Zhengchang Su, PhD

Research Description:

• Computational inference of signaling and metabolic pathways
• Characterization of transcriptional regulatory networks in prokaryotic and eukaryotic cells
• Single-cell transcriptome sequencing

Recent Publications:

• 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 doi:10.1186/1471-2164-14-520
• Zhang S, Li S, Niu M, Pham PT, Su Z. MotifClick: prediction of cis-regulatory binding sites via merging cliques.BMC Bioinformatics. 2011 Jun 16;12:238. doi: 10.1186/1471-2105-12-238. S
• Zhaoqiang 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.
• 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.
• 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.
• 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.
• Jinling Huang, Zhengchang Su and Ying Xu, The evolution of Microbial phosphonate Degradation Pathways. Journal of Molecular Evolution. 2005; 61(5):682-90.
• 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.
• 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.
• Xin Chen, Zhengchang Su, Ying Xu, Tao Jiang. Computational prediction of operons in Synechococcus sp. WH8102. Genome Informatices 2004; 15(2):211-222.
• 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.
• 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.
• 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.

Courses Taught

Undergraduate Courses

• BINF3131: Bioinformatics Algorithms: Spring 2017, Spring 2018,Spring 2019,Spring 2020, Spring 2021, Textbook and Website:  https://www.bioinformaticsalgorithms.org/

Graduate Courses

• BINF6312/8312 Computational Comparative Genomics Fall,2007, Fall 2008
• BINF6104/8104 Mathematical Systems Biology Spring 2008, Spring 2010, Spring 2012
• BINF6101/BINF8101 Molecular Sequence Analysis and Lab: Fall 2009, Fall 2010, Fall 2011, Fall 2012. Fall 2013, Fall 2014, Fall 2015, and Fall 2016, Fall 2018

Curriculum Vitae

Faculty Page