2008

  • X. Chen, M. Liu, and R. Ward, "Protein Function Assignment through Mining Cross-Species Protein-protein Interactions", PLoS ONE, 3(2): e1562, 2008.
  • X. Chen, G. Anantha, and X. Lin, "Improving Bayesian Network Structure Learning with Mutual Information-based Node Ordering in the K2 Algorithm", IEEE Transactions on Knowledge and Data Engineering, vol. 20(5): 628-640, 2008.
  • X. Chen, B. Han, J. Fang, and R. Haasl, "Large-scale protein-protein interaction prediction using novel kernel methods", International Journal of Data Mining and Bioinformatics, in press, 2008.
  • Aaron Smalter, Jun Huan, Gerald Lushington, Structure-based Pattern Mining For Chemical Compound Classification, to appear in Proceedings of the 6th Asia Pacific Bioinformatics Conference (APBC), 2008. page_white_acrobat
  • Chen. D.C.; Fang, J.W.; Yu, J.W. "Predicting Blood-Brain Barrier Penetration by Stochastic Discrimination". The International Conference on BioMedical Engineering and Informatics (BMEI2008). Accepted.
  • Li, Q.-S.; Cai, S.; Fang, J.W.; Borchardt, R.T; Kuczera, K.; Middaugh, C.R.; and Schowen, R.L. "Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolases. 2. The role of helix 18 stability". Biochemistry. Accepted.
  • Fang, J. W.; Dong Y.H.; Williams, T.D.; Lushington G.H. "Feature selection in validating mass spectrometry database search results". Journal of Bioinformatics and Computational Biology. 6(1), 2008, 223-240. page_go
  • Theerthama B.; L. Wang J.L.; Fang J.W.; and Lushington G.H. "Novel algorithms for the identification of biologically informative chemical diversity metrics". Current Computer-Aided Drug Design. Accepted.
  • Fang J.W.; Dong Y.H.; Salamat-miller N.; Middaugh C.R. "DB-PABP: a database of polyanion-binding proteins". Nucleic Acids Research. 36(Database-Issue): 303-306, 2008. page_go
  • Chen, X.W.; Han, B.; Fang, J.W.; Haasl, R.J. "A new kernel method for large-scale protein-protein interaction prediction". Int J Data Mining and Bioinformatics. Accepted.
  • Hu, C.; Fang, J.W.; Borchardt, R.T.; Schowen, R.L.; Kuczera, K. "Molecular dynamics simulations of domain motions of substrate-free S-Adenosyl-L-homocysteine hydrolase in solution". PROTEINS: Structure Function and Bioinformatics. 71(1), 131-143, 2008.
  • Jerzy W. Grzymala-Busse. "Mining incomplete data-A rough set approach". IFKT'2008 conference. (Submitted)
  • Piotr Blajdo, Jerzy W. Grzymala-Busse, Zdzislaw S. Hippe, Maksymilian Knap, Teresa Mroczek, Lukasz Piatek. "A comparison of six approaches to discretization-A rough set perspective". Accepted for the RSKT'2008 Conference, Chengdu, China, May 17-19, 2008.
  • Jerzy W. Grzymala-Busse, Zdzislaw S. Hippe, Teresa Mroczek, Adam Bucinski, Agnieszka Strepikowska and Andrzej Tutaj. "Prediction of severe brain damage outcome using two data mining methods". Accepted to the HSI'2008 conference, Krakow, Poland, May 25-27, 2008.
  • Jerzy W. Grzymala-Busse, Witold J. Grzymala-Busse, Zdzislaw S. Hippe, Wojciech Rzasa. "An improved comparison of three rough set approaches to missing attribute values". Submitted to the 16th Int Conference on Intelligent Information Systems. Zakopane, Poland, June 16-18, 2008.
