Research

Research interests

• Entropy estimation
  
• Network inference
  
• Causal discovery
  
• Bayesian networks
  
• Prior integration
  

Research group

• Machine Learning Group (MLG)
  
• Bioinformatics and Computational Genomics Laboratory of Benjamin Haibe-Kains (bhklab)
  

Research visits

• Feb-June 2015: Bioinformatics and Computational Genomics Lab, University Health Network, Princess Margaret Cancer Centre, Toronto, Canada
  
• June-July 2014: Bioinformatics and Computational Genomics Lab, University Health Network, Princess Margaret Cancer Centre, Toronto, Canada
  
• Dec 2011: Computational Biology and Functional Genomics Lab, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, USA
  
• Oct-Dec 2010: Computational Biology and Functional Genomics Lab, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, USA
  

Publications

Peer-reviewed international journals

• 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 Jayasinghe, Feng Chen, Lihua Yu, Sam Sun, Catharina Olsen, Jaegil Kim, Alison M. Taylor, 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 Claude Zenklusen, Katherine A. Hoadley, Michael C. Wendl, llya Shmulevich, Alexander J. Lazar, David A. Wheeler, Gad Getz, The Cancer Genome Atlas Research Network
  In Cell (2018),
  doi:10.1016/j.cell.2018.03.033
  
  
• Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis.
  Claudia Cava, Gloria Bertoli, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi, Isabella Castiglioni
  In BMC genomics (2018),
  doi:10.1186/s12864-017-4423-x
  
  
• SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data.
  Claudia Cava, Antonio Colaprico, Gloria Bertoli, Alex Graudenzi, Tiago C. Silva, Catharina Olsen, Houtan Noushmehr, Gianluca Bontempi, Giancarlo Mauri, and Isabella Castiglioni
  In International Journal of Molecular Sciences (2017),
  doi:10.3390/ijms18020274
  
  
• TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 1; referees: 1 approved, 1 approved with reservations].
  Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D'Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
  In F1000Research, 5:1542 (2016),
  doi:10.12688/f1000research.8923.1
  
  
• Portraying breast cancers with long noncoding RNAs.
  Olivier Van Grembergen, Martin Bizet, Eric J. de Bony, Emilie Calonne, Pascale Putmans, Sylvain Brohée, Catharina Olsen, Mingzhou Guo, Gianluca Bontempi, Christos Sotiriou, Matthieu Defrance and François Fuks
  In Science Advances (2016),
  doi:10.1126/sciadv.1600220
  
  
• 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 M. Pagnotta, Isabella Castiglioni, Michele Ceccarelli, Gianluca Bontempi and Houtan Noushmehr
  In Nucleic Acids Research (2015),
  doi:10.1093/nar/gkv1507
  
  
• 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 Selby, Deena MA Gendoo, Patrick Grossman, Andrew H Beck, Hugo JWL Aerts, Mathieu Lupien, Anna Goldenberg and Benjamin Haibe-Kains
  In Bioinformatics (2015),
  doi:10.1093/bioinformatics/btv723
  
  
• NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference.
  Pau Bellot, Catharina Olsen, Philippe Salembier, Albert Oliveras-Vergés and Patrick E. Meyer
  In BMC Bioinformatics (2015),
  doi:10.1186/s12859-015-0728-4
  
  
• Using shRNA experiments to validate gene regulatory networks.
  Catharina Olsen , Kathleen Fleming, Niall Prendergast, Renee Rubio, Frank Emmert-Streib, Gianluca Bontempi, John Quackenbush and Benjamin Haibe-Kains
  In Genomics Data (2015),
  doi:10.1016/j.gdata.2015.03.011
  
  
• Relevance of different prior knowledge sources for inferring gene interaction networks.
  Catharina Olsen , Gianluca Bontempi, Frank Emmert-Streib, John Quackenbush and Benjamin Haibe-Kains
  In Frontiers in Genetics (2014),
  doi:10.3389/fgene.2014.00177
  
