Items where Author is "Taştan, Öznur"

Article

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, 39 (10). ISSN 1367-4803 (Print) 1367-4811 (Online)

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 . ISSN 1530-437X (Print) 1558-1748 (Online) Published Online First https://dx.doi.org/10.1109/JSEN.2023.3300797

Şapcı, Ali Osman Berk and Kemik, Hasan and Yeniterzi, Reyyan and Taştan, Öznur (2023) Focusing on potential named entities during active label acquisition. Natural Language Engineering . ISSN 1351-3249 (Print) 1469-8110 (Online) Published Online First https://dx.doi.org/10.1017/S1351324923000165

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, 20 (1). pp. 330-339. ISSN 1545-5963 (Print) 1557-9964 (Online)

Nabi, Afshan and Dilekoğlu, Berke and Adebali, Ogün and Taştan, Öznur (2023) Discovering misannotated lncRNAs using deep learning training dynamics. Bioinformatics (Oxford, England), 39 (1). ISSN 1367-4803 (Print) 1367-4811 (Online)

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, 10 (3). pp. 1567-1577. ISSN 2148-2446

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, 19 (4). pp. 2334-2344. ISSN 1545-5963 (Print) 1557-9964 (Online)

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, 39 (6). ISSN 0737-4038 (Print) 1537-1719 (Online)

Olgun, Gulden and Taştan, Öznur (2022) miRCoop: identifying cooperating miRNAs via Kernel based interaction tests. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19 (3). pp. 1760-1771. ISSN 1545-5963 (Print) 1557-9964 (Online)

Özçelik, Duygu and Taştan, Öznur (2022) A weakly supervised clustering method for cancer subgroup identification. Balkan Journal of Electrical and Computer Engineering, 10 (2). pp. 178-186. ISSN 2147-284X

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, 38 (4). pp. 908-917. ISSN 1367-4803 (Print) 1460-2059 (Online)

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, 22 (1). ISSN 1471-2105

Olgun, Gulden and Nabi, Afshan and Taştan, Öznur (2021) NoRCE: non-coding RNA sets cis enrichment tool. BMC Bioinformatics, 22 (1). ISSN 1471-2105

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, 17 (5). ISSN 1553-734X (Print) 1553-7358 (Online)

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, 18 (3). pp. 1208-1216. ISSN 1545-5963 (Print) 1557-9964 (Online)

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, 28 (4). pp. 378-380. ISSN 1066-5277 (Print) 1557-8666 (Online)

Caylak, Gizem and Taştan, Öznur and Cicek, A. Ercument (2021) Potpourri: an epistasis test prioritization algorithm via diverse SNP selection. Journal of Computational Biology, 28 (4). pp. 365-377. ISSN 1066-5277 (Print) 1557-8666 (Online)

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, 36 (21). pp. 5237-5246. ISSN 1367-4803 (Print) 1460-2059 (Online)

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, 41 (8). e7-e45. ISSN 1059-7794 (Print) 1098-1004 (Online)

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, 36 (12). pp. 3652-3661. ISSN 1367-4803 (Print) 1460-2059 (Online)

Olgun, Gülden and Şahin, Özgür and Taştan, Öznur (2018) Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes. BMC Genomics, 19 (1). ISSN 1471-2164 (Print) 1471-2164 (Online)

Papers in Conference Proceedings

Alserr, Nour Almadhoun and Kale, Gulce and Mutlu, Onur and Taştan, Öznur and Ayday, Erman (2023) Tuning privacy-utility tradeoff in genomic studies using selective SNP hiding. In: 21st Asia Pacific Bioinformatics Conference (APBC 2023), Changsha, Hunan, China

Şapcı, Ali Osman Berk and Taştan, Öznur and Yeniterzi, Reyyan (2020) Active learning for Turkish text classification [Türkçe metin sınıflandırması için aktif öğrenme]. In: 28th Signal Processing and Communications Applications Conference (SIU), Gaziantep, Turkey

Olgun, Gulden and Taştan, Öznur (2020) Functional enrichment analysis of deregulated long non-coding RNAs in cancer based on their genomic neighbors. In: 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2020, Virtual, Online

Tepeli, Yasin İlkağan and Ünal, Ali Burak and Akdemir, Mustafa Furkan and Taştan, Öznur (2020) PAMOGK: A pathway graph kernel based multi-omics clustering approach for discovering cancer patient subgroups. In: Satellite Workshop on Computational Cancer Biology (RECOMB-CCB) - Jointly with RECOMB 2020, Virtual

Kuru, Halil İbrahim and Büyüközkan, Mustafa and Taştan, Öznur (2020) PRER: A patient representation with pairwise relative expression of proteins on biological networks. In: Satellite Workshop on Computational Cancer Biology (RECOMB-CCB) - Jointly with RECOMB 2020, Virtual