Bilge Karaçalı’nın Yayınları

Journal Articles

Olcay, Orkan B; ç, Bilge Kara

Evaluation of synchronization measures for capturing the lagged synchronization between EEG channels: A cognitive task recognition approach Journal Article

Computers in Biology and Medicine, pp. 103441, 2019.

BibTeX

Köktürk, Başak Esin; Karacalı, Bilge

Annealing-based model-free expectation maximisation for multi-colour flow cytometry data clustering Journal Article

International Journal of Data Mining and Bioinformatics, 2016, ISSN: 1748-5673.

Abstract | Links | BibTeX

Doty, Richard L; Tourbier, Isabelle A; Pham, Dzung L; Cuzzocreo, Jennifer L; Udupa, Jayaram K; Karacali, Bilge; Beals, Evan; Fabius, Laura; Leon-Sarmiento, Fidias E; Moonis, Gul; Kim, Taehoon; Mihama, Toru; Geckle, Rena J; Yousem, David M

Taste dysfunction in multiple sclerosis Journal Article

Journal of Neurology, 2016, ISSN: 14321459.

Abstract | Links | BibTeX

Karacalı, Bilge

An efficient algorithm for large-scale quasi-supervised learning Journal Article

Pattern Analysis and Applications, 2016, ISSN: 14337541.

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Bozkurt, Bariş; Karacali, Bilge

A computational analysis of Turkish makam music based on a probabilistic characterization of segmented phrases Journal Article

Journal of Mathematics and Music, 2015, ISSN: 17459745.

Abstract | Links | BibTeX

Onder, Devrim; Sarioglu, Sulen; Karacali, Bilge

Automated labeling of cancer textures in larynx histopathology slides using Quasi-supervised learning Journal Article

Analytical and Quantitative Cytology and Histology, 2014, ISSN: 08846812.

Abstract | BibTeX

Bozkurt, Barış; Karaosmanoğlu, Kemal M; Karacalı, Bilge; Ünal, Erdem

Usul and Makam driven automatic melodic segmentation for Turkish music Journal Article

Journal of New Music Research, 2014, ISSN: 17445027.

Abstract | Links | BibTeX

Bansal, Mukesh; Yang, Jichen; Karan, Charles; Menden, Michael P; Costello, James C; Tang, Hao; Xiao, Guanghua; Li, Yajuan; Allen, Jeffrey; Zhong, Rui; Chen, Beibei; Kim, Minsoo; Wang, Tao; Heiser, Laura M; Realubit, Ronald; Mattioli, Michela; Alvarez, Mariano J; Shen, Yao; Gallahan, Daniel; Singer, Dinah; Saez-Rodriguez, Julio; Xie, Yang; Stolovitzky, Gustavo; Califano, Andrea; Abbuehl, Jean Paul; Altman, Russ B; Balcome, Shawn; Bell, Ana; Bender, Andreas; Berger, Bonnie; Bernard, Jonathan; Bieberich, Andrew A; Borboudakis, Giorgos; Chan, Christina; Chen, Ting Huei; Choi, Jaejoon; Coelho, Luis Pedro; Creighton, Chad J; Dampier, Will; Davisson, Jo V; Deshpande, Raamesh; Diao, Lixia; Camillo, Barbara Di; Dundar, Murat; Ertel, Adam; Goswami, Chirayu P; Gottlieb, Assaf; Gould, Michael N; Goya, Jonathan; Grau, Michael; Gray, Joe W; Hejase, Hussein A; Hoffmann, Michael F; Homicsko, Krisztian; Homilius, Max; Hwang, Woochang; Ijzerman, Adriaan P; Kallioniemi, Olli; Karacali, Bilge; Kaski, Samuel; Kim, Junho; Krishnan, Arjun; Lee, Junehawk; Lee, Young Suk; Lenselink, Eelke B; Lenz, Peter; Li, Lang; Li, Jun; Liang, Han; Mpindi, John Patrick; Myers, Chad L; Newton, Michael A; Overington, John P; Parkkinen, Juuso; Prill, Robert J; Peng, Jian; Pestell, Richard; Qiu, Peng; Rajwa, Bartek; Sadanandam, Anguraj; Sambo, Francesco; Sridhar, Arvind; Sun, Wei; Toffolo, Gianna M; Tozeren, Aydin; Troyanskaya, Olga G; Tsamardinos, Ioannis; Vlijmen, Herman Van W T; Wang, Wen; Wegner, Joerg K; Wennerberg, Krister; Westen, Gerard Van J P; Xia, Tian; Yang, Yang; Yao, Victoria; Yuan, Yuan; Zeng, Haoyang; Zhang, Shihua; Zhao, Junfei; Zhou, Jian

A community computational challenge to predict the activity of pairs of compounds Journal Article

Nature Biotechnology, 2014, ISSN: 15461696.

