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Chengxin Zhang

Ph.D. in Bioinformatics, 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, Ph.D. in Bioinformatics. University of Michigan, Ann Arbor, MI.
  • 2011-2015, B.S. in Biological Science. Fudan University, Shanghai, China.
  • 2013, 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.


    8 first author papers; 5 co-first author papers; 26 in total.
  • Zhang C, Zheng W, Cheng M, Omenn GS, Freddolino P, Zhang Y (2021) Functions of Essential Genes and a Scale-free Protein Interaction Network Revealed by Structure-based Function and Interaction Prediction for a Minimal Genome. Journal of Proteome Research, in press. [Database]
  • Woodard J, Zhang C, Zhang Y (2021) ADDRESS: A database of disease-associated human variants incorporating protein structure and folding stabilities. Journal of Molecular Biology, in press. [Database]
  • Zhang C, Zheng W, Mortuza SM, Li Y, Zhang Y (2020) DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics, 36(7), 2105–2112. [Server]
  • Zhang C, Zheng W, Huang X, Bell EW, Zhou X, Zhang Y (2020) Protein structure and sequence reanalysis of 2019-nCoV genome refutes snakes as its intermediate host and the unique similarity between its spike protein insertions and HIV-1. Journal of Proteome Research, 19(4), 1351-1360. [Database][Program][News]
  • Wei X, Zhang C, Freddolino PL, Zhang Y (2020) Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. Bioinformatics, 36(16), 4383–4388. [Database] (Co-first author)
  • Huang X, Zhang C, Pearce R, Omenn GS, Zhang Y (2020) Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity Between the Spike Receptor-Binding Domain and Host ACE2. Journal of Proteome Research, 19(12), 4844–4856. [Preprint]
  • Zhang C, Lane L, Omenn GS, 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, 18(12), 4154-4166. [Database][News]
  • Li Y, Zhang C, Bell EW, Yu D, 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 EW, 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 SM, 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 DJ, 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]
  • Zhou et al. (2019) The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology, 20:244. [HTML]
  • Wei Z, Wuyun Q, Li Y, Mortuza SM, 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 GS, 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 PL, 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 SM, 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, 86(Suppl 1): 136-151.[PDF]
  • Zhang C, Freddolino PL, 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]
  • Thomas JM, Simkovic F, Keegan R, Mayans O, Zhang C, Zhang Y, Rigden DJ (2017) Approaches to ab initio molecular replacement of α-helical transmembrane proteins. Acta Crystallographica Section D: Structural Biology, 73(12), 985-996. [PDF]
  • Janson G, Zhang C, Prado MG, Paiardini A (2016) PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL. Bioinformatics, 33(3), 444-446. [Software]

  • Manuscripts under review [Google Scholar Profile]

    4 in total.
  • Li Y, Zhang C, Bell EW, Zheng W, Zhou X, Yu DJ, Zhang Y (2020) Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. bioRxiv 10.1101/2020.10.05.326140. [Server]
  • Rizvi SM, Zhang C, Freddolino PL, Zhang Y (2020) Gut Fungi Possess a Conserved Toxin Immunity Gene of Bacterial Origin. bioRxiv 2020.10.15.341461. [Preprint]
  • Gong W, Guerler A, Zhang C, Warner E, Li C, Zhang Y (2020) Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli bioRxiv 2020.10.17.343962. [Preprint]
  • Zhou X, Li Y, Zhang C, Zheng W, Zhang G, Zhang Y (2020) Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps. bioRxiv 2020.10.15.340455. [Preprint]

  • Oral Presentations at Conferences

  • Zhang C, Wei X, Freddolino PL, Zhang Y (2020) Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. ISMB, Montreal, Canada (changed to webinar due to COVID-19 pandemic).[Poster]
  • Zhang C, Wei X, Omenn GS, Freddolino PL, Zhang Y (2020) Proteome-wide detection of function misannotation by taxon-specific rate ratio comparison. US HUPO conference. Seattle, WA (changed to ePoster due to COVID-19 pandemic). [Poster]
  • 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 GS, 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 PL, 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 SM, 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 PL, 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]

  • Popular science works

  • Zhang Y, Zhang C, Zheng W (2020) Study shows pangolins may have passed new coronavirus from bats to humans. The Conversation. [HTML][PDF]
  • Zhang G, Li Y, Zhang C (2020) TripletRes: First ranked server for contact prediction in CASP13. iTASSER. [HTML][PDF]
  • Terra Mater Factual Studios (2020) Corona - The Pandemic and the Pangolin. [Trailer] (Interviewee in documentary film)

  • Grant Supports

  • Awardee. (2020) Intelligent Systems for Molecular Biology (ISMB) travel grant. Virtual conference.
  • Co-PI. (2020) MCB200078: Request computing resource for de novo protein therapeutics design simulations to treat the COVID-19 disease. COVID-19 HPC Consortium.
  • Awardee. (2019) International Conference on Supercomputing (ICS) 2019 travel support. Phoenix, AZ.
  • Co-PI. (2017-2021) MCB160124: Online Platform for I-TASSER-Based Structure and Function Prediction. The Extreme Science and Engineering Discovery Environment (XSEDE).
  • Co-PI. (2017-2021) 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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