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ORCIDBenjamin Haibe-Kains
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2020 – today
- 2024
[j40]Caryn Geady
, Farnoosh Abbas Aghababazadeh, Andres Kohan, Scott Schuetze, David Shultz, Benjamin Haibe-Kains:
Radiomic-based prediction of lesion-specific systemic treatment response in metastatic disease. Comput. Medical Imaging Graph. 116: 102413 (2024)- [i11]Shihao Ma, Andy G. X. Zeng, Benjamin Haibe-Kains, Anna Goldenberg, John E. Dick, Bo Wang:
Integrate Any Omics: Towards genome-wide data integration for patient stratification. CoRR abs/2401.07937 (2024) - 2023
- [j39]Emily So, Fengqing Yu, Bo Wang, Benjamin Haibe-Kains:
Reusability report: Evaluating reproducibility and reusability of a fine-tuned model to predict drug response in cancer patient samples. Nat. Mac. Intell. 5(7): 792-798 (2023) - [c7]Varsha Gouthamchand, Ananya Choudhury, Frank Hoebers, Frederik Wesseling, Mattea Welch, Sejin Kim, Benjamin Haibe-Kains, Joanna Kazmierska, Andre Dekker, Johan van Soest, Leonard Wee:
Privacy-Preserving Dashboard for F.A.I.R Head and Neck Cancer data supporting multi-centered collaborations. SWAT4HCLS 2023: 11-21 - [i10]George Adam, Benjamin Haibe-Kains, Anna Goldenberg:
Maintaining Stability and Plasticity for Predictive Churn Reduction. CoRR abs/2305.04135 (2023) - 2022
- [j38]Petr Smirnov, Ian Smith, Zhaleh Safikhani, Wail Ba-alawi, Farnoosh Khodakarami, Eva Lin, Yihong Yu, Scott Martin, Janosch Ortmann, Tero Aittokallio, Marc Hafner, Benjamin Haibe-Kains:
Evaluation of statistical approaches for association testing in noisy drug screening data. BMC Bioinform. 23(1): 188 (2022) - [j37]Nikta Feizi, Sisira Kadambat Nair, Petr Smirnov, Gangesh Beri, Christopher Eeles, Parinaz Nasr Esfahani, Minoru Nakano, Denis Tkachuk, Anthony Mammoliti, Evgeniya Gorobets, Arvind Singh Mer, Eva Lin, Yihong Yu, Scott Martin, Marc Hafner, Benjamin Haibe-Kains:
PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis. Nucleic Acids Res. 50(D1): 1348-1357 (2022) - [c6]George-Alexandru Adam, Chun-Hao Kingsley Chang, Benjamin Haibe-Kains, Anna Goldenberg:
Error Amplification When Updating Deployed Machine Learning Models. MLHC 2022: 715-740 - [i9]Xuelin Yang, Louis Abraham, Sejin Kim, Petr Smirnov, Feng Ruan, Benjamin Haibe-Kains, Robert Tibshirani:
FastCPH: Efficient Survival Analysis for Neural Networks. CoRR abs/2208.09793 (2022) - 2021
- [j36]Hossein Sharifi-Noghabi, Soheil Jahangiri-Tazehkand, Petr Smirnov, Casey Hon, Anthony Mammoliti, Sisira Kadambat Nair, Arvind Singh Mer, Martin Ester, Benjamin Haibe-Kains:
Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models. Briefings Bioinform. 22(6) (2021) - [j35]Reza Reiazi, Engy Abbas, Petra Famiyeh, Aria Rezaie, Jennifer Y. Y. Kwan, Tirth Patel, Scott V. Bratman, Tony Tadic, Fei-Fei Liu, Benjamin Haibe-Kains:
