{"id":2,"date":"2013-09-30T17:33:02","date_gmt":"2013-09-30T17:33:02","guid":{"rendered":"http:\/\/blog.metu.edu.tr\/vatalay\/?page_id=2"},"modified":"2023-06-27T07:24:26","modified_gmt":"2023-06-27T04:24:26","slug":"publications","status":"publish","type":"page","link":"https:\/\/blog.metu.edu.tr\/vatalay\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<h2>2023<\/h2>\n<ul>\n<li>S. \u00d6zen, V. Atalay, &#8220;<a href=\"https:\/\/www.cai.sk\/ojs\/index.php\/cai\/article\/view\/2023_1_126\" target=\"_blank\" rel=\"noopener\">Power Consumption Forecasting by Hybrid Deep Architectures with Data Fusion<\/a> &#8220;, <em>Computing and Informatics<\/em>, 42(1), 126\u2013156, 2023.<\/li>\n<li>A.S. \u00d6zdilek, A. Atakan, G. \u00d6zsar\u0131, A. Acar, M.V. Atalay, T. Do\u011fan, A.S. Rifaio\u011flu, &#8220;<a href=\"https:\/\/academic.oup.com\/bib\/article-abstract\/24\/2\/bbac627\/7025464\" target=\"_blank\" rel=\"noopener\">ProFAB\u2014open protein functional annotation benchmark<\/a>&#8220;, <em>Briefings in Bioinformatics<\/em>, 24:bbac627, 2023.<\/li>\n<li>A. Zubaro\u011flu, V. Atalay, &#8220;<a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/sam.11590\" target=\"_blank\" rel=\"noopener\">Online embedding and clustering of evolving data streams<\/a>&#8220;, <em>Statistical Analysis and Data Mining<\/em>, 16:29-44, 2023.<\/li>\n<\/ul>\n<h2>2022<\/h2>\n<ul>\n<li>G. \u00d6zsar\u0131, A.S. Rifaioglu, A. Atakan, T. Do\u011fan, M.J. Martin, R. \u00c7etin Atalay, V. Atalay, &#8220;<a href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/17\/4226\/6633921\" target=\"_blank\" rel=\"noopener\">SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins<\/a>&#8220;, <em>Bioinformatics<\/em>, 38:4226\u20134229, 2022.<\/li>\n<\/ul>\n<h2>2021<\/h2>\n<ul>\n<li>T. Do\u011fan, 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, &#8220;<a href=\"https:\/\/doi.org\/10.1093\/nar\/gkab543\" target=\"_blank\" rel=\"noopener\">CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations<\/a>&#8220;, <em>Nucleic Acids Research<\/em>, 49(16):e96, 2021.<\/li>\n<li>A.S. Rifaioglu, R. Cetin Atalay, D. Cansen Kahraman, T. Do\u011fan, M. Martin, V. Atalay, &#8220;<a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa858\" target=\"_blank\" rel=\"noopener\">MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery<\/a>&#8220;, <em>Bioinformatics<\/em>, 37(5):693\u2013704, 2021.<\/li>\n<li>A. Zubaro\u011flu, V. Atalay, &#8220;<a href=\"https:\/\/doi.org\/10.1007\/s10462-020-09874-x\" target=\"_blank\" rel=\"noopener\">Data stream clustering: a review<\/a>&#8220;, <em>Artificial Intelligence Review<\/em>,\u00a0 54:1201\u20131236, 2021.<\/li>\n<\/ul>\n<h2>2020<\/h2>\n<ul>\n<li>A.S. R\u0131faio\u011flu, E. Nalbat, V. Atalay, M. J. Martin, R. Cetin-Atalay, T. Do\u011fan, &#8220;<a href=\"https:\/\/doi.org\/10.1039\/C9SC03414E\" target=\"_blank\" rel=\"noopener\">DEEPScreen: high performance drug\u2013target interaction prediction with convolutional neural networks using 2-D structural compound representations<\/a>&#8220;,\u00a0 <em>Chemical Science<\/em>, 11:2531-2557, 2020.<\/li>\n<\/ul>\n<h2>2019<\/h2>\n<ul>\n<li>M. Din\u00e7, \u015e. Ertekin, H. \u00d6zkan, C. Meydanl\u0131, V. Atalay, &#8220;Forecasting of Product Quality Through Anomaly Detection&#8221;, <a href=\"https:\/\/abifet.wixsite.com\/iotstream2019\">ECML\/PKDD 2019 Workshop on IoT Stream for Data Driven Predictive Maintenance<\/a>, 2019.<\/li>\n<li>V. Joshi, <em>et al<\/em>, &#8220;CROssBAR: Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning&#8221;, Oral presentation, <a href=\"https:\/\/www.iscb.org\/cms_addon\/conferences\/ismbeccb2019\/bioontologies.php\" target=\"_blank\" rel=\"noopener\">Bio-Ontologies COSI<\/a> at\u00a0<em>ISMB\/ECCB 2019<\/em>.<\/li>\n<li>A.S. R\u0131faio\u011flu, A. D\u00f6nmez, A.C. Acar, M.J. Martin, T. Dogan,\u00a0 R. Cetin Atalay, V. Atalay, &#8220;iBioProVis: Interactive Visualization and Analysis of Compound Bioactivity Space&#8221;, Oral presentation,<em><a href=\"https:\/\/www.iscb.org\/cms_addon\/conferences\/ismbeccb2019\/biovis.php\" target=\"_blank\" rel=\"noopener\"> Biological Data Visualization (BioVis:) COSI<\/a> at\u00a0ISMB\/ECCB 2019<\/em>.