Abstract | Links | BibTeX

Costello, James C; Heiser, Laura M; Georgii, Elisabeth; Gönen, Mehmet; Menden, Michael P; Wang, Nicholas J; Bansal, Mukesh; Ammad-Ud-Din, Muhammad; Hintsanen, Petteri; Khan, Suleiman A; Mpindi, John Patrick; Kallioniemi, Olli; Honkela, Antti; Aittokallio, Tero; Wennerberg, Krister; Collins, James J; Gallahan, Dan; Singer, Dinah; Saez-Rodriguez, Julio; Kaski, Samuel; Gray, Joe W; Stolovitzky, Gustavo; Abbuehl, Jean Paul; Allen, Jeffrey; Altman, Russ B; Balcome, Shawn; Battle, Alexis; Bender, Andreas; Berger, Bonnie; Bernard, Jonathan; Bhattacharjee, Madhuchhanda; Bhuvaneshwar, Krithika; Bieberich, Andrew A; Boehm, Fred; Califano, Andrea; Chan, Christina; Chen, Beibei; Chen, Ting Huei; Choi, Jaejoon; Coelho, Luis Pedro; Cokelaer, Thomas; Collins, James C; Creighton, Chad J; Cui, Jike; Dampier, Will; Davisson, Jo V; Baets, Bernard De; Deshpande, Raamesh; DiCamillo, Barbara; Dundar, Murat; Duren, Zhana; Ertel, Adam; Fan, Haoyang; Fang, Hongbin; Gauba, Robinder; Gottlieb, Assaf; Grau, Michael; Gusev, Yuriy; Ha, Min Jin; Han, Leng; Harris, Michael; Henderson, Nicholas; Hejase, Hussein A; Homicsko, Krisztian; Hou, Jack P; Hwang, Woochang; IJzerman, Adriaan P; Karacali, Bilge; Keles, Sunduz; Kendziorski, Christina; Kim, Junho; Kim, Min; Kim, Youngchul; Knowles, David A; Koller, Daphne; Lee, Junehawk; Lee, Jae K; Lenselink, Eelke B; Li, Biao; Li, Bin; Li, Jun; Liang, Han; Ma, Jian; Madhavan, Subha; Mooney, Sean; Myers, Chad L; Newton, Michael A; Overington, John P; Pal, Ranadip; Peng, Jian; Pestell, Richard; Prill, Robert J; Qiu, Peng; Rajwa, Bartek; Sadanandam, Anguraj; Sambo, Francesco; Shin, Hyunjin; Song, Jiuzhou; Song, Lei; Sridhar, Arvind; Stock, Michiel; Sun, Wei; Ta, Tram; Tadesse, Mahlet; Tan, Ming; Tang, Hao; Theodorescu, Dan; Toffolo, Gianna Maria; Tozeren, Aydin; Trepicchio, William; Varoquaux, Nelle; Vert, Jean Philippe; Waegeman, Willem; Walter, Thomas; Wan, Qian; Wang, Difei; Wang, Wen; Wang, Yong; Wang, Zhishi; Wegner, Joerg K; Wu, Tongtong; Xia, Tian; Xiao, Guanghua; Xie, Yang; Xu, Yanxun; Yang, Jichen; Yuan, Yuan; Zhang, Shihua; Zhang, Xiang Sun; Zhao, Junfei; Zuo, Chandler; Vlijmen, Herman Van W T; Westen, Gerard Van J P

A community effort to assess and improve drug sensitivity prediction algorithms Journal Article

Nature Biotechnology, 2014, ISSN: 15461696.

Abstract | Links | BibTeX

Doǧan, Tunca; Karacali, Bilge

Automatic Identification of Highly Conserved Family Regions and Relationships in Genome Wide Datasets Including Remote Protein Sequences Journal Article

PLoS ONE, 2013, ISSN: 19326203.

