AGU Bilgisayar Mühendisliği

2024

Yengec-Tasdemir, S. B., Aydin, Z., Akay, E., Dogan, S., & Yilmaz, B. (2024). An effective colorectal polyp classification for histopathological images based on supervised contrastive learning. Computers in Biology and Medicine, 172, 108267.

Cini, N., & Aydin, Z. (2024). A Deep Ensemble Approach for Long-Term Traffic Flow Prediction. Arabian Journal for Science and Engineering, 1-16.

Bozkurt, B., Coskun, K., & Bakal, G. (2024). Building a challenging medical dataset for comparative evaluation of classifier capabilities. Computers in Biology and Medicine, 178, 108721.

Mahmood, R. S., Bakal, M. G., & Akbaş, A. (2024). Document Classification with Contextually Enriched Word Embeddings. Balkan Journal of Electrical and Computer Engineering, 12(1), 90-97.

Söylemez, Ü. G., Yousef, M., & Bakir-Gungor, B. (2024). Novel Antimicrobial Peptide Design Using Motif Match Score Representation. IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Dedeturk, B. A., & Bakir-Gungor, B. (2024). Aguhyper: a hyperledger-based electronic health record management framework. PeerJ Computer Science, 10, e2060.

Kuzudisli, C., Bakir-Gungor, B., Qaqish, B., & Yousef, M. (2024). RCE-IFE: Recursive Cluster Elimination with Intra-cluster Feature Elimination. bioRxiv, 2024-02.

Büyükkürkçü, H., Durmuş, A., Çolak, H., Kurban, R., Şahmetlioğlu, E., & Karaköse, E. (2024). Investigation of the performance and properties of ZnO/GO double-layer supercapacitor. Journal of Physics and Chemistry of Solids, 191, 111984.

Kevseroglu, O., & Kurban, R. (2024, May). Re-exploring the Kayseri Culture Route by Using Deep Learning for Cultural Heritage Image Classification. In Proceedings of the Cognitive Models and Artificial Intelligence Conference (pp. 196-201).

Durmus, A., Yildirim, Z., Kurban, R. & Karakose, E. (2024). An optimal concentric circular antenna array design using atomic orbital search for communication systems. Frequenz. https://doi.org/10.1515/freq-2023-0432

Kose, A., Lee, H., Foh, C. H., & Shojafar, M. (2024). Multi-Agent Context Learning Strategy for Interference-Aware Beam Allocation in mmWave Vehicular Communications. IEEE Transactions on Intelligent Transportation Systems.

Çelebi, F., Boyvat, D., Ayaz‐Guner, S., Tasdemir, K., & Icoz, K. (2024). Improved senescent cell segmentation on bright‐field microscopy images exploiting representation level contrastive learning. International Journal of Imaging Systems and Technology, 34(2), e23052.

Kolukisa, B., Dedeturk, B. K., Hacilar, H., & Gungor, V. C. (2024). An efficient network intrusion detection approach based on logistic regression model and parallel artificial bee colony algorithm. Computer Standards & Interfaces, 89, 103808.

Dedeturk, B. K., Dedeturk, B. A., & Akbaş, A. (2024). A Comparative Analysis of Passenger Flow Forecasting in Trams Using Machine Learning Algorithms. Bitlis Eren Üniversitesi Fen Bilimleri Dergisi, 13(1), 1-14.

2023

Işık, Y. E., & Aydın, Z. (2023). Comparative analysis of machine learning approaches for predicting respiratory virus infection and symptom severity. PeerJ, 11, e15552.

Yengec-Tasdemir, S. B., Aydin, Z., Akay, E., Dogan, S., & Yilmaz, B. (2023). Improved classification of colorectal polyps on histopathological images with ensemble learning and stain normalization. Computer Methods and Programs in Biomedicine, 232, 107441.

Firat, M., Bakal, M. G., & Akbaş, A. (2023). Machine learning based network intrusion detection with hybrid frequent item set mining. Politeknik Dergisi, 1-1.

Erkantarci, B., & Bakal, G. (2023). An empirical study of sentiment analysis utilizing machine learning and deep learning algorithms. Journal of Computational Social Science, 1-17.

Şen, T. Ü., & Bakal, G. (2023, July). A Transfer Learning Application on the Reliability of Psychological Drugs' Comments. In 2023 International Conference on Smart Applications, Communications and Networking (SmartNets) (pp. 1-6). IEEE.

Akkaya, A., & Bakal, G. (2023, July). A Computational Drug Repositioning Effort using Patients’ Reviews Dataset. In 2023 International Conference on Smart Applications, Communications and Networking (SmartNets) (pp. 1-6). IEEE.

Yazici, M. U., Yousef, M., Marron, J. S., & Bakir-Gungor, B. (2023, December). miRcorrNetPro: Unraveling Algorithmic Insights through Cross-Validation in Multi-Omics Integration for Comprehensive Data Analysis. In 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 3234-3240). IEEE.

Bakir-Gungor, B., Temiz, M., Jabeer, A., Wu, D., & Yousef, M. (2023). microBiomeGSM: the identification of taxonomic biomarkers from metagenomic data using grouping, scoring and modeling (GSM) approach. Frontiers in Microbiology, 14, 1264941.

Temiz, M., Yousef, M., & Bakir-Gungor, B. (2023, October). Population Specific Classification of Colorectal Cancer with Meta-Analysis of Metagenomic Data. In 2023 Innovations in Intelligent Systems and Applications Conference (ASYU) (pp. 1-5). IEEE.

Bulut, N., Bakir-Gungor, B., Qaqish, B. F., & Yousef, M. (2023, October). The Effect of Different Classifiers on Recursive Cluster Elimination in the Analysis of Transcriptomic Data. In 2023 Innovations in Intelligent Systems and Applications Conference (ASYU) (pp. 1-5). IEEE.

Kuzudisli, C., Bakir-Gungor, B., Qaqish, B. F., & Yousef, M. (2023, October). Effect of recursive cluster elimination with different clustering algorithms applied to gene expression data. In 2023 Innovations in Intelligent Systems and Applications Conference (ASYU) (pp. 1-4). IEEE.

Ersoz, N. S., Bakir-Gungor, B., & Yousef, M. (2023). GeNetOntology: identifying affected gene ontology terms via grouping, scoring, and modeling of gene expression data utilizing biological knowledge-based machine learning. Frontiers in Genetics, 14, 1139082.

Kuzudisli, C., Bakir-Gungor, B., Bulut, N., Qaqish, B., & Yousef, M. (2023). Review of feature selection approaches based on grouping of features. PeerJ, 11, e15666.

Temiz, M., Bakir-Gungor, B., Şahan, P. G., & Coskun, M. (2023). Topological feature generation for link prediction in biological networks. PeerJ, 11, e15313.

Söylemez, Ü. G., Yousef, M., & Bakir-Gungor, B. (2023). AMP-GSM: prediction of antimicrobial peptides via a grouping–scoring–modeling approach. Applied Sciences, 13(8), 5106.

Unlu Yazici, M., Marron, J. S., Bakir-Gungor, B., Zou, F., & Yousef, M. (2023). Invention of 3Mint for feature grouping and scoring in multi-omics. Frontiers in Genetics, 14, 1093326.

Kolukisa, B., & Bakir-Gungor, B. (2023). Ensemble feature selection and classification methods for machine learning-based coronary artery disease diagnosis. Computer Standards & Interfaces, 84, 103706.

Jabeer, A., Temiz, M., Bakir-Gungor, B., & Yousef, M. (2023). miRdisNET: discovering microRNA biomarkers that are associated with diseases utilizing biological knowledge-based machine learning. Frontiers in Genetics, 13, 1076554.

Yazici, M. U., Bakir-Gungor, B., & Yousef, M. (2023). Integrative analyses in omics data: Machine learning perspective.

Marcos-Zambrano, L. J., López-Molina, V. M., Bakir-Gungor, B., Frohme, M., Karaduzovic-Hadziabdic, K., Klammsteiner, T., ... & Carrillo de Santa Pau, E. (2023). A toolbox of machine learning software to support microbiome analysis. Frontiers in microbiology, 14, 1250806.

Voskergian, D., Bakir-Gungor, B., & Yousef, M. (2023). TextNetTopics Pro, a topic model-based text classification for short text by integration of semantic and document-topic distribution information. Frontiers in Genetics, 14, 1243874.

Bakir-Gungor, B., & Yousef, M. Integrative analyses in omics data: Machine learning perspective Integrative Analysen von Omics-Daten: Perspektive des maschinellen Lernens.

Söylemez, Ü. G., Yousef, M., & Bakir-Gungor, B. (2023). Prediction of Antimicrobial Peptides Using Deep Neural Networks. In BIOINFORMATICS (pp. 188-194).

