I am a professor of Computer Engineering at the Middle East Technical University (METU), Ankara, Turkey.

My research interests lie in the areas of machine learning for bioinformatics, machine learning applications, and data clustering.

I am currently a member of the International Technical Advisory Board of Arcelik (Research and Development Directorate), and  a member of the Board of Directors of Izmir Biomedicine and Genome Institute (iBG-izmir).


I have obtained “Diplôme de Docteur dans la spécialité Informatique” (Ph.D in computer science) from Université Paris Descartes, Paris, France. During sabbatical leave, I spent a year (2004) at Virginia Bioinformatics Institute, Virginia Tech, VA, USA.
From 2010 to 2016, I was the Vice President for research of METU and Chairman of Board of Directors of ODTU TEKNOKENT (METU Technopolis). My main responsibilities included strategies and policies for research and for university-industry partnership, relations with both public and private institutions, and corporate strategy management. From 2011 to 2018, I was a member of the Technology Advisory Board of Turkish Aerospace Industries (TAI).
I am still involved in activities related to technology-based innovation, technology-based entrepreneurship, technology management, and research policies and strategies.


Forecasting of Product Quality Through Anomaly Detection Workshop on IoT Stream for Data Driven Predictive Maintenance ECML/PKDD 2019
CROssBAR: Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning Bio-Ontologies COSI ISMB/ECCB 2019
iBioProVis: Interactive Visualization and Analysis of Compound Bioactivity Space Biological Data Visualization COSI ISMB/ECCB 2019
The CAFA challenge reports improved protein function prediction and new functional annotatons for hundreds of genes through experimental screens  BioRxiv
DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks   Scientific Reports 2019

list of all publications


UniGOPred  is a web-based service for automated protein function prediction based on Gene Ontology (GO) terms and it is also a database of GO term predictions for UniProtKB
ECPred  is a Java-based stand-alone program for Enzyme Commission (EC) number prediction through a command-line interface
EClerize  is a Cytoscape plugin to draw biological graphs that represent pathways in which the vertices are associated with Enzyme Commission (EC) numbers
Pathway Scoring Application  is a Cytoscape plugin that evaluates the activity of cell signaling pathways by utilizing gene expression and ChIP-seq data.


My research interests lie in the areas of machine learning for bioinformatics, machine learning applications, and data clustering.

In the last 10 years, I am involved in machine learning for bioinformatics. My research efforts are focused on developing and applying computational techniques for the analysis of biological data and modeling of biological processes at the molecular level. The broad aim is to provide computational tools to assist researchers to understand, explain and predict the behavior of complex biological systems. My research activities take place in the Cancer Systems Biology Laboratory.

I am currently involved in the following two research projects:

  • Genome Annotation based on Sequence Analysis

For the analysis of sequences, we have developed a generative system based on feature space mapping, called Subsequence Profile Map (SPMap). SPMap can be fed to a discriminative classifier for prediction purposes. Instead of focusing motifs in a sequence, SPMap considers all of the subsequences as a distribution over a quantized space by discretizing and reducing the dimension of an otherwise huge space of all possible subsequences. We have already applied SPMap and other feature generating methods to the following problems:

Automated Protein Function Prediction
Enzyme Class Prediction

  • Generating Readable Layouts for Biological Graphs

Although the force-directed layout algorithm could be used to draw biological graphs, a modification is required when we would like to embed domain-specific knowledge. We proposed a modified and improved (Kamada-Kawai) force-directed layout algorithm, EClerize, to generate more readable layouts for biological graphs that represent pathways in which the vertices are identified with EC (Enzyme Commission) numbers. While the vertices with the same EC class numbers are treated as members of the same cluster, positions of vertices in clusters are affected by the biological similarity of each vertex in the same cluster and the theoretical length between the vertices.

More about research


  • Ahmet Süreyya Rifaioğlu, Ph.D. candidate
  • Ayşe Gül Yaman, Ph.D. candidate
  • Alaettin Zubaroğlu, Ph.D. candidate
  • Alperen Dalkıran, Ph.D. candidate
  • Türkdoğan Taşdelen, Ph.D. candidate
  • Serkan Özen, Ph.D. candidate
  • Erkan Akın, MSc candidate
  • Gökhan Özsarı, MSc candidate
  • Özlem Özdoğan, MSc candidate
  • Mesut Balcı, MSc candidate
  • Fırat Aksoydan, MSc candidate
  • Ecehan Savaş, MSc candidate
  • Ahmet Atakan, MSc candidate

Graduated Doctoral and M.Sc. Students


Diplôme de Docteur dans la spécialité Informatique (Ph.D. in Computer Science), 1993, Université Paris Descartes (Paris V), Paris, France
Diplôme d’Etudes Approfondies en Informatique, 1991, Université Paris Descartes (Paris V), Paris, France
Master of Science in Electrical and Electronics Engineering, 1990, METU, Ankara, Turkey
Bachelor of Science in Electrical and Electronics Engineering, 1987, METU, Ankara, Turkey


Professor, METU, Ankara, Turkey, 2005-present
Associate Professor, METU, Ankara, Turkey, 1998-2005
Visiting Research Associate Professor, Virginia Bioinformatics Institute, Virginia Tech, VA, USA, Jan. 2004-Jan. 2005
Assistant Professor, METU, Ankara, Turkey, 1993-1998
Instructor, Université Paris Descartes (Paris V), Paris, France, 1993
Visiting Scholar, New Jersey Institute of Technology, NJ, USA, 1991-1992
Development Engineer, Aselsan Electronics Company, Ankara, Turkey, 1987-1988


Vice President for research, METU, 2010-2016
Chairman of Board, ODTÜ TEKNOKENT (METU Technopolis), 2010-2016
Member of University Senate, METU, 2010-2016
Assistant to President, METU, 2008-2010
Board Member, Informatics Association of Turkey, 2009-2011
Department Chairperson, METU Dep. of Computer Eng., 2007-2008


I enjoy teaching. The best part of teaching is to interact with young people and to learn while you teach as well. I am currently teaching

CONTACT vatalay AT metu.edu.tr