Publication

Recent Publications

38.  Chen Xu and Zhengchang Su. Prediction of the cooperative cis-regulatory elements for broadly expressed neuronal genes in Caenorhabditis elegans. (Submitted)

37. Ehsan Tabari, Shan Li, Xia Dong, Harry Lee, Jin Kim, Sunil Hwang and Zhengchang Su. Pervasive cis-antisense transcription negatively regulates gene expression in E. coli K12 in response to environmental changes. (Submitted)

36.  Chen Xu and Zhengchang Su. Identification of cell types from single-cell transcriptome using a novel clustering method. Bioinformatics 2015 (btv088) (pdf)

35.  Chen Xu and Zhengchang Su.  Identification of genes driving lineage divergence from single-cell gene expression data in C. elegans. Developmental biology. 2014 Sep 15;393(2):236-44. (pdf)

34.  Meng Niu, Ehsan Tabari and Zhengchang Su. De novo prediction of cis-regulatory modules through integrative analysis of a large number of ChIP datasets BMC Genomics. 2014 Dec 2;15:1047. (pdf)

33.  Shan Li, Xia Dong and Zhengchang Su. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics. 2013, 14:520 (pdf)

32.  Shaoqiang Zhang, Lifen Jiang Chuanbin Du and Zhengchang Su. A Novel Information Contents Based Similarity Metric for Comparing TFBS Motifs. 2012 IEEE International Conference on Systems Biology (ISB) (pdf)

31.  Shaoqiang Zhang, Huazhi Su, Guojun Li, Zhengchang Su, A simulated annealing heuristic for resource allocation and scheduling with precedence constraints, Journal of Information & Computational Science. 2011,Vol.8 (9) :1541-1550. 

30.  Shaoqiang Zhang, Huazhi Sun, Guojun Li, Zhengchang Su. A Simulated Annealing Algorithm for Resource Allocation and Scheduling with Precedence Constraints in the GLECLUBS/eGLECLUBS Pipelines. cse, pp.421-426, 2011. 14th IEEE International Conference on Computational Science and Engineering, 2011.

29.  Shaoqiang Zhang, Shan Li, Meng Niu, Phuc Pham and Zhengchang Su. MotifClick: prediction of cis-regulatory binding sites via merging cliques.BMC Bioinformatics 2011, 12:238 (pdf)

28.  Shan Li, Minli Xu and Zhengchang Su. Computational analysis of LexA regulons in Cyanobacteria. BMC Genomics 2010, 11:527. (pdf)

27.  Xu M, Su Z. A novel alignment-free method for comparing transcription factor binding site motifs. PLoS One. 2010;5(1):e8797. (pdf)

26.  Zhang S, Li S, Pham PT, Su Z. Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes. BMC Bioinformatics. 2010;11:397. PMCID: 2920276. (pdf)

25. Shaoqiang Zhang, MinLi Xu, Shan Li, and Zhengchang Su. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Research, 2009. doi:10.1093/nar/gkp248. (PMID: 19383880)

24. Minli Xu and Zhengchang Su. Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes. BMC Genomics. 2009 Jan 15;10:23. (PMID: 19146659)

23. Zhengchang Su Guojun Li and Ying Xu. Prediction of regulons through comparative genomics analyses. In Computational methods for understanding bacterial and archaeal genomes. Ying Xu and J. Peter Gogarten (eds). Imperial Colleger Press. 2008. p259-279.

22. Zhengchang Su, Victor Olman and Ying Xu. Computational prediction of Pho regulons in Cyanobacteria. BMC Genomics. 2007 Jun 8;8:156. (PMID: 17559671)

21. P. Dam, V Olman, K. Harris, Z. Su, Ying Xu, Operon prediction using both genome-specific and general genome information, Nucleic Acids Research, 2007;35(1):288-98. (PMID: 17170009)

20. T. Tran, Phuongan Dam, Zhengchang Su, Farris Poole, Michael Adams, G. Tong Zhou, Ying Xu.  Operon prediction in Pyrococcus furiosus.Nucleic Acids Res. 2007;35(1):11-20. (PMID: 17148478)

19. Zhenchang Su , Phuongan Dam, Xin Chen, Victor Olman, Tao Jiang, Brian Plaenik and Ying Xu. Computational inference and experimental validation of  nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH8102. Nucleic Acids Research. 2006; 34(3):1050-65. (PMID: 16473855)

18.  Andrea Catte, James Patterson; Gilbert Weinstein; Zhengchang Su; Ling Li; Jianguo Chen; Martin Jones; Marcela Aliste; Stephen Harvey; Jere Segrest . Novel Minimal Surface Conformations of Nascent High Density Lipoproteins through Molecular Dynamics. Biophysical Journal. 2006; 90(12):4345-60. (pdf)