Yousef, M., Ozdemir, F., Jaber, A., Allmer, J., & Bakir-Gungor, B. (2023). PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach. BMC bioinformatics, 24(1), 60.

Şentürk, R., Kurban, R., & Çakıroğlu, F., (2023). Prediction of Groundwater Level with Nonlinear Autoregressive Neural Networks . BMYZ2023 - Cognitive Models and Artificial Intelligence Conference (pp.59-63). Ankara, Turkey

Çakıroğlu, F., Kurban, R., Durmuş, A., & Karaköse, E. (2023, December). Görüntü Birleştirme Yöntemleri ile Çok-modlu Medikal Görüntülerin Kaynaştırılması. In SETSCI-Conference Proceedings (Vol. 15, pp. 70-75). SETSCI-Conference Proceedings.

Çakıroğlu, F., Kurban, R., Durmuş, A., & Karaköse, E., (2023). Comparison of Image Fusion Methods to Extend Cameras' Limited Depth of Field and Provide Improved Night Vision.Industrial Application of Intelligent Systems II (pp.129-158), Ankara: Bidge Yayınları.

Çakıroğlu, F., Kurban, R., Durmuş, A., & Karaköse, E. (2023). Multi-focus image fusion by using swarm and physics based metaheuristic algorithms: a comparative study with archimedes, atomic orbital search, equilibrium, particle swarm, artificial bee colony and jellyfish search optimizers. Multimedia Tools and Applications, 82(29), 44859-44883.

Kurban, R. (2023). Gaussian of differences: a simple and efficient general image fusion method. Entropy, 25(8), 1215.

Adige, S., Kurban, R., Durmuş, A., & Karaköse, E. (2023). Classification of apple images using support vector machines and deep residual networks. Neural Computing and Applications, 35(16), 12073-12087.

Manic, S., Foh, C. H., Kose, A., Lee, H., Leow, C. Y., Chatzimisios, P., ... & Suthaputchakun, C. (2023, December). Machine Learning based Beamwidth Adaptation for mmWave Vehicular Communications. In 2023 IEEE 16th Malaysia International Conference on Communication (MICC) (pp. 80-85). IEEE.

Hamdan, M. Q., Lee, H., Triantafyllopoulou, D., Borralho, R., Kose, A., Amiri, E., ... & Tafazolli, R. (2023). Recent advances in machine learning for network automation in the o-ran. Sensors, 23(21), 8792.

Cassillas, A. M., Kose, A., Lee, H., Foh, C. H., & Leow, C. Y. (2023, June). Contextual Multi-Armed Bandit based Beam Allocation in mmWave V2X Communication under Blockage. In 2023 IEEE 97th Vehicular Technology Conference (VTC2023-Spring) (pp. 1-6). IEEE.

Kolukisa, B., Yildirim, V. C., Ayyildiz, C., & Gungor, V. C. (2023). A deep neural network approach with hyper-parameter optimization for vehicle type classification using 3-D magnetic sensor. Computer Standards & Interfaces, 84, 103703.

Dedeturk, B. K., Kolukisa, B., & Özmen, M. (2023). ZAMAN PENCERELİ ARAÇ ROTALAMA PROBLEMLERİ İÇİN KÜMELEME TEMELLİ KLONAL SEÇİM ALGORİTMASI. Adıyaman Üniversitesi Mühendislik Bilimleri Dergisi, 10(21), 307-320. https://doi.org/10.54365/adyumbd.1381562

Dedeturk, B. A., Kolukisa, B., & Tonyalı, S. Privacy-Preserving Wireless Indoor Localization Systems. Kocaeli Journal of Science and Engineering, 6(2), 114-128.

Bulut, N., & Hacıbeyoglu, M. (2023). Hydroponic Agriculture with Machine Learning and Deep Learning Methods. Gazi Mühendislik Bilimleri Dergisi, 9(3), 508-519.

2022

Taş, M., Taş, Y., Balki, O., Aydın, Z., and Taşdemir, K., “Camera-based wildfire smoke detection for foggy environments”, Journal of Electronic Imaging, vol. 31, 2022. doi:10.1117/1.JEI.31.5.053033.

Görmez Y, Sabzekar M, Aydın Z. IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction. Proteins. 2021 Oct;89(10):1277-1288. doi: 10.1002/prot.26149. Epub 2021 May 25. Erratum in: Proteins. 2022 Aug;90(8):1613. doi: 10.1002/prot.26354. PMID: 33993559.

Görmez, Y., & Aydin, Z. (2022). IGPRED-MultiTask: a deep learning model to predict protein secondary structure, torsion angles and solvent accessibility. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(2), 1104-1113.

Dundar, M., Fahrioglu, U., Yildiz, S. H., Bakir-Gungor, B., Temel, S. G., Akin, H., ... & Tunc, B. (2022). Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium. Functional & integrative genomics, 22(3), 291-315.

Kolukısa, B., Görmez, Y., Aydın, Z. (2023). A Transfer Learning Approach for Skin Cancer Subtype Detection. 4th International Conference on Artificial Intelligence and Applied Mathematics in Engineering. ICAIAME 2022. Engineering Cyber-Physical Systems and Critical Infrastructures , vol 7. Springer, Cham. https://doi.org/10.1007/978-3-031-31956-3_28

Jabeer, A., KoÇak, A., Akkaş, H., Yenisert, F., Nalbantoğlu, Ö. U., Yousef, M., & GÜngÖr, B. B. (2022, September). Identifying taxonomic biomarkers of colorectal cancer in human intestinal microbiota using multiple feature selection methods. In 2022 Innovations in Intelligent Systems and Applications Conference (ASYU) (pp. 1-6). IEEE.

Kuzudİşlİ, C., & Güngör, B. B. (2022, September). A comparative study on psychiatric disorders: Identification of shared pathways and common agents. In 2022 Innovations in Intelligent Systems and Applications Conference (ASYU) (pp. 1-6). IEEE.

Soylemez, Ü. G., Celebiler, H. K., Harkonen, J., & Bakir-Gungor, B. (2022, September). The relationship between TSH levels, maternal characteristics and racial group of the aneuploidy screening. In 2022 Innovations in Intelligent Systems and Applications Conference (ASYU) (pp. 1-5). IEEE.

Dedeturk, B. A., Taşdemir, K., & Bakir-gungor, B. (2022). Cilt Kanseri Görüntü Sınıflandırması için Görüntü Ön İşlemenin Evrişimsel Sinir Ağları Performansı Üzerindeki Etkileri. Erciyes Üniversitesi Fen Bilimleri Enstitüsü Fen Bilimleri Dergisi, 38(2), 190-200.

Durmus, A., & Kurban, R. (2022). Optimal synthesis of concentric circular antenna arrays using political optimizer. IETE Journal of Research, 68(1), 768-777.

Kurban, R., & Bozpolat, H. (2022). AYRIK KOSİNÜS DÖNÜŞÜMÜ DC BİLEŞENLERİ VE ÇOKLU-ADAPTİF ÖLÇEKLEME FAKTÖRLERİ KULLANILARAK DAYANIKLI GÖRÜNTÜ DAMGALAMA. Eskişehir Osmangazi Üniversitesi Mühendislik ve Mimarlık Fakültesi Dergisi, 30(2), 190-200.

Çıtıl, F., Kurban, R., Durmuş, A., & Karaköse, E. (2022). Fusion of Multi-Focus Images using Jellyfish Search Optimizer. Avrupa Bilim ve Teknoloji Dergisi, (37), 147-155.

Yakupoglu, C., & Rohloff, K. (2022, October). Prefhe, prefhe-aes and prefhe-sgx: Secure multiparty computation protocols from fully homomorphic encryption and proxy reencryption with aes and intel sgx. In International Conference on Security and Privacy in Communication Systems (pp. 819-837). Cham: Springer Nature Switzerland.

Yakupoglu, C., & Rohloff, K. (2022, August). Towards Efficient FHE Based cPIR Schemes and Their Parameter Selection. In Proceedings of the 17th International Conference on Availability, Reliability and Security (pp. 1-11).

Seven, S., Yoldas, Y., Soran, A., Yalcin Alkan, G., Jung, J., Ustun, T. S., & Onen, A. (2022). Energy trading on a peer-to-peer basis between virtual power plants using decentralized finance instruments. Sustainability, 14(20), 13286.

Çelebi, F., Tasdemir, K., & Icoz, K. (2022). Deep learning based semantic segmentation and quantification for MRD biochip images. Biomedical Signal Processing and Control, 77, 103783.

Kolukisa, B., Yildirim, V. C., Elmas, B., Ayyildiz, C., & Gungor, V. C. (2022). Deep learning approaches for vehicle type classification with 3-D magnetic sensor. Computer Networks, 217, 109326.