  • Jerzy W. Grzymala-Busse and Witold J. Grzymala-Busse. "Improving quality of rule sets by increasing incompleteness of data sets". Submitted to the ICSOFT'2008 3rd Int Conference on Software and Data Technologies, Porto, Portugal, July 5-8, 2008.
  • Jerzy W. Grzymala-Busse, Edward Roj. "A rough set approach to developing an expert system for hop extraction process". Accepted for the 18-th Int Congress of Chemical and Process Engineering, Praha, Czech Republic, August 24-28, 2008.

2007

  • Xueyi Wang, Jun Huan, Jack Snoeyink,Wei Wang, "Mining RNA Tertiary Motifs with Structure Graphs", Proceedings of the 19th International Conference on Scientific and Statistical Database Management (SSDBM), 2007.
  • Xiang Zhang, Wei Wang, Jun Huan, "On demand Phenotype Ranking through Subspace Clustering", Proceedings of SIAM International Conference on Data Mining (SDM), 2007. page_white_acrobat
  • David Williams, Jun Huan, Wei Wang, "Graph Database Indexing Using Structured Graph Decomposition", Proceedings of the 23rd IEEE International Conference on Data Engineering (ICDE), 2007. page_white_acrobat
  • A. Tarca, V. Carey, X. Chen, R. Romero, and S. Draghici, "Machine Learning and Its applications to Biology", PLoS Computational Biology, vol. 3(6), e116, 2007.
  • H. Xiong, Y. Zhang, and X. Chen, "Data-dependent Kernel Machines for Microarray Data Classification", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4(4), 583-595, 2007.
  • X. Wang, R. Pal. X. Chen, K. Kumar, OJ. Kim, and E. Michaelis, "Genome-wide Transcriptome Profiling of Region-specific Vulnerability to Oxidative Stress in the Hippocampus", Genomics, doi:10.1016/j.ygeno.2007.03.007, 2007.
  • X. Chen, B. Gerlach, D. Chen, and Z. Liu, "Structural risk minimization based gene expression profiling analysis", International Journal on Bioinformatics Research and Applications, vol. 3(2), 153-169, 2007.
  • Fang, J.W.; Grzymala-Busse, J.W. "Predicting Penetration Across the Blood-Brain Barrier - a Rough Set Approach". Proceedings of 2007 IEEE International Conference on Granular Computing, IEEE Computer Society Press, pp. 231-236.
  • Sang Y, Teresa Ortega M, Rune K, Xiau W, Zhang G, Soulages JL, Lushington GH, Fang J.W., Williams TD, Blecha F, Melgarejo T. "Canine cathelicidin (K9CATH): Gene cloning, expression, and biochemical activity of a novel pro-myeloid antimicrobial peptide". Dev Comp Immunol. 2007 Apr 16.
  • Wickstrum J.R.; Skredenske J.M.; Kolin A.; Jin D.J.; Fang, J.W.; Egan S.M. "Transcription Activation by the DNA-Binding Domain of the AraC Family Protein RhaS in the Absence of its Effector-Binding Domain". Journal of Bacteriology. 189, 14, 4984-4993, 2007. page_go
  • Fang, J. W.; Grzymala-Busse, J. W. "Mining Mass Spectrometry Database Search Results—A Rough Set Approach". RSEISP 2007, LNAI 4585, pp. 340-349.
  • Fang J.W.; Salamat-miller N.; Dong Y.H.; Middaugh C.R. "Prediction of Polyanion Binding Potential in Proteins Using Random Forest". Proceedings of BIOCOMP07, 427-431, June 25-28, 2007.
