Data Compression Concepts and Algorithms and Their Applications to Bioinformatics. - Özkan U. Nalbantoglu; David J. Russell; Khalid Sayood (Entropy, 2010)

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles. - Özkan U. Nalbantoglu; Samuel F. Way; Steven H. Hinrichs; Khalid Sayood (BMC Bioinform., 2011)

Computational Genomic Signatures - Özkan U. Nalbantoglu; Khalid Sayood (Morgan & Claypool Publishers, 2011)

Data Compression. - Özkan Ufuk Nalbantoglu; Khalid Sayood (Computing Handbook, 3rd ed. (1), 2014)

Compression of Quality Factors in Next Generation Sequencing. - Özkan U. Nalbantoglu; Khalid Sayood (DCC, 2014)

Compression of Next Generation Sequencing Data. - Özkan U. Nalbantoglu; A. Riffle; Khalid Sayood (DCC, 2015)

A phylogeny-free microbiome dysbiosis detection pipeline for non-invasive disease diagnosis. - Özkan Ufuk Nalbantoglu; A. Emre Onuk (EIT, 2017)

MIMOSA: Algorithms for Microbial Profiling. - Özkan U. Nalbantoglu; Khalid Sayood (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

A comprehensive review of deep learning in colon cancer. - Ishak Paçal; Dervis Karaboga; Alper Bastürk; Bahriye Akay; Özkan Ufuk Nalbantoglu (Comput. Biol. Medicine, 2020)

Inflammatory Bowel Disease Biomarkers of Human Gut Microbiota Selected via Ensemble Feature Selection Methods. - Hilal Hacilar; Özkan Ufuk Nalbantoglu; Oya Aran; Burcu Bakir-Gungor (CoRR, 2020)

Taxonomic classification of metagenomic sequences from Relative Abundance Index profiles using deep learning. - Meryem Altin Karagöz; Özkan Ufuk Nalbantoglu (Biomed. Signal Process. Control., 2021)

Information Theoretic Metagenome Assembly Allows the Discovery of Disease Biomarkers in Human Microbiome. - Özkan Ufuk Nalbantoglu (Entropy, 2021)

A new lightweight convolutional neural network for radiation-induced liver disease classification. - Demet Alici-Karaca; Bahriye Akay; Arzu Yay; Pinar Suna; Özkan Ufuk Nalbantoglu; Dervis Karaboga; Alper Bastürk; Esra Balcioglu; Munevver Baran (Biomed. Signal Process. Control., 2022)

An efficient real-time colonic polyp detection with YOLO algorithms trained by using negative samples and large datasets. - Ishak Paçal; Ahmet Karaman; Dervis Karaboga; Bahriye Akay; Alper Bastürk; Özkan Ufuk Nalbantoglu; Seymanur Coskun (Comput. Biol. Medicine, 2022)

An unsupervised transfer learning model based on convolutional auto encoder for non-alcoholic steatohepatitis activity scoring and fibrosis staging of liver histopathological images. - Meryem Altin Karagöz; Bahriye Akay; Alper Bastürk; Dervis Karaboga; Özkan U. Nalbantoglu (Neural Comput. Appl., 2023)

Hyper-parameter optimization of deep learning architectures using artificial bee colony (ABC) algorithm for high performance real-time automatic colorectal cancer (CRC) polyp detection. - Ahmet Karaman; Dervis Karaboga; Ishak Paçal; Bahriye Akay; Alper Bastürk; Özkan Ufuk Nalbantoglu; Seymanur Coskun; Omur Sahin (Appl. Intell., 2023)

Robust real-time polyp detection system design based on YOLO algorithms by optimizing activation functions and hyper-parameters with artificial bee colony (ABC). - Ahmet Karaman; Ishak Paçal; Alper Bastürk; Bahriye Akay; Özkan Ufuk Nalbantoglu; Seymanur Coskun; Omur Sahin; Dervis Karaboga (Expert Syst. Appl., 2023)

A comparative study of YOLO models and a transformer-based YOLOv5 model for mass detection in mammograms. - Damla Coskun; Dervis Karaboga; Alper Bastürk; Bahriye Akay; Özkan Ufuk Nalbantoglu; Serap Dogan; Ishak Paçal; Meryem Altin Karagöz (Turkish J. Electr. Eng. Comput. Sci., 2023)

A self-supervised learning model based on variational autoencoder for limited-sample mammogram classification. - Meryem Altin Karagöz; Özkan Ufuk Nalbantoglu (Appl. Intell., 2024)

Residual Vision Transformer (ResViT) Based Self-Supervised Learning Model for Brain Tumor Classification. - Meryem Altin Karagöz; Özkan U. Nalbantoglu; Geoffrey C. Fox (CoRR, 2024)

Deep learning-based breast cancer diagnosis with multiview of mammography screening to reduce false positive recall rate. - Meryem Altin Karagöz; Özkan Ufuk Nalbantoglu; Dervis Karaboga; Bahriye Akay; Alper Bastürk; Halil Ulutabanca; Serap Dogan; Damla Coskun; Osman Demir (Turkish J. Electr. Eng. Comput. Sci., 2024)

Machine learning applications in detection and diagnosis of urology cancers: a systematic literature review. - Mohammed Lubbad; Dervis Karaboga; Alper Bastürk; Bahriye Akay; Özkan U. Nalbantoglu; Ishak Paçal (Neural Comput. Appl., 2024)

Disrobiom: A novel approach to discover robust biomarkers from gut microbiome datasets with deep-learning algorithms. - U. Gülfem Elgün Çiftcioglu; Özkan Ufuk Nalbantoglu (Biomed. Signal Process. Control., 2025)

Deep learning-enhanced wellness scores: A population level study on gut microbiome profiling and health prediction. - Özkan U. Nalbantoglu; Beyza Hilal Ermis; Aycan Gundogdu (Biomed. Signal Process. Control., 2025)