Benjamin Haibe-Kains

61 papers A* 1C 1Journal 52Unranked 6

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Lassoed Forests: Random Forests with Adaptive Lasso Post-selection. CoRR Jing Shang, James Bannon, Benjamin Haibe-Kains, Robert Tibshirani
2025	A*	`conf`	MorphoDiff: Cellular Morphology Painting with Diffusion Models. ICLR Zeinab Navidi, Jun Ma, Esteban Miglietta, Le Liu, Anne E. Carpenter, Beth A. Cimini, Benjamin Haibe-Kains, Bo Wang
2025	J	`jnl`	Moving towards genome-wide data integration for patient stratification with Integrate Any Omics. Nat. Mac. Intell. Shihao Ma, Andy G. X. Zeng, Benjamin Haibe-Kains, Anna Goldenberg, John E. Dick, Bo Wang
2024	J	`jnl`	Integrate Any Omics: Towards genome-wide data integration for patient stratification. CoRR Shihao Ma, Andy G. X. Zeng, Benjamin Haibe-Kains, Anna Goldenberg, John E. Dick, Bo Wang
2024	J	`jnl`	Radiomic-based prediction of lesion-specific systemic treatment response in metastatic disease. Comput. Medical Imaging Graph. Caryn Geady, Farnoosh Abbas Aghababazadeh, Andres Kohan, Scott Schuetze, David Shultz, Benjamin Haibe-Kains
2023	J	`jnl`	Maintaining Stability and Plasticity for Predictive Churn Reduction. CoRR George Adam, Benjamin Haibe-Kains, Anna Goldenberg
2023	—	`conf`	Privacy-Preserving Dashboard for F.A.I.R Head and Neck Cancer data supporting multi-centered collaborations. SWAT4HCLS Varsha Gouthamchand, Ananya Choudhury, Frank Hoebers, Frederik Wesseling, Mattea Welch, Sejin Kim, Benjamin Haibe-Kains, Joanna Kazmierska, Andre Dekker, Johan van Soest, Leonard Wee
2023	J	`jnl`	Reusability report: Evaluating reproducibility and reusability of a fine-tuned model to predict drug response in cancer patient samples. Nat. Mac. Intell. Emily So, Fengqing Yu, Bo Wang, Benjamin Haibe-Kains
2022	—	`conf`	Error Amplification When Updating Deployed Machine Learning Models. MLHC George-Alexandru Adam, Chun-Hao Kingsley Chang, Benjamin Haibe-Kains, Anna Goldenberg
2022	J	`jnl`	Evaluation of statistical approaches for association testing in noisy drug screening data. BMC Bioinform. 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
2022	J	`jnl`	FastCPH: Efficient Survival Analysis for Neural Networks. CoRR Xuelin Yang, Louis Abraham, Sejin Kim, Petr Smirnov, Feng Ruan, Benjamin Haibe-Kains, Robert Tibshirani
2022	J	`jnl`	PharmacoDB 2.0: improving scalability and transparency of Nucleic Acids Res. 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
2021	J	`jnl`	A Machine Learning Challenge for Prognostic Modelling in Head and Neck Cancer Using Multi-modal Data. CoRR 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
2021	J	`jnl`	CovidCTNet: an open-source deep learning approach to diagnose covid-19 using small cohort of CT images. npj Digit. Medicine 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
2021	—	`conf`	Deep-CR MTLR: a Multi-Modal Approach for Cancer Survival Prediction with Competing Risks. SPACA Sejin Kim, Michal Kazmierski, Benjamin Haibe-Kains
2021	J	`jnl`	Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models. Briefings Bioinform. Hossein Sharifi-Noghabi, Soheil Jahangiri-Tazehkand, Petr Smirnov, Casey Hon, Anthony Mammoliti, Sisira Kadambat Nair, Arvind Singh Mer, Martin Ester, Benjamin Haibe-Kains
2021	J	`jnl`	Lymph Node Graph Neural Networks for Cancer Metastasis Prediction. CoRR Michal Kazmierski, Benjamin Haibe-Kains
2021	J	`jnl`	The impact of the variation of imaging parameters on the robustness of Computed Tomography radiomic features: A review. Comput. Biol. Medicine 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
2020	J	`jnl`	CovidCTNet: An Open-Source Deep Learning Approach to Identify Covid-19 Using CT Image. CoRR 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
2020	J	`jnl`	Deep-CR MTLR: a Multi-Modal Approach for Cancer Survival Prediction with Competing Risks. CoRR Sejin Kim, Michal Kazmierski, Benjamin Haibe-Kains
