TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; referees: 1 approved, 2 approved with reservations]

by Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D'Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Published 2016-12-01

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

by Mohamed Mounir, Marta Lucchetta, Tiago C Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo
Published 2019-03-01

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

by Yueyuan Zheng, Guowei Huang, Tiago C. Silva, Qian Yang, Yan-Yi Jiang, H. Phillip Koeffler, De-Chen Lin, Benjamin P. Berman
Published 2021-06-01

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

by Yueyuan Zheng, Guowei Huang, Tiago C. Silva, Qian Yang, Yan-Yi Jiang, H. Phillip Koeffler, De-Chen Lin, Benjamin P. Berman
Published 2021-04-01

Sex-specific DNA methylation differences in Alzheimer’s disease pathology

by Lanyu Zhang, Juan I. Young, Lissette Gomez, Tiago C. Silva, Michael A. Schmidt, Jesse Cai, Xi Chen, Eden R. Martin, Lily Wang
Published 2021-04-01

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

by Lanyu Zhang, Tiago C. Silva, Juan I. Young, Lissette Gomez, Michael A. Schmidt, Kara L. Hamilton-Nelson, Brian W. Kunkle, Xi Chen, Eden R. Martin, Lily Wang
Published 2020-11-01

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

by Alberto Luiz P. Reyes, Tiago C. Silva, Simon G. Coetzee, Jasmine T. Plummer, Brian D. Davis, Stephanie Chen, Dennis J. Hazelett, Kate Lawrenson, Benjamin P. Berman, Simon A. Gayther, Michelle R. Jones
Published 2019-10-01

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

by Min Lu, Yifan Sha, Tiago C. Silva, Antonio Colaprico, Xiaodian Sun, Yuguang Ban, Yuguang Ban, Lily Wang, Lily Wang, Lily Wang, Lily Wang, Brian D. Lehmann, Brian D. Lehmann, X. Steven Chen, X. Steven Chen
Published 2021-08-01

Interpreting pathways to discover cancer driver genes with Moonlight

by Antonio Colaprico, Catharina Olsen, Matthew H. Bailey, Gabriel J. Odom, Thilde Terkelsen, Tiago C. Silva, André V. Olsen, Laura Cantini, Andrei Zinovyev, Emmanuel Barillot, Houtan Noushmehr, Gloria Bertoli, Isabella Castiglioni, Claudia Cava, Gianluca Bontempi, Xi Steven Chen, Elena Papaleo
Published 2020-01-01