Publications

Journal articles

  • Karaçalı, B., “Hierarchical motif vectors for prediction of functional sites in amino acid sequences using quasi-supervised learning,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press
  • Karaçalı, B., “Quasi-supervised learning for biomedical data analysis,” Pattern Recognition, 43(10), 3674-3682 (2010).
  • Gormley, M., Dampier, W., Ertel, A., Karaçalı, B., Tözeren, A., “Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets,” BMC Bioinformatics, 8(415) (2007).
  • Karaçalı, B., Vamvakidou, A.P., Tözeren, A., “Automated recognition of cell phenotypes in histology images based on membrane- and nuclei-targeting biomarkers,” BMC Medical Imaging, 7(7) (2007).
  • Karaçalı, B., Tözeren, A., “Automated detection of regions of interest for tissue microarray experiments: an image texture analysis,” BMC Medical Imaging, 7(2) (2007).
  • Karaçalı, B., “Information theoretic deformable registration using local image information,” International Journal of Computer Vision, (72)3, 219-237 (2007).
  • Xue, Z., Shen, D., Karaçalı, B., Stern, J., Rottenberg D., Davatzikos, C., “Simulating Deformations of MR Brain Images for Validation of Atlas-based Segmentation and Registration Algorithms”, NeuroImage, 33, 855-866 (2006).
  • Karaçalı, B., Davatzikos, C., “Simulation of tissue atrophy using a topology preserving transformation model,” IEEE Transactions on Medical Imaging, 25(5), 649-652 (2006).
  • Karaçalı, B., Davatzikos, C., “Estimating topology preserving and smooth displacement fields,” IEEE Transactions on Medical Imaging, 23(7), 868-880 (2004).
  • Karaçalı, B., Snyder, W., “Noise reduction in surface reconstruction from a given gradient field,” International Journal of Computer Vision, 60(1), 25-44 (2004)
  • Lao, Z., Shen, D., Karaçalı, B., Resnick, S. M., Davatzikos, C., “Morphological classification of brains via high dimensional shape transformations and machine learning methods,” NeuroImage, 21(1), 46-57 (2003).
  • Karaçalı, B., Ramanath, R., Snyder, W., “A comparative analysis of structural risk minimization by support vector machines and nearest neighbor rule,” Pattern Recognition Letters, 25(1), 63-71 (2004).
  • Karaçalı, B., Snyder, W., “Reconstructing discontinuous surfaces from a given gradient field using partial integrability,” Computer Vision and Image Understanding, 92(1), 78-111 (2003).
  • Karaçalı, B., Krim, H., “Fast minimization of structural risk by nearest neighbor method,” IEEE Trans. on Neural Networks, 14(1), 127-137 (2003).

Conference proceedings

  • Karaçalı, B., “Analytical and Predictive Quasi-Supervised Learning for Cancer Recognition in Digital Cytology,” SIU 2012. 
  • Köktürk, B., Karaçalı, B., “Automated Labeling of Electroencephalography Data Using Quasisupervised Learning,” SIU 2012.
  • Karaçalı, B., “Hierarchical Motif Vectors for Amino Acid Sequence Alignment,” Proceedings of the 9th IASTED International Conference on Biomedical Engineering, Innsbruck, 2012. 
  • Karaçalı, B., “Identification and Evaluation of Landmarks For Deformable Alignment of MultiModality Medical Images,” SIU 2011.
  • Karaçalı, B., “Deformation Field Interpolation Using Rotational Landmarks,” BİYOMUT 2010
  • Önder, D., Karaçalı, B., “Automated Classification of Cancerous Textures in Histology Images Using Quasi-supervised Learning Algorithm,” BİYOMUT 2010
  • Doğan, T., Karaçalı, B., “Evolutionary Relationships Between Gene Sequences via Nonlinear Embedding,” BİYOMUT 2010
  • Önder, D., Karaçalı, B., “Automated clustering of histology slide texture using co-occurrence based grayscale image features and manifold learning,” BİYOMUT 2009
  • Makrogiannis, S., Verma, R., Karaçalı, B., Davatzikos, C., “A joint transformation and residual image descriptor for morphometric image analysis using an equivalence class formulation,” Proceedings of the 2006 Conference on Computer Vision and Pattern Recognition Workshop (CVPRW’06), New York, 74-81, IEEE Publications, Piscataway 2006.
  • Lao, Z., Shen, D., Jawad, A., Karaçalı, B., Liu, D., Melhem, E., Bryan, N., Davatzikos, C., “Automated Segmentation of White Matter Lesions in 3D Brain MRImages, using Multivariate Pattern Classification,” Proc. 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Arlington, 307-310, IEEE Publications, Piscataway 2006.
  • Xue, Z., Shen, D., Karaçalı, B., Davatzikos, C., “Statistical representation and simulation of high-dimensional deformations: Application to synthesizing brain deformations,” Proc. MICCAI 2005, Palm Springs, J. Duncan and G. Gerig (Eds.), LNCS, Vol. 3750, 500-508, Springer, Berlin, 2005.
  • Karaçalı, B., “Fully elastic multi-modality image registration using mutual information,” Proc. 2nd IEEE International Symposium on Biomedical Imaging, Arlington, 1455-1458, IEEE Publications, Piscataway, 2004.
  • Davatzikos, C., Shen, D., Lao, Z., Xue, Z., Karaçalı, B., “Morphological classification of medical images using nonlinear support vector machines”, Proc. 2nd IEEE International Symposium on Biomedical Imaging (invited paper), Arlington, 587-590, IEEE Publications, Piscataway, 2004.
  • Karaçalı, B., Davatzikos, C., “Topology preservation and regularity in estimated deformation fields,” Proc. 18th Information Processing in Medical Imaging, Lecture Notes in Computer Science, Vol. 2732, Ambleside, 426,437, Springer, Berlin, 2003.
  • Karaçalı, B., Snyder, W., “Partial integrability in surface reconstruction from a given gradient field,” Proc. 9th International Conference on Image Processing, Rochester, Vol. 2, 525-528, IEEE Publications, Piscataway, 2002.
  • Karaçalı, B., Snyder, W., “Automatic target detection using multispectral imaging,” Proc. 31st Applied Image Pattern Recognition Workshop, Washington D.C., 55-59, IEEE Publications, Piscataway, 2002.
  • Karaçalı, B., Krim, H.,, Schick, I. C., “Wavelet-based methods in Global Positioning System signal tracking,” Proc. SPIE, Orlando, Vol. 4056, 127-136, SPIE Publications, Bellingham, 2000.