<\/li>\n<li>Zhou, N., <em>et al,<\/em> &#8220;<a href=\"https:\/\/doi.org\/10.1186\/s13059-019-1835-8\" target=\"_blank\" rel=\"noopener\">The CAFA challenge reports improved protein function prediction and new functional annotatons for hundreds of genes through experimental screens<\/a>&#8220;,\u00a0<em>Genome Biology,<\/em> 20, 244, 2019.<\/li>\n<li>A.S. R\u0131faio\u011flu, T. Dogan, M.J. Martin, R. Cetin Atalay, V. Atalay, &#8220;<a href=\"https:\/\/www.nature.com\/articles\/s41598-019-43708-3\" target=\"_blank\" rel=\"noopener\">DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks<\/a>&#8220;, <em>Scientific Reports-Nature<\/em>, <em>9<\/em>(1), 7344, 2019.<\/li>\n<\/ul>\n<h2>2018<\/h2>\n<ul>\n<li>A.S. R\u0131faio\u011flu, V. Atalay, M.J. Martin, R. Cetin Atalay,\u00a0 T. Dogan, &#8220;<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/491365v1\" target=\"_blank\" rel=\"noopener\">DEEPScreen: High Performance Drug-Target Interaction Prediction with Convolutional Neural Networks Using 2-D Structural Compound Representations<\/a>&#8220;, <em>BioRxiv <\/em> 491365, 2018. doi: <a href=\"https:\/\/doi.org\/10.1101\/491365\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.1101\/491365<\/a>.<\/li>\n<li>A. Dalk\u0131ran, A.S. R\u0131faio\u011flu, M.J. Martin, R. Cetin Atalay,\u00a0V. Atalay, T. Dogan, &#8220;<a href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2368-y\" target=\"_blank\" rel=\"noopener\">ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature<\/a>&#8220;, BMC Bioinformatics 19:334, 2018. <a href=\"https:\/\/doi.org\/10.1186\/s12859-018-2368-y\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.1186\/s12859-018-2368-y<\/a><\/li>\n<li>A.S. R\u0131faio\u011flu, H. Atas, M.J. Martin, R. Cetin Atalay, V. Atalay, T. Dogan, &#8220;<a href=\"https:\/\/academic.oup.com\/bib\/advance-article\/doi\/10.1093\/bib\/bby061\/5062947\" target=\"_blank\" rel=\"noopener\">Recent Applications of Deep Learning and Machine Intelligence on In-silico Drug Discovery: Methods, Tools and Databases<\/a>&#8220;<strong>,\u00a0<\/strong><em>Briefings in Bioinformatics<\/em> bby061, <a href=\"https:\/\/doi.org\/10.1093\/bib\/bby061\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.1093\/bib\/bby061<\/a>, 31 July 2018.<strong><br \/>\n<\/strong><\/li>\n<li>A.S. R\u0131faio\u011flu, V. Atalay, M.J. Martin, R. Cetin Atalay, T. Dogan, &#8220;Drug-Target Interaction Prediction with Deep Convolutional Neural Networks Using Compound Images&#8221;, Oral presentation, <em><a href=\"https:\/\/www.iscb.org\/cms_addon\/conferences\/ismb2018\/mlcsb.php\" target=\"_blank\" rel=\"noopener\">Machine Learning in Computational and Systems Biology (MLCSB) COSI<\/a> at\u00a0ISMB 2018<\/em>.<\/li>\n<li>T. Dogan, A.S. R\u0131faio\u011flu, R. Saidi, M.J. Martin, V. Atalay, R. Cetin Atalay, &#8220;Automated Negative Gene Ontology Based Functional Predictions for Proteins with UniGOPred&#8221;<strong>,\u00a0<\/strong>Oral presentation,\u00a0<em><a href=\"https:\/\/www.iscb.org\/cms_addon\/conferences\/ismb2018\/function.php\" target=\"_blank\" rel=\"noopener\">Function-COSI\u00a0<\/a>at\u00a0ISMB 2018<\/em>.<\/li>\n<li>H.F. Danaci, R. Cetin Atalay, V. Atalay, &#8220;<a href=\"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720018500075?src=recsys\">EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes <\/a>&#8220;, <em>Int. Journal of Bioinformatics and Computational Biology<\/em>, Vol. 16, No. 04, 1850007 (2018). doi: <a href=\"https:\/\/doi.org\/10.1142\/S0219720018500075\">10.1142\/S0219720018500075<\/a>.<\/li>\n<li>A.S. Rifaioglu, T. Do\u011fan, \u00d6.S. Sara\u00e7 , T. Ersahin, R. Saidi, M.V. Atalay, M.J. Martin, R. Cetin Atalay, <a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.25416\/full\" target=\"_blank\" rel=\"noopener\">&#8220;Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants&#8221;<\/a>, Proteins: Structure, Function, and Bioinformatics, 2018;86:135\u2013151. https:\/\/doi.org\/10.1002\/prot.25416<\/li>\n<\/ul>\n<h2>2017<\/h2>\n<ul>\n<li>A.S. R\u0131faio\u011flu, T. Dogan, M.J. Martin, R. Cetin Atalay, V. Atalay, \u201c<a href=\"https:\/\/arxiv.org\/abs\/1705.04802\" target=\"_blank\" rel=\"noopener\">Multi-task Deep Neural Networks in Automated Protein Function Prediction<\/a>&#8220;, preprint,\u00a0arXiv:1705.04802.