2020	—	`conf`	Hidden Risks of Machine Learning Applied to Healthcare: Unintended Feedback Loops Between Models and Future Data Causing Model Degradation. MLHC George-Alexandru Adam, Chun-Hao Kingsley Chang, Benjamin Haibe-Kains, Anna Goldenberg
2020	C	`conf`	Learning across label confidence distributions using Filtered Transfer Learning. ICMLA Seyed Ali Madani Tonekaboni, Andrew E. Brereton, Zhaleh Safikhani, Andreas Windemuth, Benjamin Haibe-Kains, Stephen MacKinnon
2020	J	`jnl`	Learning across label confidence distributions using Filtered Transfer Learning. CoRR Seyed Ali Madani Tonekaboni, Andrew E. Brereton, Zhaleh Safikhani, Andreas Windemuth, Benjamin Haibe-Kains, Stephen MacKinnon
2020	J	`jnl`	SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology. Nucleic Acids Res. Heewon Seo, Denis Tkachuk, Chantal Ho, Anthony Mammoliti, Aria Rezaie, Seyed Ali Madani Tonekaboni, Benjamin Haibe-Kains
2020	J	`jnl`	ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets. Nucleic Acids Res. 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
2019	J	`jnl`	Dr.VAE: improving drug response prediction via modeling of drug perturbation effects. Bioinform. Ladislav Rampásek, Daniel Hidru, Petr Smirnov, Benjamin Haibe-Kains, Anna Goldenberg
2019	—	`conf`	Machine Learning for Biomarker Discovery in Cancer Pharmacogenomics Data. BCB Arvind Singh Mer, Petr Smirnov, Benjamin Haibe-Kains
2019	J	`jnl`	Reducing Adversarial Example Transferability Using Gradient Regularization. CoRR George Adam, Petr Smirnov, Benjamin Haibe-Kains, Anna Goldenberg
2019	J	`jnl`	SIGN: similarity identification in gene expression. Bioinform. Seyed Ali Madani Tonekaboni, Venkata Satya Kumar Manem, Nehme El-Hachem, Benjamin Haibe-Kains
2019	J	`jnl`	Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer. PLoS Comput. Biol. 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
2018	J	`jnl`	A review of connectivity map and computational approaches in pharmacogenomics. Briefings Bioinform. Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina V. Glazko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib
2018	J	`jnl`	Orchestrating a community-developed computational workshop and accompanying training materials. F1000Research Sean Davis, Marcel Ramos, Lori A. Shepherd, Nitesh Turaga, Ludwig Geistlinger, Martin T. Morgan, Benjamin Haibe-Kains, Levi Waldron
2018	J	`jnl`	PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies. Nucleic Acids Res. Petr Smirnov, Victor Kofia, Alexander Maru, Mark Freeman, Chantal Ho, Nehme El-Hachem, George-Alexandru Adam, Wail Ba-alawi, Zhaleh Safikhani, Benjamin Haibe-Kains
2018	J	`jnl`	Predictive approaches for drug combination discovery in cancer. Briefings Bioinform. Seyed Ali Madani Tonekaboni, Laleh Soltan Ghoraie, Venkata Satya Kumar Manem, Benjamin Haibe-Kains
2018	J	`jnl`	Stochastic Combinatorial Ensembles for Defending Against Adversarial Examples. CoRR George-Alexandru Adam, Petr Smirnov, Anna Goldenberg, David Duvenaud, Benjamin Haibe-Kains
2018	J	`jnl`	Tissue specificity of in vitro drug sensitivity. J. Am. Medical Informatics Assoc. Fupan Yao, Seyed Ali Madani Tonekaboni, Zhaleh Safikhani, Petr Smirnov, Nehme El-Hachem, Mark Freeman, Venkata Satya Kumar Manem, Benjamin Haibe-Kains
2017	J	`jnl`	A review of connectivity map and computational approaches in pharmacogenomics. Briefings Bioinform. Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina V. Glazko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib
2017	J	`jnl`	Study of Meta-analysis strategies for network inference using information-theoretic approaches. BioData Min. Ngoc Cam Pham, Benjamin Haibe-Kains, Pau Bellot, Gianluca Bontempi, Patrick E. Meyer
2016	J	`jnl`	BatchQC: interactive software for evaluating sample and batch effects in genomic data. Bioinform. Solaiappan Manimaran, Heather Marie Selby, Kwame Okrah, Claire Ruberman, Jeffrey T. Leek, John Quackenbush, Benjamin Haibe-Kains, Héctor Corrada Bravo, W. Evan Johnson
