Benjamin Haibe-Kains

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 42

Top Topics

Machine Learning

Gene Expression

Top Venues

Briefings Bioinform.

Nucleic Acids Res.

Publications

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 (2024)
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 (2024)
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)
George Adam, Benjamin Haibe-Kains, Anna Goldenberg
Maintaining Stability and Plasticity for Predictive Churn Reduction. CoRR (2023)
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) (2023)
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) (2022)
George-Alexandru Adam, Chun-Hao Kingsley Chang, Benjamin Haibe-Kains, Anna Goldenberg
Error Amplification When Updating Deployed Machine Learning Models. MLHC (2022)
Xuelin Yang, Louis Abraham, Sejin Kim, Petr Smirnov, Feng Ruan, Benjamin Haibe-Kains, Robert Tibshirani
FastCPH: Efficient Survival Analysis for Neural Networks. CoRR (2022)
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
pharmacogenomics analysis. Nucleic Acids Res. 50 (D1) (2022)
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 (2021)
Sejin Kim, Michal Kazmierski, Benjamin Haibe-Kains
Deep-CR MTLR: a Multi-Modal Approach for Cancer Survival Prediction with Competing Risks. SPACA (2021)
Michal Kazmierski, Benjamin Haibe-Kains
Lymph Node Graph Neural Networks for Cancer Metastasis Prediction. CoRR (2021)
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)
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 (2021)
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)
Sejin Kim, Michal Kazmierski, Benjamin Haibe-Kains
Deep-CR MTLR: a Multi-Modal Approach for Cancer Survival Prediction with Competing Risks. CoRR (2020)
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) (2020)
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)
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 (2020)
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) (2020)
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)
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 (2020)
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) (2019)
George Adam, Petr Smirnov, Benjamin Haibe-Kains, Anna Goldenberg
Reducing Adversarial Example Transferability Using Gradient Regularization. CoRR (2019)
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)
Seyed Ali Madani Tonekaboni, Venkata Satya Kumar Manem, Nehme El-Hachem, Benjamin Haibe-Kains
SIGN: similarity identification in gene expression. Bioinform. 35 (22) (2019)
Arvind Singh Mer, Petr Smirnov, Benjamin Haibe-Kains
Machine Learning for Biomarker Discovery in Cancer Pharmacogenomics Data. BCB (2019)
Sean R. 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 (2018)
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) (2018)
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) (2018)
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) (2018)
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) (2018)
George-Alexandru Adam, Petr Smirnov, Anna Goldenberg, David Duvenaud, Benjamin Haibe-Kains
Stochastic Combinatorial Ensembles for Defending Against Adversarial Examples. CoRR (2018)
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) (2017)
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) (2017)
Deena M. A. Gendoo, Benjamin Haibe-Kains
MM2S: personalized diagnosis of medulloblastoma patients and model systems. Source Code Biol. Medicine 11 (1) (2016)
Petr Smirnov, Zhaleh Safikhani, Nehme Hachem, Dong Wang, Adrian She, Catharina Olsen, Mark Freeman, Heather 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) (2016)
Lavanya Kannan, Marcel Ramos, Angela Re, Nehme Hachem, Zhaleh Safikhani, Deena M. A. Gendoo, Sean R. 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) (2016)
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) (2016)
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)
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
. reply. Nat. 540 (7631) (2016)
Solaiappan Manimaran, Heather 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) (2016)
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) (2015)
Prasad Patil, Pierre-Olivier Bachant-Winner, Benjamin Haibe-Kains, Jeffrey T. Leek
Test set bias affects reproducibility of gene signatures. Bioinform. 31 (14) (2015)
Kimberly Glass, John Quackenbush, Dimitrios Spentzos, Benjamin Haibe-Kains, Guo-Cheng Yuan
A network model for angiogenesis in ovarian cancer. BMC Bioinform. 16 (2015)
Frank Emmert-Streib, Ricardo de Matos Simoes, Galina V. Glazko, Simon McDade, Benjamin Haibe-Kains, Andreas Holzinger, Matthias Dehmer, Frederick Campbell
Functional and genetic analysis of the colon cancer network. BMC Bioinform. 15 (S-6) (2014)
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) (2013)
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)
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) (2013)
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) (2013)
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) (2013)
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)
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) (2012)
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) (2012)
Gianluca Bontempi, Benjamin Haibe-Kains, Christine Desmedt, Christos P. Sotiriou, John Quackenbush
Multiple-input multiple-output causal strategies for gene selection. BMC Bioinform. 12 (2011)
Markus S. Schröder, Aedín C. Culhane, John Quackenbush, Benjamin Haibe-Kains
: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinform. 27 (22) (2011)
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 (2011)
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) (2008)