  
• Inference and validation of predictive gene networks from biomedical literature and gene expression data.
  Catharina Olsen , Kathleen Fleming, Niall Prendergast, Renee Rubio, Frank Emmert-Streib, Gianluca Bontempi, Benjamin Haibe-Kains and John Quackenbush
  In Genomics (2014),
  doi:10.1016/j.ygeno.2014.03.004
  
  
• 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
  In Bioinformatics (2013),
  doi:10.1093/bioinformatics/btt383
  
  
• Comparison and validation of genomic predictors for anticancer drug sensitivity.
  Simon Papillon-Cavanagh, Nicolas De Jay, Nehme Hachem, Catharina Olsen , Gianluca Bontempi, Hugo J W L Aerts, John Quackenbush and Benjamin Haibe-Kains
  In Journal of the American Medical Informatics Association (2013),
  doi:10.1136/amiajnl-2012-001442
  
  
• Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
  Benjamin Haibe-Kains, Catharina Olsen , Amira Djebbari, Gianluca Bontempi, Mick Correll, Christopher Bouton and John Quackenbush.
  In Nucleic Acids Research (2011),
  doi:10.1093/nar/gkr1050
  
  
• Fourier spectral factor model for prediction of multidimensional signals
  A. Alexander Miranda, Catharina Olsen and Gianluca Bontempi.
  In Signal Processing (2011),
  doi:10.1016/j.sigpro.2011.03.014
  
  
• On the Impact of Entropy Estimation on Transcriptional Regulatory Network Inference Based on Mutual Information
  Catharina Olsen , Patrick E. Meyer and Gianluca Bontempi.
  In EURASIP Journal on Bioinformatics and Systems Biology, 2008
  
  

Book chapters

• On the Integration of Prior Knowledge in the Inference of Regulatory Networks.
  Catharina Olsen, Benjamin Haibe-Kains, John Quackenbush and Gianluca Bontempi
  in "Biological Data Mining and Its Applications in Healthcare", World Scientific, 2013.
  
  
• Transcriptional Network Inference based on Information Theory
  Patrick E. Meyer, Catharina Olsen and Gianluca Bontempi
  Applied Statistics for Network Biology: Methods in Systems Biology.
  Dehmer et al. Editors. Wiley, 2011. ISBN: 978-3-527-32750-8.
  

Conferences - workshops

• Poster: A new method to identify the organ-specific role of biomarkers as oncogene or oncosuppressor in different tumor tissues
  Antonio Colaprico, Claudia Cava, Catharina Olsen, Gloria Bertoli, Isabella Castiglioni, and Gianluca Bontempi
  12th Bioinformatics ITalian Society annual meeting (BITS 2015), Milan, Italy
  
  
• Poster: Minimum Redundancy Maximum Relevance: MapReduce implementation using Apache Hadoop
  Claudio Reggiani, Yann-Aël Le Borgne, Andrea Dal Pozzolo, Catharina Olsen and Gianluca Bontempi
  BENELEARN 2014, 23rd annual Belgian-Dutch Conference on Machine Learning
  
  
• Poster & short presentation: Data-driven validation of gene regulatory networks using knock-down data
  Catharina Olsen , Gianluca Bontempi, John Quackenbush and Benjamin Haibe-Kains
  BBC13, the 8th Benelux Bioinformatics Conference, Brussels
  
  
• Poster: Inferring causal relationships using information-theoretic measures
  Catharina Olsen , Patrick E. Meyer and Gianluca Bontempi
  BBC09, the 5th Benelux Bioinformatics Conference, Liège
  file [pdf]
  
  
• Fact sheet: Using mutual information to infer causal relationships
  Catharina Olsen , Patrick E. Meyer and Gianluca Bontempi
  NIPS 2008 workshop on causality.
  file [pdf]
  
  
• On the Impact of Entropy Estimator in Transcriptional Regulatory Network Inference
  Catharina Olsen , Patrick E. Meyer and Gianluca Bontempi
  5th International Workshop on Computational Systems Biology (WSCB 08).