Research Topics
| Zhengchang SuSummaryAffiliation: University of North Carolina at Charlotte Country: USA Publications
| Collaborators
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Detail Information
Publications
Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomesShaoqiang Zhang
Department of Bioinformatics and Genomics, Center for Bioinformatics Research, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
BMC Bioinformatics 11:397. 2010..Although GLECLUBS has achieved rather high prediction accuracy of TFBSs in a target genome, it is still not efficient enough to be applied to all the sequenced prokaryotic genomes...- Computational prediction of Pho regulons in cyanobacteriaZhengchang Su
Bioinformatics Research Center and Department of Computer Science, The University of North Carolina at Charlotte, Charlotte, NC 28233, USA
BMC Genomics 8:156. 2007..However, a systematic study of the Pho regulon, the core of the phosphorus assimilation pathway in a cyanobacterium, is hitherto lacking... - Computational analysis of LexA regulons in CyanobacteriaShan Li
Bioinformatics Research Center, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
BMC Genomics 11:527. 2010..PCC 6803 might have distinct functions other than the regulation of the SOS response. To gain a general understanding of the functions of LexA and its evolution in cyanobacteria, we conducted the current study... - Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotesShaoqiang Zhang
Department of Bioinformatics and Genomics, Bioinformatics Research Center, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
Nucleic Acids Res 37:e72. 2009..When compared with the prior state-of-the-art algorithms, our algorithm outperforms them in both prediction sensitivity and specificity... - Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomesMinli Xu
Department of Bioinformatics and Genomics, Bioinformatics Research Center, The University of North Carolina at Charlotte, Charlotte, NC 28233, USA
BMC Genomics 10:23. 2009..PCC 6803 and Anabaena sp. PCC 7120; therefore, a systematic genome-scale study of the potential CRP target genes and binding sites in cyanobacterial genomes is urgently needed... - MotifClick: prediction of cis-regulatory binding sites via merging cliquesShaoqiang Zhang
Department of Bioinformatics and Genomics, Center for Bioinformatics Research, The University of North Carolina at Charlotte, 28223, USA
BMC Bioinformatics 12:238. 2011..However, some motifs may have a similar nucleotide distribution to that of their background sequences. Therefore, such binding sites can be missed by these tools... - A novel alignment-free method for comparing transcription factor binding site motifsMinli Xu
Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
PLoS ONE 5:e8797. 2010..In some applications, alignment-free methods might be preferred; however, few such methods with high accuracy have been described... - Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesisZhengchang Su
Bioinformatics Institute and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
Nucleic Acids Res 33:5156-71. 2005..We postulate for the fist time that these genes serve as the regulatory points to orchestrate these two important processes in a cyanobacterial cell... - Operon prediction in Pyrococcus furiosusThao T Tran
School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
Nucleic Acids Res 35:11-20. 2007..Using this new algorithm, we predicted 470 operons in the P.furiosus genome. Of these, 349 were validated using DNA microarray data... - Prediction of functional modules based on gene distributions in microbial genomesHongwei Wu
Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, USA
Genome Inform 16:247-59. 2005..We have also examined the predicted functional modules that are common to both Escherichia coli K12 and Bacillus subtilis subsp. subtilis str. 168, and provide explanations for some functional modules... - Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102Zhengchang Su
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
Nucleic Acids Res 34:1050-65. 2006..Moreover, for some of these genes, this coordination is probably mediated by NtcA through the canonical NtcA promoters in their regulatory regions... - Mapping of orthologous genes in the context of biological pathways: An application of integer programmingFenglou Mao
Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602, USA
Proc Natl Acad Sci U S A 103:129-34. 2006..We conclude that using genomic structure information as constraints could greatly improve the pathway-mapping accuracy over methods that use sequence-similarity information alone... - The evolution of microbial phosphonate degradative pathwaysJinling Huang
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
J Mol Evol 61:682-90. 2005..The implications of plasmids and transposition in the evolution of phosphonate degradation are also discussed... - Prediction of functional modules based on comparative genome analysis and Gene Ontology applicationHongwei Wu
Department of Biochemistry and Molecular Biology, University of Georgia 120 Green Street, Athens, GA 30602-7229, USA
Nucleic Acids Res 33:2822-37. 2005..coli. The application results have demonstrated that our approach is highly promising for the prediction of functional modules encoded in a microbial genome... - Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102Zhengchang Su
Department of Biochemistry and Molecular Biology, University of Georgia at Athens, and Computational Biology Institute, Oak Ridge National Laboratory
Genome Inform 14:3-13. 2003..To demonstrate the effectiveness of this procedure, we have applied it to the construction of the phosphorus assimilation pathways in cyanobacterium sp. WH8102. We present, in this paper, a model of the core components of this pathway... - Computational prediction of operons in Synechococcus sp. WH8102Xin Chen
Department of Computer Science and Engineering, University of California at Riverside, CA 92507, USA
Genome Inform 15:211-22. 2004..All predicted data are available at (http://www.cs.ucr.edu/~xin/operons.htm) for public use...