PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. - Emek Demir; Ozgun Babur; Ugur Dogrusöz; Attila Gürsoy; Gurkan Nisanci; Rengül Çetin-Atalay; Mehmet Ozturk (Bioinform., 2002)

Application of Data Mining Techniques to Protein-Protein Interaction Prediction. - A. Kocatas; Attila Gürsoy; Rengül Çetin-Atalay (ISCIS, 2003)

Prediction of Protein Subcellular Localization Based on Primary Sequence Data. - Mert Özarar; Volkan Atalay; Rengül Çetin-Atalay (ISCIS, 2003)

An ontology for collaborative construction and analysis of cellular pathways. - Emek Demir; Ozgun Babur; Ugur Dogrusöz; Attila Gürsoy; A. Ayaz; Gürcan Gülesir; Gurkan Nisanci; Rengül Çetin-Atalay (Bioinform., 2004)

Implicit motif distribution based hybrid computational kernel for sequence classification. - Volkan Atalay; Rengül Çetin-Atalay (Bioinform., 2005)

Subsequence-based feature map for protein function classification. - Ömer Sinan Saraç; Özge Gürsoy-Yüzügüllü; Rengül Çetin-Atalay; Volkan Atalay (Comput. Biol. Chem., 2008)

Data and Model Driven Hybrid Approach to Activity Scoring of Cyclic Pathways. - Zerrin Isik; Volkan Atalay; Cevdet Aykanat; Rengül Çetin-Atalay (ISCIS, 2010)

Bi-k-bi clustering: mining large scale gene expression data using two-level biclustering. - Levent Çarkacioglu; Rengül Çetin-Atalay; Özlen Konu; Volkan Atalay; Tolga Can (Int. J. Data Min. Bioinform., 2010)

Evaluation of Signaling Cascades Based on the Weights from Microarray and ChIP-seq Data. - Zerrin Isik; Volkan Atalay; Rengül Çetin-Atalay (MLSB, 2010)

Microscopic image classification using sparsity in a transform domain and Bayesian learning. - Alexander Suhre; Tulin Ersahin; Rengül Çetin-Atalay; A. Enis Çetin (EUSIPCO, 2011)

G-Network Modelling Based Abnormal Pathway Detection in Gene Regulatory Networks. - Haseong Kim; Rengül Çetin-Atalay; Erol Gelenbe (ISCIS, 2011)

Carcinoma cell line discrimination in microscopic images using unbalanced wavelets. - Furkan Keskin; Alexander Suhre; Tulin Ersahin; Rengül Çetin-Atalay; A. Enis Çetin (CISS, 2012)

Microscopic image classification via ℂWT-based covariance descriptors using Kullback-Leibler distance. - Furkan Keskin; A. Enis Çetin; Tulin Ersahin; Rengül Çetin-Atalay (ISCAS, 2012)

A multiplication-free framework for signal processing and applications in biomedical image analysis. - Alexander Suhre; Furkan Keskin; Tulin Ersahin; Rengül Çetin-Atalay; Rashid Ansari; A. Enis Çetin (ICASSP, 2013)

Attributed Relational Graphs for Cell Nucleus Segmentation in Fluorescence Microscopy Images. - Salim Arslan; Tulin Ersahin; Rengül Çetin-Atalay; Cigdem Gunduz Demir (IEEE Trans. Medical Imaging, 2013)

Applications of p53 interactome analysis to personalised drug discovery. - Michelle Hussain; Benjamin Stutchbury; Kun Tian; Rengül Çetin-Atalay; Jean-Marc Schwartz; Marija Krstic-Demonacos (IWBBIO, 2014)

Discriminative Modeling of Cell Signaling as Bayesian Networks. - Ayse Gul Yaman; Aybar C. Acar; Volkan Atalay; Rengül Çetin-Atalay (IWBBIO, 2014)

A supervised learning model for live cell segmentation. - Can Fahrettin Koyuncu; Irem Durmaz; Rengül Çetin-Atalay; Cigdem Gunduz Demir (SIU, 2014)

Multi-resolution super-pixels and their applications on fluorescent mesenchymal stem cells images using 1-D SIFT merging. - Onur Yorulmaz; Oguzhan Oguz; Ece Akhan; Donus Tuncel; Rengül Çetin-Atalay; A. Enis Çetin (ICIP, 2015)

Detection of Cancer Stem Cells in microscopic images by using region covariance and codifference method. - Oguzhan Oguz; Christian Münzenmayer; Thomas Wittenberg; Aysegul Uner; A. Enis Çetin; Rengül Çetin-Atalay (IWCIM, 2015)

Multiplication-free Neural Networks. - Cem Emre Akbas; Alican Bozkurt; A. Enis Çetin; Rengül Çetin-Atalay; Aysegul Uner (SIU, 2015)

Wavelet merged multi-resolution super-pixels and their applications on fluorescent MSC images. - Onur Yorulmaz; Oguzhan Oguz; Ece Akhan; Donus Tuncel; Rengül Çetin-Atalay; A. Enis Çetin (SIU, 2015)

Classification of human carcinoma cells using multispectral imagery. - Umut Çinar; Yasemin Yardimci Çetin; Rengül Çetin-Atalay; A. Enis Çetin (Digital Pathology, 2016)