  • Hanzlik RP, Koen TM, Theertham B, Dong YH, and Fang J.W. "The Reactive Metabolite Target Protein Database - A Web-Accessible Resource". BMC Bioinformatics. 2007, 8:95. page_go
  • Li, Q.-S.; Cai, S.; Borchardt, R.T; Fang, J.W.; Kuczera, K.; Middaugh, C.R.; and Schowen, R.L. "Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolases. 1. Basic features of the association and dissociation processes". Biochemistry, 46 (19), 5798 -5809, 2007. page_go
  • Salamat-Miller, N.; Fang, J.W.; Seidel, C.; Smalter, A.; Assenov, Y.; Albrechat, M.; Middaugh, C.R. "A Network-Based Analysis of Polyanion Binding Proteins Utilizing Human Protein Arrays". J. Biol. Chem. 282, 14, 10153-10163, 2007. page_go
  • Suprenant, K.A.; Nathan Bloom1, N.; Fang, J.W.; Lushington, G.H. "The Major Vault Protein is Related to the Toxic Anion Resistance Protein (TELA) Family". J. Exp. Biol. 210, 946-955, 2007. page_go
  • Jerzy W. Grzymala-Busse and Witold J. Grzymala-Busse. "An experimental comparison of three rough set approaches to missing attribute values." Transactions on Rough Sets, Lecture Notes in Computer Science Journal Subline, Springer-Verlag, vol. 6 (2007), 31–50.
  • Jerzy W. Grzymala-Busse, Zdzislaw S. Hippe and Teresa Mroczek. "Deriving belief networks and belief rules from data: A progress report." Transactions on Rough Sets, Lecture Notes in Computer Science Journal Subline, Springer-Verlag, vol. 7 (2007), 53–69.
  • Jerzy W. Grzymala-Busse and Wojciech Rzasa. "Definability of approximations for a generalization of the indiscernibility relation:. Proceedings of the 2007 IEEE Symposium on Foundations of Computational Intelligence (FOCI'2007), Honolulu, Hawaii, April 1-5, 2007, IEEE Computer Society, 65-72.
  • Jerzy W. Grzymala-Busse, Zdzislaw S. Hippe, Agnieszka Kordek, Teresa Mroczek, Wojciech Podraza. "Neonatal infection diagnosis using constructive induction in data mining". Proceedings of the 11-th International Conference on Rough Sets, Fuzzy Sets, Data Mining and Granular Computing (RSFDGrC' 2007), Toronto, Canada, May 14-16, 2007, Springer: Berlin, Heidelberg, New York, Lecture Notes in AI, vol. 4482, ed. by A. An, J. Stefanowski, S. Ramana, C. J. Butz, W. Pedrycz and G. Wang, 289-296.
  • Jianwen Fang and Jerzy W. Grzymala-Busse. "Mining mass spectrometry database search results-A rough set approach". Proceedings of the RSEISP'2007, the International Conference of Rough Sets and Emerging Intelligent Systems Paradigms, Warsaw, Poland, June 28-30, 2007. Springer, Berlin, Heidelberg, New York, Lecture Notes in AI, vol. 4585, ed. by M. Kryszkiewicz, J. F. Peters, H. Rybinski and A. Skowron, 340-349.
  • Jerzy W. Grzymala-Busse. "Mining numerical data-A rough set approach". Proceedings of the RSEISP'2007, the International Conference of Rough Sets and Emerging Intelligent Systems Paradigms, Warsaw, Poland, June 28-30, 2007. Springer, Berlin, Heidelberg, New York, Lecture Notes in AI, vol. 4585, ed. by M. Kryszkiewicz, J. F. Peters, H. Rybinski and A. Skowron, 12-21.
  • Jerzy W. Grzymala-Busse and Wojciech Rzasa. "Discovery of decision rules in incomplete data Modified LEM2 algorithm for local approximations". Proceedings of the Thirteen International Conference on Mathematics and Computer Science, Chelm, Poland, July 1-4, 2007, 46-47.
  • Zdzislaw S. Hippe, Jerzy W. Grzymala-Busse and Lukasz Piatek. "Synthesis of static images of melanocytic skin lesions". Proc of the Int Conference on Computers in Medical Activity, Lodz, Poland, September 19-21, 2007, 201-208.
