Oznur Taştan

Türkçe sürüm

Oznur Taştan

E-mail : otastansabanciuniv.edu

Personal web page

Education :

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,

Awards :

  • Mustafa N. PARLAR Eğitim ve Araştırma Vakfı'nın 2019 yılı Araştırma Teşvik Ödülü - Mustafa N. PARLAR Eğitim ve Araştırma Vakfı  2019

Membership :

International Society for Computational Biology, ISCB

Publications :

Article
Kuru, Halil Ibrahim and Taştan, Öznur and Cicek, Ercument (2022) "MatchMaker: a deep learning framework for drug synergy prediction", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol.19, No.4, 2334-2344 (SCI)
Kuru, Halil İbrahim and Tepeli, Yasin İlkağan and Taştan, Öznur (2022) "GEGE: predicting gene essentiality with graph embeddings", Duzce University Journal of Science and Technology, Vol.10, No.3, 1567-1577 (NA)
Kuru, Nurdan and Dereli, Onur and Akkoyun, Emrah and Bircan, Aylin and Taştan, Öznur and Adebali, Ogün (2022) "PHACT: phylogeny-aware computing of tolerance for missense mutations", Molecular Biology and Evolution, Vol.39, No.6 (SCI)
Olgun, Gulden and Taştan, Öznur (2022) "miRCoop: identifying cooperating miRNAs via Kernel based interaction tests", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol.19, No.3, 1760-1771 (SCI)
Özçelik, Duygu and Taştan, Öznur (2022) "A weakly supervised clustering method for cancer subgroup identification", Balkan Journal of Electrical and Computer Engineering, Vol.10, No.2, 178-186 (NA)
Yilmaz, Serhan and Fakhouri, Mohamad and Koyuturk, Mehmet and Ercument Cicek, A. and Taştan, Öznur (2022) "Uncovering complementary sets of variants for predicting quantitative phenotypes", Bioinformatics, Vol.38, No.4, 908-917 (SCI)
Uner, Onur Can and Kuru, Halil Ibrahim and Cinbis, Ramazan Gokberk and Taştan, Öznur and Cicek, Ercument (2022) "DeepSide: a deep learning approach for drug side effect prediction". Published Online First https://dx.doi.org/10.1109/TCBB.2022.3141103
Olgun, Gulden and Nabi, Afshan and Taştan, Öznur (2021) "Correction to: NoRCE: non‑coding RNA sets cis enrichment tool (BMC Bioinformatics, (2021), 22, 1, (294), 10.1186/s12859-021-04112-9)", BMC Bioinformatics, Vol.22, No.1 (SCI)
Olgun, Gulden and Nabi, Afshan and Taştan, Öznur (2021) "NoRCE: non-coding RNA sets cis enrichment tool", BMC Bioinformatics, Vol.22, No.1 (SCI)
Kuru, Halil Ibrahim and Buyukozkan, Mustafa and Taştan, Öznur (2021) "PRER: a patient representation with pairwise relative expression of proteins on biological networks", PLoS Computational Biology, Vol.17, No.5 (SCI)
Yilmaz, Serhan and Taştan, Öznur and Cicek, A. Ercument (2021) "SPADIS: an algorithm for selecting predictive and diverse SNPs in GWAS", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol.18, No.3, 1208-1216 (SCI)
Caylak, Gizem and Taştan, Öznur and Cicek, A. Ercument (2021) "A tool for detecting complementary single nucleotide polymorphism pairs in genome-wide association studies for epistasis testing", Journal of Computational Biology, Vol.28, No.4, 378-380 (SCI)
Caylak, Gizem and Taştan, Öznur and Cicek, A. Ercument (2021) "Potpourri: an epistasis test prioritization algorithm via diverse SNP selection", Journal of Computational Biology, Vol.28, No.4, 365-377 (SCI)
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
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:

Journal 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.