<\/li>\n<li>A.S. R\u0131faio\u011flu, M.J. Martin, R. Cetin Atalay, V. Atalay, T. Dogan, \u201cInvestigation of Multi-task Deep Neural Networks in Automated Protein Function Prediction\u201d, Oral Presentation at <em>Function COSI ISMB\/ECCB 2017: 25th\u00a0Annual International Conference on Intelligent Systems for Molecular Biology<\/em>, Prague, Czech Republic, July 2017.<\/li>\n<li>A. Dalk\u0131ran, A.S. R\u0131faio\u011flu, T. Dogan, V. Atalay, M.J. Martin, R. Cetin Atalay, \u201cPrediction of Enzymatic Properties of Protein Sequences Based on the EC Nomenclature\u201d, Poster Presentation at <em>ISMB\/ECCB 2017: 25th\u00a0Annual International Conference on Intelligent Systems for Molecular Biology<\/em>, Prague, Czech Republic,\u00a0July 2017.<\/li>\n<li>A.S. R\u0131faio\u011flu, M.J. Martin, R. Cetin Atalay, V. Atalay, T. Dogan \u201cInvestigation of Multi-task Deep Neural Networks in Automated Protein Function Prediction\u201d, Oral Presentation at <em>HIBIT 2017: The International Symposium on Health Informatics and Bioinformatics<\/em>, \u00a0METU Northern Cyprus Campus, June 28 \u2013 30, 2017.<\/li>\n<li>A. Dalk\u0131ran, A.S. R\u0131faio\u011flu, T. Dogan, V. Atalay, M.J. Martin, R. Cetin Atalay, \u201cPrediction of Enzymatic Properties of Protein Sequences Based on the EC Nomenclature\u201d, Poster Presentation at <em>HIBIT 2017: The International Symposium on Health Informatics and Bioinformatics<\/em>, METU Northern Cyprus Campus, June 28 \u2013 30, 2017.<\/li>\n<li>H.F. Danac\u0131, R. Cetin Atalay, V. Atalay, \u201cEClerize: A Customized Force-Directed Layout Algorithm for Biological Networks with EC Attributes\u201d, Oral Presentation at <em>GLBIO 2017: Great Lakes Bioinformatics Conference<\/em>, Chicago, USA, May 15-17, 2017.<\/li>\n<li>A.S. R\u0131faio\u011flu, T. Dogan, \u00d6.S. Sarac, R. Saidi, V. Atalay, M.J. Martin, R. Cetin Atalay, \u201cUniGOPred: A Large Scale Automated GO Term Annotation System for UniProtKB\u201d,\u00a0Poster presentation at <em>GLBIO 2017: Great Lakes Bioinformatics Conference<\/em>, Chicago, USA, May 15-17, 2017\u00a0\u00a0(Best Poster Award).<\/li>\n<\/ul>\n<h2>2015<\/h2>\n<ul>\n<li>S Gen\u00e7, M Ba\u015ftan, U G\u00fcd\u00fckbay, V Atalay, \u00d6 Ulusoy, \u201c<a href=\"http:\/\/link.springer.com\/article\/10.1007\/s11760-014-0631-x\" target=\"_blank\" rel=\"noopener noreferrer\">HandVR: a hand-gesture-based interface to a video retrieval system\u201d,\u00a0<em>Signal, Image and Video Processing<\/em>,<\/a>\u00a09 (7), 1717-1726, 2015, doi:10.1007\/s11760-014-0631-x.<\/li>\n<\/ul>\n<h2>2014<\/h2>\n<ul>\n<li>T. Ersahin, L. Carkacioglu, T. Can, O. Konu, V. Atalay, R. Cetin-Atalay, \u201c<a href=\"http:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0093341\" target=\"_blank\" rel=\"noopener noreferrer\">Identification of novel reference genes based on MeSH categories<\/a>\u201d,\u00a0<em>PLoS ONE<\/em>, Public Library of Science (PLoS), 9(3): e93341, 2014, doi:10.1371\/journal.pone.0093341.<\/li>\n<li>A.G. Yaman, A.C. Acar, V. Atalay, R. \u00c7etin-Atalay, \u201cDiscriminative Modeling of Cell Signaling as Bayesian Networks\u201d, 2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBE 2014), Granada, Spain, April 7-9, 2014.<\/li>\n<\/ul>\n<h2>2012<\/h2>\n<ul>\n<li>Z. Isik, T. Ersahin, V. Atalay, C. Aykanat, R. Cetin-Atalay, \u201c<a href=\"http:\/\/pubs.rsc.org\/en\/Content\/ArticleLanding\/2012\/MB\/c2mb25215e#!divAbstract\" target=\"_blank\" rel=\"noopener noreferrer\">A signal transduction score flow algorithm for cyclic cellular pathway analysis, which combines transcriptome and ChIP-seq data<\/a>\u201d,\u00a0<em>Molecular BioSystems<\/em>, 8, p.3224-3231, 2012, doi:10.1039\/C2MB25215E.<\/li>\n<li>A.G. Yaman, V. Atalay, R. Cetin-Atalay, &#8220;Prediction Of Enzyme Classes In A Hierarchical Approach By Using SPMap&#8221;, <em>11th European Conference on Computational Biology (ECCB&#8217;12)<\/em>, p.H29, 2012.<\/li>\n<\/ul>\n<h2>2010<\/h2>\n<ul>\n<li>O.S. Sarac, V. Atalay, R. \u00c7etin-Atalay, \u201c<a href=\"http:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0012382\" target=\"_blank\" rel=\"noopener noreferrer\">GOPred: GO Molecular Function Prediction by Combined Classi\ufb01ers<\/a>\u201d,\u00a0<em>PLoS ONE<\/em>, Public Library of Science (PLoS), 5(8): e12382, 2010, doi:10.1371\/journal.pone.0012382.