  • Jerzy W. Grzymala-Busse and Wojciech Rzasa. "Approximation space and LEM2-like algorithms for local approximations". Proceedings of the Concurrency, Specification and Programming Workshop, Lagow, Poland, September 27-29, 2007, 279-289.
  • Jianwen Fang and Jerzy W. Grzymala-Busse. "Predicting penetration across the blood-brain barrier-A rough set approach". Proceedings of the IEEE Int Conference on Granular Computing GrC 2007, Silicon Valley, USA, November 2-4, 2007, IEEE Computer Society, 231-236.
  • Jerzy W. Grzymala-Busse, Witold J. Grzymala-Busse, Zdzislaw S. Hippe and W. Rzasa. "A comparison of three approximation strategies for incomplete data sets". Proceedings of the IEEE Int Conference on Granular Computing GrC 2007, Silicon Valley, USA, November 2-4, 2007, IEEE Computer Society, 301-306.

2006

  • X. Chen, G. Anantha, and X. Wang, "An effective structure learning method for constructing gene networks", Bioinformatics, 22(11):1367-1374, 2006.
  • H. Xiong and X. Chen, "Kernel-Based Distance Metric Learning for Microarray Data Classification", BMC Bioinformatics, 7:299, 2006.
  • X. Chen, X. Zeng, and D. van Alphen, "Multi-class feature selection for texture classification", Pattern Recognition Letters, vol. 27(14), pp. 1685-1691, 2006.
  • X. Chen, "Margin based wrapper methods for gene identification using microarray", Neurocomputing, vol. 69 (16-18): 2236-2243, 2006.
  • Jun Huan, "Graph Based Pattern Discovery in Protein Structures", PhD Dissertation, Department of Computer Science, University of North Carolina, 2006.
  • Stephen Olivier, Jun Huan, Jinze Liu, Jan Prins, James Dinan, P Sadayappan and Chau-Wen Tseng. "UTS: An Unbalanced Tree Search Benchmark". in Proceedings of the 19th Intl. Workshop on Languages and Compilers for Parallel Computing (LCPC 2006). New Orleans, LA, November 2-4, 2006. page_white_acrobat
  • Jun Huan, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, Alex Tropsha, Wei Wang, "Distance-based Identification of Spatial Motifs in Proteins Using Constrained Frequent Subgraph Mining", Proceedings of the IEEE Computational Systems Bioinformatics (CSB), 2006. page_white_acrobat
  • Jun Huan, Wei Wang, and Jan Prins, "Protein Local Structure Comparison: Methods and Future Directions", Advances in Computers by Chau-Wen Tseng (eds. ), Elsevier, 2006.
  • Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha, "Structure-based Function Inference Using Protein Family-specific Fingerprints ", Journal of Protein Science, Vol. 15, Page: 1537-1543. page_go
  • Salamat-Miller, N. S.; Fang, J. W.; Seidel, C.; Smalter, A.; Assenov, Y.; Albrecht, M.; Middaugh1, C. R. "A Network-Based Analysis of Polyanion Binding Proteins Utilizing Yeast Protein Arrays". Molecular and Cellular Proteomics, 5, 12, 2263-2278, 2006. page_go
  • Fang, J. W.; Grzymala-Busse, J. W. "Leukemia Prediction from Gene Expression Data: A Rough Set Approach". Lecture Notes in Computer Science: 4062, 758-765, 2006.
  • Fang, J. W.; Grzymala-Busse, J. W. "Mining of MicroRNA Expression Data: A Rough Set Approach". Lecture Notes in Computer Science: 4029, 899-908, 2006.
  • Fang, J. W.; Dong, Y. H.; Lushington, G. H.; Ye, Q. Z.; Georg, G. I. "Support Vector Machines in HTS Data Mining: Type I MetAPs Inhibition Study". Journal of Biomolecular Screening. 11 (2): 138-144, 2006.
