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BioLiP E. coli GLASS GPCR-HGmod GPCR-RD GPCR-EXP TM-fold DECOYS POTENTIAL RW/RWplus HPSF THE-DB CASP7 CASP8 CASP9 CASP10 CASP11 CASP12 CASP13


Chengxin Zhang

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

Contact

RM 2035B, Palmer Commons
100 Washtenaw Ave
Ann Arbor, MI 48109-2218
zcxumich.edu
https://github.com/kad-ecoli/

Education

  • 2015-2020 (expected), Ph.D. candidate in Bioinformatics. University of Michigan, Ann Arbor, MI.
  • 2011-2015, B.S. in Biological Science. Fudan University, Shanghai, China.
  • 2014, Exchange Student. National Tsing Hua University, Hsinchu, Taiwan.


  • Research Interests

    Algorithm development for protein and RNA structure prediction, function annotation, structure alignment and interaction prediction.


    6 first author papers; 4 co-first author papers; 21 in total.
  • Zhang, C., Zheng, W., Mortuza, S.M., Li, Y., Zhang, Y. (2019) DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics, in press. [Server]
  • Zhang, C., Lane, L., Omenn, G.S., Zhang, Y. (2019) A blinded testing of function annotation for uPE1 proteins by the I-TASSER/COFACTOR pipeline using the 2018-2019 additions to neXtProt and the CAFA3 challenge. Journal of Proteome Research, DOI:10.1021/acs.jproteome.9b00537. [Database][News]
  • Li, Y., Zhang, C., Eric W. Bell, Dong-Jun Yu, Zhang, Y. (2019) Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13. Proteins: Structure, Function, and Bioinformatics, 87, 1082-1091. [Server] (Co-first author)
  • Gong, S., Zhang, C., Zhang, Y. (2019) RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA. Bioinformatics, 35(21), 4459-4461,. [Server] (Co-first author)
  • Zheng, W., Zhang, C., Bell, E.W., Zhang, Y. (2019) I-TASSER gateway: a protein structure and function prediction server powered by XSEDE. Future Generation Computer Systems, 99, 73-85. (Co-first author) [Server]
  • Wang, Y., Shi, Q., Yang, P., Zhang, C., Mortuza, S.M., Xue, Z, Ning, K, Zhang, Y. (2019) Fueling ab initio folding with oceanic metagenomics enables structure and function predictions of new protein families. Genome Biology, 20 (229). (Co-first author) [Database]
  • Zheng, W., Zhang, C., Wuyun, Q., Pearce, R., Li, Y., Zhang, Y. (2019) LOMETS2: Improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acid Research, 47 (W1), W429-W436. [Server]
  • Wei, X., Zhang, C., Xie, Z., Teng, X., Wang, Z., Zheng, H., Zou, S., Huang, N., Cui, K., Li, J. (2019) EGF-like repeats and discoidin I-like domain 3 (EDIL3) deficiency improves post-myocardial infarction healing via neutrophil extracellular traps (NETs) mediated pro-inflammatory macrophage polarization. The Journal of Immunology 202 (1 Supplement), 117.9. [HTML]
  • Zhou, X., Hu, J., Zhang, C., Zhang, G., Zhang, Y. (2019) Assembling multi-domain protein structures through analogous global structural alignments. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 116 (32), 15930-15938. [Server]
  • Wei, Z., Li, Y., Zhang, C., Pearce, R., Zhang, Y. (2019) Deep-learning contact-map guided protein structure prediction in CASP13. Proteins: Structure, Function, and Bioinformatics, 87, 1149-1164. [Server]
  • Li, Y., Hu, J., Zhang, C., Yu, D.J., Zhang, Y. (2019) ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. Bioinformatics, 35(22), 4647–4655. [Server]
  • Wu, J., Yin, Q., Zhang, C., Geng, J., Wu, H., Hu, H., Ke, X., Zhang, Y. (2019) Function prediction for G protein-coupled receptors through text mining and induction matrix completion. ACS Omega, 4(2), 3045-3054. [Software]
  • The CAFA consortium (2019) The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology, in press. [bioRxiv preprint]
  • Wei, Z., Wuyun, Q., Li, Y., Mortuza, S.M., Zhang, C., Pearce, R., Ruan, J., Zhang, Y. (2019) Detecting distant-homology protein structures by aligning deep neural-network based contact maps. PLOS Computational Biology, 15(10): e1007411. [Server]
  • Zhang, C., Wei, X., Omenn, G.S., Zhang, Y. (2018) Structure and protein interaction-based Gene Ontology annotations reveal likely functions of uncharacterized proteins on human chromosome 17. Journal of Proteome Research, 17(12), 4186-4196. [Database]
  • 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]
  • Zhang, C., Mortuza, S.M., He, B., Wang, Y., Zhang, Y. (2018) 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]
  • 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., Freddolino, P.L., Zhang, Y. (2017) COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research, 45(W1), W291-W299. [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]

  • Oral Presentations at Conferences

  • Zhang, C., Pearce, R., Zhang, Y. (2019) C-QUARK: contact-assisted de novo protein structure prediction on XSEDE Comet. International Conference on Supercomputing (ICS). Phoenix, AZ. [Abstract]
  • Zhang, C., Wei, X., Omenn, G.S., Zhang, Y. (2018) Structure and Protein Interaction-based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17. HUPO world congress. Orlando, FL. [Abstract][Poster]
  • 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]

  • Invited talks

  • Zhang, C. (2019) Application of artificial intelligence in biomedical research and clinical diagnosis. West China Hospital. Chengdu, Sichuan, China.
  • Zhang, C. (2017) I-TASSER science gateway for protein structure and function prediction. The Science Gateway Institute. (Webinar). [Slides]

  • Grant Supports

  • Awardee. (2019) International Conference on Supercomputing (ICS) 2019 travel support. Phoenix, AZ.
  • Co-PI. (2017-2020) MCB160124: Online Platform for I-TASSER-Based Structure and Function Prediction. The Extreme Science and Engineering Discovery Environment (XSEDE).
  • Co-PI. (2017-2020) MCB160101: 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).
  • Participant of General Program. (2019) 81973243: Computer-aided Design and Optimization of Artificial Protein Drugs. National Natural Science Foundation of China.
  • Awardee. (2018) Rackham Travel Grant. University of Michigan.

  • Other Awards

  • Awardee. (2019) C-HPP young investigator award. 18th Human Proteome Organization (HUPO) World Congress. Aldelaide, Australia.
  • Lead member of "Zhang-Freddolino lab" group. (2019) Second, third, fourth, and fifth ranked group in Critical Assessment of Function Annotation (CASP) 3 "Motility", "Biofilm formation", "Cellular Component" and "Biological Process" categories. [Assessment Website]
  • Awardee. (2019) Biological Chemistry Retreat "Outstanding Talk Award". University of Michigan. [Certificate]
  • Team member of "TripletRes" group. (2018) First ranked server in Critical Assessment of protein Structure Prediction (CASP) 13 "Contact prediction" category. [Assessment Website]
  • Nominee. (2018) Office of Graduate and Postdoctoral Studies Annual Graduate Student Award "Excellence in Research". University of Michigan. [News]
  • Team member of "Zhang-Server" group. (2016) First ranked server in Critical Assessment of protein Structure Prediction (CASP) 12. [Assessment Website]

  • 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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