Dedeturk, B. A., & Gungor, B. B. (2022). Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. Pamukkale Üniversitesi Mühendislik Bilimleri Dergisi, 28(2), 292-298.

Y.E. IŞIK, Y. GÖRMEZ, Z. AYDIN, B. Bakir-Gungor, "The Determination of Distinctive Single Nucleotide Polymorphism Sets for the Diagnosis of Behcet's Disease," IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,vol. 19 no. 3, 2022.

B. Bakir-Gungor, H. Hacılar, A. Jabeer, O.U. Nalbantoglu, O. Aran, M. Yousef. "Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods," PeerJ, 2022.

M. Yousef, G. Goy, B. Bakir-Gungor, "miRModuleNet: Detecting miRNA-mRNA regulatory modules," Frontiers in Genetics, 2022.

Ü.G. Söylemez, M. Yousef, Z. Kesmen, M.E. Büyükkiraz, B. Bakir-Gungor, "Prediction of Linear Cationic Antimicrobial Peptides Active against Gram-Negative and Gram-Positive Bacteria Based on Machine Learning Models," Applied Sciences, vol. 12 no. 7, 2022.

B. Bakir-Gungor, Z. Aydın, et. al., "Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium," Functional & Integrative Genomics, 2022.

P. GÜNER, B. GÜNGÖR, M. COŞKUN, "Developing a label propagation approach for cancer subtype identification problem," Turkish Journal of Biology, vol. 46, no.2, 2022.

B. Kolukisa, V.C. Yildirim, B. Elmas, C. Ayyildiz, V.C. Gungor, "Deep learning approaches for vehicle type classification with 3-D magnetic sensor," Computer Networks, 2022.

O.G. Uyan, A. Akbas, V.C. Gungor, "A Reliable and Secure Multi-Path Routing Strategy for Underwater Acoustic Sensor Networks," Computer Networks, vol. 24, 2021.

2021

Kolukisa, B., Dedeturk, B. K., Dedeturk, B. A., Gulsen, A., & Bakal, G. (2021, September). A comparative analysis on medical article classification using text mining & machine learning algorithms. In 2021 6th International Conference on Computer Science and Engineering (UBMK) (pp. 360-365). IEEE.

Z. Aydın, et. al., "A Continuously Benchmarked and Crowdsourced Challenge for Rapid Development and Evaluation of Models to Predict COVID-19 Diagnosis and Hospitalization," JAMA NETWORK OPEN,vol.4, no.10 2021.

Y. Görmez, M. Sabzekar, Z. Aydın, "IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction," Proteins: Structure, Function, and Bioinformatics,vol.89, no.10, 2021.

Z. Aydın, et. al., "Crowdsourcing digital health measures to predict Parkinson’s disease severity: the Parkinson’s Disease Digital Biomarker DREAM Challenge," NPJ digital medicine, vol.4, no.1, 2021.

M. Sabzekar, Z. Aydin, "A noise-aware feature selection approach for classification," Soft Computing, vol.25, no.8 2021.

S. Atasever, N. Azgınoglu, H. Erbay, Z. Aydın, "3-State Protein Secondary Structure Prediction based on SCOPe Classes," Brazilian Archives of Biology and Technology, vol. 64, 2021.

B. Adanur Dedeturk, A. Soran, B. Bakir-Gungor, "Blockchain for genomics and healthcare: a literature review, current status, classification and open issues," PeerJ, 2021.

B. Bakir-Gungor, O. Bulut, A. Jabeer, O.U. Nalbantoglu, M. Yousef, "Discovering potential taxonomic biomarkers of type 2 diabetes from human gut microbiota via different feature selection methods," Frontiers in microbiology, 2021.

M. Yousef, G. Goy, R. Mitra, C.M. Eischen, A. Jabeer, B. Bakir-Gungor, "miRcorrNet: machine learning-based integration of miRNA and mRNA expression profiles, combined with feature grouping and ranking," PeerJ, vol. 9, 2021.

B. Bakir-Gungor, et al., "Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions," Frontiers in Microbiology, vol. 277, 2021.

M. Yousef, A. Kumar, B. Bakir-Gungor, "Application of biological domain knowledge based feature selection on gene expression data," Entropy, vol. 23, no. 1, 2021.

M. Faheem, R.A. Butt, R. Ali, B. Raza, M.A. Ngadi, V.C. Gungor, "CBI4. 0: A cross-layer approach for big data gathering for active monitoring and maintenance in the manufacturing industry 4.0," Journal of Industrial Information Integration, vol. 24, 2021.

C. Ayyildiz, R. Cetin, Z. Khodzhaev, T. Kocak, E.G. Soyak, V.C. Gungor, G.K. Kurt, "Physical layer authentication for extending battery life," Ad Hoc Networks, vol. 123, 2021.

N. Tekin, H.U. Yildiz, V.C. Gungor, "Node-Level Error Control Strategies for Prolonging the Lifetime of Wireless Sensor Networks," IEEE Sensors Journal, vol. 21, no.13, 2021.

2020

S.B: Yengec Tasdemir, K. Tasdemir, Z. Aydin, "A review of mammographic region of interest classification," Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, vol. 10, no. 5, 2020

Z. Kesmen, Ö. Kılıç, Y. Gormez, M. Celik, B. Bakir-Gungor, "Multi fragment melting analysis system (MFMAS) for one-step identification of lactobacilli," Journal of Microbiological Methods, vol. 177, 2020

Y. Gormez, Z. Aydin, R. Karademir, V. C. Gungor, "A deep learning approach with Bayesian optimization and ensemble classifiers for detecting denial of service attacks," International Journal of Communication Systems (Wiley), vol. 33, no.11, 2020.

H. Erdem, V.C. Gungor, "Analyzing lifetime of energy harvesting underwater wireless sensor nodes," International Journal of Communication Systems (Wiley), vol. 33, no.3, 2020.

N. Tekin, V.C. Gungor,"The impact of error control schemes on lifetime of energy harvesting wireless sensor networks in industrial environments," Computer Standards & Interfaces (Elsevier), vol. 70, 2020.

N. Tekin, V.C. Gungor,"Analysis of compressive sensing and energy harvesting for wireless multimedia sensor networks," Ad Hoc Networks (Elsevier), vol. 103, no. 1, 2020.

J: T. Cowman, M. Coşkun, A. Grama, and M. Koyuturk. Integrated Querying and Version Control of Context-Specific Biological Networks (The Journal of Biological Databases and Curation, Oxford) 2020.

J: M. Coşkun, A. Baggag, M. Koyutürk Fast Computation of Katz Index for Efficient Processing of Link Prediction Queries, Data Mining and Knowledge Discovery, DMKD, 2020 (Revised).

Saputro, N., Tonyali, S., Aydeger, A., Akkaya, K., Rahman, M.A. and Uluagac, S., 2020. A Review of Moving Target Defense Mechanisms for Internet of Things Applications. Modeling and Design of Secure Internet of Things, pp.563-614.

Sena B Yengec Tasdemir, Kasim Tasdemir, and Zafer Aydin. A review of mammographic region of interest classification. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, page e1357, 2020.

Fatma Uslu, Kutay Icoz, Kasim Tasdemir, Refika S Doğan, and Bulent Yilmaz. Automated quantification of immunomagnetic beads, micropads and patient leukemia cells: A readout method for biochip. Micron, page 102863, 2020.

Fatma Uslu, Kutay Icoz, Kasim Tasdemir, Refika S Doğan, and Bulent Yilmaz. Image-analysis based readout method for biochip: Automated quantification of immunomagnetic beads, micropads and patient leukemia cell. Micron (Oxford, England: 1993), 133:102863-102863, 2020.

Nuh Azgınoğlu, Zafer Aydın, Mete Çelik, "Structural profile matrices for predicting structural properties of proteins," Journal of Bioinformatics and Computational Biology, 2050022, 2020.

Rukiye Nur Kaçmaz, Bülent Yılmaz, Zafer Aydın, "Effect of interpolation on specular reflections in texture‐based automatic colonic polyp detection," International Journal of Imaging Systems and Technology, 1-9, 2020

Yasin Görmez, Zafer Aydın, Ramazan Karademir, Vehbi Çağrı Güngör, "A deep learning approach with Bayesian optimization and ensemble classifiers for detecting denial of service attacks," International Journal of Communication Systems, 33:e4401, 2020.

Sena Büşra Yengeç Taşdemir, Kasım Tasdemir, Zafer Aydın, "A review of mammographic region of interest classification," WIREs Data Mining and Knowledge Discovery, e1357, 2020.

Zafer Aydın, "Performance analysis of machine learning and bioinformatics applications on high performance computing systems," Academic Platform Journal of Engineering and Science, 8(1):1-14, 2020.