Mixture of learners for cancer stem cell detection using CD13 and H and E stained images. - Oguzhan Oguz; Cem Emre Akbas; Maen Mallah; Kasim Tasdemir; Ece Akhan Güzelcan; Christian Münzenmayer; Thomas Wittenberg; Aysegül Üner; A. Enis Çetin; Rengül Çetin-Atalay (Digital Pathology, 2016)

Phase and TV Based Convex Sets for Blind Deconvolution of Microscopic Images. - Mohammad Tofighi; Onur Yorulmaz; Kivanç Köse; Deniz Cansen Yildirim; Rengül Çetin-Atalay; A. Enis Çetin (IEEE J. Sel. Top. Signal Process., 2016)

Classification of Hematoxylin and Eosin Images Using Local Binary Patterns and 1-D SIFT Algorithm. - Oguzhan Oguz; A. Enis Çetin; Rengül Çetin-Atalay (IWCIM@EUSIPCO, 2017)

Automated cancer stem cell recognition in H and E stained tissue using convolutional neural networks and color deconvolution. - Wolfgang Aichinger; Sebastian Krappe; A. Enis Çetin; Rengül Çetin-Atalay; Aysegül Üner; Michaela Benz; Thomas Wittenberg; Marc Stamminger; Christian Münzenmayer (Digital Pathology, 2017)

Contrast Enhancement of Microscopy Images Using Image Phase Information. - Serdar Çakir; Deniz Cansen Kahraman; Rengül Çetin-Atalay; A. Enis Çetin (IEEE Access, 2018)

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. - Alperen Dalkiran; Ahmet Süreyya Rifaioglu; Maria Jesus Martin; Rengül Çetin-Atalay; Volkan Atalay; Tunca Dogan (BMC Bioinform., 2018)

EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes. - Hasan Fehmi Danaci; Rengül Çetin-Atalay; Volkan Atalay (J. Bioinform. Comput. Biol., 2018)

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. - Ahmet Süreyya Rifaioglu; Heval Atas; Maria Jesus Martin; Rengül Çetin-Atalay; Volkan Atalay; Tunca Dogan (Briefings Bioinform., 2019)

Synthesis, anticancer activity, toxicity evaluation and molecular docking studies of novel phenylaminopyrimidine - (thio)urea hybrids as potential kinase inhibitors. - Asli Türe; Deniz Cansen Kahraman; Rengül Çetin-Atalay; Sinem Helvacioglu; Mohammad Charehsaz; Ilkay Küçükgüzel (Comput. Biol. Chem., 2019)

DeepDistance: A Multi-task Deep Regression Model for Cell Detection in Inverted Microscopy Images. - Can Fahrettin Koyuncu; Gozde Nur Gunesli; Rengül Çetin-Atalay; Cigdem Gunduz Demir (CoRR, 2019)

A visual object tracking benchmark for cell motility in time-lapse imaging. - H. Seckin Demir; A. Enis Çetin; Rengül Çetin-Atalay (Signal Image Video Process., 2019)

iBioProVis: interactive visualization and analysis of compound bioactivity space. - Ataberk Donmez; Ahmet Süreyya Rifaioglu; Aybar C. Acar; Tunca Dogan; Rengül Çetin-Atalay; Volkan Atalay (Bioinform., 2020)

iBioProVis: interactive visualization and analysis of compound bioactivity space. - Ataberk Donmez; Ahmet Süreyya Rifaioglu; Aybar C. Acar; Tunca Dogan; Rengül Çetin-Atalay; Volkan Atalay; Wren Jonathan (Bioinform., 2020)

DeepDistance: A multi-task deep regression model for cell detection in inverted microscopy images. - Can Fahrettin Koyuncu; Gozde Nur Gunesli; Rengül Çetin-Atalay; Cigdem Gunduz Demir (Medical Image Anal., 2020)

MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery. - Ahmet Süreyya Rifaioglu; Rengül Çetin-Atalay; Deniz Cansen Kahraman; Tunca Dogan; Maria Jesus Martin; Volkan Atalay (Bioinform., 2021)

Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases. - Tunca Dogan; Ece Akhan Güzelcan; Marcus Baumann; Altay Koyas; Heval Atas; Ian R. Baxendale; Maria Jesus Martin; Rengül Çetin-Atalay (PLoS Comput. Biol., 2021)

SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins. - Gökhan Özsari; Ahmet Süreyya Rifaioglu; Ahmet Atakan; Tunca Dogan; Maria Jesus Martin; Rengül Çetin-Atalay; Volkan Atalay (Bioinform., 2022)

Transfer learning for drug-target interaction prediction. - Alperen Dalkiran; Ahmet Atakan; Ahmet Süreyya Rifaioglu; Maria Jesus Martin; Rengül Çetin-Atalay; Aybar C. Acar; Tunca Dogan; Volkan Atalay (Bioinform., 2023)

Human Hepatocellular Carcinoma Classification from H&E Stained Histopathology Images with 3D Convolutional Neural Networks and Focal Loss Function. - Umut Çinar; Rengül Çetin-Atalay; Yasemin Yardimci Çetin (J. Imaging, 2023)

An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data. - Mona Shojaei; Navid Mohammadvand; Tunca Dogan; Can Alkan; Rengül Çetin-Atalay; Aybar C. Acar (Comput. Biol. Medicine, 2024)