Publications

2022

1. PharmacoDB 2.0: Improving Scalability and Transparency of in Vitro Pharmacogenomics Analysis

   Feizi, Nikta, Nair, Sisira Kadambat, Smirnov, Petr, Beri, Gangesh, Eeles, Christopher, Esfahani, Parinaz Nasr, Nakano, Minoru, Tkachuk, Denis, Mammoliti, Anthony, Gorobets, Evgeniya, and others,

   Nucleic acids research 2022

2021

1. The Mevalonate Pathway Is an Actionable Vulnerability of t (4; 14)-Positive Multiple Myeloma

   Longo, Joseph, Smirnov, Petr, Li, Zhihua, Branchard, Emily, van Leeuwen, Jenna E, Licht, Jonathan D, Haibe-Kains, Benjamin, Andrews, David W, Keats, Jonathan J, Pugh, Trevor J, and others,

   Leukemia 2021
2. Orchestrating and Sharing Large Multimodal Data for Transparent and Reproducible Research

   Mammoliti, Anthony, Smirnov, Petr, Nakano, Minoru, Safikhani, Zhaleh, Eeles, Christopher, Seo, Heewon, Nair, Sisira Kadambat, Mer, Arvind S, Smith, Ian, Ho, Chantal, and others,

   Nature communications 2021
3. Drug Sensitivity Prediction from Cell Line-Based Pharmacogenomics Data: Guidelines for Developing Machine Learning Models

   Sharifi-Noghabi, Hossein, Jahangiri-Tazehkand, Soheil, Smirnov, Petr, Hon, Casey, Mammoliti, Anthony, Nair, Sisira Kadambat, Mer, Arvind Singh, Ester, Martin, and Haibe-Kains, Benjamin

   Briefings in Bioinformatics 2021

2020

1. Machine Learning Approaches to Drug Response Prediction: Challenges and Recent Progress

   Adam, George, Rampášek, Ladislav, Safikhani, Zhaleh, Smirnov, Petr, Haibe-Kains, Benjamin, and Goldenberg, Anna

   NPJ precision oncology 2020
2. Bimodality of Gene Expression in Cancer Patient Tumors as Interpretable Biomarkers for Drug Sensitivity

   Ba-Alawi, Wail, Nair, Sisira Kadambat, Li, Bo, Mammoliti, Anthony, Smirnov, Petr, Mer, Arvind Singh, Penn, Linda, and Haibe-Kains, Benjamin

   bioRxiv 2020
3. ToxicoDB: An Integrated Database to Mine and Visualize Large-Scale Toxicogenomic Datasets

   Nair, Sisira Kadambat, Eeles, Christopher, Ho, Chantal, Beri, Gangesh, Yoo, Esther, Tkachuk, Denis, Tang, Amy, Nijrabi, Parwaiz, Smirnov, Petr, Seo, Heewon, and others,

   Nucleic acids research 2020
4. Assessment of Genetic Drift in Large Pharmacogenomic Studies

   Quevedo, Rene, Smirnov, Petr, Tkachuk, Denis, Ho, Chantal, El-Hachem, Nehme, Safikhani, Zhaleh, Pugh, Trevor J, and Haibe-Kains, Benjamin

   Cell systems 2020

2019

1. Reducing Adversarial Example Transferability Using Gradient Regularization

   Adam, George, Smirnov, Petr, Haibe-Kains, Benjamin, and Goldenberg, Anna

   arXiv preprint arXiv:1904.07980 2019
2. Creating Reproducible Pharmacogenomic Analysis Pipelines

   Mammoliti, Anthony, Smirnov, Petr, Safikhani, Zhaleh, Ba-Alawi, Wail, and Haibe-Kains, Benjamin

   Scientific Data 2019
3. Modeling Cellular Response in Large-Scale Radiogenomic Databases to Advance Precision Radiotherapy

   Manem, Venkata SK, Lambie, Meghan, Smith, Ian, Smirnov, Petr, Kofia, Victor, Freeman, Mark, Koritzinsky, Marianne, Abazeed, Mohamed E, Haibe-Kains, Benjamin, and Bratman, Scott V

   Cancer research 2019
4. Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts

   Mer, Arvind S, Ba-Alawi, Wail, Smirnov, Petr, Wang, Yi X, Brew, Ben, Ortmann, Janosch, Tsao, Ming-Sound, Cescon, David W, Goldenberg, Anna, and Haibe-Kains, Benjamin

