Silva TC - Search Results

1

Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes.

Lehmann BD, Colaprico A, Silva TC, Chen J, An H, Ban Y, Huang H, Wang L, James JL, Balko JM, Gonzalez-Ericsson PI, Sanders ME, Zhang B, Pietenpol JA, Chen XS. Lehmann BD, et al. Among authors: silva tc. Nat Commun. 2021 Nov 1;12(1):6276. doi: 10.1038/s41467-021-26502-6. Nat Commun. 2021. PMID: 34725325 Free PMC article.

2

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.

3

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.

4

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.

5

Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer's disease.

Zhang L, Silva TC, Young JI, Gomez L, Schmidt MA, Hamilton-Nelson KL, Kunkle BW, Chen X, Martin ER, Wang L. Zhang L, et al. Among authors: silva tc. Nat Commun. 2020 Nov 30;11(1):6114. doi: 10.1038/s41467-020-19791-w. Nat Commun. 2020. PMID: 33257653 Free PMC article.

6

Sex-specific DNA methylation differences in Alzheimer's disease pathology.

Zhang L, Young JI, Gomez L, Silva TC, Schmidt MA, Cai J, Chen X, Martin ER, Wang L. Zhang L, et al. Among authors: silva tc. Acta Neuropathol Commun. 2021 Apr 26;9(1):77. doi: 10.1186/s40478-021-01177-8. Acta Neuropathol Commun. 2021. PMID: 33902726 Free PMC article.

7

A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes.

Zheng Y, Huang G, Silva TC, Yang Q, Jiang YY, Koeffler HP, Lin DC, Berman BP. Zheng Y, et al. Among authors: silva tc. Nat Commun. 2021 Apr 30;12(1):2485. doi: 10.1038/s41467-021-22720-0. Nat Commun. 2021. PMID: 33931649 Free PMC article.

8

LR Hunting: A Random Forest Based Cell-Cell Interaction Discovery Method for Single-Cell Gene Expression Data.

Lu M, Sha Y, Silva TC, Colaprico A, Sun X, Ban Y, Wang L, Lehmann BD, Chen XS. Lu M, et al. Among authors: silva tc. Front Genet. 2021 Aug 20;12:708835. doi: 10.3389/fgene.2021.708835. eCollection 2021. Front Genet. 2021. PMID: 34497635 Free PMC article.

9

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.

10

MethReg: estimating the regulatory potential of DNA methylation in gene transcription.

Silva TC, Young JI, Martin ER, Chen XS, Wang L. Silva TC, et al. Nucleic Acids Res. 2022 May 20;50(9):e51. doi: 10.1093/nar/gkac030. Nucleic Acids Res. 2022. PMID: 35100398 Free PMC article.

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