TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages. - Tiago Chedraoui Silva; Antonio Colaprico; Catharina Olsen; Fulvio D'Angelo; Gianluca Bontempi; Michele Ceccarelli; Houtan Noushmehr (F1000Research, 2016)

TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data. - Tiago Chedraoui Silva; Antonio Colaprico; Catharina Olsen; Tathiane M. Malta; Gianluca Bontempi; Michele Ceccarelli; Benjamin P. Berman; Houtan Noushmehr (F1000Research, 2018)

ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. - Tiago Chedraoui Silva; Simon G. Coetzee; Nicole Gull; Lijing Yao; Dennis J. Hazelett; Houtan Noushmehr; De-Chen Lin; Benjamin P. Berman (Bioinform., 2019)

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx. - Mohamed Mounir; Marta Lucchetta; Tiago Chedraoui Silva; Catharina Olsen; Gianluca Bontempi; Xi Chen; Houtan Noushmehr; Antonio Colaprico; Elena Papaleo (PLoS Comput. Biol., 2019)