====== Publications ======

===== 2009 =====
  * L. Çarkacıoğlu, R. Çetin-Atalay, Ö. Konu, V. Atalay, T. Can, “Bi-k-Bi Clustering: Mining Large Scale Gene Expression Data Using Two-Level Biclustering”, __International Journal of Data Mining and Bioinformatics__, Inderscience, to appear.
  * S. Genç, V. Atalay, “Which Shape Representation is the best for Real-Time Hand Interface System?”, __5th International Symposium on Visual Computing__, Las Vegas, Nevada, USA, November 30-December 2, 2009.
  * Z. Isik, V. Atalay, R. Cetin-Atalay, “Evaluation of Signaling Cascades Based on the Weights from Microarray and ChIP-seq Data”, __Third International Workshop on Machine Learning in Systems Biology__ (MLSB 2009), Ljubljana, Slovenia, September 5-6 2009.

===== 2008 =====
  * O.S. Sarac, R. Cetin-Atalay, V. Atalay, “GOPred: Combining classifiers on the GO”, __Second International Workshop on Machine Learning in Systems Biology__(MLSB08), Brussels, September 13-14, 2008. 
  * O.S. Sarac, Ö. Gürsoy-Yüzügüllü, R. Cetin-Atalay, V. Atalay, “Subsequence based feature map for protein function classification”, __Journal of Computational Biology and Chemistry__, Elsevier, Vol.32, pp.122-130, 2008.
===== 2007 =====
  * O.S. Sarac, Ö. Gürsoy-Yüzügüllü,, R. Cetin-Atalay and V. Atalay, “Protein Function Annotation by Subsequence based Feature Map”, __Automated Function Prediction (AFP) and Biosapiens Special Interest Group (SIG) meeting at ISMB/ECCB 2007__, Vienna, Austria, July 19-20, 2007.
  * Z.Sokmen, M.Ozturk, V.Atalay, R.Cetin Atalay, “A Hybrid Method For The Identification of Expression Patterns From Microarray Data”, __15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference on Computational Biology (ECCB)__, Vienna, Austria, July 21-25, 2007.
  * O.Sinan Sarac, O.Gursoy-Yuzugullu, R.Cetin-Atalay and V. Atalay, “Function Annotation via a Discriminative Classifier Database on GO hierarchy”, __15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference on Computational Biology (ECCB)__, Vienna, Austria, July 21-25, 2007.
  * O.Sinan Sarac, P.Bezek, R.Cetin-Atalay, V.Atalay, “Spectral Clustering based Subsequence Feature Map for Protein Classification”, __11th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007)__, Oakland, California, USA, April 21-25, 2007.

===== 2006 =====

  * A. Teke and V. Atalay, “Texture Classification and Retrieval Using the Random Neural Network Model”, __Computational Management Science__,  Springer, Vol.3, No.3, pp.193-205, 2006.
  * R. Hassanpour and V. Atalay, “An Experimental Study on the Sensitivity of Auto-Calibration to Projective Camera Models Parameters”, __Optical Engineering__, Vol. 45, 047002,  2006.
  * B. Otlu, V. Atalay, R. Hassanpour, “Relative Consistency of Projective Reconstructions Obtained from the Same Image Pair”, __International Journal of Pattern Recognition and Artificial Intelligence__, World Scientific, Vol.20, No.5, pp.649-664, 2006.
  * O.S. Sarac, V. Atalay, R. Cetin-Atalay, "Subsequence Feature Map for Protein Classification and Remote Homology Detection", __5th European Conference on Computational Biology (ECCB)__, Eliat, Israel, September 10-13, 2006.
  * L. Carkacioglu, T. Can, O. Konu, V. Atalay, R. Cetin-Atalay, "Expression Pattern Analysis of Housekeeping Genes Across Large Number of Microarray Experiments", __5th European Conference on Computational Biology (ECCB)__, Eliat, Israel, September 10-13, 2006.
  * O.S. Sarac, V. Atalay, R. Cetin-Atalay, “HMM-based subsequence feature map for Protein Classification and Remote Homology Detection”, __14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2006)__, Forteleza, Brazil, August 6-10, 2006.