The impact of the variation of imaging parameters on the robustness of Computed Tomography radiomic features: A review. Comput. Biol. Medicine 133: 104400 (2021) - [j34]Tahereh Javaheri, Morteza Homayounfar, Zohreh Amoozgar, Reza Reiazi, Fatemeh Homayounieh, Engy Abbas, Azadeh Laali, Amir Reza Radmard, Mohammad Hadi Gharib, Seyed Ali Javad Mousavi, Omid Ghaemi, Rosa Babaei, Hadi Karimi Mobin, Mehdi Hosseinzadeh, Rana Jahanban-Esfahlan, Khaled Seidi, Mannudeep K. Kalra, Guanglan Zhang, Lubomir T. Chitkushev, Benjamin Haibe-Kains, Reza Malekzadeh, Reza Rawassizadeh:
CovidCTNet: an open-source deep learning approach to diagnose covid-19 using small cohort of CT images. npj Digit. Medicine 4 (2021) - [c5]Sejin Kim, Michal Kazmierski, Benjamin Haibe-Kains:
Deep-CR MTLR: a Multi-Modal Approach for Cancer Survival Prediction with Competing Risks. SPACA 2021: 223-231 - [i8]Michal Kazmierski, Mattea Welch, Sejin Kim, Chris McIntosh, Katrina Rey-McIntyre, Shao-Hui Huang, Tirth Patel, Tony Tadic, Michael F. Milosevic, Fei-Fei Liu, Andrew Hope, Scott V. Bratman, Benjamin Haibe-Kains:
A Machine Learning Challenge for Prognostic Modelling in Head and Neck Cancer Using Multi-modal Data. CoRR abs/2101.11935 (2021) - [i7]Michal Kazmierski, Benjamin Haibe-Kains:
Lymph Node Graph Neural Networks for Cancer Metastasis Prediction. CoRR abs/2106.01711 (2021) - 2020
- [j33]Sisira Kadambat Nair, Christopher Eeles, Chantal Ho, Gangesh Beri, Esther Yoo, Denis Tkachuk, Amy Tang, Parwaiz Nijrabi, Petr Smirnov, Heewon Seo, Danyel Jennen, Benjamin Haibe-Kains:
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets. Nucleic Acids Res. 48(Webserver-Issue): W455-W462 (2020) - [j32]Heewon Seo, Denis Tkachuk, Chantal Ho, Anthony Mammoliti, Aria Rezaie, Seyed Ali Madani Tonekaboni, Benjamin Haibe-Kains:
SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology. Nucleic Acids Res. 48(Webserver-Issue): W494-W501 (2020) - [c4]Seyed Ali Madani Tonekaboni, Andrew E. Brereton, Zhaleh Safikhani, Andreas Windemuth, Benjamin Haibe-Kains, Stephen MacKinnon:
Learning across label confidence distributions using Filtered Transfer Learning. ICMLA 2020: 1117-1123 - [c3]George-Alexandru Adam, Chun-Hao Kingsley Chang, Benjamin Haibe-Kains, Anna Goldenberg:
Hidden Risks of Machine Learning Applied to Healthcare: Unintended Feedback Loops Between Models and Future Data Causing Model Degradation. MLHC 2020: 710-731 - [i6]Tahereh Javaheri, Morteza Homayounfar, Zohreh Amoozgar, Reza Reiazi, Fatemeh Homayounieh, Engy Abbas, Azadeh Laali, Amir Reza Radmard, Mohammad Hadi Gharib, Seyed Ali Javad Mousavi, Omid Ghaemi, Rosa Babaei, Hadi Karimi Mobin, Mehdi Hosseinzadeh, Rana Jahanban-Esfahlan, Khaled Seidi, Mannudeep K. Kalra, Guanglan Zhang, Lubomir T. Chitkushev, Benjamin Haibe-Kains, Reza Malekzadeh, Reza Rawassizadeh:
CovidCTNet: An Open-Source Deep Learning Approach to Identify Covid-19 Using CT Image. CoRR abs/2005.03059 (2020) - [i5]Seyed Ali Madani Tonekaboni, Andrew E. Brereton, Zhaleh Safikhani, Andreas Windemuth, Benjamin Haibe-Kains, Stephen MacKinnon:
Learning across label confidence distributions using Filtered Transfer Learning. CoRR abs/2006.02528 (2020) - [i4]Sejin Kim, Michal Kazmierski, Benjamin Haibe-Kains:
Deep-CR MTLR: a Multi-Modal Approach for Cancer Survival Prediction with Competing Risks. CoRR abs/2012.05765 (2020)
