E-mail : otastansabanciuniv.edu
Personal web page
PhD, Carnegie Mellon University, School of Computer Science
MSc, Carnegie Mellon University, School of Computer Science
BSc, Sabanci University, Biological Sciences and Bioengineering
Work Experience :
Bilkent University, Department of Computer Engineering
Microsoft Research New England, Cambridge, USA
Areas of Interest :
Computational Biology, Bioinformatics, Machine learning,
- Mustafa N. PARLAR Eğitim ve Araştırma Vakfı'nın 2019 yılı Araştırma Teşvik Ödülü - Mustafa N. PARLAR Eğitim ve Araştırma Vakfı 2019
International Society for Computational Biology, ISCB
|Tepeli, Yasin İlkağan and Ünal, Ali Burak and Furkan, Mustafa Akdemir and Taştan, Öznur (2020) "PAMOGK: A pathway graph kernel-based multiomics approach for patient clustering". Published Online First http://dx.doi.org/10.1093/bioinformatics/btaa655|
|Yılmaz, Serhan and Taştan, Öznur and Çiçek, Ercüment (2019) "SPADIS: an algorithm for selecting predictive and diverse SNPs in GWAS". Published Online First http://dx.doi.org/10.1109/TCBB.2019.2935437|
|Olgun, Gülden and Şahin, Özgür and Taştan, Öznur (2018) "Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes", BMC Genomics, Vol.19 (SCI)|
|Papers in Conference Proceedings|
|Kuru, Halil İbrahim and Büyüközkan, Mustafa and Taştan, Öznur, "PRER: A patient representation with pairwise relative expression of proteins on biological networks", Satellite Workshop on Computational Cancer Biology (RECOMB-CCB) - Jointly with RECOMB 2020, biorxiv.org, June 2020|
|Tepeli, Yasin İlkağan and Ünal, Ali Burak and Akdemir, Mustafa Furkan and Taştan, Öznur, "PAMOGK: A pathway graph kernel based multi-omics clustering approach for discovering cancer patient subgroups", Satellite Workshop on Computational Cancer Biology (RECOMB-CCB) - Jointly with RECOMB 2020, biorxiv.org, June 2020|
Before SU Publications:
- G. Kale, E. Ayday, and O. Tastan (2018). A utility-maximizing and privacy preserving approach for protecting kinship in genomic databases, Bioinformatics, 34(2):181-189.
- B. Otlu, C. Fırtına, S. Keles, and O. Tastan (2017). GLANET: A tool for annotation and enrichment analysis of variable length genomic loci, Bioinformatics, 33(18), pp. 2818-28.
- C. Yao, B.H. Chen, R. Joehanes, B. Otlu, X. Zhang, C. Liu, T. Huan, O. Tastan, L. A. Cupples, J. B. Meigs, C. S. Fox, J.E. Freedman, P. Courchesne, C. J. O'Donnell, P. J. Munson, S. Keles, D. Levy (2015). Integrated analysis of genetic variation and gene expression identifies networks for cardiovascular disease phenotypes. Circulation. 131(6):536-49.
- T. Jartti, O. Palomares, M, Waris, O. Tastan, R. Nieminen, T. Puhakka, B. Rückert, A. Aab, T. Vuorinen, A. Tobias, T. Vahlberg, O. Ruuskanen, M. Akdis, and C. Akdis (2014). Distinct regulation of tonsillar immune response in virus infections. Allergy. 69(5):658-67.
- O. Tastan, A. Dutta, P. Booth, and J. Klein-Seetharaman (2014). Retinal proteins as model systems for membrane protein folding. Biochimica et Biophysica Acta; 1837(5):656-63.
- Z. Zhao, J. Xia, O. Tastan, I. Singh, M. Kshirsagar, J.G. Carbonell, and J. Klein-Seetharaman (2011). Virus interactions with human signal transduction pathways. International Journal of Computational Biology and Drug Design. 4(1), p83-105.
- S. Uguroglu, O. Tastan, J. Klein-Seetharaman, and S.H. Leuba (2011). Identification of potentially relevant citeable articles using association rule mining. Medicinal Chemistry. 1:e101.
- Y. Qi, O. Tastan, J.G. Carbonell, J. Klein-Seetharaman and J. Weston (2010). Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins. Bioinformatics, 26(18):645-52.
- N.J. Venkatachari, T. Le, O. Tastan, M.D. Timothy, L. Walker, A. Ricciuti, N. Yanamala, A. Srinivasan, J. Klein-Seetharaman, M. Ramachandran, R.C. Montelaro, and V. Ayyavoo (2010). Oligomerization of HIV-1 Vpr: Identification of essential domains/residues using structure based approaches and evaluation of its relevance to Vpr functions. Virology Journal, 7:119.
- S. Balakrishnan, O. Tastan, J.G. Carbonell and J. Klein-Seetharaman (2009). Alternative paths in HIV-1 targeted human signal transduction pathways. BMC Genomics 10 Suppl. 3, S30.
- O. Tastan, J. Klein-Seetharaman, and H. Meirovitch (2009). The effect of loops on the structural organization of alpha-helical membrane proteins. Biophysical Journal, 96:2299-312.
- O. Tastan, E. Yu, M. Ganapathiraju, A. Aref, A.J. Rader, and J. Klein-Seetharaman (2007). Comparison of stability predictions and simulated unfolding of rhodopsin structures. Photochemistry and Photobiology, 83:351-62.
Reviewed conference and workshop publications
- I. Deznabi, A. A. Celik and O. Tastan. MEMNAR: Finding mutually exclusive mutation sets through negative association rule mining. The 11th International Workshop on Machine Learning in Systems Biology, 25th ISMB/ECCB, Prag, Czech Republic, Jul 25, 2017.
- A. B. Unal, O. Tastan, Identification of cancer patient subgroups via smoothed shortest path graph kernel, NIPS Workshop on Machine Learning in Computational Biology, Barcelona, Dec 10, 2016.
- . Orhan and O. Tastan, ALEVS: Active learning by statistical leverage sampling, 32nd International Conference on Machine Learning (ICML), Lille, France, Jul 6 – 11, 2015.
- O. Tastan, Y. Qi, J.G. Carbonell and J. Klein-Seetharaman. Refining literature-curated HIV-1, human protein-protein interactions using expert opinions. Pacific Symposium on Biocomputing, Big Island of Hawaii, 318-29, Jan 2 – 9, 2015.
- Z. Zhao, J. Xia, O. Tastan, I. Singh, M. Kshirsagar, J. Carbonell and J. Klein-Seetharaman. Virus interactions with human signal transduction pathways. International journal of computational biology and drug design 4 (1), 83-105, 2011.
- . Singh, O. Tastan and J. Klein-Seetharaman Comparison of virus interactions with human signal transduction pathways. Proceedings ACM International Conference on Bioinformatics and Computational Biology, p17-24, 2010.
- O. Tastan, Y. Qi, JG Carbonell, and J. Klein-Seetharaman. Prediction of interactions between HIV-1 and human proteins by information integration. Pacific Symposium on Biocomputing (PSB), Big Island of Hawaii, 13, p516-27, 2009.