Hilal Hacılar, Yasin Görmez, Burcu Bakır Güngör, Cengiz Gezer, Zafer Aydın, Vehbi Çağrı Güngör, "Classification of cardiovascular artery diseases using artificial neural network," International Journal of Bioscience, Biochemistry and Bioinformatics, 10(1):34-41, 2000.

Oğuzhan Ayyıldız, Zafer Aydın, Bülent Yılmaz, Seyhan Karaçavuş, Kübra Şenkaya, Semra İçer, Arzu Taşdemir, Eser Kaya, "Lung cancer subtype differentiation from positron emission tomography images," Turkish Journal of Electrical Engineering and Computer Sciences, 28(1):262-274, 2020.

2019

H. U. Yildiz, V.C. Gungor, B. Tavli, "Packet Size Optimization for Lifetime Maximization in Underwater Acoustic Sensor Networks," IEEE Trans. Ind. Informatics, vol. 15, no. 2, pp. 719-729, 2019.

O.G. Uyan, V.C. Gungor, "QoS-aware LTE-A downlink scheduling algorithm: A case study on edge users. International Journal of Communication Systems (Wiley), vol. 32, no. 15, 2019.

J: H. Jiang, M. Coşkun, A. Badokhon, M. Liu, M-C. Huang Hidden Smile Correlation Discovery Across Subjects Using Random Walk with Restart IEEE Transaction On Affective Computing, Volume: 10 Issue: 1 Pages: 76-84 Special Issue: SI, ISSN: 1949-3045 (SCIE), Jan 2019.

C: M. Coşkun, V. Ç. Güngör, H. Hacılar. OFFER: Referee Suggester Algorithm for Journal Editors. The 24th IEEE* Symposium on Computers and Communications, March 2019.

Enes Altinisik, Kasim Tasdemir, and Husrev Taha Sencar. Mitigation of h. 264 and h. 265 video compression for reliable prnu estimation. IEEE Transactions on information forensics and security, 15:1557-1571, 2019.

Fatma Uslu, Kutay Icoz, Kasim Tasdemir, and Bulent Yilmaz. Automated quantification of immunomagnetic beads and leukemia cells from optical microscope images. Biomedical Signal Processing and Control, 49:473-482, 2019.

Fatma Uslu, Kutay İҫöz, and Kasim Tasdemir. Image-processing based signal readout method for mrd biochip. In 2019 27th Signal Processing and Communications Applications Conference (SIU), pages 1-4. IEEE, 2019.

Sema Atasever, Zafer Aydın, Hasan Erbay, Mostafa Sabzekar, "Sample reduction strategies for protein secondary structure prediction," Applied Sciences, 9(20):4429, 2019.

Zafer Aydın, Nuh Azgınoğlu, Halil İbrahim Bilgin, Mete Çelik, "Developing structural profile matrices for protein secondary structure and solvent accessibility prediction," Bioinformatics, 35(20):4004-4010, 2019.

2018

M. Yigit, V.C. Gungor, P. Sarisaray-Boluk, "Performance analysis of Hamming code for WSN-based smart grid applications," Turkish Journal of Electrical Engineering & Computer Sciences, vol. 26, no.1, pp. 125137, 2018.

M. Faheem, V.C. Gungor, "MQRP: Mobile sinks-based QoS-aware data gathering protocol for wireless sensor networks-based smart grid applications in the context of industry 4.0-based on internet of things," Future Generation Computer Systems (Elsevier), vol. 82, pp. 358-374, May 2018.

N. Tekin, H.E. Erdem, V.C. Gungor, "Analyzing lifetime of energy harvesting wireless multimedia sensor nodes in industrial environments," Computer Standards & Interfaces (Elsevier), vol. 58, pp. 109-117, May 2018.

H.E. Erdem, V.C. Gungor, "On the Lifetime Analysis of Energy Harvesting Sensor Nodes in Smart Grid Environments," Ad Hoc Networks (Elsevier), vol. 75, pp. 98-105, June 2018.

M. Faheem, V.C. Gungor, "Energy Efficient and Qos-Aware Routing Protocol for Wireless Sensor NetworkBased Smart Grid Applications in the Context of Industry 4.0," Applied Soft Computing (Elsevier), vol. 68, pp. 910-922, July 2018.

M. Yigit, H.U. Yildiz, S. Kurt, B. Tavli, V.C. Gungor, "A Survey on Packet Size Optimization for Terrestrial, Underwater, Underground, And Body Area Sensor Networks," International Journal of Communication Systems (Wiley), vol. 31 no. 11, July 2018.

C. Ayyildiz, H.E. Erdem, T. Dirikgil, O. Dugenci, T. Kocak, F. Altun, V.C. Gungor, "Structure Health Monitoring Using Wireless Sensor Networks on Structural Elements," Ad Hoc Networks (Elsevier), July 2018.

C. Deniz, O.G. Uyan, V.C. Gungor, “On the Performance of LTE Downlink Scheduling Algorithms: A Case Study on Edge Throughput," Computer Standards & Interfaces (Elsevier), vol. 59, pp. 96-108, Aug. 2018.

J: M. Coşkun, A. Grama, M. Koyuturk Indexed Fast Network Proximity Querying. 44th Very Large Databases VLDB Endowment ,Volume: 11 Issue: 8 Pages: 840-852.ISSN: 2150-8097 (ESCI), Aug 2018.

C: M. Coşkun, A. Baggag, S. Chawla. Deep Learning Approaches for Traffic Light Optimization International Conf. Data Mining (ICDM) Workshops,Nov, 2018

Yusuf Cagatay Ersan, Damian Palin, Sena Busra Yengec Tasdemir, Kasim Tasdemir, Henk M Jonkers, Nico Boon, and Nele De Belie. Volume fraction, thickness, and permeability of the sealing layer in microbial self-healing concrete containing biogranules. Frontiers in Built Environment, 4:70, 2018.

Enes Altinisik, Kasim Tasdemir, and Husrev Taha Sencar. Extracting prnu noise from h. 264 coded videos. In 2018 26th European signal processing conference (EUSIPCO), pages 1367-1371. IEEE, 2018.

Sena Busra Yengec Tasdemir, Kasim Tasdemir, and Zafer Aydin. Roi detection in mammogram images using wavelet-based haralick and hog features. In 2018 17th IEEE International Conference on Machine Learning and Applications (ICMLA), pages 105-109. IEEE, 2018.

Fourati et al. "A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection," Nature Communications, 9(1):1-11, 2018.

Zafer Aydın, Oğuz Kaynar, Yasin Görmez, "Dimensionality reduction for protein secondary structure and solvent accesibility prediction," Journal of Computational Biology and Bioinformatics, 16(5):1850020-1-1850020-16, 2018.

Vehbi Çağrı Güngör, Zafer Aydın, Ramazan Karademir, “Intelligent anomaly detection techniques for denial of service attacks,” International Journal of Computer and Communication Enginering, 7(2): 20-31, 2018.

Yunus Emre Işık, Yasin Görmez, Oğuz Kaynar, Zafer Aydın, "NSEM: Novel Stacked Ensemble Method for Sentiment Analysis," IEEE International Conference on Artificial Intelligence and Data Processing (IDAP), 1-4, Malatya, Turkey, 28-30 September 2018.

Zafer Aydın, Vehbi Çağrı Güngör, "A novel feature design and stacking approach for non technical electricity loss detection," IEEE Innovative Smart Grid Technologies – Asia (ISGT Asia), 867-872, Singapore, 2018.

Sena Büşra Yengeç Taşdemir, Kasım Taşdemir, Zafer Aydın, "ROI detection in mammogram images using wavelet-based Haralick and HOG features," IEEE International Conference on Machine Learning Applications, 105-109, Orlando, Florida, 2018.

Zafer Aydın, Oğuz Kaynar, Yasin Görmez, Yunus Emre Işık, “Comparison of machine learning classifiers for protein secondary structure prediction,” IEEE 26th Signal Processing and Communication Applications Conference (SIU), 1-4, Çeşme, İzmir, Turkey, 2018.

Zafer Aydın, Oğuz Kaynar, Yasin Görmez, “Comparison of NR and Uniclust databases for protein secondary structure prediction,” IEEE 26th Signal Processing and Communication Applications Conference (SIU), 1-4, Çeşme, İzmir, Turkey, 2018.

Nuh Azgınoğlu, Mehmet Akif Eren, Mete Çelik, Zafer Aydın, “Ceph-based storage server application,” IEEE 6th International Symposium on Digital Forensics and Security (ISDFS), 1-4, Antalya, Turkey, 2018.

2017

S. Kurt, Sinan; H.U. Yildiz, M. Yigit, B. Tavli, V.C. Gungor, "Packet Size Optimization in Wireless Sensor Networks for Smart Grid Applications," IEEE Transactions on Industrial Electronics, vol. 64, no. 3, pp. 2392-2401, March 2017.

