Hacettepe Üniversitesi Bilişim Enstitüsü

Araştırma

Bu sayfada Enstitümüzde yürütülen veya Enstitümüz tarafından desteklenen araştırmalara ve yayınlanan araştırma makalelerine (Scopus Q1/Q2) dair bilgi bulabilirsiniz.

2026
	"Physical and transition climate risks and financial risk predictability in the US banking sector," P. Caraiani, O. Polat, R. Gupta, E. Bouri, International Review of Economics & Finance, 107, 105099, 2026.
	"University journals in the global academic publishing landscape: Mapping over 19,000 diverse titles based on Ulrichsweb data," M. Nazarovets, M. Laakso, Z. Taskin, Scientometrics, 2026.
	"Weight stability intervals for multi-criteria decision analysis using the weighted sum model," R. O'Shea, P. Deeney, E. Triantaphyllou, L. Diaz-Balteiro, S. A. Tarim, Expert Systems with Applications, 296, 128460, 2026.
	"Experimental insights into muscle and joint roles in stumble recovery: A scoping review," O. F. Seven, M. Bicer, M. A. Adli, Gait and Posture, 123, 109963, 2026.
	"OmniPath: integrated knowledgebase for multi-omics analysis," D. Türei, J. Schaul, N. Palacio-Escat, B. Bohár, Y. Bai, F. Ceccarelli, E. Çevrim, M. Daley, M. Darcan, D. Dimitrov, T. Doğan, D. Domingo-Fernández, A. Dugourd, A. Gábor, L. Gul, B. A. Hall, C. T. Hoyt, O. Ivanova, M. Klein, T. Lawrence, D. Mañanes, D. Módos, S. Müller-Dott, M. Ölbei, C. Schmidt, B. Şen, F. J. Theis, A. Ünlü, E. Ulusoy, A. Valdeolivas, T. Korcsmáros, J. Saez-Rodriguez, Nucleic Acids Research, gkaf1126, 2026.
	"Climate risks and predictability of the conditional distributions of rare earth stock returns and volatility," O. Polat, R. Gupta, E. Bouri, M. Brahim, Journal of Economics and Finance, 50 (1), 15, 2026.


2025
	"AI-driven discovery of antiretroviral drug bictegravir and etravirine as inhibitors against monkeypox and related poxviruses," Y. Wang, A. Ünlü, X. Wang, E. Çevrim, D. M. Offermans, M. P. Flesseman, L. M. Zaeck, L. Wu, M. J. C. Bijvelds, N. A. Sam-Agudu, R. D. de Vries, K. Raymond, P. Li, A. Olğaç, W. Wang, T. Doğan, Q. Pan, Communications Biology, 8 (1), 1734, 2025.
	"MoDeST: A dataset for Multi Domain Scientific Title Generation," N. Bölücü, Y. C. Bilge, D. Çetintaş, Z. Yücel, Knowledge-Based Systems, 321, 113557, 2025.
	"Mpox: disease manifestations and therapeutic development," Y. Wang, X. Wang, T. Doğan, N. A. Sam-Agudu, J. A. Al-Tawfiq, Q. Pan, Journal of Virology, 99 (9), 2025.
	"A heuristic method for perishable inventory management under non-stationary demand," S. Gulecyuz, B. O'Sullivan, S. A. Tarim, Omega, 133, 103267, 2025.
	"Target-specific de novo design of drug candidate molecules with graph-transformer-based generative adversarial networks," A. Ünlü, E. Çevrim, M. G. Yiğit, A. Sarıgün, H. Çelikbilek, O. Bayram, D. C. Kahraman, A. Olğaç, A. S. Rifaioglu, E. Banoğlu, T. Doğan, Nature Machine Intelligence, 7 (9), pp. 1524–1540, 2025.
	"Simple heuristics for the joint inventory and pricing models with fixed replenishment costs," M. E. Gurkan, H. Tunc, S. A. Tarim, Journal of the Operational Research Society, 76 (3), pp. 567–580, 2025.
	"Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions," A. Ünlü, E. Ulusoy, M. G. Yiğit, M. Darcan, T. Doğan, Current Opinion in Structural Biology, 91, 103017, 2025.