===== 2005 =====
  * V. Atalay, R. Cetin-Atalay, “Implicit Motif Distribution based Hybrid Computational Kernel for Sequence Classification”, __Bioinformatics Journal__, Oxford University Press, vol.21, No.8, pp.1429-1436, 2005. 
  * O. Dalay and V. Atalay, “Interactive classification of satellite image content based on query by example”, __ISPRS Spatial Data Mining Workshop__, Ankara, Turkey, 24-25 November, 2005.
  * S. Genc and V. Atalay, “ITouch: Vision-based Intelligent Touch Screen in a Distributed Environment”,  doctoral spotlight paper at __Seventh International Conference on Multimodal Interfaces (ICMI)__, Trento, Italy, October 4-6, 2005.

===== 2004 =====
  * M. Musa, D. de Ridder, R. Duin and V. Atalay, “Almost Autonomous Training of Mixtures of Principal Component Analyzers”, __Pattern Recognition Letters__, vol.25, No.9, pp.1085-1095, 2004. 
  * R. Hassanpour and V. Atalay, “Camera auto-calibration using a sequence of 2D images with small rotations”, __Pattern Recognition Letters__, vol.25, No.9, pp.989-997, 2004. 
  * I.A. Erdem, M.E. Erdem,  V. Atalay, A.E. Çetin, “Vision-based Continuous Graffiti-like Text Entry System”, __Optical Engineering__, vol.43, pp.553-558, 2004. 
  * R. Hassanpour and V. Atalay, “Delaunay Triangulation based 3D human face modeling from uncalibrated images”, __The First IEEE Workshop on Face Processing in Video__, Washington, D.C., USA, June 28, 2004.   
  * A. Teke and V. Atalay, “Texture Classification and Retrieval Using Random Neural Network Model”, __IEEE 6th Southwest Symposium on Image Analysis and Interpretation__, Lake Tahoe, Nevada, USA, March 28-30, 2004, IEEE Press, pp.109-113.

===== 2003 =====

  * A.Y. Mulayim, Y. Ulas,  V. Atalay, “Silhouette-based 3D Model Reconstruction from Multiple Images”, __IEEE Trans. On Systems, Man, and Cybernetics-Part B__, Special Issue on 3D Image Analysis and Modeling, Vol.33, No.4, pp.582-591, 2003.  
  * U. Yilmaz, A.Y. Mulayim, V. Atalay, “An Image based Inexpensive 3D Scanner”, __Int. Journal of Image and Graphics__, Special Issue on Virtual Reality and Virtual Environment, World Scientific, Vol.3, No.2, pp.235-264, 2003.  
  * C. Guray, N. Celebi, V. Atalay, A.Gunhan, “Ore-Age: An Hybrid system for Assisting and Teaching Mining Method Selection”, __Expert Systems with Applications Journal__, Pergamon-Elsevier Science, Vol.24, pp.261-271, 2003. 
  * M. Ozarar, V. Atalay, R. Cetin-Atalay, “Prediction of protein subcellular localization based on primary sequence data”, __18th International Symposium on Computer and Information Sciences (ISCIS XVII)__, Antalya, Turkey, 3-5 November, 2003, LNCS 2869, pp.611-618, Springer.
  * M.Musa, R.Duin, D. deRidder, V.Atalay, “Texture Segmentation Using the Mixtures of Principal Component Analyzers”,  __18th International Symposium on Computer and Information Sciences (ISCIS XVII)__, Antalya, Turkey,  3-5 November, 2003, LNCS 2869, pp.505-512, Springer.
  * M.E. Erdem, I.A. Erdem, V. Atalay, “Image based extraction of material reflectance properties of a 3D rigid object”, __Eurographics 2003 Annual Conference of the European Association for Computer Graphics__, Granada, Spain, 1-6 September 2003.
  * I.S. Sen, V. Atalay, “Occlusion culling for image based rendering with warping”, __Eurographics 2003 Annual Conference of the European Association for Computer Graphics__, Granada, Spain, 1-6 September 2003.
  * G.K. Akinci, S.U. Korkmaz, V. Atalay, “A character recognizer for Turkish language”, __7th Int. Conf. on Document Analysis and Recognition__, Edinburgh, Scotland, 3-6 August 2003.
  * A. Erdem, E. Erdem, V. Atalay, E. Cetin, “Computer vision based unistroke keyboard system and mouse for the handicapped”, __Int. Conf. on Multimedia and Expo-ICME 03__, Baltimore, Maryland, USA, 6-9 July 2003.