17.  H. Wu, F. Mao, Z. Su, V Olman, Ying Xu, Prediction of functional modules based on gene distributions in microbial genomes. Genome Inform.2005;16(2):247-59. (pdf)

16.  Zhengchang Su, Victor Olman,  Fenglou Mao,  and Ying Xu. Comparative genomics analysis of ntcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis. Nucleic Acids Research.  2005, 33(16): 5156-5171. (pdf)

15.  Jinling Huang,  Zhengchang Su and Ying Xu, The evolution of Microbial phosphonate Degradation Pathways.  Journal of Molecular Evolution. 2005; 61(5):682-90. (pdf)

14.  Fenglou Mao, Zhengchang Su, Victor Olman, Phuongan Dam, Zhijie Liu, Ying Xu. Mapping of Orthologous Genes in the Context of Biological Pathways: an Application of Integer Programming. Proceedings of  National Academy of Sciences  U S A . 2005; 103(1):129-34. (pdf)

13.  Hongwei Wu, Zhengchang Su, Victor Olman and Ying Xu. Prediction of functional gene modules based on comparative genome analysis and gene otology application, Nucleic Acids Research. 2005;33(9):2822-37. (pdf)

12.  Zhengchang Su,  Xiaochuan Guo, Richard L. Shoemaker, Richard B. Marchase, and J. Edwin Blalock. A Store-operated Nonselective Cation Channel in Human Lymphocytes. Cellular and Molecular Neurobiology. 2005; 25(3-4):625-47. (pdf)

11.  Phuongan  Dam and Zhengchang Su and Victor Olman Ying Xu. In sillco reconstruction of the carbon fixation pathway in Synechococcus sp. WH8102. Journal of Biological Systems. 2004; 12:97-125. (pdf)

10.  Xin Chen, Zhengchang Su, Ying Xu, Tao Jiang. Computational  prediction of operons in Synechococcus sp. WH8102. Genome Informatices 2004; 15(2):211-222. (pdf)

9.    Victor Olman, Hanchun Peng, Zhengchang Su, Ying Xu. Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes.  Proceedings of CSB 2004 Conference.  p363-370. (pdf)

8.    Zhengchang Su, Richard L. Shoemaker Richard B. Marchase and J. Edwin Blalock. Ca2+  dependent inactivation of monovalent cation current through Ca2+  release activated Ca channels. Biophys J. 2004;86(2):805-14. (pdf)

7.    X. Chen, Z. Su, P. Dam, B. Palenik, Y. Xu and T. Jiang. Operon prediction by comparative genomics. Nucleic Acid Research. 2004; 19;32(7):2147-57. (pdf)

6.    Zhenchang Su , Phuongan Dam, Xin Chen Vicor Olman, Tao Jiang, Brian Plaenik and Ying Xu. Computational inference of regulatory pathway in microbes. An application to phosphorus assimilation pathway. Genome Informatics 2003; 14:1-10. (pdf)

5.   Zhengchang Su, Douglas S. Barker, Peter Csutora, Theresa Chang, Richard L. Shoemaker, Richard B. Marchase and J. Edwin Blalock. Regulation of Ca2+ release activated Ca2+ channel by INAD and Calcium influx factors. Am J Physiol Cell Physiol. 2003;284(2):C497-505. (pdf)

4.   Zhengchang Su, Peter Csutora, Dacia Hunton,  Richard L. Shoemaker, Richard B. Marchase, and J. Edwin Blalock A Store-operated Non-selective Cation Channel in Lymphocytes is Activated Directly by Ca2+ Influx Factor (CIF) and Diacylglycerol. American Journal of Physiology. 2001;280(5):C1284-92. (pdf)

3.   Manion MK, Su Z, Villain M, Blalock JE. A new type of Ca(2+) channel blocker that targets Ca(2+) sensors and prevents Ca(2+)-mediated apoptosis. FASEB Journal. 2000;14(10):1297-306. (pdf)

2.   Villain M, Jackson PL, Manion MK, Dong WJ, Su Z, Fassina G, Johnson TM, Sakai TT, Krishna NR, Blalock JE. De novo design of peptides targeted to the EF hands of calmodulin. Journal of  Biological Chemistry 2000; 275(4):2676-85. (pdf)

1.   Csutora P, Su Z, Kim HY, Bugrim A, Cunningham KW, Nuccitelli R, Keizer JE, Hanley MR, Blalock JE, Marchase RB. Calcium influx factor is synthesized by yeast and mammalian cells depleted of organellar calcium stores. Proceedings of  National Academy of Sciences  U S A. 1999;96(1):121-6. (pdf)