2024
	"An IRP Model to Improve the Sustainability of Cold Food Supply Chains under Stochastic Demand," S. Jahdi, S. Gulecyuz, S. O’Reilly, B. O’Sullivan, S. A. Tarim, Journal of Cleaner Production, 462, 142615, 2024.
	"A Simple Heuristic for Computing Non-Stationary Inventory Policies Based on Function Approximation," O. A. Kilic, S. A. Tarim, European Journal of Operational Research, 316, pp.899–905, 2024.
	"On the Stochastic Inventory Problem Under Order Capacity Constraints," R. Rossi, Z. Chen, S. A. Tarim, European Journal of Operational Research, 312, pp.541-555, 2024.
	"The trade-off between bias and imprecision: Debunking the myth of bias as the primary culprit in patient result misclassification," H. C. Çubukçu, American Journal of Clinical Pathology, 161 (5), pp. 513–516, 2024.
	"Describing the Flick Movement Kinematic Biomechanically and Investigating the Effect of Thrower’s Ten Exercises in Underwater Hockey Players," D. Deniz, L. Eraslan, C. Bas, V. B. Tunay, Journal of Sport Rehabilitation, 33 (7), pp. 522–530, 2024.
	"Machine learning-based clinical decision support using laboratory data," H. C. Çubukçu, D. İ. Topcu, S. Yenice, Clinical Chemistry and Laboratory Medicine, 62 (5), pp. 793–823, 2024.
	"APS calculator: A data-driven tool for setting outcome-based analytical performance specifications for measurement uncertainty using specific clinical requirements and population data," H. C. Çubukçu, F. Vanstapel, M. Thelen, M. Van Schrojenstein Lantman, F. A. Bernabeu-Andreu, P. Meško Brguljan, N. Milinkovic, S. Linko, M. Panteghini, G. Boursier, Clinical Chemistry and Laboratory Medicine, 62 (4), pp. 597–607, 2024.


2023
	"ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations," F. Cankara, T. Doğan, Computational and Structural Biotechnology Journal, 21, pp. 4743–4758, 2023.
	"How to approach machine learning-based prediction of drug/compound–target interactions," H. Atas Guvenilir, T. Doğan, Journal of Cheminformatics, 15 (1), 16, 2023.
	"SELFormer: molecular representation learning via SELFIES language models," A. Yüksel, E. Ulusoy, A. Ünlü, T. Doğan, Machine Learning: Science and Technology, 4 (2), 025035, 2023.


2022
	"Learning functional properties of proteins with language models," S. Unsal, H. Atas, M. Albayrak, K. Turhan, A. C. Acar, T. Doğan, Nature Machine Intelligence, 4 (3), pp. 227–245, 2022.
	"Cloudy/clear weather classification using deep learning techniques with cloud images," M. Kalkan, G. E. Bostancı, M. S. Güzel, B. Kalkan, Ş. Özsarı, Ö. Soysal, G. Köse, Computers and Electrical Engineering, 102, 108271, 2022.
	"Machine learning-based prediction of drug approvals using molecular, physicochemical, clinical trial, and patent-related features," F. Ciray, T. Doğan, Expert Opinion on Drug Discovery, 17 (12), pp. 1425–1441, 2022.


2021
	"Protein domain-based prediction of drug/ compound-target interactions and experimental validation on LIM kinases," T. Doğan, E. A. Güzelcan, M. Baumann, A. Koyas, H. Atas, I. R. Baxendale, M. Martin, R. Cetin-Atalay, PLoS Computational Biology, 17 (11), e1009171, 2021.
	"MDeePred: Novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery," A. S. Rifaioglu, R. C. Atalay, D. C. Kahraman, T. Doğan, M. Martin, V. Atalay, Bioinformatics, 37 (5), pp. 693–704, 2021.
	"X-Ray microtomography imaging of red lentil puffed snacks: Processing conditions, microstructure and texture," R.-M. Guillermic, E. C. Aksoy, S. Aritan, C. Erkinbaev, J. Paliwal, F. Koksel, Food Research International, 140, 109996, 2021.
	"CROssBAR: Comprehensive resource of biomedical relations with knowledge graph representations," T. Doğan, H. Atas, V. Joshi, A. Atakan, A. S. Rifaioglu, E. Nalbat, A. Nightingale, R. Saidi, V. Volynkin, H. Zellner, R. Cetin-Atalay, M. Martin, V. Atalay, Nucleic Acids Research, 49 (16), e96, 2021.


2020
	"DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations," A. S. Rifaioglu, E. Nalbat, V. Atalay, M. J. Martin, R. Cetin-Atalay, T. Doğan, Chemical Science, 11 (9), pp. 2531–2557, 2020.
	"iBioProVis: interactive visualization and analysis of compound bioactivity space," A. Donmez, A. S. Rifaioglu, A. Acar, T. Doğan, R. Cetin-Atalay, V. Atalay, Bioinformatics, 36 (14), pp. 4227–4230, 2020.
	"Evaluating cross-lingual textual similarity on dictionary alignment problem," Y. Sever, G. Ercan, Language Resources and Evaluation, 54 (4), pp. 1059–1078, 2020.
	"Selective personalization and group profiles for improved web search personalization," S. Karimi Mansoub, G. Ercan, I. Çiçekli, Turkish Journal of Electrical Engineering and Computer Sciences, 28 (3), pp. 1631–1643, 2020.