<\/li>\n<li>\n<div>L. \u00c7arkac\u0131o\u011flu, R. \u00c7etin-Atalay, \u00d6. Konu, V. Atalay, T. Can, \u201cBi-k-Bi Clustering: Mining Large Scale Gene Expression Data Using Two-Level Biclustering\u201d,\u00a0<em>International Journal of Data Mining and Bioinformatics<\/em>, Inderscience, Vol. 4, No.6 pp.701-721, 2010, doi:10.1504\/IJDMB.2010.037548.<\/div>\n<\/li>\n<li>\n<div>Z. I\u015f\u0131k, V. Atalay, R. \u00c7etin-Atalay, \u201cEvaluation of Signaling Cascades Based on the Weights from Microarray and ChIP-seq Data\u201d,\u00a0<em>Journal of Machine Learning Research W&amp;C Proceedings<\/em>,\u00a0<acronym title=\"Massachusetts Institute of Technology\">MIT<\/acronym>\u00a0Press, Vol.8, pp.44-54, 2010.<\/div>\n<\/li>\n<li>\n<div>Z. I\u015f\u0131k, V. Atalay, C. Aykanat, R. \u00c7etin-Atalay, \u201cData and Model Driven Hybrid Approach to Activity Scoring of Cyclic Pathways\u201d,\u00a0<em>25th International Symposium on Computer and Information Sciences<\/em>\u00a0(ISCIS 2010), London, UK, September 22-24, 2010, Lecture Notes in Electrical Engineering, Springer, Vol. 62 pp.91-94.<\/div>\n<\/li>\n<\/ul>\n<h2>2009<\/h2>\n<div>\n<ul>\n<li>\n<div>S. Gen\u00e7, V. Atalay, \u201cWhich Shape Representation is the best for Real-Time Hand Interface System?\u201d,\u00a0<em>5th International Symposium on Visual Computing<\/em>, Las Vegas, Nevada, USA, November 30-December 2, 2009.<\/div>\n<\/li>\n<li>\n<div>Z. Isik, V. Atalay, R. Cetin-Atalay, \u201cEvaluation of Signaling Cascades Based on the Weights from Microarray and ChIP-seq Data\u201d,\u00a0<em>Third International Workshop on Machine Learning in Systems Biology<\/em>\u00a0(MLSB 2009), Ljubljana, Slovenia, September 5-6, 2009.<\/div>\n<\/li>\n<\/ul>\n<\/div>\n<h2><a id=\"section2\" name=\"section2\"><\/a>2008<\/h2>\n<div>\n<ul>\n<li>\n<div>O.S. Sarac, R. Cetin-Atalay, V. Atalay, \u201cGOPred: Combining classifiers on the GO\u201d,\u00a0<em>Second International Workshop on Machine Learning in Systems Biology<\/em>(MLSB08), Brussels, September 13-14, 2008.<\/div>\n<\/li>\n<li>\n<div>O.S. Sarac, \u00d6. G\u00fcrsoy-Y\u00fcz\u00fcg\u00fcll\u00fc, R. Cetin-Atalay, V. Atalay, \u201c<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18243801\" target=\"_blank\" rel=\"noopener\">Subsequence based feature map for protein function classification<\/a>\u201d,\u00a0<em>Journal of Computational Biology and Chemistry<\/em>, Elsevier, Vol.32, pp.122-130, 2008.<\/div>\n<\/li>\n<\/ul>\n<\/div>\n<h2><a id=\"section3\" name=\"section3\"><\/a>2007<\/h2>\n<div>\n<ul>\n<li>\n<div>O.S. Sarac, \u00d6. G\u00fcrsoy-Y\u00fcz\u00fcg\u00fcll\u00fc,, R. Cetin-Atalay and V. Atalay, \u201cProtein Function Annotation by Subsequence based Feature Map\u201d,\u00a0<em>Automated Function Prediction (AFP) and Biosapiens Special Interest Group (SIG) meeting at ISMB\/ECCB 2007<\/em>, Vienna, Austria, July 19-20, 2007.<\/div>\n<\/li>\n<li>\n<div>Z.Sokmen, M.Ozturk, V.Atalay, R.Cetin Atalay, \u201cA Hybrid Method For The Identification of Expression Patterns From Microarray Data\u201d,\u00a0<em>15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference on Computational Biology (ECCB)<\/em>, Vienna, Austria, July 21-25, 2007.<\/div>\n<\/li>\n<li>\n<div>O.Sinan Sarac, O.Gursoy-Yuzugullu, R.Cetin-Atalay and V. Atalay, \u201cFunction Annotation via a Discriminative Classifier Database on GO hierarchy\u201d,\u00a0<em>15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference on Computational Biology (ECCB)<\/em>, Vienna, Austria, July 21-25, 2007.<\/div>\n<\/li>\n<li>\n<div>O.Sinan Sarac, P.Bezek, R.Cetin-Atalay, V.Atalay, \u201cSpectral Clustering based Subsequence Feature Map for Protein Classification\u201d,\u00a0<em>11th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007)<\/em>, Oakland, California, USA, April 21-25, 2007.<\/div>\n<\/li>\n<\/ul>\n<\/div>\n<h2><a id=\"section4\" name=\"section4\"><\/a>2006<\/h2>\n<div>\n<ul>\n<li>\n<div>A. Teke and V. Atalay, \u201cTexture Classification and Retrieval Using the Random Neural Network Model\u201d,\u00a0<em>Computational Management Science<\/em>, Springer, Vol.3, No.3, pp.193-205, 2006.<\/div>\n<\/li>\n<li>\n<div>R. Hassanpour and V. Atalay, \u201cAn Experimental Study on the Sensitivity of Auto-Calibration to Projective Camera Models Parameters\u201d,\u00a0<em>Optical Engineering<\/em>, Vol. 45, 047002, 2006.