| Faculty of Engineering and Natural Sciences

Öznur Taştan Faculty of Engineering and Natural Sciences Faculty Member (216) 483 9883 oznurtastansabanciunivedu

Personal Web

http://people.sabanciuniv.edu/otastan/

Jobs

Faculty Member

Education

PhD, Carnegie Mellon University, School of Computer Science

MSc, Carnegie Mellon University, School of Computer Science

BSc, Sabanci University, Biological Sciences and Bioengineering

Areas of Interest

Computational Biology, Bioinformatics, Machine learning,

Memberships

International Society for Computational Biology, ISCB, EACR

Dereli, Onur and Kuru, Nurdan and Akkoyun, Emrah and Bircan, Aylin and Taştan, Öznur and Adebali, Ogün (2024) "PHACTboost: a phylogeny-aware pathogenicity predictor for missense mutations via boosting", Molecular Biology and Evolution, Vol.41, No.7 (SCI)

Kuru, Halil Ibrahim and Cicek, A. Ercument and Taştan, Öznur (2024) "From cell lines to cancer patients: personalized drug synergy prediction", Bioinformatics (Oxford, England), Vol.40, No.5 (SCI)

Şapcı, Ali Osman Berk and Kemik, Hasan and Yeniterzi, Reyyan and Taştan, Öznur (2024) "Focusing on potential named entities during active label acquisition", Natural Language Engineering, Vol.30, No.3, 602-624 (SCI, SSCI, AHCI)

Şapcı, Ali Osman Berk and Lu, Shan and Yan, Shuchen and Ay, Ferhat and Taştan, Öznur and Keleş, Sündüz (2023) "MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing", Bioinformatics, Vol.39, No.10 (SCI)

Cagatay Karakan, M. and Ari, Atakan B. and Kelleci, Mehmet and Yanık, Cenk and Kaya, İsmet İnönü and Taştan, Öznur and Selim Hanay, M. (2023) "Vapor sensing of colorectal cancer biomarkers in isolation by bare and functionalized nanoelectromechanical sensors", IEEE Sensors Journal, Vol.23, No.18, 21113-21120 (SCI)

Nabi, Afshan and Dilekoğlu, Berke and Adebali, Ogün and Taştan, Öznur (2023) "Discovering misannotated lncRNAs using deep learning training dynamics", Bioinformatics (Oxford, England), Vol.39, No.1 (SCI)

Uner, Onur Can and Kuru, Halil Ibrahim and Cinbis, Ramazan Gokberk and Taştan, Öznur and Cicek, Ercument (2023) "DeepSide: a deep learning approach for drug side effect prediction", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol.20, No.1, 330-339 (SCI)

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)

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 Akdemir, Furkan Mustafa and Taştan, Öznur (2020) "PAMOGK: a pathway graph kernel-based multiomics approach for patient clustering", Bioinformatics, Vol.36, No.21, 5237-5246 (SCI)

Tunca, Ceren and Şeker, Tuncay and Akçimen, Fulya and Coşkun, Cemre and Bayraktar, Elif and Palvadeau, Robin and Zor, Seyit and Koçoğlu, Cemile and Kartal, Ece and Şen, Nesli Ece and Hamzeiy, Hamid and Özoğuz Erimiş, Aslıhan and Norman, Utku and Karakahya, Oğuzhan and Olgun, Gülden and Akgün, Tahsin and Durmuş, Hacer and Şahin, Erdi and Çakar, Arman and Başar Gürsoy, Esra and Babacan Yıldız, Gülsen and İşak, Barış and Uluç, Kayıhan and Hanağası, Haşmet and Bilgiç, Başar and Turgut, Nilda and Aysal, Fikret and Ertaş, Mustafa and Boz, Cavit and Kotan, Dilcan and İdrisoğlu, Halil and Soysal, Aysun and Uzun Adatepe, Nurten and Akalın, Mehmet Ali and Koç, Filiz and Tan, Ersin and Oflazer, Piraye and Deymeer, Feza and Taştan, Öznur and Çiçek, A. Ercüment and Kavak, Erşen and Parman, Yeşim and Başak, A. Nazlı (2020) "Revisiting the complex architecture of ALS in Turkey: expanding genotypes, shared phenotypes, molecular networks, and a public variant database", Human Mutation, Vol.41, No.8, e7-e45 (SCI)

Deznabi, Iman and Arabaci, Busra and Koyuturk, Mehmet and Taştan, Öznur (2020) "DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving understudied kinases", Bioinformatics, Vol.36, No.12, 3652-3661 (SCI)

Olgun, Gülden and Şahin, Özgür and Taştan, Öznur (2018) "Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes", BMC Genomics, Vol.19, No.1 (SCI)

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.