Peng Y - Search Results

1

Detection of new pioneer transcription factors as cell-type-specific nucleosome binders.

Peng Y, Song W, Teif VB, Ovcharenko I, Landsman D, Panchenko AR. Peng Y, et al. Elife. 2024 Jan 31;12:RP88936. doi: 10.7554/eLife.88936. Elife. 2024. PMID: 38293962 Free PMC article.

2

Interpretable deep residual network uncovers nucleosome positioning and associated features.

Masoudi-Sobhanzadeh Y, Li S, Peng Y, Panchenko AR. Masoudi-Sobhanzadeh Y, et al. Among authors: peng y. Nucleic Acids Res. 2024 Aug 27;52(15):8734-8745. doi: 10.1093/nar/gkae623. Nucleic Acids Res. 2024. PMID: 39036965 Free PMC article.

3

Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis.

Xu W, Zhang H, Guo W, Jiang L, Zhao Y, Peng Y. Xu W, et al. Among authors: peng y. Brief Bioinform. 2024 Jan 22;25(2):bbad532. doi: 10.1093/bib/bbad532. Brief Bioinform. 2024. PMID: 38329268 Free PMC article.

4

SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein-protein complexes.

Rimal P, Panday SK, Xu W, Peng Y, Alexov E. Rimal P, et al. Among authors: peng y. Bioinformatics. 2024 Sep 2;40(9):btae544. doi: 10.1093/bioinformatics/btae544. Bioinformatics. 2024. PMID: 39240325 Free PMC article.

5

Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model.

Peng Y, Alexov E. Peng Y, et al. Proteins. 2016 Dec;84(12):1797-1809. doi: 10.1002/prot.25162. Epub 2016 Oct 1. Proteins. 2016. PMID: 27696497 Free PMC article.

6

SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions.

Li G, Panday SK, Peng Y, Alexov E. Li G, et al. Among authors: peng y. Bioinformatics. 2021 Nov 5;37(21):3760-3765. doi: 10.1093/bioinformatics/btab567. Bioinformatics. 2021. PMID: 34343273 Free PMC article.

7

Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.

Peng Y, Sun L, Jia Z, Li L, Alexov E. Peng Y, et al. Bioinformatics. 2018 Mar 1;34(5):779-786. doi: 10.1093/bioinformatics/btx698. Bioinformatics. 2018. PMID: 29091991 Free PMC article.

8

Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes.

Peng Y, Alexov E. Peng Y, et al. Proteins. 2017 Feb;85(2):282-295. doi: 10.1002/prot.25221. Epub 2017 Jan 5. Proteins. 2017. PMID: 27936518 Free PMC article.

9

Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding.

Peng Y, Alexov E. Peng Y, et al. Proteins. 2016 Feb;84(2):232-9. doi: 10.1002/prot.24968. Epub 2016 Jan 11. Proteins. 2016. PMID: 26650512 Free PMC article.

10

Rare missense variant p.Ala505Ser in the ZAK protein observed in a patient with split-hand/foot malformation from a non-consanguineous pedigree.

Funk CR, Huey ES, May MM, Peng Y, Michonova E, Best RG, Schwartz CE, Blenda AV. Funk CR, et al. Among authors: peng y. J Int Med Res. 2020 Apr;48(4):300060519879293. doi: 10.1177/0300060519879293. J Int Med Res. 2020. PMID: 32266845 Free PMC article.

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