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Education

• D.Sc., Systems Research Institute, Polish Academy of Sciences, 1999
• M.B.A., University of Toledo, Ohio, 1994
• Ph.D., Computer Science, AGH University of Science and Technology, Krakow, 1984
• M.S., Electrical Engineering, AGH University of Science and Technology, Krakow, 1973

Publications

• Allison Gehrke, Shaojun Sun, Lukasz Kurgan, Natalie Ahn, Katheryn Resing, Karen Kafadar and Krzysztof Cios. 2008. Improved machine learning method for analysis of gas phase chemistry of peptides. BMC Bioinformatics 9:515, DOI:10.1186/1471-2105-9-515
• Kurgan LA, Cios KJ, Zhang H, Zhang T, Chen K, Shen S, Ruan J, 2008. Sequence-based Methonds for Real Value Predictions of Protein Structure. Current Bioinformatics 3(3):183-196.
• C-Y. Yen, K.J. Cios. 2008. Image recognition system based on novel measures of image similarity and cluster validity. Neurocomputing 72, pp. 401-412, DOI:10.1016/j.neucom.2007.12.018.
• C.D. Nguyen, K.J. Cios. 2008. GAKREM: A novel hybrid clustering algorithm. Information Sciences 178, pp. 4205-4227, DOI information:10.1016/ j.ins.2008.07.016.
• Kurgan L., Cios, K.J., Chen K. 2008. SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences. BMC Bioinformatics 2008, 9:226 doi:10.1186/1471-2105-9-226
• Staley K., Swiercz, W., Cios, K.J. 2008. Validating Models Of Epilepsy. In: Computational Neuroscience in Epilepsy(Computational Neuroscience), Soltesz I., Staley K. (eds.), Academic Press.
• Nguyen C., Mannino M., Gardiner K. and Cios K. 2008. ClusFCM: Algorithm for Prediction of Protein Functions Using Homologies and Protein Interactions. Journal of Bioinformatics and Computational Biology 6(1):203-222.
• Lovelace J. and Cios K.J. 2008. A Very Simple Spiking Neuron Model that Allows for Efficient Modeling of Complex Systems. Neural Computation, 20(1):65-90
• Nguyen C., Gardiner K. and Cios K.J. 2007. A Hidden Markov Model for Prediction of Protein Interfaces. Journal of Bioinformatics and Computational Biology, 5(3):739-753
• Swiercz W., Cios K., Hellier J., Yee A., Staley K. 2007 Effects of Synaptic Depression and Recovery on Synchronous Network Activity. J Clin Neurophysiol, 24, 165-174
• Homaeian L., Kurgan A.K., Ruan J., Cios K.J. and Chen K. 2007. Prediction of Protein Secondary Structure Content for the Twilight Zone Sequences. Proteins, DOI: 10.1002/prot.21527
• Tripet B., Jayadev M.R., Blow D., Nguyen C., Hodges R.S. and Cios K.J. 2007. Proteomic Data Mining Using Predicted Peptide Chromatographic Retention Times. International Journal of Bioinformatics Research and Applications, 3(4):431-445
• Schuyler R.,White A., Staley K. and Cios K. 2007 Epileptic seizure detection. IEEE Engineering In Medicine And Biology Magazine, 26(2), 86-93
• Nguyen C., Thaicharoen S., Lacroix T., Gardiner K. and Cios K. 2007. A Comprehensive Human Chromosome 21 Database. IEEE Engineering In Medicine And Biology Magazine, 26(2), 86-93
• Sun S., Meyer-Arendt K., Eichelberger B., Brown R., Yen CY, Old W, Pierce K, Cios KJ, Ahn N and Resing K. 2007 Improved Validation of Peptide MS/MS Assignments Using Spectral Intensity Prediction. Molecular & Cellular Proteomics, 6(1):1-17
• Balasubramanian N., Wilson B.J. and Cios K.J. 2006. Innovative Methods of Teaching Science and Engineering in Middle Schools. Journal of Systemics, Cybernetics and Informatics, 4(6)
• Siebert J., Newell K., Villa-Lobos E. and Cios K.J. 2006 A rich analytical environment for flow cytometry experimental results. Int. J. Bioinformatics Research and Applications, 2(1), 52-62
• Yen CY., Russell S., Mendoza A., Meyer-Arendt K., Sun S., Cios K.J., Ahn N. G. and Resing K. 2006 Improving Sensitivity in Shotgun Using a Peptide-Centric Database with Reduced Complexity: Protease Cleavage and SCX Elution Rules from Data Mining of MS/MS Spectra. Analytical Chemistry, 78(4):1071-1084
• Swiercz W., Cios K.J., Staley K., Kurgan L., Accurso F. and Sagel S. 2006 New Synaptic Plasticity Rule For Networks Of Spiking Neurons, IEEE Transactions on Neural Networks, 17(1):94-105
• Kurgan L., Cios K.J. and Scott D. 2006. Highly Scalable and Robust Rule Learner: Performance Evaluation and Comparison. IEEE Transactions Systems Man And Cybernetics, part B, 36(1):32-53
• Nikolaienko A., Nguyen C., Crinc L., Cios K.J. and Gardiner K. 2005 Human chromosome 21/Down syndrome gene function and pathway database. Gene, 364: 90-98
• Hamady M., Cheung T., Resing K., Cios K.J. and Knight R. 2005 Key Challenges in Proteomics and Proteoinformatics. IEEE Engineering in Medicine and Biology Magazine, 24(3):34-40
• Yen C., Helmke S.N., Cios K.J., Perryman M.B. and Duncan M. 2005 Quantitative Analysis of Proteomics Using Data Mining. IEEE Engineering in Medicine and Biology Magazine, 24(3):67-72
• Dvorkin  D.,  Fadok V. and Cios K.J. 2005 SiMCAL 1 algorithm for analysis of gene expression data related to the phosphatidylserine receptor. Artificial Intelligence in Medicine, (35):49-60
• Ruan  J.,  Wang K., Yang J., Kurgan L. and Cios K.J. 2005  Highly accurate and consistent method prediction of helix and strand content from primary protein sequences. Artificial Intelligence in Medicine, (35):19-35
• Cios K.J., Mamitshuka H., Nagashima T. and Tadeusiewicz R. 2005, Computational intelligence in solving bioinformatics problems. editorial paper, Artificial Intelligence in Medicine, (35):1-8
• Cios K.J., Swiercz W. and Jackson W. 2004  Networks of Spiking Neurons in Modeling and problem Solving. Neurocomputing , 61(2004): 99-119
• Helmke S.M., Yen C., Cios K.J., Nunley K., Bristow M.R., Duncan M.W. and Perryman M.B., 2004 Simultaneous Quantification of Human Cardiac a- and b-Myosin Heavy Chain Proteins by MALDI-TOF Mass Spectometry. Analytical Biochemistry, 76(6), 1683-1689
• Kurgan, L. and Cios, K.J. 2004. CAIM Discretization Algorithm. IEEE Tr. on Knowledge and Data Engineering, 16(2), 145-153
• Cios K.J and Kurgan L.A. 2004. CLIP4: Hybrid inductive machine learning algorithm that generates inequality rules, Information Sciences, 163(1-3), 37-83

Research Interests

• Biomedical informatics, data mining and learning algorithms

Research Lab

• Data Mining and Biomedical Informatics