2010 – 2019
- 2019
- [j31]Ladislav Rampásek, Daniel Hidru, Petr Smirnov, Benjamin Haibe-Kains, Anna Goldenberg:
Dr.VAE: improving drug response prediction via modeling of drug perturbation effects. Bioinform. 35(19): 3743-3751 (2019) - [j30]Seyed Ali Madani Tonekaboni, Venkata Satya Kumar Manem, Nehme El-Hachem, Benjamin Haibe-Kains:
SIGN: similarity identification in gene expression. Bioinform. 35(22): 4830-4833 (2019) - [j29]Deena M. A. Gendoo, Robert E. Denroche, Amy Zhang, Nikolina Radulovich, Gun Ho Jang, Mathieu Lemire, Sandra Fischer, Dianne Chadwick, Ilinca M. Lungu, Emin Ibrahimov, Ping-Jiang Cao, Lincoln D. Stein, Julie M. Wilson, John M. S. Bartlett, Ming-Sound Tsao, Neesha Dhani, David Hedley, Steven Gallinger, Benjamin Haibe-Kains:
Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer. PLoS Comput. Biol. 15(1) (2019) - [c2]Arvind Singh Mer, Petr Smirnov, Benjamin Haibe-Kains:
Machine Learning for Biomarker Discovery in Cancer Pharmacogenomics Data. BCB 2019: 557 - [i3]George Adam, Petr Smirnov, Benjamin Haibe-Kains, Anna Goldenberg:
Reducing Adversarial Example Transferability Using Gradient Regularization. CoRR abs/1904.07980 (2019) - 2018
- [j28]Seyed Ali Madani Tonekaboni, Laleh Soltan Ghoraie, Venkata Satya Kumar Manem, Benjamin Haibe-Kains:
Predictive approaches for drug combination discovery in cancer. Briefings Bioinform. 19(2): 263-276 (2018) - [j27]Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina V. Glazko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib:
A review of connectivity map and computational approaches in pharmacogenomics. Briefings Bioinform. 19(3): 506-523 (2018) - [j26]Fupan Yao, Seyed Ali Madani Tonekaboni, Zhaleh Safikhani, Petr Smirnov, Nehme El-Hachem, Mark Freeman, Venkata Satya Kumar Manem, Benjamin Haibe-Kains:
Tissue specificity of in vitro drug sensitivity. J. Am. Medical Informatics Assoc. 25(2): 158-166 (2018) - [j25]Petr Smirnov, Victor Kofia, Alexander Maru, Mark Freeman, Chantal Ho, Nehme El-Hachem, George-Alexandru Adam, Wail Ba-alawi, Zhaleh Safikhani, Benjamin Haibe-Kains:
PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies. Nucleic Acids Res. 46(Database-Issue): D994-D1002 (2018) - [i2]George-Alexandru Adam, Petr Smirnov, Anna Goldenberg, David Duvenaud, Benjamin Haibe-Kains:
Stochastic Combinatorial Ensembles for Defending Against Adversarial Examples. CoRR abs/1808.06645 (2018) - [i1]Sean Davis, Marcel Ramos, Lori A. Shepherd, Nitesh Turaga, Ludwig Geistlinger, Martin T. Morgan, Benjamin Haibe-Kains, Levi Waldron:
Orchestrating a community-developed computational workshop and accompanying training materials. F1000Research 7: 1656 (2018) - 2017
- [j24]Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina V. Glazko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib:
A review of connectivity map and computational approaches in pharmacogenomics. Briefings Bioinform. 18(5): 903 (2017) - [j23]Ngoc Cam Pham, Benjamin Haibe-Kains, Pau Bellot, Gianluca Bontempi, Patrick E. Meyer:
Study of Meta-analysis strategies for network inference using information-theoretic approaches. BioData Min. 10(1): 15:1-15:14 (2017) - 2016
- [j22]Lavanya Kannan, Marcel Ramos, Angela Re, Nehme Hachem, Zhaleh Safikhani, Deena M. A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe-Kains, Levi Waldron:
Public data and open source tools for multi-assay genomic investigation of disease. Briefings Bioinform. 17(4): 603-615 (2016) - [j21]Deena M. A. Gendoo, Natchar Ratanasirigulchai, Markus S. Schröder, Laia Paré, Joel S. Parker, Aleix Prat, Benjamin Haibe-Kains:
Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer. Bioinform. 32(7): 1097-1099 (2016) - [j20]Petr Smirnov, Zhaleh Safikhani, Nehme Hachem, Dong Wang, Adrian She, Catharina Olsen, Mark Freeman, Heather Marie Selby, Deena M. A. Gendoo, Patrick Grossmann, Andrew H. Beck, Hugo J. W. L. Aerts, Mathieu Lupien, Anna Goldenberg, Benjamin Haibe-Kains:
PharmacoGx: an R package for analysis of large pharmacogenomic datasets. Bioinform. 32(8): 1244-1246 (2016) - [j19]Solaiappan Manimaran, Heather Marie Selby, Kwame Okrah, Claire Ruberman, Jeffrey T. Leek, John Quackenbush, Benjamin Haibe-Kains, Héctor Corrada Bravo, W. Evan Johnson:
BatchQC: interactive software for evaluating sample and batch effects in genomic data. Bioinform. 32(24): 3836-3838 (2016) - [j18]Zhaleh Safikhani, Nehme Hachem, Petr Smirnov, Mark Freeman, Anna Goldenberg, Nicolai J. Birkbak, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush, Benjamin Haibe-Kains:
Safikhani et al. reply. Nat. 540(7631): E2-E4 (2016) - [j17]Deena M. A. Gendoo, Benjamin Haibe-Kains:
MM2S: personalized diagnosis of medulloblastoma patients and model systems. Source Code Biol. Medicine 11(1): 6 (2016) - [c1]Ngoc Cam Pham, Benjamin Haibe-Kains, Pau Bellot, Gianluca Bontempi, Patrick E. Meyer:
Study of Meta-analysis Strategies for Network Inference Using Information-Theoretic Approaches. DEXA Workshops 2016: 76-83 - 2015
- [j16]Prasad Patil, Pierre-Olivier Bachant-Winner, Benjamin Haibe-Kains, Jeffrey T. Leek:
Test set bias affects reproducibility of gene signatures. Bioinform. 31(14): 2318-2323 (2015) - [j15]Swneke D. Bailey, Carl Virtanen, Benjamin Haibe-Kains, Mathieu Lupien:
ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments. Bioinform. 31(18): 3057-3059 (2015) - [j14]Kimberly Glass, John Quackenbush, Dimitrios Spentzos, Benjamin Haibe-Kains, Guo-Cheng Yuan:
A network model for angiogenesis in ovarian cancer. BMC Bioinform. 16: 115:1-115:17 (2015) - 2014
- [j13]Frank Emmert-Streib, Ricardo de Matos Simoes, Galina V. Glazko, Simon S. McDade, Benjamin Haibe-Kains, Andreas Holzinger, Matthias Dehmer, Frederick Campbell:
Functional and genetic analysis of the colon cancer network. BMC Bioinform. 15(S-6): S6 (2014) - 2013
- [j12]Benjamin Frederick Ganzfried, Markus Riester, Benjamin Haibe-Kains, Thomas Risch, Svitlana Tyekucheva, Ina Jazic, Xin Victoria Wang, Mahnaz Ahmadifar, Michael J. Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron:
curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database J. Biol. Databases Curation 2013 (2013) - [j11]Markus S. Schröder, Daniel Gusenleitner, John Quackenbush, Aedín C. Culhane, Benjamin Haibe-Kains:
RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. Bioinform. 29(5): 666-668 (2013) - [j10]Nicolas De Jay, Simon Papillon-Cavanagh, Catharina Olsen, Nehme Hachem, Gianluca Bontempi, Benjamin Haibe-Kains:
mRMRe: an R package for parallelized mRMR ensemble feature selection. Bioinform. 29(18): 2365-2368 (2013) - [j9]Simon Papillon-Cavanagh, Nicolas De Jay, Nehme Hachem, Catharina Olsen, Gianluca Bontempi, Hugo J. W. L. Aerts, John Quackenbush, Benjamin Haibe-Kains:
Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity. J. Am. Medical Informatics Assoc. 20(4): 597-602 (2013) - [j8]Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai J. Birkbak, Andrew C. Jin, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush:
Inconsistency in large pharmacogenomic studies. Nat. 504(7480): 389-393 (2013) - [j7]Andrew H. Beck, Nicholas W. Knoblauch, Marco M. Hefti, Jennifer Kaplan, Stuart J. Schnitt, Aedín C. Culhane, Markus S. Schröder, Thomas Risch, John Quackenbush, Benjamin Haibe-Kains:
Significance Analysis of Prognostic Signatures. PLoS Comput. Biol. 9(1) (2013) - 2012
- [j6]Benjamin Haibe-Kains, Catharina Olsen, Amira Djebbari, Gianluca Bontempi, Mick Correll, Christopher Bouton, John Quackenbush:
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Res. 40(Database-Issue): 866-875 (2012) - [j5]Aedín C. Culhane, Markus S. Schröder, Razvan Sultana, Shaita C. Picard, Enzo N. Martinelli, Caroline Kelly, Benjamin Haibe-Kains, Misha Kapushesky, Anne-Alyssa St Pierre, William Flahive, Kermshlise C. Picard, Daniel Gusenleitner, Gerald Papenhausen, Niall O'Connor, Mick Correll, John Quackenbush:
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res. 40(Database-Issue): 1060-1066 (2012) - 2011
- [j4]Markus S. Schröder, Aedín C. Culhane, John Quackenbush, Benjamin Haibe-Kains:
survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinform. 27(22): 3206-3208 (2011) - [j3]Qiyuan Li, Aron C. Eklund, Nicolai J. Birkbak, Christine Desmedt, Benjamin Haibe-Kains, Christos P. Sotiriou, W. Fraser Symmans, Lajos Pusztai, Søren Brunak, Andrea L. Richardson, Zoltan Szallasi:
Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. BMC Bioinform. 12: 310 (2011) - [j2]Gianluca Bontempi, Benjamin Haibe-Kains, Christine Desmedt, Christos P. Sotiriou, John Quackenbush:
Multiple-input multiple-output causal strategies for gene selection. BMC Bioinform. 12: 458 (2011)
2000 – 2009
- 2008
- [j1]Benjamin Haibe-Kains, Christine Desmedt, Christos P. Sotiriou, Gianluca Bontempi:
A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? Bioinform. 24(19): 2200-2208 (2008) - [p1]Benjamin Haibe-Kains, Christine Desmedt, Sherene Loi, Mauro Delorenzi, Christos P. Sotiriou, Gianluca Bontempi:
Computational Intelligence in Clinical Oncology: Lessons Learned from an Analysis of a Clinical Study. Computational Intelligence in Biomedicine and Bioinformatics 2008: 237-268
Coauthor Index
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