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Items: 12

1.

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.

PLoS Comput Biol. 2019 Apr 19;14(4):e1006935. doi: 10.1371/journal.pcbi.1006935. eCollection 2018 Jun.

2.

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.

Genome Med. 2018 May 23;10(1):37. doi: 10.1186/s13073-018-0545-2.

3.

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.

Bioinformatics. 2018 Jun 1;34(11):1859-1867. doi: 10.1093/bioinformatics/bty004.

4.

KRAS mutation status is highly homogeneous between areas of the primary tumor and the corresponding metastasis of colorectal adenocarcinomas: one less problem in patient care.

Petaccia de Macedo M, Melo FM, Ribeiro HSC, Marques MC, Kagohara LT, Begnami MD, Neto JC, Ribeiro JS, Soares FA, Carraro DM, Cunha IW.

Am J Cancer Res. 2017 Sep 1;7(9):1978-1989. eCollection 2017.

5.

Epigenetic regulation of gene expression in cancer: techniques, resources and analysis.

Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA, Fertig EJ.

Brief Funct Genomics. 2018 Jan 1;17(1):49-63. doi: 10.1093/bfgp/elx018.

6.

Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity.

Kulkarni P, Jolly MK, Jia D, Mooney SM, Bhargava A, Kagohara LT, Chen Y, Hao P, He Y, Veltri RW, Grishaev A, Weninger K, Levine H, Orban J.

Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2644-E2653. doi: 10.1073/pnas.1700082114. Epub 2017 Mar 13.

7.

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.

Br J Cancer. 2017 Feb 14;116(4):515-523. doi: 10.1038/bjc.2016.450. Epub 2017 Jan 24.

8.

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.

Oncotarget. 2016 Nov 8;7(45):73845-73864. doi: 10.18632/oncotarget.12075.

9.

Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA.

Izumchenko E, Chang X, Brait M, Fertig E, Kagohara LT, Bedi A, Marchionni L, Agrawal N, Ravi R, Jones S, Hoque MO, Westra WH, Sidransky D.

Nat Commun. 2015 Sep 16;6:8258. doi: 10.1038/ncomms9258.

10.

Global and gene-specific DNA methylation pattern discriminates cholecystitis from gallbladder cancer patients in Chile.

Kagohara LT, Schussel JL, Subbannayya T, Sahasrabuddhe N, Lebron C, Brait M, Maldonado L, Valle BL, Pirini F, Jahuira M, Lopez J, Letelier P, Brebi-Mieville P, Ili C, Pandey A, Chatterjee A, Sidransky D, Guerrero-Preston R.

Future Oncol. 2015;11(2):233-49. doi: 10.2217/fon.14.165. Epub 2014 Jul 28.

11.

Epigenetic inactivation of VGF associated with Urothelial Cell Carcinoma and its potential as a non-invasive biomarker using urine.

Hayashi M, Bernert H, Kagohara LT, Maldonado L, Brait M, Schoenberg M, Bivalacqua T, Netto GJ, Koch W, Sidransky D, Hoque MO.

Oncotarget. 2014 May 30;5(10):3350-61.

12.

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.

Cancer Immunol Res. 2013 Jul;1(1):54-63. doi: 10.1158/2326-6066.CIR-13-0034.

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