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 member of the International Technical Advisory Board of Arcelik (Research and Development Directorate), the Technology Advisory Board of Turkish Aerospace Industries (TAI) and 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.
I am still involved in activities related to technology based innovation, technology based entrepreneurship, technology management, and research policies and strategies.

RECENT SELECTED PUBLICATIONS

Recent Applications of Deep Learning and Machine Intelligence on In-silico Drug Discovery: Methods, Tools and Databases Briefings in Bioinformatics to appear
Drug-Target Interaction Prediction with Deep Convolutional Neural Networks Using Compound Images
  Oral presentation Machine Learning in Computational and Systems Biology (MLCSB) COSI at ISMB 2018
Automated Negative Gene Ontology Based Functional Predictions for Proteins with UniGOPred   Oral presentation Function-COSI at ISMB 2018
EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes  Int. Journal of Bioinformatics and Computational Biology 2018
Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants  Proteins: Structure, Function, and Bioinformatics 2018
Multi-task Deep Neural Networks in Automated Protein Function Prediction arXiv.org 2017

list of all publications

SOFTWARE TOOLS and WEB-BASED SERVICES

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 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.

RESEARCH

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 force-directed layout algorithm could be used to draw biological graphs, 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

CURRENT GRADUATE STUDENTS

  • Ahmet Süreyya Rifaioğlu, PhD candidate
  • Ayşe Gül Yaman, PhD candidate
  • Alaettin Zubaroğlu, PhD canidate
  • Alperen Dalkıran, PhD candidate
  • Türkdoğan Taşdelen, PhD candidate
  • Serkan Özen, MSc candidate
  • Erkan Akın, MSc candidate
  • Özlem Özdoğan, MSc candidate
  • Mesut Balcı, MSc candidate
  • Fırat Aksoydan, MSc candidate
  • Ecehan Savaş, MSc candidate

Graduated Doctoral and M.Sc. Students

EDUCATION

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

PROFESSIONAL POSITIONS

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

MAJOR ADMINISTRATIONAL POSITIONS

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

TEACHING

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