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Chengxin Zhang

Ph.D. Candidate, Department of Computational Medicine and Bioinformatics

Contact

RM 2035, Palmer Commons
100 Washtenaw Ave
Ann Arbor, MI 48109-2218
zcxumich.edu

Education

2011-2015, B.S. in Biological Science. Fudan University, Shanghai, China.

Research Interests

Algorithm development for protein structure prediction, structure-based protein function prediction, and protein-protein interaction.

Publications

  • Zhang, C., Zheng, W., Freddolino, P. L., Zhang, Y., (2018). MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein-protein network mapping. Journal of Molecular Biology, 430(15), 2256-2265. [Server]
  • Thomas, J. M., Simkovic, F., Keegan, R., Mayans, O., Zhang, C., Zhang, Y., Rigden, D. J. (2017). Approaches to ab initio molecular replacement of α-helical transmembrane proteins. Acta Crystallographica Section D: Structural Biology, 73(12), 985-996. [PDF]
  • Zhang, C., Mortuza, S.M., Zhang, Y. (2017). Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12. Proteins: Structure, Function, and Bioinformatics, 10.1002/prot.25414. [PDF].
  • Zhang, C., Freddolino, P. L., Zhang, Y. (2017). COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information. Nucleic Acids Research, gkx366. [Server]
  • Xiong, P., Zhang, C., Zheng, W., Zhang, Y. (2017). BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts. Journal of molecular biology, 429(3), 426-434. [Server]
  • Janson, G., Zhang, C., Prado, M. G., Paiardini, A. (2016). PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL. Bioinformatics, 33(3), 444-446. [Software]

  • Conferences

  • Zhang, C., Rahimpour, M., Freddolino, P. L., Zhang, Y. (2018). Proteome-wide Structure-Based Function Prediction Reveals Roles of Proteins Responsible for E. coli Fitness. US HUPO conference. Minneapolis, MN. [Abstract]
  • Zhang, C., Mortuza, S.M., Zhang, Y. (2017). Demo: I-TASSER Gateway for Protein Structure Prediction and Structure-based Function Annotation. The 12th Gateway Computing Environments Conference (Gateways 2017). Ann Arbor, MI. [Paper and Slides]
  • Zhang, C., Freddolino, P. L., Zhang, Y. (2017). Protein Function Prediction by COFACTOR in CAFA3. ISMB/ECCB 2017. Prague, Czech Republic. [Abstract]
  • Zhang, C.. (2017). Structure-based Protein Function Prediction. I-TASSER Workshop 2017. Greensboro, NC. [Slides]

  • Grant Supports

  • Co-PI. (2017-2018). Online Platform for I-TASSER-Based Structure and Function Prediction. The Extreme Science and Engineering Discovery Environment (XSEDE) project TG-MCB160124.
  • Co-PI. (2017-2018). Development of New Methods for Template-Based and Ab Initio Protein Structure Prediction and Structure-Based Function Annotation. The Extreme Science and Engineering Discovery Environment (XSEDE) project TG-MCB160101.

  • Professional Experiences

  • 2016-. Graduate Student Research Assistant. Yang Zhang lab, Department of Computational Medicine and Bioinformatics, University of Michigan.
  • 2016-. Rotation Student. Peter Freddolino lab, Department of Biological Chemistry, University of Michigan.
  • 2017. Graduate Student Instructor. BIOINF-528: Structural Bioinformatics, University of Michigan.
  • 2012-2015. Undergraduate Research Assistant. Yan-Wen Tan lab, State Key Laboratory of Surface Physics, Fudan University.
  • 2014. Intern Student. Richard Lewis lab, Institute for Molecular Bioscience, University of Queensland.
  • 2013. Exchange Student. Ping-Chiang Lyu lab, Institute of Bioinformatics and Structural Biology, National Tsing Hua University.

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