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Bi-order multimodal integration of single-cell data.
Dou J, Liang S, Mohanty V, Miao Q, Huang Y, Liang Q, Cheng X, Kim S, Choi J, Li Y, Li L, Daher M, Basar R, Rezvani K, Chen R, Chen K. Dou J, et al. Among authors: cheng x. Genome Biol. 2022 May 9;23(1):112. doi: 10.1186/s13059-022-02679-x. Genome Biol. 2022. PMID: 35534898 Free PMC article.
A multi-omics atlas of the human retina at single-cell resolution.
Liang Q, Cheng X, Wang J, Owen L, Shakoor A, Lillvis JL, Zhang C, Farkas M, Kim IK, Li Y, DeAngelis M, Chen R. Liang Q, et al. Among authors: cheng x. Cell Genom. 2023 Apr 11;3(6):100298. doi: 10.1016/j.xgen.2023.100298. eCollection 2023 Jun 14. Cell Genom. 2023. PMID: 37388908 Free PMC article.
Single-nucleotide variant calling in single-cell sequencing data with Monopogen.
Dou J, Tan Y, Kock KH, Wang J, Cheng X, Tan LM, Han KY, Hon CC, Park WY, Shin JW, Jin H, Wang Y, Chen H, Ding L, Prabhakar S, Navin N, Chen R, Chen K. Dou J, et al. Among authors: cheng x. Nat Biotechnol. 2024 May;42(5):803-812. doi: 10.1038/s41587-023-01873-x. Epub 2023 Aug 17. Nat Biotechnol. 2024. PMID: 37592035 Free PMC article.
DeMixSC: a deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for improved analysis of cell-type ratios in complex tissue samples.
Guo S, Liu X, Cheng X, Jiang Y, Ji S, Liang Q, Koval A, Li Y, Owen LA, Kim IK, Aparicio A, Shen JP, Kopetz S, Weinstein JN, DeAngelis MM, Chen R, Wang W. Guo S, et al. Among authors: cheng x. bioRxiv [Preprint]. 2023 Nov 11:2023.10.10.561733. doi: 10.1101/2023.10.10.561733. bioRxiv. 2023. Update in: Genome Res. 2025 Jan 6. doi: 10.1101/gr.278822.123 PMID: 37873318 Free PMC article. Updated. Preprint.
To be or not to be - Decoding the Trabecular Meshwork Cell Identity.
Tian A, Baidouri H, Kim S, Li J, Cheng X, Li Y, Chen R, Raghunathan V. Tian A, et al. Among authors: cheng x. bioRxiv [Preprint]. 2024 Apr 29:2024.04.26.591346. doi: 10.1101/2024.04.26.591346. bioRxiv. 2024. PMID: 38746421 Free PMC article. Preprint.
Comprehensive single-cell atlas of the mouse retina.
Li J, Choi J, Cheng X, Ma J, Pema S, Sanes JR, Mardon G, Frankfort BJ, Tran NM, Li Y, Chen R. Li J, et al. Among authors: cheng x. iScience. 2024 May 8;27(6):109916. doi: 10.1016/j.isci.2024.109916. eCollection 2024 Jun 21. iScience. 2024. PMID: 38812536 Free PMC article.
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