My published or arxived works.


  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


  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


  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


  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


  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


  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


  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