   Cancer Research 2019
5. Dr. VAE: Improving Drug Response Prediction via Modeling of Drug Perturbation Effects

   Rampášek, Ladislav, Hidru, Daniel, Smirnov, Petr, Haibe-Kains, Benjamin, and Goldenberg, Anna

   Bioinformatics 2019

2018

1. Stochastic Combinatorial Ensembles for Defending against Adversarial Examples

   Adam, George A, Smirnov, Petr, Duvenaud, David, Haibe-Kains, Benjamin, and Goldenberg, Anna

   arXiv preprint arXiv:1808.06645 2018
2. PharmacoDB: An Integrative Database for Mining in Vitro Anticancer Drug Screening Studies

   Smirnov, Petr, Kofia, Victor, Maru, Alexander, Freeman, Mark, Ho, Chantal, El-Hachem, Nehme, Adam, George-Alexandru, Ba-Alawi, Wail, Safikhani, Zhaleh, and Haibe-Kains, Benjamin

   Nucleic acids research 2018
3. 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, and others,

   Proceedings of the National Academy of Sciences 2018
4. Tissue Specificity of in Vitro Drug Sensitivity

   Yao, Fupan, Madani Tonekaboni, Seyed Ali, Safikhani, Zhaleh, Smirnov, Petr, El-Hachem, Nehme, Freeman, Mark, Manem, Venkata Satya Kumar, and Haibe-Kains, Benjamin

   Journal of the American Medical Informatics Association 2018

2017

1. Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy

   El-Hachem, Nehme, Gendoo, Deena MA, Ghoraie, Laleh Soltan, Safikhani, Zhaleh, Smirnov, Petr, Chung, Christina, Deng, Kenan, Fang, Ailsa, Birkwood, Erin, Ho, Chantal, and others,

   Cancer research 2017
2. Gene Isoforms as Expression-Based Biomarkers Predictive of Drug Response in Vitro

   Safikhani, Zhaleh, Smirnov, Petr, Thu, Kelsie L, Silvester, Jennifer, El-Hachem, Nehme, Quevedo, Rene, Lupien, Mathieu, Mak, Tak W, Cescon, David, and Haibe-Kains, Benjamin

   Nature communications 2017

2016

1. Consistency in Drug Response Profiling Reply

   Safikhani, Zhaleh, El-Hachem, Nehme, Smirnov, Petr, Freeman, Mark, Goldenberg, Anna, Birkbak, Nicolai J, Beck, Andrew H, Aerts, Hugo JWL, Quackenbush, John, and Haibe-Kains, Benjamin

   Nature 2016
2. Drug Response Consistency in CCLE and CGP Reply

   Safikhani, Zhaleh, El-Hachem, Nehme, Smirnov, Petr, Freeman, Mark, Goldenberg, Anna, Birkbak, Nicolai J, Beck, Andrew H, Aerts, Hugo JWL, Quackenbush, John, and Haibe-Kains, Benjamin

   Nature 2016
3. Revisiting Inconsistency in Large Pharmacogenomic Studies

   Safikhani, Zhaleh, Smirnov, Petr, Freeman, Mark, El-Hachem, Nehme, She, Adrian, Rene, Quevedo, Goldenberg, Anna, Birkbak, Nicolai J, Hatzis, Christos, Shi, Leming, and others,

   F1000Research 2016
4. Safikhani et al. Reply

   Safikhani, Zhaleh, El-Hachem, Nehme, Smirnov, Petr, Freeman, Mark, Goldenberg, Anna, Birkbak, Nicolai J, Beck, Andrew H, Aerts, Hugo JWL, Quackenbush, John, and Haibe-Kains, Benjamin

   Nature 2016
5. PharmacoGx: An R Package for Analysis of Large Pharmacogenomic Datasets.

   Smirnov, Petr, Safikhani, Zhaleh, El-Hachem, Nehme, Wang, Dong, She, Adrian, Olsen, Catharina, Freeman, Mark, Selby, Heather, Gendoo, Deena M. A., Grossmann, Patrick, Beck, Andrew H., Aerts, Hugo J. W. L., Lupien, Mathieu, Goldenberg, Anna, and Haibe-Kains, Benjamin

   Bioinformatics Apr 2016

   Abs

   Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data. AVAILABILITY AND IMPLEMENTATION: PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub. CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.