A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? - Benjamin Haibe-Kains; Christine Desmedt; Christos P. Sotiriou; Gianluca Bontempi (Bioinform., 2008)

Computational Intelligence in Clinical Oncology: Lessons Learned from an Analysis of a Clinical Study. - Benjamin Haibe-Kains; Christine Desmedt; Sherene Loi; Mauro Delorenzi; Christos P. Sotiriou; Gianluca Bontempi (Computational Intelligence in Biomedicine and Bioinformatics, 2008)

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. - Markus S. Schröder; Aedín C. Culhane; John Quackenbush; Benjamin Haibe-Kains (Bioinform., 2011)

Multiple-input multiple-output causal strategies for gene selection. - Gianluca Bontempi; Benjamin Haibe-Kains; Christine Desmedt; Christos P. Sotiriou; John Quackenbush (BMC Bioinform., 2011)

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. - 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 (BMC Bioinform., 2011)

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. - 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; et al. (Nucleic Acids Res., 2012)

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. - Benjamin Haibe-Kains; Catharina Olsen; Amira Djebbari; Gianluca Bontempi; Mick Correll; Christopher Bouton; John Quackenbush (Nucleic Acids Res., 2012)

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. - 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 (Database J. Biol. Databases Curation, 2013)

mRMRe: an R package for parallelized mRMR ensemble feature selection. - Nicolas De Jay; Simon Papillon-Cavanagh; Catharina Olsen; Nehme Hachem; Gianluca Bontempi; Benjamin Haibe-Kains (Bioinform., 2013)

RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. - Markus S. Schröder; Daniel Gusenleitner; John Quackenbush; Aedín C. Culhane; Benjamin Haibe-Kains (Bioinform., 2013)

Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity. - Simon Papillon-Cavanagh; Nicolas De Jay; Nehme Hachem; Catharina Olsen; Gianluca Bontempi; Hugo J. W. L. Aerts; John Quackenbush; Benjamin Haibe-Kains (J. Am. Medical Informatics Assoc., 2013)

Inconsistency in large pharmacogenomic studies. - Benjamin Haibe-Kains; Nehme El-Hachem; Nicolai J. Birkbak; Andrew C. Jin; Andrew H. Beck; Hugo J. W. L. Aerts; John Quackenbush (Nat., 2013)

Significance Analysis of Prognostic Signatures. - 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 (PLoS Comput. Biol., 2013)

Functional and genetic analysis of the colon cancer network. - Frank Emmert-Streib; Ricardo de Matos Simoes; Galina V. Glazko; Simon S. McDade; Benjamin Haibe-Kains; Andreas Holzinger; Matthias Dehmer; Frederick Campbell (BMC Bioinform., 2014)

ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments. - Swneke D. Bailey; Carl Virtanen; Benjamin Haibe-Kains; Mathieu Lupien (Bioinform., 2015)

Test set bias affects reproducibility of gene signatures. - Prasad Patil; Pierre-Olivier Bachant-Winner; Benjamin Haibe-Kains; Jeffrey T. Leek (Bioinform., 2015)

A network model for angiogenesis in ovarian cancer. - Kimberly Glass; John Quackenbush; Dimitrios Spentzos; Benjamin Haibe-Kains; Guo-Cheng Yuan (BMC Bioinform., 2015)

Public data and open source tools for multi-assay genomic investigation of disease. - Lavanya Kannan; Marcel Ramos; Angela Re; Nehme Hachem; Zhaleh Safikhani; Deena M. A. Gendoo; Sean Davis 001; David Gomez-Cabrero; Robert Castelo; Kasper D. Hansen; Vincent J. Carey; Martin Morgan; et al. (Briefings Bioinform., 2016)

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer. - Deena M. A. Gendoo; Natchar Ratanasirigulchai; Markus S. Schröder; Laia Paré; Joel S. Parker; Aleix Prat; Benjamin Haibe-Kains (Bioinform., 2016)

