C
Catharina Olsen
Researcher at Université libre de Bruxelles
Publications - 38
Citations - 3934
Catharina Olsen is an academic researcher from Université libre de Bruxelles. The author has contributed to research in topics: Bioconductor & Inference. The author has an hindex of 15, co-authored 32 publications receiving 2419 citations. Previous affiliations of Catharina Olsen include Princess Margaret Cancer Centre & Harvard University.
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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
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.
Journal ArticleDOI
Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics
Li Ding,Matthew H. Bailey,Eduard Porta-Pardo,Vesteinn Thorsson,Antonio Colaprico,Denis Bertrand,David L Gibbs,Amila Weerasinghe,Kuan-lin Huang,Collin Tokheim,Isidro Cortes-Ciriano,Reyka G Jayasinghe,Feng Chen,Lihua Yu,Sam Q. Sun,Catharina Olsen,Jaegil Kim,Alison M. Taylor,Andrew D. Cherniack,Andrew D. Cherniack,Rehan Akbani,Chayaporn Suphavilai,Niranjan Nagarajan,Joshua M. Stuart,Gordon B. Mills,Matthew A. Wyczalkowski,Benjamin G. Vincent,Carolyn M. Hutter,Jean C. Zenklusen,Katherine A Hoadley,Michael C. Wendl,llya Shmulevich,Alexander J. Lazar,David A. Wheeler,Gad Getz,Gad Getz +35 more
TL;DR: Results from the TCGA PanCancer Atlas project will anchor future characterization of rare and common tumor types, primary and relapsed tumors, and cancers across ancestry groups and will guide the deployment of clinical genomic sequencing.
Journal ArticleDOI
PharmacoGx: an R package for analysis of large pharmacogenomic datasets
Petr Smirnov,Zhaleh Safikhani,Nehme El-Hachem,Dong Wang,Adrian She,Catharina Olsen,Mark Freeman,Heather M. Selby,Deena M.A. Gendoo,Patrick Grossmann,Andrew H. Beck,Hugo J.W.L. Aerts,Mathieu Lupien,Anna Goldenberg,Benjamin Haibe-Kains +14 more
TL;DR: The implementation of PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets, is implemented and the utility of the package is demonstrated in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia.
Journal ArticleDOI
mRMRe: an R package for parallelized mRMR ensemble feature selection.
Nicolas De Jay,Simon Papillon-Cavanagh,Catharina Olsen,Nehme El-Hachem,Gianluca Bontempi,Benjamin Haibe-Kains +5 more
TL;DR: The mRMRe R package is described, in which the mRMR technique is extended by using an ensemble approach to better explore the feature space and build more robust predictors, and shows significant gains in terms of run-time speed when compared with previously released packages.