E. Fadel, M. Faheem, V.C. Gungor, et al. "Spectrum-Aware Bio-Inspired Routing in Cognitive Radio Sensor Networks for Smart Grid Applications," Computer Communications (Elsevier), vol. 101, pp. 106-120, March 2017.

M. Faheem, G. Tuna, V.C. Gungor, "QERP: Quality-of-Service (QoS) Aware Evolutionary Routing Protocol for Underwater Wireless Sensor Networks," IEEE Systems Journal, March 2017.

M. Yigit, O. Durmaz Incel, S. Baktir, V.C. Gungor, "QoS‐Aware MAC Protocols Utilizing Sectored Antenna For Wireless Sensor Networks‐Based Smart Grid Applications," International Journal of Communication Systems (Wiley), vol. 30, no. 7, May 2017.

G. Tuna, V.C. Gungor, "A Survey On Deployment Techniques, Localization Algorithms, And Research Challenges For Underwater Acoustic Sensor Networks," International Journal of Communication Systems (Wiley), June 2017.

M. Faheem, V.C. Gungor, "Capacity and Spectrum-Aware Communication Framework for Wireless Sensor Network-Based Smart Grid Applications," Computer Standards & Interfaces (Elsevier), vol. 53, pp. 48-58, August 2017.

M. Faheem, G. Tuna, V.C. Gungor, "LRP: Link quality-aware queue-based spectral clustering routing protocol for underwater acoustic sensor networks," International Journal of Communication Systems (Wiley), vol. 30, no. 12, August 2017.

G. Tuna, D.G. Kogias, V.C. Gungor, C. Gezer, E. Taşkın, E. Ayday, "A Survey On Information Security Threats And Solutions For Machine To Machine (M2M) Communications," Journal of Parallel and Distributed Computing (Elsevier), vol. 109, pp. 142-154, November 2017.

J: Z. Stanfield, M. Coşkun, M. Koyuturk. Drug Response Prediction as a Link Prediction Problem. Nature Scientific Reports Volume: 7 Article Number: 44961. ISSN: 2045-2322 (SCI / SCIE), Aug 2017.

C: Zachary Stanfield, Mustafa Coşkun, Mehmet Koyuturk. Drug Response Prediction as a Link Prediction Problem. 8th ACM International Conference On Bioinformatics (BCB) Aug, 2017

Ahmet Kerim Aggirman and Kasim Tasdemir. Short to mid-range night fire detection. In 2017 25th Signal Processing and Communications Applications Conference (SIU), pages 1-4. IEEE, 2017.

Mostafa Sabzekar, Mahmoud Naghibzadeh, Mahdie Eghdami, Zafer Aydin, "Protein beta-sheet prediction using an efficient dynamic programming algorithm," Computational Biology and Chemistry, 70:142-155, 2017.

Oğuz Kaynar, Zafer Aydın, Yasin Görmez, “Sentiment analizinde öznitelik düşürme yöntemlerinin oto kodlayıcı derin öğrenme makinaları ile karşılaştırılması,” Gazi Üniversitesi Bilişim Teknolojileri Dergisi, 10(3):319-326, 2017.

Ashrf Aoad, Murat Şimşek, Zafer Aydın, "Knowledge based response correction method for design of reconfigurable N-shaped microstrip patch antenna using inverse ANNs," International Journal of Numerical Modeling: Electronic Networks, Devices and Fields, 30:e2129, 2017.

Zafer Aydın, Ömmu Gülsüm Uzut, “Combining Classifiers for Protein Secondary Structure Prediction,” IEEE International Conference on Computational Intelligence and Communication Networks, Girne, Cyprus, pp. 29-33, 2017.

Zafer Aydın, Oğuz Kaynar, Yasin Görmez, “Feature Selection for Protein Dihedral Angle Prediction,” IEEE International Conference on Computational Intelligence and Communication Networks, Girne Cyprus, pp. 48-52, 2017.

Nuh Azgınoğlu, Umut Atasever, Zafer Aydın, Mete Çelik, Hasan Erbay, “Open Source SLURM Computer Cluster System Design and a Sample Application, IEEE International Conference on Computer Science and Engineering, Antalya, Turkey, 2017.

2016

M. Yigit, M. Macit, V.C. Gungor, T. Kocak, O. Ozhan, "Operator User Management System Based on TMF615 Standard," Journal of Network and Systems Management (Springer), vol. 24, no. 1, pp. 161-188 January 2016.

S. Kaya, N. Kilic, T. Kocak, V.C. Gungor, "A Battery-Friendly Data Acquisition Model for Vehicular Speed Estimation," Computers & Electrical Engineering (Elsevier), vol. 50, pp. 79-90, February 2016.

M. Yigit, V.C. Gungor, E. Fadel, et al. "Channel-Aware Routing and Priority-Aware Multi-Channel Scheduling for WSN-Based Smart Grid Applications," Journal of Network and Computer Applications (Elsevier), vol. 71, pp. 50-58, August 2016.

B.E. Bilgin, S. Baktir, V.C. Gungor, "Collecting Smart Meter Data via Public Transportation Buses," IET Intelligent Transport Systems, vol. 10, no. 8, pp. 515-523, October 2016.

C: M. Coşkun , A. Grama, and M. Koyuturk. Efficient processing of network proximity queries via Chebyshev acceleration. ACM SIGKDD Conf. Knowledge Discovery and Data Mining (KDD), Aug, 2016.

Oğuzhan Oğuz, Cem Emre Akbas, Maen Mallah, Kasim Tasdemir, Ece Akhan Güzelcan, Christian Muenzenmayer, Thomas Wittenberg, Aysegül Üner, A Enis Cetin, and Rengül Çetin Atalay. Mixture of learners for cancer stem cell detection using cd13 and h and e stained images. In Medical Imaging 2016: Digital Pathology, volume 9791, page 97910Y. International Society for Optics and Photonics, 2016.

Kasim Tasdemir, Fatih Kurugollu, and Sakir Sezer. Spatio-temporal rich model based video steganalysis on cross sections of motion vector planes. IEEE Transactions on Image Processing, 25(7):3316-3328, 2016.

Cem Emre Akbas, Osman Günay, Kasim Tasdemir, and A Enis Çetin. Energy efficient cosine similarity measures according to a convex cost function. Signal, Image and Video Processing, pages 1-8, 2016.

2015

A. A. Aoad, M. Simsek, and Z. Aydin, "Development of Knowledge Based Response Correction for a Reconfigurable N-Shaped Microstrip Antenna Design," accepted to IEEE MTT-S International Conference on Numerical Electromagnetic and Multiphysics Modeling and Optimization, Ottawa, Canada, 2015.

B. Tepekule, A. E. Pusane, M. Ş. Kuran ve T. Tugcu, "A Novel Pre-Equalization Method for Molecular Communication via Diffusion in Nanonetworks," to appear in IEEE Communications Letters, 2015.

Z. Aydin, D. Baker, and W. S. Noble, "Constructing structural profiles for protein torsion angle prediction," 6th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2015), pp. 26-35, Lisbon, Portugal, 2015.

M. Yigit, M. Macit, V.C. Gungor, T. Kocak, O. Ozhan, "Operator User Management System-Based on the TMF615 Standard," to appear in Journal of Network System Management (Springer), 2015.

G. Tuna, V.C. Gungor, "Energy harvesting and battery technologies for powering wireless sensor networks," Book Chapter, Industrial Wireless Sensor Networks (Edited Book), Woodhead Publishing, 2015.

M. S. Kuran, A. C. Viana, L. Iannone, D. Kofman, G. Mermoud, and J. P. Vasseur “A Smart Parking Lot Management System for Scheduling the Recharging of Electric Vehicles,”, to appear in IEEE Transactions on Smart Grid, 2015.

C: M. Coşkun and M. Koyuturk. Link prediction in large networks by comparing the global view of nodes in the network. International Conf. Data Mining (ICDM) Workshops, 485?492. Nov, 2015

Kasim Tasdemir, Fatih Kurugollu, and Sakir Sezer. A steganalysis system utilizing temporal pixel correlation of hevc video. In 2015 23nd Signal Processing and Communications Applications Conference (SIU), pages 2446-2449. IEEE, 2015.

Kasim Tasdemir, Fatih Kurugollu, and Sakir Sezer. Spatio-temporal rich model for motion vector steganalysis. In 2015 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), pages 1717-1721. IEEE, 2015.

Zafer Aydın, David Baker, William Stafford Noble, "Template scoring methods for protein torsion angle prediction," Communications in Computer and Information Science, 574:206-223, 2015.

