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PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.
Stein-O'Brien GL, Carey JL, Lee WS, Considine M, Favorov AV, Flam E, Guo T, Li S, Marchionni L, Sherman T, Sivy S, Gaykalova DA, McKay RD, Ochs MF, Colantuoni C, Fertig EJ. Stein-O'Brien GL, et al. Among authors: sherman t. Bioinformatics. 2017 Jun 15;33(12):1892-1894. doi: 10.1093/bioinformatics/btx058. Bioinformatics. 2017. PMID: 28174896 Free PMC article.
CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer.
Sherman TD, Kagohara LT, Cao R, Cheng R, Satriano M, Considine M, Krigsfeld G, Ranaweera R, Tang Y, Jablonski SA, Stein-O'Brien G, Gaykalova DA, Weiner LM, Chung CH, Fertig EJ. Sherman TD, et al. PLoS Comput Biol. 2019 Apr 19;14(4):e1006935. doi: 10.1371/journal.pcbi.1006935. eCollection 2018 Jun. PLoS Comput Biol. 2019. PMID: 31002670 Free PMC article.
Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification.
Clark BS, Stein-O'Brien GL, Shiau F, Cannon GH, Davis-Marcisak E, Sherman T, Santiago CP, Hoang TV, Rajaii F, James-Esposito RE, Gronostajski RM, Fertig EJ, Goff LA, Blackshaw S. Clark BS, et al. Among authors: sherman t. Neuron. 2019 Jun 19;102(6):1111-1126.e5. doi: 10.1016/j.neuron.2019.04.010. Epub 2019 May 22. Neuron. 2019. PMID: 31128945 Free PMC article.
Differential Variation Analysis Enables Detection of Tumor Heterogeneity Using Single-Cell RNA-Sequencing Data.
Davis-Marcisak EF, Sherman TD, Orugunta P, Stein-O'Brien GL, Puram SV, Roussos Torres ET, Hopkins AC, Jaffee EM, Favorov AV, Afsari B, Goff LA, Fertig EJ. Davis-Marcisak EF, et al. Among authors: sherman td. Cancer Res. 2019 Oct 1;79(19):5102-5112. doi: 10.1158/0008-5472.CAN-18-3882. Epub 2019 Jul 23. Cancer Res. 2019. PMID: 31337651 Free PMC article.
Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development.
Lu Y, Shiau F, Yi W, Lu S, Wu Q, Pearson JD, Kallman A, Zhong S, Hoang T, Zuo Z, Zhao F, Zhang M, Tsai N, Zhuo Y, He S, Zhang J, Stein-O'Brien GL, Sherman TD, Duan X, Fertig EJ, Goff LA, Zack DJ, Handa JT, Xue T, Bremner R, Blackshaw S, Wang X, Clark BS. Lu Y, et al. Among authors: sherman td. Dev Cell. 2020 May 18;53(4):473-491.e9. doi: 10.1016/j.devcel.2020.04.009. Epub 2020 May 7. Dev Cell. 2020. PMID: 32386599 Free PMC article.
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS.
Johnson JAI, Tsang AP, Mitchell JT, Zhou DL, Bowden J, Davis-Marcisak E, Sherman T, Liefeld T, Loth M, Goff LA, Zimmerman JW, Kinny-Köster B, Jaffee EM, Tamayo P, Mesirov JP, Reich M, Fertig EJ, Stein-O'Brien GL. Johnson JAI, et al. Among authors: sherman t. Nat Protoc. 2023 Dec;18(12):3690-3731. doi: 10.1038/s41596-023-00892-x. Epub 2023 Nov 21. Nat Protoc. 2023. PMID: 37989764 Free PMC article. Review.
176 results