Hasan Oğul I am a postdoctoral researcher in the Statistical Machine Learning and Bioinformatics research group of Helsinki University of Technology. I received my PhD degree from Information Systems at Middle East Technical University, Turkey. My research interests include protein homology modeling and pattern discovery in molecular data. I reviewed for the journals: Information Sciences, Int. Journal of Data Mining and Bioinformatics, Artificial Intelligence in Medicine and Digital Signal Processing. I am an advisory board member of the Informatics Technologies journal. I have been a program committe member of ISCIS'2006, HIBIT'2006-2008, BASARIM'2009 and BIOSIGNALS'2009.

Publications

H.Oğul, (2009), Variable context Markov chains for HIV Protease Clevage Site Prediction
Biosystems (accepted for publication)

Ç.Beyan, H.Oğul, (2008), A fuzzy kNN aprroach for cancer diagnosis with microarray gene expression data
Proceedings of 3rd International Sympoisum on Health Informatics and Bioinformatics (HIBIT,2008), İstanbul, Turkey.

H.Oğul, (2008), Prediction of disulfide connectivity patterns from protein sequence
Proceedings of International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC'08), Orlando, FL, USA

A.C.Polatkan, H.Oğul, H.Sever, (2008), A data fusion approach in protein homology detection
Proceedings of International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies (BIOTECHNO'08)
Bucharest, Romania.

Ö.Eren, H.Oğul, (2008), Automated classification of allergen proteins
Proceedings of 14th Annual Biomedical Engineering Conference (BIYOMUT'08), Ankara, Turkey.

H.Oğul, E.Mumcuoğlu, (2007), Subcellular Localization Prediction with New Protein Encoding Schemes
IEEE/ACM Transactions on Computational Biology and Bioinformatics 4, 227-232 (IEEE Computer Society).

H.Oğul, E.Mumcuoğlu, (2007), A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets
Biosystems 87, 75-81 (Elsevier).

H.Oğul, E.Mumcuoğlu, (2006), SVM-based Detection of Distant Protein Structural Relationships Using Pairwise Probabilistic Suffix Trees
Computational Biology and Chemistry 30, 292-299 (Elsevier).

H.Oğul, E.Mumcuoğlu, (2006), Protein solvent accessibility prediction using support vector machines and sequence conservations
Artificial Intelligence and Neural Networks, LNAI 3949, 141-148 (Springer-Verlag), also presented in Turkish Symposium on Artificial Intelligence and Neural Networks, Çeşme, Turkey.

H.Oğul, E.Mumcuoğlu, (2005), Discriminative remote homology detection using maximal unique sequence matches
Advances in Intelligent Data Analysis, LNCS 3546, 283-292 (Springer-Verlag), also presented in International Symposium on Intelligent Data Analysis, Madrid, Spain.

H.Oğul, E.Mumcuoğlu, (2005), Prediction of protein subcellular localization using support vector machines and probabilistic suffix trees
Proceedings of 1st International Symposium on Health Informatics and Bioinformatics (HIBIT'05 56-62), Antalya, Turkey.

H.Oğul, E.Mumcuoğlu, (2004), Finding maximal unique secondary structure matches in protein families (in Turkish)
Proceedings of 10th Annual Biomedical Engineering Conference (BIYOMUT'04 107-113), İstanbul, Turkey.

H.Oğul, K. Erciyes, (2001), Identifying all local and global alignments between two DNA sequences
Proceedings of 16th International Symposium on Computer and Information Sciences (ISCIS'01 468-475), Antalya, Turkey.

H.Oğul, K. Erciyes, (2001), Parallel Sequence Alignment Using a Cluster of Workstations
Ege University, International Computing Institute, Technical Report.

Theses

H.Oğul, PhD Thesis, (Jan, 2006) Computational Representation of Protein Sequences for Homology Detection and Classification, METU Informatics Institute, Department of Information Systems, Ankara, Turkey.(Advisor: Assoc.Prof.Dr.Erkan Mumcuoğlu) Award winning: (1) Young Scientist of the Year 2007, Turkey - S.Ozyar Award (2) Best Thesis of the Year 2007, METU

H.Oğul, MS Thesis, (Sep, 2001) Algorithms for DNA Sequence Comparison and Alignment, Ege Univ., International Computing Institute, Department of Information Technologies, İzmir, Turkey.(Advisor: Prof.Dr.Kayhan Erciyes)

Contact information

Mail address:	Helsinki University of Technology Department of Information and Computer Science P.O. Box 5400 FI-02015 HUT FINLAND
Location:	Otaniemi, Computer Science Building, room A317
E-Mail:	hasan.ogul@hut.fi