Çiğdem Eroğlu Erdem, Çiğdem Turan, Zafer Aydın, "BAUM-2: A multilingual audio-visual affective face database," Multimedia Tools and Applications, 74(18): 7429-7459, 2015.

Ashrf Aoad, Murat Şimşek, Zafer Aydın, "Development of Knowledge Based Response Correction for a Reconfigurable N-Shaped Microstrip Antenna Design," IEEE MTT-S International Conference on Numerical Electromagnetic and Multiphysics Modeling and Optimization (NEMO'15), Ottawa, Canada, August 2015.

Muhammed Yasin, Tolga Göze, İhsan Özcan, Vehbi Çağrı Güngör, Zafer Aydın, "Short Term Electricity Load Forecasting: A Case Study of Electric Utility Market in Turkey," International Istanbul Smart Grid Congress And Exhibition (ICSG'15), İstanbul, Turkey, April 2015.

Zafer Aydın, David Baker, William Stafford Noble, "Constructing structural profiles for protein torsion angle prediction," In Proc. 6th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS'15), pages 26-35, Lisbon, Portugal, January 2015.

2014

A. Aoad, M. Simsek and Z. Aydin, "Design of a Reconfigurable 5-Fingers Shaped Microstrip Patch Antenna by Artificial Neural Networks," International Journal of Advanced Research in Computer Science and Software Engineering (IJARCSSE), 4(10): 61-70, 2014

A. Aoad, Z. Aydın, and E. Korkmaz, "Design of a tri band 5-fingers shaped microstrip patch antenna with an adjustable resistor," IEEE International Conference on Antenna Measurements and Applications, pp 1-4, Antibes Juan-les-Pins, France, 2014.

C. E. Erdem, C. T., and Z. Aydin, "BAUM-2: A multilingual audio-visual affective face database," Multimedia Tools and Applications, 2014.

B. Yılmaz, S. Korkmaz, D.B. Arslan, E. Güngör, M.H. Asyalı “Like/Dislike Analysis Using EEG: Determination of Most Discriminative Channels and Frequencies”, Computer Methods and Programs in Biomedicine, 2014.

G. Ataş, V.C. Gungor, "Performance Evaluations of Cloud Computing Platforms using Statistical Methods", to appear in Computers and Electrical Engineering (Elsevier), 2014.

G. Tuna, V.C. Gungor, K. Gulez, "An Autonomous Wireless Sensor Network Deployment System using Mobile Robots for Human Existence Detection in Case of Disasters," in Ad Hoc Networks Journal (Elsevier), vol. 13, pp. 54-68, 2014.

B. Bakir-Gungor, E. Egemen, O.U. Sezerman, "PANOGA: a web-server for identification of SNP targeted pathways from genome-wide association study data”, in Bioinformatics, 2014.

Z. Görmez, B. Bakir-Gungor, M. Ş. Sağıroğlu, "HomSI: a homozygous stretch identifier from next-generation sequencing data”, in Bioinformatics, vol. 30, pp. 445-447, 2014.

Y. Wang, V. D. Ta, Y. Gao, T. C. He, R. Chen, E. Mutlugün, H. V. Demir, H. D. Sun, "Stimulated emission and lasing from CdSe/CdS/ZnS core-multi-shell quantum dots by simultaneous three-photon absorption," Advanced Materials, in press 2014.

B. Peng, Z. Li, E. Mutlugun, P. L. Hernandez-Martinez, D. Li, Q. Zhang, Y. Gao, H. V. Demir and Q. Xiong, "Quantum Dots on Vertically Aligned Gold Nanorod Monolayer: Plasmon Enhanced Fluorescence," Nanoscale, in press 2014.

Y. Zhao, J. Zhang, S. Liu, Y. Gao, X. Yang, K. S. Leck, A. P. Abiyasa, Y. Divayana, E. Mutlugun, S. T. Tan, Q. Xiong, H.V. Demir, X. W. Sun, “Transition metal oxides on organic semiconductors,” Organic Electronics, in press 2014.

2013

H. Caglayan, S.-H. Hong, B. Edwards, C. R. Kagan, and N. Engheta, “Near-IR Metatronic Nanocircuits by Design” Phys. Rev. Lett. 111, 2013.

T. Gordon, T. Paik, D. Klein, G. Naik, H. Caglayan, A. Boltasseva, and C. Murray, “Shape-Dependent Plasmonic Response and Directed Self-Assembly in a New Semiconductor Building Block, Indium-Doped Cadmium Oxide (ICO)” Nano Lett. 13 (6), 2857-63, 2013.

E. J. R. Vesseur, T. Coenen, H. Caglayan, N. Engheta, and A. Polman, “Experimental verification of n=0 structures for visible light” Phys. Rev. Lett. 110, 2013.

G.A. Shah, V. C. Gungor, O. B. Akan, "A Cross-Layer QoS-Aware Communication Framework in Cognitive Radio Sensor Networks for Smart Grid Applications", to appear in IEEE Transactions on Industrial Informatics, 2013.

G. Tuna, V.C. Gungor, K. Gulez, "An Autonomous Wireless Sensor Network Deployment System using Mobile Robots for Human Existence Detection in Case of Disasters," to appear in Ad Hoc Networks Journal (Elsevier), 2013.

G. Tuna, K. Gulez, V. C. Gungor, "The Effects of Exploration Strategies and Communication Models on the Performance of Cooperative Exploration", to appear in Ad Hoc Networks (Elsevier), 2013.

B. Yılmaz, E. Çiftçi “An FDTD-Based Computer Simulation Platform for Shock Wave Propagation in Electrohydraulic Lithotripsy”, Computer Methods and Programs in Biomedicine, 110, 389-398, 2013.

K.A. Kaya, B. Yılmaz, “A new tool for QT interval analysis during sleep in healthy and obstructive sleep apnea subjects: A study on women”, Turkish Journal of Electrical Engineering and Computer Sciences, 21, 1504-1513, 2013.

I. Ozdur, P. Toliver, A. Agarwal and T. K. Woodward, “Free-space to single-mode collection efficiency enhancement using photonic lanterns” Optics Letters, 38, 3554-3557, 2013.

X. Yang, Y. Ma, E. Mutlugun, Y. Zhao, K. S. Leck, S. T. Tan, H. V. Demir, Q. Zhang, H. Du, X. W. Sun, " Stable, Efficient, and All Solution-Processed Quantum Dot Light-Emitting Diodes with Double-Sided Metal-Oxide Nanoparticle Charge Transport Layers," accepted for publication, ACS Appl. Mater. Interfaces, 2013.

U. O. S Seker*, E. Mutlugun*, P. L. Hernandez-Martinez, V. K. Sharma, V. Lesnyak, N. Gaponik, A. Eychmuller and H. V. Demir "Excitonic Bio-Nanohybrids of Quantum Dots and Photoproteins Facilitating Strong Nonradiative Energy Transfer," (*equal contribution), Nanoscale, 5, 7034-7040, 2013.

Y. Zhao, R. Chen, Y. Gao, K. S. Leck, X. Yang, S. Liu, A. P. Abiyasa, Y. Divayana, E. Mutlugun, S. T. Tan, H. Sun, H. V. Demir, X. W. Sun, "AC-driven, color- and brightness-tunable organic light-emitting diodes constructed from an electron only device," Organic Electronics,in press 2013.

X. Yang, E. Mutlugun, Y. B. Zhao, K. S. Leck, S. T. Tan, H. V. Demir, and X. W. Sun, "Solution Processed Tungsten Oxide Interfacial Layer for Efficient Hole-Injection in Quantum Dot Light-Emitting Diodes, " in press, Small, 2013.

T. Ozel, P. L. Hernandez-Martinez, E. Mutlugun, O. Akin, S. Nizamoglu, I. O. Ozel, Q. Zhang, Q. Xiong and H. V. Demir, "Observation of Selective Plasmon-Exciton Coupling in Nonradiative Energy Transfer: Donor-Selective vs. Acceptor-Selective Plexcitons," Nano Letters, 13 (7), 3065–3072, 2013.

A. F. Cihan, P. L. Hernandez-Martinez, Y. Kelestemur, E. Mutlugun and H. V. Demir "Observation of Biexcitons in Nanocrystal Solids in the
Presence of Photocharging," ACS Nano, 7 (6), 4799–4809, 2013.

K. S. Leck, Y. Divayana, D. Zhao, X. Yang, A. P. Abiyasa, E. Mutlugun, Y. Gao, S. Liu, S. T. Tan, X. W. Sun, and H. V. Demir, "A Quantum Dot Light-Emitting Diode with Quantum Dots Inside the Hole Transporting Layers," ACS Appl. Mater. Interfaces, 5 (14), 6535–6540, 2013.

