2010

Brain MRI Image Segmentation Using Fuzzy C-Means Clustering
Y. Wei, HK Brown, X. Tao, S. Moore, and Dongsheng Che
The 2010 International Conference on Image Processing, Computer Vision, and Pattern Recognition (IPCV2010), in press.
A Multi-Objective Evolutionary Approach for Haplotype Inference
P. Lakshminarasimhan, Q. Liu, R. Marmelstein, M. Devito, and Dongsheng Che
The 2010 International Conference on Bioinformatics & Computational Biology (BioComp2010), 202-208.
A Maximum Likelihood Based Genetic Algorithm for Inferring Haplotypes from Genotypes.
P. Lakshminarasimhan, Q. Liu, R. Marmelstein, M. Devito, and Dongsheng Che
The 2010 International Conference on Educational Technology and Computers (ICETC 2010), V5, 92-96.
RNACompare: an efficient computational framework for RNA secondary structure comparison and classification based on grammar inference and indefinite kernel learning
Q. Liu, R. Zhu, Dongsheng Che, Y. Yang, and Z. Cao
RNA, submitted.
Classification of genomic islands using decision trees and their ensemble algorithms
Dongsheng Che, C. Hockenbury, R. Marmelsteinand, and K. Rasheed
BMC Genomics, accepted.
Decision tree and ensemble learning algorithms with their applications in bioinformatics
Dongsheng Che,Q. Liu, K. Rasheed and X. Tao
In: Software Tools and Algorithms for Biological Systems, Springer Publisher, in press.

2009

Computational methods in unravelling transcriptional regulatory networks in prokaryotes
Dongsheng Che and G. Li.
In: Jake Chen and Stefano Lonardi (ed.), Biological Data Mining, Chapman & Hall/CRC Press, 2009. 377-396.
Classification of genomic islands using decision-tree based algorithms.
Dongsheng Che, C. Hockenbury, R. Marmelsteinand, and K. Rasheed
The 2009 International Conference on Bioinformatics & Computational Biology (BioComp2009), 252-258.
Haplotype Inference Using A Genetic Algorithm
Dongsheng Che, H. Tang, and Y. Song
Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB2009), 31-37.
A universal operon predictor for prokaryotic genomes
G. Li, Dongsheng Che and Y. Xu
Journal of Bioinformatics and Computational Biology, (2009), 7(1):19-38
[PMID:19226658 | pdf ]

Computational elucidation of operons and uber-operons
P. Dam, F. Mao, Dongsheng Che, P. Wan, T. Tran, G. Li, Y. Xu
In: Y. Xu and J. P. Gogarten (ed.), Computational Methods for Understanding Bacterial and Archaeal Genomes, World Scientific Publishing, 2008,233-257.
Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source
Y. Li, P. Bahti, N. Shaw, G. Song, S. Chen 1, X. Zhang, M. Zhang, C. Cheng, J. Yin, J. Zhu, H. Zhang, Dongsheng Che, H. Xu, A. Abbas, B. Wang, Z. Liu
Proteins: Structure, Function, and Bioinformatics, (2008), 71(4):2109 - 2113.
[ PMID: 18361456 | 10.1002/prot.22025 ]
PFP: a computational framework for phylogenetic footprinting in prokaryotic genomes
Dongsheng Che, G. Li, S. Jensen, J.S. Liu and Y. Xu
Proceedings of International Symposium on Bioinformatics Research and Applications (ISBRA2008), 110-121.
[ Conference website | pdf ]
Purification, crystallization and preliminary crystallographic analysis of the non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304
P. Bahti, S. Chen, Y. Li, N. Shaw, X. Zhang, M. Zhang, C. Cheng, G. Song, J. Yin, H. Zhang, Dongsheng Che, A. Abbas, H. Xu, B. Wang and Z. Liu
Acta Cryst., (2008) F64,91-93
[doi:10.1107/S1744309107068649 | pdf ]

Decision tree modeling predicts operon structures of prokaryotic genomes
Dongsheng Che, J. Zhao, L. Cai, Y. Xu
International Journal of Information Technology and Intelligent Computing, (2007), 2(1)
Comparative pathway annotation with protein-DNA interaction and operon information via graph tree decomposition
J. Zhao, Dongsheng Che and L. Cai.
Pac Symp Biocomput., 2007 496-507
[ PMID 17990513 | pdf ]
Operon prediction in microbial genomes using decision tree approach
Dongsheng Che, J. Zhao, L. Cai and Y. Xu
Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB2007), 135-142.
[ IEEE Xplore ]
Comparative pathway prediction via unified graph modeling of genomic structure
J. Zhao, Dongsheng Che and L. Cai.
Proceedings of International Symposium on Bioinformatics Research and Applications (ISBRA2007), 627-637
[ DOI 10.1007/978-3-540-72031-7 | pdf ]

Detecting uber-operons in prokaryotic genomes
Dongsheng Che, G. Li, F. Mao, H. Wu and Y. Xu.
Nucleic Acids Res., 34(8):2418-2427
[ PMID: 16682449 | doi: 10.1093/nar/gkl294 | pdf ]
Expression of organomecurial lyase in eastern cottonwood enhances organomercury resistance
Dongsheng Che, R. Meagher, C. Rugh, T. Kim, A. Heaton, S. Merkle
In Vitro Cellular and Developmental Biology, (2006) 228-234
[ dx.doi.org/10.1079/IVP2006771 | pdf ]

BEST: binding-site estimation suite of tools
Dongsheng Che, S. Jensen, L. Cai and J.S. Liu.
Bioinformatics, 2005 21(12):2909-2911
[ PMID 15814553 | doi:10.1093/bioinformatics/bti425 | pdf ]
MDGA: motif discovery using a genetic algorithm
Dongsheng Che, Y. Song and K. Rasheed
Genetic and Evolutionary Computation Conference (GECCO2005), 447-452.
[ ACM Link | pdf ]

Expression of mercuric ion reductase in Eastern cottonwood (Populus deltoides) confers mercuric ion reduction and resistance
Dongsheng Che, R. Meagher, A. Heaton, A. Lima, C. Rugh and S. Merkle
Plant Biotechnol J., 2003 1(4):311-319
[ PMID: 17163907 | doi:10.1046/j.1467-7652.2003.00031.x (on the cover) ]

Designing an XML database engine: API and performance
S. Sipani, K. Verma, S. Chandrasekaran, X. Zeng, J. Zhu, Dongsheng Che and K. Wang
Proceedings of the 40th Annual ACM Southeast Conference (ACMSE2002), 239-245.
[ Conference website | pdf ]