Chengxin Zhang

Education

2021-2023, HHMI Postdoctoral Associate, Yale University, New Haven, CT.

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.

Publications [Google Scholar Profile]

16 first author papers; 7 co-first author papers; 54 in total.

Perry ZR, Pyle AM , Zhang C (2023) Arena: rapid and accurate reconstruction of full atomic RNA structures from coarse-grained models. Journal of Molecular Biology, 435 (18), 168210.

Zhang C, Zhang X, Freddolino PL, Zhang Y (2023) BioLiP2: an updated structure database for biologically relevant ligand–protein interactions. Nucleic Acids Research, gkad630.

Zhang C, Zhang Y, Pyle AM (2023) rMSA: a sequence search and alignment algorithm to improve RNA structure modeling. Journal of Molecular Biology, 435 (14), 167904.

Zhang C, Pyle AM (2023) PDC: a highly compact file format to store protein 3D coordinates. Database, baad018.

Zhang C (2023) BeEM: fast and faithful conversion of mmCIF format structure files to PDB format. BMC Bioinformatics, 24 (1), 1-6.

Zhang C, Shine M, Pyle AM, Zhang Y (2022) US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods, 19 (9), 1109-1115

Zhang C, Pyle AM (2022) CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures. Acta Crystallographica Section D: Structural Biology, 78 (4)

Zhang C, Zhang Y, Pyle AM (2022) rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling. Journal of Molecular Biology, 167904.

Zhang C, AM Pyle (2022) A unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs. iScience, 25 (10), 105218.

Zhu YH, Zhang C, Yu DJ, Zhang Y (2022) Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLOS Computational Biology, 18 (12), e1010793

Li Y, Zhang C, Yu DJ, Zhang Y (2022) Deep learning geometrical potential for high-accuracy ab initio protein structure prediction. iScience, 25 (6), 104425.

Shine M, Zhang C, Pyle AM (2022) AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. Bioinformatics, 38 (10), 2937-2939

Zhu YH, Zhang C, Liu Y, Omenn GS, Freddolino PL, Yu DJ, Zhang Y (2022) Integrating transcript expression profiles with protein homology inferences for gene function prediction. Genomics, Proteomics & Bioinformatics, 20(5), 1013-1027.

MacCarthy EA, Zhang C, Zhang Y, KC D (2022) GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool. Bioinformatics 38 (6), 1754-1755.

Zhou X, Li Y, Zhang C, Zheng W, Zhang G, Zhang Y (2022) Progressive assembly of multi-domain protein structures from cryo-EM density maps.Nature computational science 2 (4), 265-275.

Zhou X, Zheng W, Li Y, Pearce R, Zhang C, Bell EW, Zhang G, Zhang Y (2022) I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction. Nature Protocols 17 (10), 2326-2353

Si L, Shen Q, Li J, Chen L, Shen J, Xiao X, Bai H, Feng T, Ye AY, Li L, Zhang C, Li Z, Wang P, Oh CY, Nurani A, Niu S, Zhang C, Wei X, Yuan W, Liao H, Huang X, Wang N, Tian WX, Tian H, Li L, Liu X, Plebani R (2022) Generation of a live attenuated influenza A vaccine by proteolysis targeting. Nature Biotechnology 40 (9), 1370-1377

Tsou PS, Lu C, Gurrea-Rubio M, Muraoka S, Campbell PL, Wu Q, Model EN, Lind ME, Vichaikul S, Mattichak MN, Brodie WD, Hervoso JL, Ory S, Amarista CI, Pervez R, Junginger L, Ali M, Hodish G, O’Mara MM, Ruth JH, Robida AM, Alt AJ, Zhang C, Urquhart AG, Lawton JN, Chung KC, Maerz T, Saunders TL, Groppi VE, Fox DA, Amin MA (2022) Soluble CD13 induces inflammatory arthritis by activating the bradykinin receptor B1. The Journal of Clinical Investigation 132(11)

Wei X, Zou S, Xie Z, Wang Z, Huang N, Cen Z, Hao Y, Zhang C, Chen Z, Zhao F, Hu Z, Teng X, Gui Y, Liu X, Zheng H, Zhou H, Chen S, Cheng J, Zeng F, Zhou Y, Wu W, Hu J, Wei Y, Cui K, Li J (2022) EDIL3 deficiency ameliorates adverse cardiac remodeling by neutrophil extracellular traps (NET)-mediated macrophage polarization. Cardiovascular Research, 118 (9), 2179-2195.

Mohan HM, Trzeciakiewicz H, Pithadia A, Crowley EV, Pacitto R, Safren N, Trotter B, Zhang C, Zhou X, Zhang Y, Basrur V, Paulson HL, Sharkey LM (2022) RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control. Cellular and Molecular Life Sciences 79 (3), 176

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, 20(2), 1178-1189. [Database]

Li Y, Zhang C, Bell EW, Zheng W, Zhou X, Yu DJ, Zhang Y (2021) Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLOS Computational Biology, 17(3), e1008865. [Server] (Co-first author)

Chang J, Zhang C, Cheng H, Tan YW (2021) Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis. International Journal of Molecular Sciences, 22(5), 2768. (Co-first author)

Zheng W, Zhang C, Li Yang, Pearce R, Bell EW, Zhang Y (2021) Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods, 1(3), 100014. [Server] (Co-first author)

Li Y, Zhang C, Zheng W, Zhou X, Bell EW, Yu DJ, Zhang Y (2021) Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14. Proteins: Structure, Function, and Bioinformatics, 89(12), 1911-1921.

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, 433(11), 166840. [Database]

Mortuza SM, Zheng W, Zhang C, Li Y, Pearce R, Zhang Y (2021) Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature Communications, 12, 5011. [Server]

Zheng W, Li Y, Zhang C, Zhou X, Pearce R, Bell EW, Zhang Y (2021) Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14. Proteins: Structure, Function, and Bioinformatics, 89(12), 1734-1751. [Server]

Gong W, Guerler A, Zhang C, Warner E, Li C, Zhang Y (2021) Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli. Journal of Molecular Biology. 433(10), 166944. [Server]

Zhou D, Feng H, Huang T, Yang Y, Qiu P, Zhang C, Olsen TR, Zhang J, Chen YE, Mizrak D, Yang B (2021) hiPSC modeling of lineage-specific smooth muscle cell defects caused by TGFBR1A230T variant, and its therapeutic implications for Loeys-Dietz Syndrome. Circulation. 144(14), 1145-1159.

Kryshtafovych A, Moult J, Billings WM, Corte DD, Fidelis K, Kwon S, Olechnovič K, Seok C, Venclovas C, Won J, CASP-COVID participants. (2021) Modeling SARS-CoV-2 proteins in the CASP-commons experiment. Proteins: Structure, Function, and Bioinformatics, 89 (12), 1987-1996.

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]

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]

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

2021-2023. Postdoc Fellow. Anna Pyle lab, Department of Molecular, Cellular and Developmental Biology, Yale University.

2016-2020. Graduate Student Research Assistant. Yang Zhang lab, Department of Computational Medicine and Bioinformatics, 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.