S. Akhavan, K. Gungor, E. Mutlugun and H. V. Demir, "Plasmonic light-sensitive skins of nanocrystal monolayers,"Nanotechnology, 24, 155201, 2013.

G. Ablay, "Online condition monitoring of battery systems with a nonlinear estimator", IEEE Energy Conversion, pp. 1-8, 2013.

G. Ablay, “A modeling and control approach to advanced nuclear power plants with gas turbines,” Energy Conversion and Management, vol. 76, pp. 899-909, 2013.

G. Ablay, “Robust reactivity, neutron source, and precursor estimators for nuclear reactors,” Nuclear Engineering and Design, pp. 526-533, 2013.

G. Ablay, "A robust restimator-based optimal algebraic approach to steam generator feedwater control system", Turkish Journal of Electrical Engineering and Computer Sciences, 2013.

G. Ablay and T. Aldemir, “Fault detection in nuclear systems using sliding mode observers,” Nuclear Science and Engineering, vol. 173, no.1, pp. 82-98, 2013.

G. Tuna, V. C. Gungor, K. Gulez, "Wireless Sensor Networks for Smart Grid Applications: A Case Study on Link Reliability and Node Lifetime Evaluations in Power Distribution Systems", in International Journal of Distributed Sensor Networks, 2013.

2012

V.C. Gungor, D. Sahin, T. Kocak, S. Ergut, C. Buccella, C. Cecati, G.P. Hancke, "Smart Grid Technologies: Communication Technologies and Standards," in IEEE Transactions on Industrial Informatics, vol. 7, no. 4, pp. 529-539, 2011. (Received Best Paper Award from IEEE Transactions on Industrial Informatics in 2012. Ranked 8th in the Top Accessed Article List in IEEE Xplore as of May 2012.)

A. T. Fafarman, S.-H. Hong, H. Caglayan, X. Ye, B. T. Diroll, T. Paik, N. Engheta, C. Murray, and C. R. Kagan, “Chemically tailored dielectric-to-metal transition for the design of metamaterials from nanoimprinted colloidal nanocrystals” Nano Lett. 13 (2), 350-357, 2012.

V.C. Gungor, D. Sahin, T. Kocak, S. Ergut, C. Buccella, C. Cecati, G.P. Hancke, "Smart Grid and Smart Homes: Key Players and Pilot Projects," in Industrial Electronics Magazine, vol. 6, no. 4, pp. 18-34, 2012.

A.O. Bicen, V.C. Gungor, O.B. Akan, "Delay-sensitive and Multimedia Communication in Cognitive Radio Sensor Networks," in Ad Hoc Networks Journal (Elsevier), vol. 10, no. 5, pp. 816-830, 2012.

V.C. Gungor, D. Sahin, T. Kocak, S. Ergut, C. Buccella, C. Cecati, G.P. Hancke, "A Survey on Smart Grid Potential Applications and Communication Requirements," to appear in IEEE Transactions on Industrial Informatics, 2012.

B.E. Bilgin, V.C. Gungor, "Performance Evaluations of ZigBee in Different Smart Grid Environments," in Computer Networks Journal( Elsevier), vol. 56, no. 8, pp. 2196-2205, 2012.

A.O. Bicen, V. C. Gungor, O. B. Akan, "Spectrum-Aware and Cognitive Sensor Networks for Smart Grid Applications," in IEEE Communications Magazine, vol. 50 , no. 5, pp. 158-165, 2012.

B.E. Bilgin, V.C. Gungor, "Adaptive Error Control in Wireless Sensor Networks Under Harsh Smart Grid Environments," in Sensor Review, vol. 32, no. 3, 2012.

S. Cakmakyapan, A. Serebryannikov, H. Caglayan, and E. Ozbay, “Spoof-plasmon relevant one-way collimation and multiplexing at beaming from a slit in metallic grating” accepted for publication in Opt. Expr. 20, 26636–26648, 2012.

X. Ye, L. Jin, H. Caglayan, J. Chen, G. Xing, C. Zheng, V. Doan-Nguyen, Y. Kang, N. Engheta, C. R. Kagan, and C. Murray, “Improved size-tunable synthesis of monodispersed gold nanorods through the use of aromatic additives” ACS Nano 6, 2804-2817, 2012.

V.C. Gungor, D.Sahin, "Cognitive Radio Networks for Smart Grid Applications: A Promising Technology to Overcome Spectrum Inefficiency," in IEEE Vehicular Technology Magazine, vol. 7, no. 2, pp. 41-46, 2012.

Z. Li, K. B. Alici, H. Caglayan, M. Kafesaki, C. M. Soukoulis, and E. Ozbay, “Composite chiral metamaterials with negative refractive index and high values of the figure of merit” Opt. Expr. 20, 6146-6156, 2012.

I. Ozdur, H. Shu, Michael Bass and Guifang Li, “Think Outside the Fiber: Imaging Amplifier for Space-Multiplexed Optical Transmission”, IEEE Photonics Journal, Vol. 4 , Issue: 5 pp. 1316 – 1324, 2012.

P. J. Delfyett, I. Ozdur, J. Davila-Rodriguez, N. Hoghooghi, M. Akbulut, S. Bhooplapur,”Advanced Ultrafast Technologies based on Optical Frequency Combs”, Selected Topics in Quantum Electronics, IEEE, Volume: 18 , Issue: 1, Page(s): 258 – 274, 2012.

J. Davila-Rodriguez, I. Ozdur, M. Bagnell, P. J. Delfyett, J. J. Plant, and P. W. Juodawlkis, “Ultralow Noise, Etalon Stabilized, 10 GHz Optical Frequency Comb Based on a SCOW Amplifier” Photonics Technology Letters, IEEE , vol.24, no.23, pp.2159 - 2162, 2012

E. Mutlugun, P. L. Hernandez-Martinez, C. Eroğlu, Y. Coşkun, T. Erdem, V. K. Sharma, E. Ünal, S. K. Panda, S. G. Hickey, N. Gaponik, A. Eychmuller and H. V. Demir, "Large-area (over 50 cm × 50 cm) freestanding films of colloidal InP/ZnS quantum dots," Nano Letters, 12, 3986, 2012.

S. Nizamoglu, P. L. Hernandez-Martinez, E. Mutlugun, D. U. Karatay and H. V. Demir, "Excitonic enhancement of nonradiative energy transfer from a quantum well in the optical near field of energy gradient quantum dots," Applied Physics Letters, 100, 241109, 2012.

G. Ablay, C. E. Koksal and T. Aldemir, “Chaotic data encryption for long-distance monitoring of nuclear reactors,” Nuclear Science and Engineering, vol. 170, no.1, pp. 16-26, 2012.

2011

Z. Aydin, A. Singh, J. Bilmes, and W. S. Noble, "Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure," BMC Bioinformatics , 12:154, 2011.

Z. Aydin, Y. Altunbasak, and H. Erdogan, "Bayesian models and algorithms for protein beta-sheet prediction," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(2):395-409, 2011.

S. Cakmakyapan, H. Caglayan, A. Serebryannikov, and E. Ozbay, “Experimental validation of strong directional selectivity in nonsymmetric metallic gratings with subwavelength slit” Appl. Phys. Lett. 98, 051103, 2011.

B. Aygun, V.C. Gungor, "Wireless Sensor Networks for Structure Health Monitoring: Recent Advances and Future Research Directions," in Sensor Review, vol. 31, no. 3, pp. 261-276, 2011.

E. Şener, N. Yüksel, D. K. Yıldız, B. Yılmaz, Ö. Özdemir, Y. Çağlar, E. Değirmenci, “The Impact of Subconjuctivally Injected EGF and VEGF Inhibitor on Experimental Corneal Neovascularization in Rat Model”, Current Eye Research, 36(11), 1005–1013, 2011.

I. Ozdur, D. Mandridis, M. U. Piracha, M. Akbulut, N. Hoghooghi, and P. J. Delfyett,”Optical frequency stability measurement using an etalon based Optoelectronic Oscillator” Photonics Technology Letters, IEEE , vol.23, no.4, pp.263-265, 2011

C. Xia, N. Bai, I. Ozdur, X. Zhou and Guifang Li, “Supermodes for Optical Transmission” Optics Express, Vol. 19, Issue 17, pp. 16653-16664, 2011.

M. Akbulut, J. Davila-Rodriguez, I. Ozdur, F. Quinlan S. Ozharar, N. Hoghooghi and P.J. Delfyett,” Measurement of Carrier Envelope Offset Frequency for a 10 GHz Etalon-stabilized Semiconductor Optical Frequency Comb”, Optics Express, Vol. 19, Issue 18, pp. 16851-16865, 2011.

P. Sarisaray, V.C. Gungor, E. Harmanci, "Quality-Aware Image Transmission over Underwater Multimedia Sensor Networks," in Ad Hoc Networks Journal (Elsevier), vol.9, no. 7, pp. 1287-1301, 2011.

