Li Y - Search Results

1

Deep generative design of RNA aptamers using structural predictions.

Wong F, He D, Krishnan A, Hong L, Wang AZ, Wang J, Hu Z, Omori S, Li A, Rao J, Yu Q, Jin W, Zhang T, Ilia K, Chen JX, Zheng S, King I, Li Y, Collins JJ. Wong F, et al. Among authors: li y, li a. Nat Comput Sci. 2024 Nov;4(11):829-839. doi: 10.1038/s43588-024-00720-6. Epub 2024 Nov 6. Nat Comput Sci. 2024. PMID: 39506080

2

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis.

Han W, Cheng Y, Chen J, Zhong H, Hu Z, Chen S, Zong L, Hong L, Chan TF, King I, Gao X, Li Y. Han W, et al. Among authors: li y. Brief Bioinform. 2022 Sep 20;23(5):bbac377. doi: 10.1093/bib/bbac377. Brief Bioinform. 2022. PMID: 36089561 Free PMC article.

3

Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis.

Chen Y, Wang Y, Chen Y, Cheng Y, Wei Y, Li Y, Wang J, Wei Y, Chan TF, Li Y. Chen Y, et al. Among authors: li y. Nat Commun. 2022 Nov 8;13(1):6735. doi: 10.1038/s41467-022-34550-9. Nat Commun. 2022. PMID: 36347853 Free PMC article.

4

AcrNET: predicting anti-CRISPR with deep learning.

Li Y, Wei Y, Xu S, Tan Q, Zong L, Wang J, Wang Y, Chen J, Hong L, Li Y. Li Y, et al. Bioinformatics. 2023 May 4;39(5):btad259. doi: 10.1093/bioinformatics/btad259. Bioinformatics. 2023. PMID: 37084259 Free PMC article.

5

Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model.

Shen J, Yu Q, Chen S, Tan Q, Li J, Li Y. Shen J, et al. Among authors: li y, li j. Nat Comput Sci. 2024 Jan;4(1):29-42. doi: 10.1038/s43588-023-00576-2. Epub 2023 Dec 13. Nat Comput Sci. 2024. PMID: 38177492

6

scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics.

Zheng C, Wang Y, Cheng Y, Wang X, Wei H, King I, Li Y. Zheng C, et al. Among authors: li y. Brief Bioinform. 2024 Mar 27;25(3):bbae112. doi: 10.1093/bib/bbae112. Brief Bioinform. 2024. PMID: 38555470 Free PMC article.

7

RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models.

Huang H, Lin Z, He D, Hong L, Li Y. Huang H, et al. Among authors: li y. Bioinformatics. 2024 Jun 28;40(Suppl 1):i347-i356. doi: 10.1093/bioinformatics/btae259. Bioinformatics. 2024. PMID: 38940178 Free PMC article.

8

Fast, sensitive detection of protein homologs using deep dense retrieval.

Hong L, Hu Z, Sun S, Tang X, Wang J, Tan Q, Zheng L, Wang S, Xu S, King I, Gerstein M, Li Y. Hong L, et al. Among authors: li y. Nat Biotechnol. 2024 Aug 9. doi: 10.1038/s41587-024-02353-6. Online ahead of print. Nat Biotechnol. 2024. PMID: 39123049

9

A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data.

Chen S, Wang J, Jung I, Qiu Z, Gao X, Li Y. Chen S, et al. Among authors: li y. Genome Res. 2024 Sep 20;34(8):1174-1184. doi: 10.1101/gr.279274.124. Genome Res. 2024. PMID: 39137961 Free PMC article.

10

Learning meaningful representation of single-neuron morphology via large-scale pre-training.

Fan Y, Li Y, Zhong Y, Hong L, Li L, Li Y. Fan Y, et al. Among authors: li y, li l. Bioinformatics. 2024 Sep 1;40(Suppl 2):ii128-ii136. doi: 10.1093/bioinformatics/btae395. Bioinformatics. 2024. PMID: 39230697 Free PMC article.

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