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Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion.
Jeong YJ, Knutsdottir H, Shojaeian F, Lerner MG, Wissler MF, Henriet E, Ng T, Datta S, Navarro-Serer B, Chianchiano P, Kinny-Köster B, Zimmerman JW, Stein-O'Brien G, Gaida MM, Eshleman JR, Lin MT, Fertig EJ, Ewald AJ, Bader JS, Wood LD. Jeong YJ, et al. J Clin Invest. 2023 Apr 17;133(8):e162054. doi: 10.1172/JCI162054. J Clin Invest. 2023. PMID: 36881486 Free PMC article.
CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network.
Fertig EJ, Ozawa H, Thakar M, Howard JD, Kagohara LT, Krigsfeld G, Ranaweera RS, Hughes RM, Perez J, Jones S, Favorov AV, Carey J, Stein-O'Brien G, Gaykalova DA, Ochs MF, Chung CH. Fertig EJ, et al. Oncotarget. 2016 Nov 8;7(45):73845-73864. doi: 10.18632/oncotarget.12075. Oncotarget. 2016. PMID: 27650546 Free PMC article.
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. Bioinformatics. 2017 Jun 15;33(12):1892-1894. doi: 10.1093/bioinformatics/btx058. Bioinformatics. 2017. PMID: 28174896 Free PMC article.
Enter the Matrix: Factorization Uncovers Knowledge from Omics.
Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Stein-O'Brien GL, et al. Trends Genet. 2018 Oct;34(10):790-805. doi: 10.1016/j.tig.2018.07.003. Epub 2018 Aug 22. Trends Genet. 2018. PMID: 30143323 Free PMC article. Review.
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. 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.
44 results