Zhang Y - Search Results

1

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, … See abstract for full author list ➔ Zhou N, et al. Among authors: zhang c, zhang s, zhang f, zhang z, zhang y. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 Free PMC article.

2

Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons.

Wei X, Zhang C, Freddolino PL, Zhang Y. Wei X, et al. Among authors: zhang c, zhang y. Bioinformatics. 2020 Aug 15;36(16):4383-4388. doi: 10.1093/bioinformatics/btaa548. Bioinformatics. 2020. PMID: 32470107 Free PMC article.

3

PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning.

Bell EW, Schwartz JH, Freddolino PL, Zhang Y. Bell EW, et al. Among authors: zhang y. J Mol Biol. 2022 Jun 15;434(11):167530. doi: 10.1016/j.jmb.2022.167530. Epub 2022 Mar 5. J Mol Biol. 2022. PMID: 35662463 Free PMC article.

4

TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction.

Zhu YH, Zhang C, Liu Y, Omenn GS, Freddolino PL, Yu DJ, Zhang Y. Zhu YH, et al. Among authors: zhang c, zhang y. Genomics Proteomics Bioinformatics. 2022 Oct;20(5):1013-1027. doi: 10.1016/j.gpb.2022.03.001. Epub 2022 May 11. Genomics Proteomics Bioinformatics. 2022. PMID: 35568117 Free PMC article.

5

ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities.

Woodard J, Zhang C, Zhang Y. Woodard J, et al. Among authors: zhang c, zhang y. J Mol Biol. 2021 May 28;433(11):166840. doi: 10.1016/j.jmb.2021.166840. Epub 2021 Feb 2. J Mol Biol. 2021. PMID: 33539887 Free PMC article.

6

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks.

Li Y, Hu J, Zhang C, Yu DJ, Zhang Y. Li Y, et al. Among authors: zhang c, zhang y. Bioinformatics. 2019 Nov 1;35(22):4647-4655. doi: 10.1093/bioinformatics/btz291. Bioinformatics. 2019. PMID: 31070716 Free PMC article.

7

I-TASSER gateway: A protein structure and function prediction server powered by XSEDE.

Zheng W, Zhang C, Bell EW, Zhang Y. Zheng W, et al. Among authors: zhang c, zhang y. Future Gener Comput Syst. 2019 Oct;99:73-85. doi: 10.1016/j.future.2019.04.011. Epub 2019 Apr 9. Future Gener Comput Syst. 2019. PMID: 31427836 Free PMC article.

8

Deep learning geometrical potential for high-accuracy ab initio protein structure prediction.

Li Y, Zhang C, Yu DJ, Zhang Y. Li Y, et al. Among authors: zhang c, zhang y. iScience. 2022 May 18;25(6):104425. doi: 10.1016/j.isci.2022.104425. eCollection 2022 Jun 17. iScience. 2022. PMID: 35663033 Free PMC article.

9

RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA.

Gong S, Zhang C, Zhang Y. Gong S, et al. Among authors: zhang c, zhang y. Bioinformatics. 2019 Nov 1;35(21):4459-4461. doi: 10.1093/bioinformatics/btz282. Bioinformatics. 2019. PMID: 31161212 Free PMC article.

10

Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion.

Wu J, Yin Q, Zhang C, Geng J, Wu H, Hu H, Ke X, Zhang Y. Wu J, et al. Among authors: zhang c, zhang y. ACS Omega. 2019 Feb 12;4(2):3045-3054. doi: 10.1021/acsomega.8b02454. eCollection 2019 Feb 28. ACS Omega. 2019. PMID: 31459527 Free PMC article.

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