021 - Present Postdoctoral Researcher, Institute for Computational Biomedicine, Heidelberg University, Germany
2020 - Present Faculty Member, İskenderun Technical University, Hatay, Turkey
2011-2020 Teaching/Research Assistant, Computer Engineering Department, Middle East Technical University, Ankara, Turkey
2019-2020 Predoctoral Visiting Researcher, EMBL-EBI, Automatic Annotation Team, Cambridge, UK
2011-2011 Software Engineer, ISIS Information Technologies, İstanbul, Turkey


2015-2020 Ph.D. in Computer Engineering, Middle East Technical University, Ankara, Turkey
2012-2015 M.Sc. in Computer Engineering, Middle East Technical University, Ankara, Turkey
2006-2010 B.Sc. in Computer Engineering, İstanbul Doğuş University, İstanbul, Turkey