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Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces.
Deshpande A, Loth M, Sidiropoulos DN, Zhang S, Yuan L, Bell ATF, Zhu Q, Ho WJ, Santa-Maria C, Gilkes DM, Williams SR, Uytingco CR, Chew J, Hartnett A, Bent ZW, Favorov AV, Popel AS, Yarchoan M, Kiemen A, Wu PH, Fujikura K, Wirtz D, Wood LD, Zheng L, Jaffee EM, Anders RA, Danilova L, Stein-O'Brien G, Kagohara LT, Fertig EJ. Deshpande A, et al. Among authors: kagohara lt. Cell Syst. 2023 Apr 19;14(4):285-301.e4. doi: 10.1016/j.cels.2023.03.004. Cell Syst. 2023. PMID: 37080163 Free PMC article.
PD-L1 expression in the Merkel cell carcinoma microenvironment: association with inflammation, Merkel cell polyomavirus and overall survival.
Lipson EJ, Vincent JG, Loyo M, Kagohara LT, Luber BS, Wang H, Xu H, Nayar SK, Wang TS, Sidransky D, Anders RA, Topalian SL, Taube JM. Lipson EJ, et al. Among authors: kagohara lt. Cancer Immunol Res. 2013 Jul;1(1):54-63. doi: 10.1158/2326-6066.CIR-13-0034. Cancer Immunol Res. 2013. PMID: 24416729 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. Among authors: kagohara lt. Oncotarget. 2016 Nov 8;7(45):73845-73864. doi: 10.18632/oncotarget.12075. Oncotarget. 2016. PMID: 27650546 Free PMC article.
Comparative mutational landscape analysis of patient-derived tumour xenografts.
Brait M, Izumchenko E, Kagohara LT, Long S, Wysocki PT, Faherty B, Fertig EJ, Khor TO, Bruckheimer E, Baia G, Ciznadija D, Sloma I, Ben-Zvi I, Paz K, Sidransky D. Brait M, et al. Among authors: kagohara lt. Br J Cancer. 2017 Feb 14;116(4):515-523. doi: 10.1038/bjc.2016.450. Epub 2017 Jan 24. Br J Cancer. 2017. PMID: 28118322 Free PMC article.
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.
Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Zambo KD, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ. Afsari B, et al. Among authors: kagohara lt. Bioinformatics. 2018 Jun 1;34(11):1859-1867. doi: 10.1093/bioinformatics/bty004. Bioinformatics. 2018. PMID: 29342249 Free PMC article.
Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.
Stein-O'Brien G, Kagohara LT, Li S, Thakar M, Ranaweera R, Ozawa H, Cheng H, Considine M, Schmitz S, Favorov AV, Danilova LV, Califano JA, Izumchenko E, Gaykalova DA, Chung CH, Fertig EJ. Stein-O'Brien G, et al. Among authors: kagohara lt. Genome Med. 2018 May 23;10(1):37. doi: 10.1186/s13073-018-0545-2. Genome Med. 2018. PMID: 29792227 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. Among authors: kagohara lt. 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.
Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines.
Kagohara LT, Zamuner F, Davis-Marcisak EF, Sharma G, Considine M, Allen J, Yegnasubramanian S, Gaykalova DA, Fertig EJ. Kagohara LT, et al. Br J Cancer. 2020 Jul;123(1):101-113. doi: 10.1038/s41416-020-0851-5. Epub 2020 May 4. Br J Cancer. 2020. PMID: 32362655 Free PMC article.
37 results