  • Haasl, R. J.; Fang, J. W. "Mining protein-protein interaction data". Current Bioinformatics 1, 2: 197-205, 2006. (invited review)
  • Jerzy W. Grzymala-Busse and Wojciech Ziarko. "Rough sets and data mining". Encyclopedia of Data Warehousing and Mining, ed. by J. Wang, Information-Science Publishing, 2006, 973-977.
  • Jerzy W. Grzymala-Busse. "Rough set strategies to data with missing attribute values". Foundations and Novel Approaches in Data Mining, ed. by T. Y. Lin, S. Ohsuga, C.-J. Liau and X. Hu. Studies in Computational Intelligence, vol. 9, Springer-Verlag, 2006, 197-212.
  • Jerzy W. Grzymala-Busse, Zdzislaw S. Hippe, Edward Roj, Boleslaw Skowronski. "Applying expert systems to hop extraction monitoring and prediction". Polish Journal of Chemical Technology 8 (2006), 1-3.
  • Zdzislaw S. Hippe, Jerzy W. Grzymala-Busse and Lukasz Piatek. "Randomized dynamic generation of selected melanocytic skin lesion features". Proceedings of the IIS'2006 International Conference on Intelligent Information Systems, New Trends in Intelligent Information Processing and WEB Mining, Springer-Verlag, Ustron, Poland, June 19-22, 2006, 21-29.
  • Jerzy W. Grzymala-Busse and Steven Santoso. "Experiments on data with three interpretations of missing attribute values—A rough set approach". Proceedings of the IIS'2006 International Conference on Intelligent Information Systems, New Trends in Intelligent Information Processing and WEB Mining, Springer-Verlag, Ustron, Poland, June 19-22, 2006, 143-152.
  • Jianwen Fang, Jerzy W. Grzymala-Busse. "Leukemia prediction from gene expression data—A rough set approach". Proceedings of the ICAISC'2006, the Eighth International Conference on Artificial Intelligence and Soft Computing, Lecture Notes in Artificial Intelligence, vol. 4029, Springer-Verlag, Zakopane, Poland, June 25-29, 2006, 899-908.
  • Jerzy W. Grzymala-Busse. "Experiments on mining incomplete data—A rough set approach". Proceedings of the IPMU'2006, the 11th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems, Paris, France, July 2-7, 2006, 2586-2593.
  • Jerzy W. Grzymala-Busse. "A rough set approach to data with missing attribute values". Proceedings of the RSKT'2006, the First International Conference on Rough Sets and Knowledge Technology, Lecture Notes in Artificial Intelligence, vol. 4062, Springer-Verlag, Chongqing, P. R. China, July 24-26, 2006, 58-67.
  • Jianwen Fang, Jerzy W. Grzymala-Busse. "Mining of microRNA expression data—A rough set approach". Proceedings of the RSKT'2006, the First International Conference on Rough Sets and Knowledge Technology, Lecture Notes in Artificial Intelligence, vol. 4062, Springer-Verlag, Chongqing, P.R. China, July 24-26, 2006, 785-765.
  • Zdzislaw S. Hippe, Jerzy W. Grzymala-Busse, Teresa Mroczek. "Belief networks vs. belief rules: basic theory and practical issues". Proceedings of the 3-rd Conference Chemometrics - Methods and Applications, Zakopane, Poland, October 19-22, 2006, 47-67.
  • Jerzy W. Grzymala-Busse and Wojciech Rzasa. "Local and global approximations for incomplete data". Proceedings of the RSCTC 2006, the Fifth International Conference on Rough Sets and Current Trends in Computing, Kobe, Japan, November 6-8, 2006 Lecture Notes in AI, 4259. ed. by: S. Greco, Y. Hata, S. Hirano, M. Inuiguchi, H.-S. Nguyen, R. Slowinski, Springer Verlag, Berlin, Heidelberg, 2006, 244-253.