===== 2002 =====

  * S. Baskan, M.M. Bulut and V. Atalay, “Projection based Method for Segmentation of Human Faces and its Evaluation”,  //Pattern Recognition Letters//, Vol.23, No.14, pp.1623-1629, Elsevier Science, December 2002. 
  * P. Duygulu and V. Atalay, “A Hierarchical Representation of Form Documents for Identification and  Retrieval”, //Int. Journal of Document Analysis and Recognition//, Vol.5, No.1, pp.17-27, Elsevier Science, 2002. 
  * R. Hassanpour and V. Atalay, “Head Modeling with Camera Auto-calibration and Deformation”, //7th Int. Fall Workshop on Vision, Modeling and Visualization-VMV 2002//, Erlangen, Germany, 20-22 November 2002.
  * B. Otlu, R. Hassanpour, V. Atalay, “Consistency of projective reconstructions from an image pair”, //9th International Workshop on Systems, Signals and Image Processing//, Manchester Town Hall, UK, 7-8 November 2002.
  * A. Erdem, E. Erdem, V. Atalay, E. Cetin, “Vision based gesture-based text entry” demonstration at the //6th Int. Symposium on Wearable Computers//, Seattle, Washington, USA, October 7-10, 2002.
  * M. Yaman, V. Atalay, M. Turker, O.N. Gerek, A.E. Cetin, “Texture Segmentation by Using Adaptive Polyphase Subband Decomposition”, //17th International Symposium on Computer and Information Sciences (ISCIS XVII)//, Orlando, Florida, USA, 28-30 October, 2002.
  * K.Balci and V.Atalay, “PCA for Gender Estimation: Which Eigenvectors Contribute?”, //16th Int. Conference on Pattern Recognition//, Quebec City, Canada, August 11-15, 2002, IEEE Press, Vol.3, 363-366. 
  * U.Yilmaz, A.Mulayim, and V.Atalay, “Reconstruction of Three Dimensional Models from Real Images”, //3D Data Processing, Visualization, Transmission (3DPVT)//, Padova, Italy, June 19-21, 2002, IEEE press, eds. G.M.Cortelazzo, C.Guerra, pp.554-557.

===== 2001 =====
  * G. Ongun, U. Halıcı, K. Leblebicioğlu, V. Atalay, S. Beksaç, M. Beksaç, “Automated Contour Detection in Blood Cell Images by an Efficient Snake Algorithm”, //Nonlinear Analysis//, Vol.47, pp.5839-5847, Pergamon-Elsevier Science, 2001.
  * Ö.F. Özer, O. Özün, C.Ö. Tüzel, V. Atalay, A.E. Çetin, “Vision-based Single-stroke Character Recognition for Wearable Computing”, //IEEE Intelligent Systems//, Vol.16, pp.33-37, 2001. 
  * A.Y. Mulayim and V. Atalay, “Stereo correction on the silhouette-based 3D model reconstruction from multiple images", //SPIE's 13th International Symposium on Three-Dimensional Image Capture and Applications IV//, 24-25 January 2001, Proceedings of SPIE Vol. 4298.
  * S. Baskan, M.M. Bulut, V. Atalay, “Segmentation of facial features using gradient-based approach", //SPIE's 13th International Symposium on Machine Vision Applications in Industrial Inspection IX//, 22-23 January 2001, Proceedings of SPIE Vol. 4301.
 
