Peer-reviewed journal articles

1. A universal operon predictor for prokaryotic genomes
   G. Li, Dongsheng Che and Y. Xu
   Journal of Bioinformatics and Computational Biology, (2009), in press
2. 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 ]
3. 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 ]
4. 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)
5. 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 ]
6. 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 ]
7. 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 ]
8. 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) ]

Peer-reviewed conference contributions

9. 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), accepted.
10. 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 ]
11. 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 ]
12. 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 ]
13. 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 ]
14. 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 ]
15. 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 ]

Book chapters

16. Computational methods in unravelling transcriptional regulatory networks in prokaryotes
    Dongsheng Che, G. Li.
    In: Jake Chen and Stefano Lonardi (ed.), Biological Data Mining, Chapman & Hall/CRC Press, 2009. in press.
17. 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, 2009.

Submitted

18. Classification of Genomic Islands Using Decision-tree Based Algorithms
    Dongsheng Che, C. Hockenbury and R. Marmelsteinand
    
19. Motif Length Could Be Computationally Recognized
    G. Li, B. Liu, Dongsheng Che, J.Z. Sun and Y. Xu
    
20. Operon structural diversity is a reflection of adaptive evolution
    P. Wan, F. Mao, V. Olman, Dongsheng Che, H. Liu and Y. Xu
    
21. Co-evolution analysis of protein complexes and its applications in predicting residue interactions
    F. Pan, Dongsheng Che, M. Momany, L. Cai and R. Malmberg
    

Conference poster abstracts

• A General Framework for the Whole-Genome Regulon Prediction Across Prokaryotic Genomes
  Dongsheng Che, G. Li and Ying Xu
  The Third Computational & Systems Biology Symposium, Athens, GA, March, 21, 2008
  [ Symposium website | poster ]
• Co-evolution Analysis of Protein Complexes and Its Applications in Predicting Residue Interactions
  F. Pan, Dongsheng Che, M. Momany, L. Cai and R. Malmberg
  Proceedings of International Symposium on Bioinformatics Research and Applications (ISBRA2007), Atlanta, May, 7-10, 2007
  [ Conference website ]
• A universal operon predictor for prokaryotic genomes
  Dongsheng Che, G. Li and Ying Xu
  The Second Computational & Systems Biology Symposium, Athens, GA, March, 23, 2007
  [ Symposium website | poster ]
• SGXPRO: A Versatile Structure Solving Engine for Structural Biology/Genomics
  BC Wang, Z. Fu, Y. Wu, Dongsheng Che, J. Zhao, H. Yan and J. Rose
  American Crystallographic Association Meeting, Chicago, July, 25-31, 2004.
  [ Conference website ]