V.C. Gungor, B. Lu, G.P. Hancke, "Opportunities and Challenges of Wireless Sensor Networks in Smart Grid," in IEEE Transactions on Industrial Electronics, vol. 57, no. 10, pp. 3557-3564, 2010. (Ranked 4th in the Top Accessed TIE Article List in IEEE Xplore as of April 2011)

M. U. Piracha, D. Nguyen, I. Ozdur and P. J Delfyett, ”Simultaneous ranging and velocimetry of fast moving targets using oppositely chirped pulses from a mode locked laser” Optics. Express 19, 11213-11219, 2011.

D. Mandridis, C. Williams, I. Ozdur, and P. J. Delfyett, " Low noise performance of a Theta laser using an intra-cavity Fabry-Pérot etalon," Optics Express 19, 8994-8999, 2011.

H. V. Demir, S. Nizamoglu, T. Erdem, E. Mutlugun, N. Gaponik, A. Eychmüller, "Quantum dot integrated LEDs using photonic and excitonic color conversion," Nano Today, 6, 632, 2011.

H. V. Demir, U. O. S. Seker, G. Zengin, E. Mutlugun, E. Sari, C. Tamerler and M. Sarikaya, "Spatially Selective Assembly of Quantum Dot Light Emitters in an LED Using Engineered Peptides," ACS Nano, 5, 2735, 2011.

T. Ozel, S. Nizamoglu, M. A. Sefunc, O. Samarskaya, I. O. Ozel, E. Mutlugun, V. Lesnyak, N. Gaponik, A. Eychmuller, S. V. Gaponenko, and H. V. Demir, “Anisotropic Emission from Multilayered Plasmon Resonator Nanocomposites of Isotropic Semiconductor Quantum Dots,” ACS Nano, 5, 1328, 2011.

N. K. Perkgoz, R. S. Toru, E. Unal, M. A. Sefunc, S. Tek, E. Mutlugun, I. M. Soganci, H. Celiker, G. Celiker and H. V. Demir,"Photocatalytic hybrid nano-composites of metal oxide nano-particles enhanced towards the visible spectral range," Applied Catalysis B: Environmental, 105, 77, 2011.

G. Ablay and T. Aldemir, “Observation of the dynamics of nuclear systems using sliding mode observers,” Nuclear Technology, vol. 174, no.1, pp. 64-76, 2011.

2010

S. A. Addae, M. A. Pinard, H. Caglayan, S. Cakmakyapan, D. Caliskan, E. Ozbay, and K. Aslan, “Rapid and sensitive colorimetric ELISA using silver Nanoparticles, microwaves and split ring resonator structures” Nano Biomed. Eng. 2, 155-164, 2010.

H. Caglayan and E. Ozbay, “Observation of cavity structures in left-handed metamaterials” J. Nanophotonics 4, 041790, 2010.

H. Caglayan, S. Cakmakyapan, S. A. Addae, M. A. Pinard, D. Caliskan, K. Aslan, and E. Ozbay, “Ultrafast and and sensitive bioassay using SRR structures and microwave heating” Appl. Phys. Lett. 97, 093701, 2010.

Z. Li, R. Zhao, T. Koschny, M. Kafesaki, K. B.Alici, E. Colak, H. Caglayan, E. Ozbay, and C. M. Soukoulis, “Chiral metamaterials with negative refractive index based on Four-U-SRRs” Appl. Phys. Lett. 97, 081901, 2010.

S. Cakmakyapan, H. Caglayan, A. Serebryannikov, and E. Ozbay, “One-way transmission through the subwavelength slit in non-symmetric metallic gratings” Opt. Lett. 35, 2597, 2010.

Z. Li, H. Caglayan, E. Colak, J. Zhou, C. M. Soukoulis, and E. Ozbay, “Coupling effect between two adjacent chiral structure layers” Opt. Expr. 18, 5375 -5383, 2010.

Yılmaz, B., U. Cunedioğlu, E. Baysoy, Usage of Spline Interpolation in Catheter-based Cardiac Mapping”, Turkish Journal of Electrical Engineering and Computer Sciences, 18(6), 989-1002, 2010.

B. Yılmaz, M. H. Asyalı, E. Arıkan, S. Yetkin, F. Özgen, “Sleep stage and obstructive apneaic epoch classification using single-lead ECG”, BioMedical Engineering Online, 9:39, 2010.

E. Baysoy, U. Cunedioğlu, B. Yılmaz, “Simultaneous Mapping of Endocardium and Epicardium from Multielectrode Intrachamber and Intravenous Catheters: A Computer Simulation-based Validation”, Journal of Electrocardiology, 43(1), 56-62, 2010.

I. Ozdur, D. Mandridis, N. Hoghooghi, and Delfyett P., J., “Low noise tunable opto electronic oscillator with Fabry-Perot Etalon”, Journal of Lightwave Technology, vol.28, no.21, pp.3100-3106, 2010.

J. Davila-Rodriguez, I. Ozdur, C. Williams, and P. J. Delfyett,” A semiconductor-based, frequency-stabilized mode-locked laser using a phase modulator and an intracavity etalon”, Optics Letters, Vol. 35, 2010.

N. Hoghooghi, I. Ozdur, S. Bhooplapur, and P. J. Delfyett,”Direct demodulation and channel filtering of phase modulated signals using an injection locked VCSEL”, Photonics Technology Lett., Vol. 22, No 20, 2010

D. Mandridis, I. Ozdur, M. Bagnell, and P. J. Delfyett” Free Spectral Range Measurement of a Fiberized Fabry – Perot Etalon with Sub-Hz Accuracy”, Optics Express, 18, 11264-11269, 2010.

M. Akbulut, S. Bhooplapur, I. Ozdur, J. Davila-Rodriguez, P.J. Delfyett ” Dynamic Line-by-Line Pulse Shaping with GHz Update Rate”, Optics Express 18, 18284-18291, 2010.

I. Ozdur, M. Akbulut, N. Hoghooghi, D. Mandridis, M. U. Piracha, and P. J. Delfyett, “An optoelectronic loop design with 1000 finesse Fabry-Perot etalon” Optics Letters, Vol. 35, No. 6, 2010

D. Mandridis, I. Ozdur, F. Quinlan, M. Akbulut, Delfyett P. J, Plant J. J, Juodawlkis P. W., “A Low Noise, Low Repetition Rate, Semiconductor Based Mode-Locked Laser Source Suitable For High Bandwidth Photonic ADC” Applied Optics, vol. 49, pp. 2850-2857, 2010

M. U. Piracha, D. Nguyen, D. Mandridis, Yilmaz T., I. Ozdur, S. Ozharar, and Delfyett P. J., “Range Resolved Lidar for Long Distance Ranging with Sub-millimeter Resolution”. Optics Express Vol. 18, Iss. 7, pp. 7184–7189, 2010

I. Ozdur, M. Akbulut, N. Hoghooghi, D. Mandridis, S. Ozharar, F. Quinlan, and P. J. Delfyett,” A semiconductor based 10-GHz optical comb source with 3 fs integrated timing jitter (1Hz-100MHz) and ~500 Hz comb linewidth” Photonic Technology Letters Vol. 22, No. 6, 2010.

N. Hoghooghi, I. Ozdur, J. Davila-Rodriguez, M. Akbulut and Delfyett Jr. P. J., “Resonant Cavity Linear Interferometric Intensity Modulator” Optics Letters , Vol. 35, No. 8, 2010

D. Mandridis, I. Ozdur, M. Akbulut, P. J. Delfyett, "A Photonic Method for Measuring the AM Noise of Periodic Electrical Signals" Photonics Technology Letters, IEEE, Vol. 22, pp. 790-792, 2010.

B. Güzeltürk*, E. Mutlugun*, X.Wang, K. L. Pey and H. V. Demir, "Photovoltaic nanopillar radial junction diode architecture enhanced by integrating semiconductor quantum dot nanocrystals as light harvesters," Applied Physics Letters, 97, 093111, 2010. (*equal contribution)

E. Mutlugun, O. Samarskaya, T. Ozel, N. Cicek, N. Gaponik, A. Eychmuller, and H. V. Demir, "Highly efficient nonradiative energy transfer mediated light harvesting in water using aqueous CdTe quantum dot antennas," Optics Express, 18, 10, 10720-10730, 2010.

İ. Alan, “A novel approach for a sinusoidal output inverter”, Electrical Engineering, Vol. 92, Issue: 7-8, pp. 239-244, 2010.

İ. Alan “The use of FPGA in Field-Oriented Control of an Induction Machine”, Turk J Elec Eng & Comp Sci, Vol.18, No.6, pp. 943-962, TÜBİTAK, 2010.