===== Selected Publications prior to 2001 =====

  * A.Y. Mülayim, V. Atalay, O. Özün, F. Schmitt, “On the Silhouette Based 3D Reconstruction and Initial Bounding Cube Estimation", //5th Int. Fall Workshop on Vision, Modeling and isualization-VMV 2000//, Max-Planck-Institut für Informatik, Saarbrucken, Germany, 22-24 November 2000.
   * N. Dicle and V. Atalay, “Image matching using singular value decompositionand Godel coding scheme”, //SPIE's 12th International Symposium on Electronic Imaging-Image and Video Communications and Processing//, 26-28 January, Proceedings of SPIE Vol. 3974, 2000.
   * O.N. Gerek , A.E. Cetin , A. Tewfik, and V. Atalay, “Subband Domain Coding of Binary Textual Images for Document Archiving”, //IEEE Transactions on Image Processing//, Vol.8, No.10, pp.1438-1446, October 1999.
  * E. Oztop, A.Y. Mulayim,  V. Atalay, and F. Yarman-Vural,  “Repulsive Attractive Network for Baseline Extraction on Document Images”,  //Signal  Processing//, Vol.75, No.1, pp.1-10, 1999. 
  * Sinan Beksac, Aydan J. Erkmen, Sezer Aksel, Ugur Halici, Kemal Leblebicioglu, Meral Beksac, Volkan Atalay, Lakhmi C. Jain,  //Intelligent diagnostic systems in maternal and fetal medicine//, pp.137-199,  in Soft-Computing in Human-Related Sciences, editors: Jain, L. C., Kandel, Abraham, Teodorescu, Horia-Nicolai, CRC press, Singapore, 1999.
  * A.Y. Mulayim, Y. Yener, F. Schmitt, and V. Atalay, “Rotation Axis Extraction of a Turn Table Viewed by a Fixed Camera”, Workshop on Vision, Modelling, and Visualization - VMV'99, Erlangen, Germany, November 17-19, 1999.
   * S. Genc, and V. Atalay, “Texture Extraction from Photographs and Rendering with Dynamic Texture Mapping”, //International Conference on Image Analysis and Processing (ICIAP99)//, Venice, Italy, September 27-29, 1999. 
  * V. Atalay, and E. Arslan, ”An SGML Based Viewer for Form Documents”, //Fouth International Conference on Document Analysis and Recognition//, Bangalore, India, September 20-22, 1999.
   * V. Atalay, and U. Yilmaz,  “A Matching Algorithm Based on Linear Features”, //Pattern Recognition Letters//, Vol.19, No.9, pp.857-867, Elsevier Science,1998.
  * M. Goktepe, V. Atalay, N. Yalabik,  and C. Yalabik, “Unsupervised Texture Based Image Segmentation by Simulated Annealing with Markov Random Field and Potts Models”, Proceedings of the //Fourteenth International Conference on Pattern Recognition (ICPR)//, Brisbane, Australia, 16-20 August, pp.820-822, IEEE Computer Society Press, 1998.
  * P. Duygulu, V. Atalay, and E. Dincel, “A Heuristic Algorithm for Hierarchical Representation of Form Documents”, Proceedings of the //Fourteenth International Conference on Pattern Recognition (ICPR)//, Brisbane, Australia, 16-20 August, pp.929-931, IEEE Computer Society Press, 1998.
  * M. Borchani, V. Atalay, and G. Stamon, “Classification d'Images par des Attributs de Texture", //Colloque de Recherche Doctorale Automatique, Genie Informatique et Image//, Angers, France, December, 1997. 
  * M. Borchani, V. Atalay, and G. Stamon, “Classification d'Images par des Statistiques d'Ordres Differents", //Cinquiemes Rencontres de la  Societe Francophone de Classification//, Lyon, France, September 1997. 
  * E. Oztop, A.Y. Mulayim, F.T. Yarman-Vural, and V. Atalay, “Baseline Extraction on Document Images by Repulsive/ Attractive Network”, //IEEE Int. Conf. on Acustics, Signal, and Speech Processing (ICASSP)//, Munich, Germany, April 1997.   
  * M. Goktepe, V. Atalay and N. Yalabik, "Unsupervised Segmentation of Gray Level Markov Model Textures with Hierarchical Self Organizing Maps", Proceedings of the //Thirteenth International Conference on Pattern Recognition (ICPR)//, Wien, Austria, August 25-29 , vol.4, pp.90-94, IEEE Computer Society Press,1996.
  * M. Koksal, H. Vural, and V. Atalay, “The Investigation of Hydrodynamics of a 2-D Fluidized Bed with Moving Double Plate Distributors Using Image Analysis”, //5th World Congress of Chemical Engineers//, San Diego, USA, July 1996.
   * V. Atalay, and E. Gelenbe, “Parallel algorithm for color texture generation using the random neural network model”, //International Journal of Pattern Recognition and Artificial Intelligence//, Vol.6, No.2-3, pp. 437-446, World Scientific, 1992. 
  * V. Atalay, E. Gelenbe, and N. Yalabik, “Texture generation with the random neural network model”, //International Journal of Pattern Recognition and Artificial Intelligence//, Vol-6, No.1, pp. 131-142, World Scientific,1992. 
  * V. Atalay, E. Gelenbe, and N. Yalabik, “Texture generation with the random neural network model", Proc. //International Conference on Artificial Neural Networks (ICANN 91)//, Helsinki, Finland, July 1991. 
  * V. Atalay, and E. Gelenbe, “Parallel algorithm for color texture generation using the random neural network model", Proc. //International Colloqium on Parallel Image Processing//, Paris, France, June 1991. 
  * V. Atalay, M. Ozcilingir, N. Yalabik, “Computer recognition of Ottoman text", Proc. //International Symposium on Computer and Information Sciences-V (ISCIS)//, Capadoccia, Turkey, November 1990.