Abstract | Links | BibTeX

Unlu, Mehtat; Cetinayak, Hasan Oguz; Onder, Devrim; Ecevit, Cenk; Akman, Fadime; Ikiz, Ahmet Omer; Ada, Emel; Karacali, Bilge; Sarioglu, Sulen

The prognostic value of tumor-stroma proportion in laryngeal squamous cell carcinoma Journal Article

Turkish Journal of Pathology, 2013, ISSN: 1018-5615.

Abstract | Links | BibTeX

Ünlü, Mehtat; cetinayak, Hasan Oǧuz; Önder, Devrim; Ecevit, Cenk; Akman, Fadime; Ikiz, Ahmet Ömer; Ada, Emel; Karacali, Bilge; Sarioǧlu, Sülen

Laringeal skuamöz hücreli karsinomlarda tümör-stroma oranidotlessnidotlessn prognostik deǧeri Journal Article

Turk Patoloji Dergisi/Turkish Journal of Pathology, 2013, ISSN: 10185615.

Abstract | Links | BibTeX

Karacali, Bilge

Hierarchical motif vectors for prediction of functional sites in amino acid sequences using quasi-supervised learning Journal Article

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012, ISSN: 15455963.

Abstract | Links | BibTeX

Karacali, Bilge

Quasi-supervised learning for biomedical data analysis Journal Article

Pattern Recognition, 2010, ISSN: 00313203.

Abstract | Links | BibTeX

Karacali, Bilge; Tözeren, Aydin

Automated detection of regions of interest for tissue microarray experiments: An image texture analysis Journal Article

BMC Medical Imaging, 2007, ISSN: 14712342.

Abstract | Links | BibTeX

Karacali, Bilge

Information theoretic deformable registration using local image information Journal Article

International Journal of Computer Vision, 2007, ISSN: 09205691.

Abstract | Links | BibTeX

Karacali, Bilge; Vamvakidou, Alexandra P; Tözeren, Aydin

Automated recognition of cell phenotypes in histology images based on membrane- and nuclei-targeting biomarkers. Journal Article

BMC medical imaging, 2007, ISSN: 14712342.

Abstract | Links | BibTeX

Gormley, Michael; Dampier, William; Ertel, Adam; Karacali, Bilge; Tozeren, Aydin

Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets Journal Article

BMC Bioinformatics, 2007, ISSN: 14712105.

Abstract | Links | BibTeX

Karacali, Bilge; Davatzikos, Christos

Simulation of tissue atrophy using a topology preserving transformation model Journal Article

IEEE Transactions on Medical Imaging, 2006, ISSN: 02780062.

Abstract | Links | BibTeX

Xue, Zhong; Shen, Dinggang; Karacali, Bilge; Stern, Joshua; Rottenberg, David; Davatzikos, Christos

Simulating deformations of MR brain images for validation of atlas-based segmentation and registration algorithms Journal Article

NeuroImage, 2006, ISSN: 10538119.

Abstract | Links | BibTeX

Karacali, Bilge; Davatzikos, Christos

Estimating topology preserving and smooth displacement fields Journal Article

IEEE Transactions on Medical Imaging, 2004, ISSN: 02780062.

Abstract | Links | BibTeX

Lao, Zhiqiang; Shen, Dinggang; Xue, Zhong; Karacali, Bilge; Resnick, Susan M; Davatzikos, Christos

Morphological classification of brains via high-dimensional shape transformations and machine learning methods Journal Article

NeuroImage, 2004, ISSN: 10538119.

Abstract | Links | BibTeX

Karacali, Bilge; Snyder, Wesley

Reconstructing discontinuous surfaces from a given gradient field using partial integrability Journal Article

Computer Vision and Image Understanding, 2003, ISSN: 10773142.

Abstract | Links | BibTeX

Karacali, Bilge; Krim, Hamid

Fast minimization of structural risk by nearest neighbor rule Journal Article

IEEE Transactions on Neural Networks, 2003, ISSN: 10459227.

Abstract | Links | BibTeX

Incollections

Karacalı, Bilge; Davatzikos, Christos

Topology Preservation and Regularity in Estimated Deformation Fields Incollection

2010.

Abstract | Links | BibTeX

Inproceedings

caǧdaş, Serhat; Karacali, Bilge

Novel techniques for model-free and fast computation of mutual information Inproceedings

26th IEEE Signal Processing and Communications Applications Conference, SIU 2018, 2018, ISBN: 9781538615010.

Links | BibTeX

Olcay, Bilal Orkan; Karacali, Bilge; Ozgoren, Murat; Guducu, Cagdas

Brain activity characterization by entropic clustering of EEG signals Inproceedings

2017.