2019
	"Synset expansion on translation graph for automatic wordnet construction," G. Ercan, F. Haziyev, Information Processing and Management, 56 (1), pp. 130–150, 2019.
	"Assessing risks and threats with layered approach to Internet of Things security," M. Aydos, Y. Vural, A. Tekerek, Measurement and Control, 52 (5–6), pp. 338–353, 2019.


2016
	"Topic segmentation using word-level semantic relatedness functions," G. Ercan, I. Cicekli, Journal of Information Science, 42 (5), pp. 597–608, 2016.


Seçilmiş Yayınlar
	"Masked Multiple State Space Model Identification Using FRD and Evolutionary Optimization," M. Ö. Efe, B. Kürkçü, C. Kasnakoglu, Z. Mohamed, Z. Liu, IEEE Transactions on Industrial Informatics, 20 (7), pp. 9861–9869, 2024.
	"Single parameter adaptive neural network control for multi-agent deployment with prescribed tracking performance," Z. Liu, Z. Lu, Z. Zhao, M. Ö. Efe, K.-S. Hong, Automatica, 156, 111207, 2023.
	"Structural Results for Average-Cost Inventory Models with Markov-Modulated Demand and Partial Information," H. Avci, K. Gokbayrak, E. Nadar, Production and Operations Management, 29 (1), pp. 156–173, 2020.
	"An Extended MIP Formulation and Dynamic Cut Generation Approach for the Stochastic Lot Sizing Problem," H. Tunc, O. A. Kilic, S. A. Tarim, R. Rossi, INFORMS Journal on Computing, 30, pp.492-506, 2018.
	"Disturbance/Uncertainty Estimator Based Integral Sliding-Mode Control," B. Kürkçü, C. Kasnakoǧlu, M. Ö. Efe, IEEE Transactions on Automatic Control, 63 (11), pp. 3940–3947, 2018.
	"Confidence-Based Reasoning in Stochastic Constraint Programming," R. Rossi, B. Hnich, S. A. Tarim, S. Prestwich, Artificial Intelligence, 228, pp.129-152, 2015.
	"Statistical Constraints," R. Rossi, S. D. Prestwich, S. A. Tarim, ECAI European Conference on Artificial Intelligence, 263, pp. 777–782, 2014.
	"Constraint-based local search for inventory control under stochastic demand and lead time," R. Rossi, S. A. Tarim, R. Bollapragada, INFORMS Journal on Computing, 24 (1), pp. 66–80, 2012.
	"Filtering Algorithms for Global Chance Constraints," B. Hnich, R. Rossi, S. A. Tarim, S. Prestwich, Artificial Intelligence, 189, pp.69-94, 2012.
	"Finding (α, υ)-solutions via sampled SCSPs," R. Rossi, B. Hnich, S. A. Tarim, S. Prestwich, IJCAI International Joint Conference on Artificial Intelligence, pp. 2172–2177, 2011.
	"Service time optimization of mixed-line flow shop systems," K. Gokbayrak, O. Selvi, IEEE Transactions on Automatic Control, 55 (2), pp. 395–404, 2010.
	"Optimization of a flow shop system of initially controllable machines," K. Gokbayrak, O. Selvi, IEEE Transactions on Automatic Control, 53 (11), pp. 2665–2668, 2008.
	"Constrained optimal hybrid control of a flow shop system," K. Gokbayrak, O. Selvi, IEEE Transactions on Automatic Control, 52 (12), pp. 2270–2281, 2007.
	"Stochastic Constraint Programming: A Scenario-Based Approach," S. A. Tarim, S. Manandhar, T. Walsh, Constraints, 11, pp.53-80, 2006.
	"Scenario-based stochastic constraint programming," S. Manandhar, S. A. Tarim, T. Walsh, IJCAI International Joint Conference on Artificial Intelligence, pp. 257–262, 2003.
	"Generalized surrogate problem methodology for online stochastic discrete optimization," K. Gokbayrak, C. G. Cassandras, Journal of Optimization Theory and Applications, 114 (1), pp. 97–132, 2002.
	"Adaptive call admission control in circuit-switched networks," K. Gokbayrak, C. G. Cassandras, IEEE Transactions on Automatic Control, 47 (6), pp. 1004–1015, 2002.