Li M - Search Results

1

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network.

Hu J, Li X, Coleman K, Schroeder A, Ma N, Irwin DJ, Lee EB, Shinohara RT, Li M. Hu J, et al. Among authors: li x, li m. Nat Methods. 2021 Nov;18(11):1342-1351. doi: 10.1038/s41592-021-01255-8. Epub 2021 Oct 28. Nat Methods. 2021. PMID: 34711970

2

PennDiff: detecting differential alternative splicing and transcription by RNA sequencing.

Hu Y, Lin J, Hu J, Hu G, Wang K, Zhang H, Reilly MP, Li M. Hu Y, et al. Among authors: li m. Bioinformatics. 2018 Jul 15;34(14):2384-2391. doi: 10.1093/bioinformatics/bty097. Bioinformatics. 2018. PMID: 29474557 Free PMC article.

3

SAVER: gene expression recovery for single-cell RNA sequencing.

Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR. Huang M, et al. Among authors: li m. Nat Methods. 2018 Jul;15(7):539-542. doi: 10.1038/s41592-018-0033-z. Epub 2018 Jun 25. Nat Methods. 2018. PMID: 29941873 Free PMC article.

4

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference.

Wang X, Park J, Susztak K, Zhang NR, Li M. Wang X, et al. Among authors: li m. Nat Commun. 2019 Jan 22;10(1):380. doi: 10.1038/s41467-018-08023-x. Nat Commun. 2019. PMID: 30670690 Free PMC article.

5

Pathologic gene network rewiring implicates PPP1R3A as a central regulator in pressure overload heart failure.

Cordero P, Parikh VN, Chin ET, Erbilgin A, Gloudemans MJ, Shang C, Huang Y, Chang AC, Smith KS, Dewey F, Zaleta K, Morley M, Brandimarto J, Glazer N, Waggott D, Pavlovic A, Zhao M, Moravec CS, Tang WHW, Skreen J, Malloy C, Hannenhalli S, Li H, Ritter S, Li M, Bernstein D, Connolly A, Hakonarson H, Lusis AJ, Margulies KB, Depaoli-Roach AA, Montgomery SB, Wheeler MT, Cappola T, Ashley EA. Cordero P, et al. Among authors: li h, li m. Nat Commun. 2019 Jun 24;10(1):2760. doi: 10.1038/s41467-019-10591-5. Nat Commun. 2019. PMID: 31235787 Free PMC article.

6

ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing.

Fan J, Hu J, Xue C, Zhang H, Susztak K, Reilly MP, Xiao R, Li M. Fan J, et al. Among authors: li m. PLoS Genet. 2020 May 11;16(5):e1008786. doi: 10.1371/journal.pgen.1008786. eCollection 2020 May. PLoS Genet. 2020. PMID: 32392242 Free PMC article.

7

Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis.

Li X, Wang K, Lyu Y, Pan H, Zhang J, Stambolian D, Susztak K, Reilly MP, Hu G, Li M. Li X, et al. Among authors: li m. Nat Commun. 2020 May 11;11(1):2338. doi: 10.1038/s41467-020-15851-3. Nat Commun. 2020. PMID: 32393754 Free PMC article.

8

APOE and TREM2 regulate amyloid-responsive microglia in Alzheimer's disease.

Nguyen AT, Wang K, Hu G, Wang X, Miao Z, Azevedo JA, Suh E, Van Deerlin VM, Choi D, Roeder K, Li M, Lee EB. Nguyen AT, et al. Among authors: li m. Acta Neuropathol. 2020 Oct;140(4):477-493. doi: 10.1007/s00401-020-02200-3. Epub 2020 Aug 25. Acta Neuropathol. 2020. PMID: 32840654 Free PMC article.

9

Iterative transfer learning with neural network for clustering and cell type classification in single-cell RNA-seq analysis.

Hu J, Li X, Hu G, Lyu Y, Susztak K, Li M. Hu J, et al. Among authors: li x, li m. Nat Mach Intell. 2020 Oct;2(10):607-618. doi: 10.1038/s42256-020-00233-7. Epub 2020 Oct 5. Nat Mach Intell. 2020. PMID: 33817554 Free PMC article.

10

A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics.

Lakkis J, Wang D, Zhang Y, Hu G, Wang K, Pan H, Ungar L, Reilly MP, Li X, Li M. Lakkis J, et al. Among authors: li x, li m. Genome Res. 2021 Oct;31(10):1753-1766. doi: 10.1101/gr.271874.120. Epub 2021 May 25. Genome Res. 2021. PMID: 34035047 Free PMC article.

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