<\/div>\n<\/li>\n<li>\n<div>B. Otlu, V. Atalay, R. Hassanpour, \u201cRelative Consistency of Projective Reconstructions Obtained from the Same Image Pair\u201d,\u00a0<em>International Journal of Pattern Recognition and Artificial Intelligence<\/em>, World Scientific, Vol.20, No.5, pp.649-664, 2006.<\/div>\n<\/li>\n<li>\n<div>O.S. Sarac, V. Atalay, R. Cetin-Atalay, \u201cSubsequence Feature Map for Protein Classification and Remote Homology Detection\u201d,\u00a0<em>5th European Conference on Computational Biology (ECCB)<\/em>, Eliat, Israel, September 10-13, 2006.<\/div>\n<\/li>\n<li>\n<div>L. Carkacioglu, T. Can, O. Konu, V. Atalay, R. Cetin-Atalay, \u201cExpression Pattern Analysis of Housekeeping Genes Across Large Number of Microarray Experiments\u201d,\u00a0<em>5th European Conference on Computational Biology (ECCB)<\/em>, Eliat, Israel, September 10-13, 2006.<\/div>\n<\/li>\n<li>\n<div>O.S. Sarac, V. Atalay, R. Cetin-Atalay, \u201cHMM-based subsequence feature map for Protein Classification and Remote Homology Detection\u201d,\u00a0<em>14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2006)<\/em>, Forteleza, Brazil, August 6-10, 2006.<\/div>\n<\/li>\n<\/ul>\n<\/div>\n<h2><a id=\"section5\" name=\"section5\"><\/a>2005<\/h2>\n<div>\n<ul>\n<li>\n<div>V. Atalay, R. Cetin-Atalay, \u201cImplicit Motif Distribution based Hybrid Computational Kernel for Sequence Classification\u201d,\u00a0<em>Bioinformatics Journal<\/em>, Oxford University Press, vol.21, No.8, pp.1429-1436, 2005.<\/div>\n<\/li>\n<li>\n<div>O. Dalay and V. Atalay, \u201cInteractive classification of satellite image content based on query by example\u201d,\u00a0<em>ISPRS Spatial Data Mining Workshop<\/em>, Ankara, Turkey, 24-25 November, 2005.<\/div>\n<\/li>\n<li>\n<div>S. Genc and V. Atalay, \u201cITouch: Vision-based Intelligent Touch Screen in a Distributed Environment\u201d, doctoral spotlight paper at\u00a0<em>Seventh International Conference on Multimodal Interfaces (ICMI)<\/em>, Trento, Italy, October 4-6, 2005.<\/div>\n<\/li>\n<\/ul>\n<\/div>\n<h2><a id=\"section6\" name=\"section6\"><\/a>2004<\/h2>\n<div>\n<ul>\n<li>\n<div>M. Musa, D. de Ridder, R. Duin and V. Atalay, \u201cAlmost Autonomous Training of Mixtures of Principal Component Analyzers\u201d,\u00a0<em>Pattern Recognition Letters<\/em>, vol.25, No.9, pp.1085-1095, 2004.<\/div>\n<\/li>\n<li>\n<div>R. Hassanpour and V. Atalay, \u201cCamera auto-calibration using a sequence of 2D images with small rotations\u201d,\u00a0<em>Pattern Recognition Letters<\/em>, vol.25, No.9, pp.989-997, 2004.<\/div>\n<\/li>\n<li>\n<div>I.A. Erdem, M.E. Erdem, V. Atalay, A.E. \u00c7etin, \u201cVision-based Continuous Graffiti-like Text Entry System\u201d,\u00a0<em>Optical Engineering<\/em>, vol.43, pp.553-558, 2004.<\/div>\n<\/li>\n<li>\n<div>R. Hassanpour and V. Atalay, \u201cDelaunay Triangulation based 3D human face modeling from uncalibrated images\u201d,\u00a0<em>The First IEEE Workshop on Face Processing in Video<\/em>, Washington, D.C., USA, June 28, 2004.<\/div>\n<\/li>\n<li>\n<div>A. Teke and V. Atalay, \u201cTexture Classification and Retrieval Using Random Neural Network Model\u201d,\u00a0<em>IEEE 6th Southwest Symposium on Image Analysis and Interpretation<\/em>, Lake Tahoe, Nevada, USA, March 28-30, 2004, IEEE Press, pp.109-113.<\/div>\n<\/li>\n<\/ul>\n<\/div>\n<h2><a id=\"section7\" name=\"section7\"><\/a>2003<\/h2>\n<div>\n<ul>\n<li>\n<div>A.Y. Mulayim, Y. Ulas, V. Atalay, \u201cSilhouette-based 3D Model Reconstruction from Multiple Images\u201d,\u00a0<em>IEEE Trans. On Systems, Man, and Cybernetics-Part B<\/em>, Special Issue on 3D Image Analysis and Modeling, Vol.33, No.4, pp.582-591, 2003.<\/div>\n<\/li>\n<li>\n<div>U. Yilmaz, A.Y. Mulayim, V. Atalay, \u201cAn Image based Inexpensive 3D Scanner\u201d,\u00a0<em>Int. Journal of Image and Graphics<\/em>, Special Issue on Virtual Reality and Virtual Environment, World Scientific, Vol.3, No.2, pp.235-264, 2003.<\/div>\n<\/li>\n<li>\n<div>C. Guray, N. Celebi, V. Atalay, A.Gunhan, \u201cOre-Age: An Hybrid system for Assisting and Teaching Mining Method Selection\u201d,\u00a0<em>Expert Systems with Applications Journal<\/em>, Pergamon-Elsevier Science, Vol.24, pp.261-271, 2003.