T
Tiago C. Silva
Researcher at University of Miami
Publications - 45
Citations - 4444
Tiago C. Silva is an academic researcher from University of Miami. The author has contributed to research in topics: DNA methylation & Bioconductor. The author has an hindex of 15, co-authored 43 publications receiving 2414 citations. Previous affiliations of Tiago C. Silva include University of São Paulo & Cedars-Sinai Medical Center.
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Journal ArticleDOI
TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.
Antonio Colaprico,Tiago C. Silva,Catharina Olsen,Luciano Garofano,Claudia Cava,Davide Garolini,Thais S. Sabedot,Tathiane M. Malta,Stefano Maria Pagnotta,Isabella Castiglioni,Michele Ceccarelli,Gianluca Bontempi,Houtan Noushmehr +12 more
TL;DR: An R/Bioconductor package called TCGAbiolinks is developed to address bioinformatics challenges of the Cancer Genome Atlas data by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data.
Journal ArticleDOI
The chromatin accessibility landscape of primary human cancers
M. Ryan Corces,Jeffrey M. Granja,Shadi Shams,Bryan H. Louie,Jose A. Seoane,Wanding Zhou,Tiago C. Silva,Tiago C. Silva,Clarice S. Groeneveld,Christopher K. Wong,Seung Woo Cho,Ansuman T. Satpathy,Maxwell R. Mumbach,Katherine A. Hoadley,A. Gordon Robertson,Nathan C. Sheffield,Ina Felau,Mauro A. A. Castro,Benjamin P. Berman,Louis M. Staudt,Jean C. Zenklusen,Peter W. Laird,Christina Curtis,William J. Greenleaf,Howard Y. Chang +24 more
TL;DR: These chromatin accessibility profiles identify cancer- and tissue-specific DNA regulatory elements that enable classification of tumor subtypes with newly recognized prognostic importance, and identify distinct TF activities in cancer based on differences in the inferred patterns of TF-DNA interaction and gene expression.
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New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEX
Mohamed Mounir,Marta Lucchetta,Tiago C. Silva,Catharina Olsen,Gianluca Bontempi,Xi Chen,Houtan Noushmehr,Houtan Noushmehr,Antonio Colaprico,Antonio Colaprico,Elena Papaleo +10 more
TL;DR: New features and enhancements of TCGAbiolinks are introduced, including more accurate and flexible pipelines for differential expression analyses, different methods for tumor purity estimation and filtering, and integration of normal samples from other platforms iv) support for other genomics datasets, exemplified by the TARGET data.
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Glioma CpG island methylator phenotype (G-CIMP): biological and clinical implications.
Tathiane M. Malta,Tathiane M. Malta,Camila F de Souza,Camila F de Souza,Thais S. Sabedot,Thais S. Sabedot,Tiago C. Silva,Maritza S Mosella,Steven N. Kalkanis,James Snyder,Ana Valeria B Castro,Houtan Noushmehr,Houtan Noushmehr +12 more
TL;DR: The evolution of the understanding of the G-CIMP subsets is highlighted and how recent advances in characterizing the genome and epigenome of gliomas may influence future basic and translational research is highlighted.
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