Abstract | Links | BibTeX

Güzel, Başak Esin Köktürk; Karacalı, Bilge

Fisher's Linear Discriminant Analysis Based Prediction using Transient Features of Seismic Events in Coal Mines Inproceedings

Proceedings of the 2016 Federated Conference on Computer Science and Information Systems, 2016.

Links | BibTeX

Olcay, Orkan B; Ozgoren, Murat; Karacali, Bilge

Imaginary activity recognition using inter-channel time coherence profiles in EEG data Inproceedings

2016.

Abstract | Links | BibTeX

Köktürk, Başak Esin; Karacali, Bilge

Model-free expectation maximization for divisive hierarchical clustering of multicolor flow cytometry data Inproceedings

Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014, 2014, ISBN: 9781479956692.

Abstract | Links | BibTeX

Bozkurt, Baris; Karaosmanoglu, Kemal M; Karacali, Bilge; Unal, Erdem

Automatic melodic segmentation of Turkish makam music scores Inproceedings

2014.

Abstract | Links | BibTeX

Bozkurt, Baris; Karaosmanoglu, Kemal M; Karacali, Bilge; Unal, Erdem

Türk makam müziǧi notalari icin otomatik ezgi bölütleme Inproceedings

2014 22nd Signal Processing and Communications Applications Conference, SIU 2014 - Proceedings, 2014, ISBN: 9781479948741.

Abstract | Links | BibTeX

Bozkurt, Barış; Karaosmanoğlu, Kemal M; Karacalı, Bilge; Ünal, Erdem

Türk makam müziği notaları icin otomatik ezgi bölütleme Inproceedings

IEEE 22. Sinyal İşleme ve İletişim Uygulamaları Kurultayı (SIU), 2014, ISBN: 9781479948741.

Abstract | BibTeX

Doğan, Tunca; Karacalı, Bilge

2-D Thresholding of the Connectivity Map Following the Multiple Sequence Alignments of Diverse Datasets Inproceedings

2013.

Abstract | Links | BibTeX

Kokturk, Basak Esin; Karacali, Bilge

Automated labeling of electroencephalography data using quasi-supervised learning Inproceedings

2012.

Links | BibTeX

Karacalı, Bilge

Hierarchical Motif Vectors for Amino Acid Sequence Alignment Inproceedings

2012.

Links | BibTeX

Karacali, Bilge

Analytical and predictive quasi-supervised learning for cancer recognition in digital cytology Inproceedings

2012.

Links | BibTeX

Karacali, Bilge

Identification and evaluation of landmarks for deformable alignment of multi-modality medical images Inproceedings

2011.

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Onder, Devrim; Sarioglu, Sulen; Karacali, Bilge

Automated classification of cancerous textures in histology images using quasi-supervised learning algorithm Inproceedings

2010.

Abstract | Links | BibTeX

Karacali, Bilge

Deformation field interpolation using rotational landmarks Inproceedings

2010.

Links | BibTeX

Onder, Devrim; Karacali, Bilge

Automated clustering of histology slide texture using co-occurrence based grayscale image features and manifold learning Inproceedings

2009.

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Makrogiannis, Sokratis; Verma, Ragini; Karacali, Bilge; Davatzikos, Christos

A joint transformation and residual image descriptor for morphometric image analysis using an equivalence class formulation Inproceedings

Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2006, ISSN: 10636919.

Abstract | Links | BibTeX

Xue, Zhong; Shen, Dinggang; Karacali, Bilge; Davatzikos, Christos

Statistical representation and simulation of high-dimensional deformations: Application to synthesizing brain deformations Inproceedings

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2005, ISSN: 03029743.

Abstract | Links | BibTeX

Hamza, Ben A; Krim, Hamid; Karacali, Bilge

Structural risk minimization using nearest neighbor rule Inproceedings

Proceedings - IEEE International Conference on Multimedia and Expo, 2003, ISSN: 1945788X.

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Karacali, Bilge; Krim, Hamid A; Schick, Irvin C

textlesstitletextgreaterWavelet-based methods in Global Positioning System signal trackingtextless/titletextgreater Inproceedings

Wavelet Applications VII, 2003.

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Karacali, Bilge; Snyder, Wesley

Automatic target detection using multispectral imaging Inproceedings

Proceedings - Applied Imagery Pattern Recognition Workshop, 2002, ISSN: 21642516.

Abstract | Links | BibTeX