Silva TC - Search Results

1

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages.

Silva TC, Colaprico A, Olsen C, D'Angelo F, Bontempi G, Ceccarelli M, Noushmehr H. Silva TC, et al. F1000Res. 2016 Jun 29;5:1542. doi: 10.12688/f1000research.8923.2. eCollection 2016. F1000Res. 2016. PMID: 28232861 Free PMC article.

2

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.

Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot TS, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G, Noushmehr H. Colaprico A, et al. Among authors: silva tc. Nucleic Acids Res. 2016 May 5;44(8):e71. doi: 10.1093/nar/gkv1507. Epub 2015 Dec 23. Nucleic Acids Res. 2016. PMID: 26704973 Free PMC article.

3

SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data.

Cava C, Colaprico A, Bertoli G, Graudenzi A, Silva TC, Olsen C, Noushmehr H, Bontempi G, Mauri G, Castiglioni I. Cava C, et al. Among authors: silva tc. Int J Mol Sci. 2017 Jan 27;18(2):274. doi: 10.3390/ijms18020274. Int J Mol Sci. 2017. PMID: 28134831 Free PMC article.

4

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx.

Mounir M, Lucchetta M, Silva TC, Olsen C, Bontempi G, Chen X, Noushmehr H, Colaprico A, Papaleo E. Mounir M, et al. Among authors: silva tc. PLoS Comput Biol. 2019 Mar 5;15(3):e1006701. doi: 10.1371/journal.pcbi.1006701. eCollection 2019 Mar. PLoS Comput Biol. 2019. PMID: 30835723 Free PMC article.

5

Interpreting pathways to discover cancer driver genes with Moonlight.

Colaprico A, Olsen C, Bailey MH, Odom GJ, Terkelsen T, Silva TC, Olsen AV, Cantini L, Zinovyev A, Barillot E, Noushmehr H, Bertoli G, Castiglioni I, Cava C, Bontempi G, Chen XS, Papaleo E. Colaprico A, et al. Among authors: silva tc. Nat Commun. 2020 Jan 3;11(1):69. doi: 10.1038/s41467-019-13803-0. Nat Commun. 2020. PMID: 31900418 Free PMC article.

6

ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles.

Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, Lin DC, Berman BP. Silva TC, et al. Bioinformatics. 2019 Jun 1;35(11):1974-1977. doi: 10.1093/bioinformatics/bty902. Bioinformatics. 2019. PMID: 30364927 Free PMC article.

7

Glioma CpG island methylator phenotype (G-CIMP): biological and clinical implications.

Malta TM, de Souza CF, Sabedot TS, Silva TC, Mosella MS, Kalkanis SN, Snyder J, Castro AVB, Noushmehr H. Malta TM, et al. Among authors: silva tc. Neuro Oncol. 2018 Apr 9;20(5):608-620. doi: 10.1093/neuonc/nox183. Neuro Oncol. 2018. PMID: 29036500 Free PMC article. Review.

8

PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data.

Odom GJ, Ban Y, Colaprico A, Liu L, Silva TC, Sun X, Pico AR, Zhang B, Wang L, Chen X. Odom GJ, et al. Among authors: silva tc. Proteomics. 2020 Nov;20(21-22):e1900409. doi: 10.1002/pmic.201900409. Epub 2020 Jul 2. Proteomics. 2020. PMID: 32430990 Free PMC article.

9

DNA methylation-based signatures classify sporadic pituitary tumors according to clinicopathological features.

Mosella MS, Sabedot TS, Silva TC, Malta TM, Dezem FS, Asmaro KP, Wells M, Mukherjee A, Poisson LM, Snyder J, deCarvalho AC, Walbert T, Aho T, Kalkanis S, Elias PC, Antonini SR, Rock J, Noushmehr H, Castro M, Castro AV. Mosella MS, et al. Among authors: silva tc. Neuro Oncol. 2021 Aug 2;23(8):1292-1303. doi: 10.1093/neuonc/noab044. Neuro Oncol. 2021. PMID: 33631002 Free PMC article.

10

PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples.

Odom GJ, Colaprico A, Silva TC, Chen XS, Wang L. Odom GJ, et al. Among authors: silva tc. Front Genet. 2021 Dec 22;12:783713. doi: 10.3389/fgene.2021.783713. eCollection 2021. Front Genet. 2021. PMID: 35003218 Free PMC article.

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