Reproducible Research

Making our research fully reproducible is part of the mission of the Haibe-Kains laboratory. This is made possible when all data and software are publicly available. We do our best to make all our publications easy to reproduce and, for the following studies, we even developed companion websites to facilitate this process.

 

Characterization of conserved toxicogenomic responses in chemically exposed hepatocytes across species and platforms

Nehme, Patrick Grossmann, Alexis Blanchet-Cohen, Alain R. Bateman, Nicolas Bouchard, Jacques Archambault, Hugo J.W.L. Aerts and Benjamin Haibe-Kains

Publication: http://ehp.niehs.nih.gov/1409157/

URL: https://www.pmgenomics.ca/bhklab/pubs/tggates/

 

APOBEC3B expression in breast cancer reflects cellular proliferation while a deletion polymorphism is associated with immune activation

David W. Cescon, Benjamin Haibe-Kains and Tak W. Mak

Publication: To be announced

URL: https://www.pmgenomics.ca/bhklab/pubs/apobec/

 

Inconsistency in large pharmacogenomic studies

Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai Juul Birkbak, Andrew C. Jin, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush

Publication: http://www.nature.com/nature/journal/v504/n7480/full/nature12831.html

URL: https://github.com/bhaibeka/cdrug

 

A Three-Gene Model to Robustly Identify Breast Cancer Molecular Subtypes

Benjamin Haibe-Kains, Christine Desmedt, Sherene Loi, Aedin C Culhane, Gianluca Bontempi, John Quackenbush, Christos Sotiriou

Publication: http://jnci.oxfordjournals.org/content/104/4/311.long

URL: http://compbio.dfci.harvard.edu/pubs/sbtpaper/

 

A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?

Benjamin Haibe-Kains, Christine Desmedt, Christos Sotiriou and Gianluca Bontempi

Publication: http://bioinformatics.oxfordjournals.org/content/24/19/2200.short

URL: http://www.ulb.ac.be/di/map/bhaibeka/survcompaper/