PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis.

Feizi N, Nair SK, Smirnov P, Beri G, Eeles C, Esfahani PN, Nakano M, Tkachuk D, Mammoliti A, Gorobets E, Mer AS, Lin E, Yu YH, Martin S, Hafner M, Haibe-Kains B

Nucleic Acids Research, 2022

doi:10.1093/nar/gkab1084.

The mevalonate pathway is an actionable vulnerability oft(4;14)-positive multiple myeloma.

Longo J, Smirnov P, Li ZH, Branchard E, van Leeuwen JE, Licht JD, Haibe-Kains B, Andrews DW, Keats JJ, Pugh TJ, Trudel S, Penn LZ

Leukemia , 2021

doi:10.1038/s41375-020-0962-2.

ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets.

Nair SK, Eeles C, Ho C, Beri G, Yoo E, Tkachuk D, Tang A, Nijrabi P, Smirnov P, Seo H, Jennen D, Haibe-Kains B

Nucleic Acids Research, 2020

doi:10.1093/nar/gkaa390.

Machine learning approaches to drug response prediction: challenges and recent progress.

Adam G, Rampasek L, Safikhani Z, Smirnov P, Haibe-Kains B, Goldenberg A

NPJ precision oncology, 2020

doi:10.1038/s41698-020-0122-1.

Modeling cellular response in large-scale radiogenomic databases to advance precision radiotherapy.

Manem VSK, Lambie M, Smith I, Smirnov P, Kofia V, Freeman M, Koritzinsky M, Abazeed ME, Haibe-Kains B, Bratman SV

Cancer Research, 2019

doi:10.1158/0008-5472.CAN-19-0179.

Dr.VAE: improving drug response prediction via modeling of drug perturbation effects.

Rampasek L, Hidru D, Smirnov P, Haibe-Kains B, Goldenberg A

Bioinformatics , 2019

doi:10.1093/bioinformatics/btz158.

Integrative pharmacogenomics analysis of patient-derived xenografts.

Mer AS, Ba-Alawi W, Smirnov P, Wang YX, Brew B, Ortmann J, Tsao MS, Cescon DW, Goldenberg A, Haibe-Kains B

Cancer Research, 2019

doi:10.1158/0008-5472.CAN-19-0349.

Disruption of the anaphase-promoting complex confers resistance to TTK inhibitors in triple-negative breast cancer.

Thu KL, Silvester J, Elliott MJ, Ba-Alawi W, Duncan MH, Elia AC, Mer AS, Smirnov P, Safikhani Z, Haibe-Kains B, Mak TW, Cescon DW

Proceedings of the National Academy of Sciences of the United States of America., 2018

doi:10.1073/pnas.1719577115.

Author Correction:gene isoforms as expression-based biomarkers predictive of drug response in vitro

Safikhani Z, Smirnov P, Thu KL, Silvester J, El-Hachem N, Quevedo R, Lupien M, Mak TW, Cescon D, Haibe-Kains B

Nature Communications, 2018

doi:10.1038/s41467-017-02136-5.

Gene isoforms as expression-based biomarkers predictive of drug response in vitro.

Safikhani Z, Smirnov P, Thu KL, Silvester J, El-Hachem N, Quevedo R, Lupien M, Mak TW, Cescon D, Haibe-Kains B

Nature communications, 2017

doi:10.1038/s41467-017-01153-8.

Assessment of pharmacogenomic agreement.

Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B

F1000Research, 2016

doi:10.12688/f1000research.8705.1.

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.

Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo DMA, Grossmann P, Beck AH, Aerts HJWL, Lupien M, Goldenberg A, Haibe-Kains B

Bioinformatics , 2016

doi:10.1093/bioinformatics/btv723.

Personalized diagnosis of medulloblastoma subtypes across patients and model systems.

Gendoo DMA, Smirnov P, Lupien M, Haibe-Kains B

Genomics , 2015

doi:10.1016/j.ygeno.2015.05.002.