<\/div>\n<\/li>\n<li>\n<div>M. Ozarar, V. Atalay, R. Cetin-Atalay, \u201cPrediction of protein subcellular localization based on primary sequence data\u201d,\u00a0<em>18th International Symposium on Computer and Information Sciences (ISCIS XVII)<\/em>, Antalya, Turkey, 3-5 November, 2003, LNCS 2869, pp.611-618, Springer.<\/div>\n<\/li>\n<li>\n<div>M.Musa, R.Duin, D. deRidder, V.Atalay, \u201cTexture Segmentation Using the Mixtures of Principal Component Analyzers\u201d,\u00a0<em>18th International Symposium on Computer and Information Sciences (ISCIS XVII)<\/em>, Antalya, Turkey, 3-5 November, 2003, LNCS 2869, pp.505-512, Springer.<\/div>\n<\/li>\n<li>\n<div>M.E. Erdem, I.A. Erdem, V. Atalay, \u201cImage based extraction of material reflectance properties of a 3D rigid object\u201d,\u00a0<em>Eurographics 2003 Annual Conference of the European Association for Computer Graphics<\/em>, Granada, Spain, 1-6 September 2003.<\/div>\n<\/li>\n<li>\n<div>I.S. Sen, V. Atalay, \u201cOcclusion culling for image based rendering with warping\u201d,\u00a0<em>Eurographics 2003 Annual Conference of the European Association for Computer Graphics<\/em>, Granada, Spain, 1-6 September 2003.<\/div>\n<\/li>\n<li>\n<div>G.K. Akinci, S.U. Korkmaz, V. Atalay, \u201cA character recognizer for Turkish language\u201d,\u00a0<em>7th Int. Conf. on Document Analysis and Recognition<\/em>, Edinburgh, Scotland, 3-6 August 2003.<\/div>\n<\/li>\n<li>\n<div>A. Erdem, E. Erdem, V. Atalay, E. Cetin, \u201cComputer vision based unistroke keyboard system and mouse for the handicapped\u201d,\u00a0<em>Int. Conf. on Multimedia and Expo-ICME 03<\/em>, Baltimore, Maryland, USA, 6-9 July 2003.<\/div>\n<\/li>\n<\/ul>\n<\/div>\n<h2><a id=\"section8\" name=\"section8\"><\/a>2002<\/h2>\n<div>\n<ul>\n<li>\n<div>S. Baskan, M.M. Bulut and V. Atalay, \u201cProjection based Method for Segmentation of Human Faces and its Evaluation\u201d,\u00a0<em>Pattern Recognition Letters<\/em>, Vol.23, No.14, pp.1623-1629, Elsevier Science, December 2002.<\/div>\n<\/li>\n<li>\n<div>P. Duygulu and V. Atalay, \u201cA Hierarchical Representation of Form Documents for Identification and Retrieval\u201d,\u00a0<em>Int. Journal of Document Analysis and Recognition<\/em>, Vol.5, No.1, pp.17-27, Elsevier Science, 2002.<\/div>\n<\/li>\n<li>\n<div>R. Hassanpour and V. Atalay, \u201cHead Modeling with Camera Auto-calibration and Deformation\u201d,\u00a0<em>7th Int. Fall Workshop on Vision, Modeling and Visualization-VMV 2002<\/em>, Erlangen, Germany, 20-22 November 2002.<\/div>\n<\/li>\n<li>\n<div>B. Otlu, R. Hassanpour, V. Atalay, \u201cConsistency of projective reconstructions from an image pair\u201d,\u00a0<em>9th International Workshop on Systems, Signals and Image Processing<\/em>, Manchester Town Hall, UK, 7-8 November 2002.<\/div>\n<\/li>\n<li>\n<div>A. Erdem, E. Erdem, V. Atalay, E. Cetin, \u201cVision based gesture-based text entry\u201d demonstration at the\u00a0<em>6th Int. Symposium on Wearable Computers<\/em>, Seattle, Washington, USA, October 7-10, 2002.<\/div>\n<\/li>\n<li>\n<div>M. Yaman, V. Atalay, M. Turker, O.N. Gerek, A.E. Cetin, \u201cTexture Segmentation by Using Adaptive Polyphase Subband Decomposition\u201d,\u00a0<em>17th International Symposium on Computer and Information Sciences (ISCIS XVII)<\/em>, Orlando, Florida, USA, 28-30 October, 2002.<\/div>\n<\/li>\n<li>\n<div>K.Balci and V.Atalay, \u201cPCA for Gender Estimation: Which Eigenvectors Contribute?\u201d,\u00a0<em>16th Int. Conference on Pattern Recognition<\/em>, Quebec City, Canada, August 11-15, 2002, IEEE Press, Vol.3, 363-366.<\/div>\n<\/li>\n<li>\n<div>U.Yilmaz, A.Mulayim, and V.Atalay, \u201cReconstruction of Three Dimensional Models from Real Images\u201d,\u00a0<em>3D Data Processing, Visualization, Transmission (3DPVT)<\/em>, Padova, Italy, June 19-21, 2002, IEEE press, eds. G.M.Cortelazzo, C.Guerra, pp.554-557.<\/div>\n<\/li>\n<\/ul>\n<\/div>\n<h2><a id=\"section9\" name=\"section9\"><\/a>2001<\/h2>\n<div>\n<ul>\n<li>\n<div>G. Ongun, U. Hal\u0131c\u0131, K. Leblebicio\u011flu, V. Atalay, S. Beksa\u00e7, M. Beksa\u00e7, \u201cAutomated Contour Detection in Blood Cell Images by an Efficient Snake Algorithm\u201d,\u00a0<em>Nonlinear Analysis<\/em>, Vol.47, pp.5839-5847, Pergamon-Elsevier Science, 2001.