Silva TC - Search Results

1

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.

2

Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas.

Pan J, Silva TC, Gull N, Yang Q, Plummer JT, Chen S, Daigo K, Hamakubo T, Gery S, Ding LW, Jiang YY, Hu S, Xu LY, Li EM, Ding Y, Klempner SJ, Gayther SA, Berman BP, Koeffler HP, Lin DC. Pan J, et al. Among authors: silva tc. Cancer Res. 2020 Jul 1;80(13):2722-2736. doi: 10.1158/0008-5472.CAN-20-0390. Epub 2020 Apr 24. Cancer Res. 2020. PMID: 32332020

3

Publisher Correction: 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 Jun 28;12(1):4106. doi: 10.1038/s41467-021-24389-x. Nat Commun. 2021. PMID: 34183671 Free PMC article. No abstract available.

4

Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas.

Lin DC, Dinh HQ, Xie JJ, Mayakonda A, Silva TC, Jiang YY, Ding LW, He JZ, Xu XE, Hao JJ, Wang MR, Li C, Xu LY, Li EM, Berman BP, Phillip Koeffler H. Lin DC, et al. Among authors: silva tc. Gut. 2018 Oct;67(10):1769-1779. doi: 10.1136/gutjnl-2017-314607. Epub 2017 Aug 31. Gut. 2018. PMID: 28860350 Free PMC article.

5

Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma.

Chen L, Huang M, Plummer J, Pan J, Jiang YY, Yang Q, Silva TC, Gull N, Chen S, Ding LW, An O, Yang H, Cheng Y, Said JW, Doan N, Dinjens WN, Waters KM, Tuli R, Gayther SA, Klempner SJ, Berman BP, Meltzer SJ, Lin DC, Koeffler HP. Chen L, et al. Among authors: silva tc. Gut. 2020 Apr;69(4):630-640. doi: 10.1136/gutjnl-2019-318325. Epub 2019 Aug 13. Gut. 2020. PMID: 31409603 Free PMC article.

6

RNA-Binding Protein ZFP36L1 Suppresses Hypoxia and Cell-Cycle Signaling.

Loh XY, Sun QY, Ding LW, Mayakonda A, Venkatachalam N, Yeo MS, Silva TC, Xiao JF, Doan NB, Said JW, Ran XB, Zhou SQ, Dakle P, Shyamsunder P, Koh AP, Huang RY, Berman BP, Tan SY, Yang H, Lin DC, Koeffler HP. Loh XY, et al. Among authors: silva tc. Cancer Res. 2020 Jan 15;80(2):219-233. doi: 10.1158/0008-5472.CAN-18-2796. Epub 2019 Sep 24. Cancer Res. 2020. PMID: 31551365

7

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.

8

Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma.

Huang Y, Yang Q, Zheng Y, Lin L, Xu X, Xu XE, Silva TC, Hazawa M, Peng L, Cao H, Ding Y, Lu D, Berman BP, Xu LY, Li EM, Yin D. Huang Y, et al. Among authors: silva tc. Nucleic Acids Res. 2021 Sep 20;49(16):9246-9263. doi: 10.1093/nar/gkab679. Nucleic Acids Res. 2021. PMID: 34370013 Free PMC article.

9

GENAVi: a shiny web application for gene expression normalization, analysis and visualization.

Reyes ALP, Silva TC, Coetzee SG, Plummer JT, Davis BD, Chen S, Hazelett DJ, Lawrenson K, Berman BP, Gayther SA, Jones MR. Reyes ALP, et al. Among authors: silva tc. BMC Genomics. 2019 Oct 16;20(1):745. doi: 10.1186/s12864-019-6073-7. BMC Genomics. 2019. PMID: 31619158 Free PMC article.

10

The chromatin accessibility landscape of primary human cancers.

Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network; Greenleaf WJ, Chang HY. Corces MR, et al. Among authors: silva tc. Science. 2018 Oct 26;362(6413):eaav1898. doi: 10.1126/science.aav1898. Science. 2018. PMID: 30361341 Free PMC article.

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