2016	J	`jnl`	Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer. Bioinform. Deena M. A. Gendoo, Natchar Ratanasirigulchai, Markus S. Schröder, Laia Paré, Joel S. Parker, Aleix Prat, Benjamin Haibe-Kains
2016	J	`jnl`	MM2S: personalized diagnosis of medulloblastoma patients and model systems. Source Code Biol. Medicine Deena M. A. Gendoo, Benjamin Haibe-Kains
2016	J	`jnl`	PharmacoGx: an R package for analysis of large pharmacogenomic datasets. Bioinform. 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
2016	J	`jnl`	Public data and open source tools for multi-assay genomic investigation of disease. Briefings Bioinform. 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
2016	J	`jnl`	Safikhani Nat. 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
2016	—	`conf`	Study of Meta-analysis Strategies for Network Inference Using Information-Theoretic Approaches. DEXA Workshops Ngoc Cam Pham, Benjamin Haibe-Kains, Pau Bellot, Gianluca Bontempi, Patrick E. Meyer
2015	J	`jnl`	A network model for angiogenesis in ovarian cancer. BMC Bioinform. Kimberly Glass, John Quackenbush, Dimitrios Spentzos, Benjamin Haibe-Kains, Guo-Cheng Yuan
2015	J	`jnl`	ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments. Bioinform. Swneke D. Bailey, Carl Virtanen, Benjamin Haibe-Kains, Mathieu Lupien
2015	J	`jnl`	Test set bias affects reproducibility of gene signatures. Bioinform. Prasad Patil, Pierre-Olivier Bachant-Winner, Benjamin Haibe-Kains, Jeffrey T. Leek
2014	J	`jnl`	Functional and genetic analysis of the colon cancer network. BMC Bioinform. Frank Emmert-Streib, Ricardo de Matos Simoes, Galina V. Glazko, Simon S. McDade, Benjamin Haibe-Kains, Andreas Holzinger, Matthias Dehmer, Frederick Campbell
2013	J	`jnl`	Inconsistency in large pharmacogenomic studies. Nat. Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai J. Birkbak, Andrew C. Jin, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush
2013	J	`jnl`	RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. Bioinform. Markus S. Schröder, Daniel Gusenleitner, John Quackenbush, Aedín C. Culhane, Benjamin Haibe-Kains
2013	J	`jnl`	Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity. J. Am. Medical Informatics Assoc. Simon Papillon-Cavanagh, Nicolas De Jay, Nehme Hachem, Catharina Olsen, Gianluca Bontempi, Hugo J. W. L. Aerts, John Quackenbush, Benjamin Haibe-Kains
2013	J	`jnl`	Significance Analysis of Prognostic Signatures. PLoS Comput. Biol. 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
2013	J	`jnl`	curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database J. Biol. Databases Curation 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
2013	J	`jnl`	mRMRe: an R package for parallelized mRMR ensemble feature selection. Bioinform. Nicolas De Jay, Simon Papillon-Cavanagh, Catharina Olsen, Nehme Hachem, Gianluca Bontempi, Benjamin Haibe-Kains
2012	J	`jnl`	GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res. 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
2012	J	`jnl`	Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Res. Benjamin Haibe-Kains, Catharina Olsen, Amira Djebbari, Gianluca Bontempi, Mick Correll, Christopher Bouton, John Quackenbush
2011	J	`jnl`	Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. BMC Bioinform. 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
2011	J	`jnl`	Multiple-input multiple-output causal strategies for gene selection. BMC Bioinform. Gianluca Bontempi, Benjamin Haibe-Kains, Christine Desmedt, Christos P. Sotiriou, John Quackenbush
2008	J	`jnl`	A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? Bioinform. Benjamin Haibe-Kains, Christine Desmedt, Christos P. Sotiriou, Gianluca Bontempi
2008	—	`ch.`	Computational Intelligence in Clinical Oncology: Lessons Learned from an Analysis of a Clinical Study. Computational Intelligence in Biomedicine and Bioinformatics Benjamin Haibe-Kains, Christine Desmedt, Sherene Loi, Mauro Delorenzi, Christos P. Sotiriou, Gianluca Bontempi