<\/div>\n<\/li>\n<li>\n<div>\u00d6.F. \u00d6zer, O. \u00d6z\u00fcn, C.\u00d6. T\u00fczel, V. Atalay, A.E. \u00c7etin, \u201cVision-based Single-stroke Character Recognition for Wearable Computing\u201d,\u00a0<em>IEEE Intelligent Systems<\/em>, Vol.16, pp.33-37, 2001.<\/div>\n<\/li>\n<li>\n<div>A.Y. Mulayim and V. Atalay, \u201cStereo correction on the silhouette-based 3D model reconstruction from multiple images\u201d,\u00a0<em>SPIE\u2019s 13th International Symposium on Three-Dimensional Image Capture and Applications IV<\/em>, 24-25 January 2001, Proceedings of SPIE Vol. 4298.<\/div>\n<\/li>\n<li>\n<div>S. Baskan, M.M. Bulut, V. Atalay, \u201cSegmentation of facial features using gradient-based approach\u201d,\u00a0<em>SPIE\u2019s 13th International Symposium on Machine Vision Applications in Industrial Inspection IX<\/em>, 22-23 January 2001, Proceedings of SPIE Vol. 4301.<\/div>\n<\/li>\n<\/ul>\n<\/div>\n<h2><a id=\"selected_publications_prior_to_2001\" name=\"selected_publications_prior_to_2001\"><\/a>Selected Publications prior to 2001<\/h2>\n<div>\n<ul>\n<li>\n<div>A.Y. M\u00fclayim, V. Atalay, O. \u00d6z\u00fcn, F. Schmitt, \u201cOn the Silhouette Based 3D Reconstruction and Initial Bounding Cube Estimation\u201d,\u00a0<em>5th Int. Fall Workshop on Vision, Modeling and isualization-VMV 2000<\/em>, Max-Planck-Institut f\u00fcr Informatik, Saarbrucken, Germany, 22-24 November 2000.<\/div>\n<\/li>\n<li>\n<div>N. Dicle and V. Atalay, \u201cImage matching using singular value decompositionand Godel coding scheme\u201d,\u00a0<em>SPIE\u2019s 12th International Symposium on Electronic Imaging-Image and Video Communications and Processing<\/em>, 26-28 January, Proceedings of SPIE Vol. 3974, 2000.<\/div>\n<\/li>\n<li>\n<div>O.N. Gerek , A.E. Cetin , A. Tewfik, and V. Atalay, \u201cSubband Domain Coding of Binary Textual Images for Document Archiving\u201d,\u00a0<em>IEEE Transactions on Image Processing<\/em>, Vol.8, No.10, pp.1438-1446, October 1999.<\/div>\n<\/li>\n<li>\n<div>E. Oztop, A.Y. Mulayim, V. Atalay, and F. Yarman-Vural, \u201cRepulsive Attractive Network for Baseline Extraction on Document Images\u201d,\u00a0<em>Signal Processing<\/em>, Vol.75, No.1, pp.1-10, 1999.<\/div>\n<\/li>\n<li>\n<div>Sinan Beksac, Aydan J. Erkmen, Sezer Aksel, Ugur Halici, Kemal Leblebicioglu, Meral Beksac, Volkan Atalay, Lakhmi C. Jain,\u00a0<em>Intelligent diagnostic systems in maternal and fetal medicine<\/em>, pp.137-199, in Soft-Computing in Human-Related Sciences, editors: Jain, L. C., Kandel, Abraham, Teodorescu, Horia-Nicolai, CRC press, Singapore, 1999.<\/div>\n<\/li>\n<li>\n<div>A.Y. Mulayim, Y. Yener, F. Schmitt, and V. Atalay, \u201cRotation Axis Extraction of a Turn Table Viewed by a Fixed Camera\u201d, Workshop on Vision, Modelling, and Visualization &#8211; VMV\u201999, Erlangen, Germany, November 17-19, 1999.<\/div>\n<\/li>\n<li>\n<div>S. Genc, and V. Atalay, \u201cTexture Extraction from Photographs and Rendering with Dynamic Texture Mapping\u201d,\u00a0<em>International Conference on Image Analysis and Processing (ICIAP99)<\/em>, Venice, Italy, September 27-29, 1999.<\/div>\n<\/li>\n<li>\n<div>V. Atalay, and E. Arslan, \u201dAn\u00a0<acronym title=\"Standard General Markup Language\">SGML<\/acronym>\u00a0Based Viewer for Form Documents\u201d,\u00a0<em>Fouth International Conference on Document Analysis and Recognition<\/em>, Bangalore, India, September 20-22, 1999.<\/div>\n<\/li>\n<li>\n<div>V. Atalay, and U. Yilmaz, \u201cA Matching Algorithm Based on Linear Features\u201d,\u00a0<em>Pattern Recognition Letters<\/em>, Vol.19, No.9, pp.857-867, Elsevier Science,1998.<\/div>\n<\/li>\n<li>\n<div>M. Goktepe, V. Atalay, N. Yalabik, and C. Yalabik, \u201cUnsupervised Texture Based Image Segmentation by Simulated Annealing with Markov Random Field and Potts Models\u201d, Proceedings of the\u00a0<em>Fourteenth International Conference on Pattern Recognition (ICPR)<\/em>, Brisbane, Australia, 16-20 August, pp.820-822, IEEE Computer Society Press, 1998.<\/div>\n<\/li>\n<li>\n<div>P. Duygulu, V. Atalay, and E. Dincel, \u201cA Heuristic Algorithm for Hierarchical Representation of Form Documents\u201d, Proceedings of the\u00a0<em>Fourteenth International Conference on Pattern Recognition (ICPR)<\/em>, Brisbane, Australia, 16-20 August, pp.929-931, IEEE Computer Society Press, 1998.<\/div>\n<\/li>\n<li>\n<div>M. Borchani, V. Atalay, and G. Stamon, \u201cClassification d\u2019Images par des Attributs de Texture\u201d,\u00a0<em>Colloque de Recherche Doctorale Automatique, Genie Informatique et Image<\/em>, Angers, France, December, 1997.<\/div>\n<\/li>\n<li>\n<div>M. Borchani, V. Atalay, and G. Stamon, \u201cClassification d\u2019Images par des Statistiques d\u2019Ordres Differents\u201d,\u00a0<em>Cinquiemes Rencontres de la Societe Francophone de Classification<\/em>, Lyon, France, September 1997.<\/div>\n<\/li>\n<li>\n<div>E. Oztop, A.Y. Mulayim, F.T. Yarman-Vural, and V. Atalay, \u201cBaseline Extraction on Document Images by Repulsive\/ Attractive Network\u201d,\u00a0<em>IEEE Int. Conf. on Acustics, Signal, and Speech Processing (ICASSP)<\/em>, Munich, Germany, April 1997.<\/div>\n<\/li>\n<li>\n<div>M. Goktepe, V. Atalay and N. Yalabik, \u201cUnsupervised Segmentation of Gray Level Markov Model Textures with Hierarchical Self Organizing Maps\u201d, Proceedings of the\u00a0<em>Thirteenth International Conference on Pattern Recognition (ICPR)<\/em>, Wien, Austria, August 25-29 , vol.4, pp.90-94, IEEE Computer Society Press,1996.<\/div>\n<\/li>\n<li>\n<div>M. Koksal, H. Vural, and V. Atalay, \u201cThe Investigation of Hydrodynamics of a 2-D Fluidized Bed with Moving Double Plate Distributors Using Image Analysis\u201d,\u00a0<em>5th World Congress of Chemical Engineers<\/em>, San Diego, USA, July 1996.<\/div>\n<\/li>\n<li>\n<div>V. Atalay, and E. Gelenbe, \u201cParallel algorithm for color texture generation using the random neural network model\u201d,\u00a0<em>International Journal of Pattern Recognition and Artificial Intelligence<\/em>, Vol.6, No.2-3, pp. 437-446, World Scientific, 1992.<\/div>\n<\/li>\n<li>\n<div>V. Atalay, E. Gelenbe, and N. Yalabik, \u201cTexture generation with the random neural network model\u201d,\u00a0<em>International Journal of Pattern Recognition and Artificial Intelligence<\/em>, Vol-6, No.1, pp. 131-142, World Scientific,1992.<\/div>\n<\/li>\n<li>\n<div>V. Atalay, E. Gelenbe, and N. Yalabik, \u201cTexture generation with the random neural network model\u201d, Proc.\u00a0<em>International Conference on Artificial Neural Networks (<acronym title=\"Internet Corporation for Assigned Names and Numbers\">ICANN<\/acronym>\u00a091)<\/em>, Helsinki, Finland, July 1991.<\/div>\n<\/li>\n<li>\n<div>V. Atalay, and E. Gelenbe, \u201cParallel algorithm for color texture generation using the random neural network model\u201d, Proc.\u00a0<em>International Colloqium on Parallel Image Processing<\/em>, Paris, France, June 1991.<\/div>\n<\/li>\n<li>\n<div>V. Atalay, M. Ozcilingir, N. Yalabik, \u201cComputer recognition of Ottoman text\u201d, Proc.\u00a0<em>International Symposium on Computer and Information Sciences-V (ISCIS)<\/em>, Capadoccia, Turkey, November 1990.<\/div>\n<\/li>\n<\/ul>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>2023 S. \u00d6zen, V. Atalay, &#8220;Power Consumption Forecasting by Hybrid Deep Architectures with Data Fusion &#8220;, Computing and Informatics, 42(1), 126\u2013156, 2023. A.S. \u00d6zdilek, A. Atakan, G. \u00d6zsar\u0131, A. Acar, M.V. Atalay, T. Do\u011fan, A.S. Rifaio\u011flu, &#8220;ProFAB\u2014open protein functional annotation benchmark&#8220;, Briefings in Bioinformatics, 24:bbac627, 2023. A. Zubaro\u011flu, V. Atalay, &#8220;Online embedding and clustering of [&hellip;]<\/p>\n","protected":false},"author":1875,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/blog.metu.edu.tr\/vatalay\/wp-json\/wp\/v2\/pages\/2","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blog.metu.edu.tr\/vatalay\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/blog.metu.edu.tr\/vatalay\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/blog.metu.edu.tr\/vatalay\/wp-json\/wp\/v2\/users\/1875"}],"replies":[{"embeddable":true,"href":"https:\/\/blog.metu.edu.tr\/vatalay\/wp-json\/wp\/v2\/comments?post=2"}],"version-history":[{"count":0,"href":"https:\/\/blog.metu.edu.tr\/vatalay\/wp-json\/wp\/v2\/pages\/2\/revisions"}],"wp:attachment":[{"href":"https:\/\/blog.metu.edu.tr\/vatalay\/wp-json\/wp\/v2\/media?parent=2"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}