BatchQC: interactive software for evaluating sample and batch effects in genomic data. - Solaiappan Manimaran; Heather Marie Selby; Kwame Okrah; Claire Ruberman; Jeffrey T. Leek; John Quackenbush; Benjamin Haibe-Kains; Héctor Corrada Bravo; W. Evan Johnson (Bioinform., 2016)

PharmacoGx: an R package for analysis of large pharmacogenomic datasets. - Petr Smirnov; Zhaleh Safikhani; Nehme Hachem; Dong Wang; Adrian She; Catharina Olsen; Mark Freeman 002; Heather Marie Selby; Deena M. A. Gendoo; Patrick Grossmann; Andrew H. Beck; Hugo J. W. L. Aerts; et al. (Bioinform., 2016)

Safikhani et al. reply. - Zhaleh Safikhani; Nehme Hachem; Petr Smirnov; Mark Freeman 002; Anna Goldenberg; Nicolai J. Birkbak; Andrew H. Beck; Hugo J. W. L. Aerts; John Quackenbush; Benjamin Haibe-Kains (Nat., 2016)

MM2S: personalized diagnosis of medulloblastoma patients and model systems. - Deena M. A. Gendoo; Benjamin Haibe-Kains (Source Code Biol. Medicine, 2016)

A review of connectivity map and computational approaches in pharmacogenomics. - Aliyu Musa; Laleh Soltan Ghoraie; Shu-Dong Zhang; Galina V. Glazko; Olli Yli-Harja; Matthias Dehmer; Benjamin Haibe-Kains; Frank Emmert-Streib (Briefings Bioinform., 2017)

Study of Meta-analysis strategies for network inference using information-theoretic approaches. - Ngoc Cam Pham; Benjamin Haibe-Kains; Pau Bellot; Gianluca Bontempi; Patrick E. Meyer 001 (BioData Min., 2017)

Predictive approaches for drug combination discovery in cancer. - Seyed Ali Madani Tonekaboni; Laleh Soltan Ghoraie; Venkata Satya Kumar Manem; Benjamin Haibe-Kains (Briefings Bioinform., 2018)

Stochastic Combinatorial Ensembles for Defending Against Adversarial Examples. - George-Alexandru Adam; Petr Smirnov; Anna Goldenberg; David Duvenaud; Benjamin Haibe-Kains (CoRR, 2018)

Orchestrating a community-developed computational workshop and accompanying training materials. - Sean Davis 001; Marcel Ramos; Lori A. Shepherd; Nitesh Turaga; Ludwig Geistlinger; Martin T. Morgan; Benjamin Haibe-Kains; Levi Waldron (F1000Research, 2018)

Tissue specificity of in vitro drug sensitivity. - Fupan Yao; Seyed Ali Madani Tonekaboni; Zhaleh Safikhani; Petr Smirnov; Nehme El-Hachem; Mark Freeman 002; Venkata Satya Kumar Manem; Benjamin Haibe-Kains (J. Am. Medical Informatics Assoc., 2018)

PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies. - Petr Smirnov; Victor Kofia; Alexander Maru; Mark Freeman 002; Chantal Ho; Nehme El-Hachem; George-Alexandru Adam; Wail Ba-alawi; Zhaleh Safikhani; Benjamin Haibe-Kains (Nucleic Acids Res., 2018)

Machine Learning for Biomarker Discovery in Cancer Pharmacogenomics Data. - Arvind Singh Mer; Petr Smirnov; Benjamin Haibe-Kains (BCB, 2019)

Dr.VAE: improving drug response prediction via modeling of drug perturbation effects. - Ladislav Rampásek; Daniel Hidru; Petr Smirnov; Benjamin Haibe-Kains; Anna Goldenberg (Bioinform., 2019)

SIGN: similarity identification in gene expression. - Seyed Ali Madani Tonekaboni; Venkata Satya Kumar Manem; Nehme El-Hachem; Benjamin Haibe-Kains (Bioinform., 2019)

Reducing Adversarial Example Transferability Using Gradient Regularization. - George Adam; Petr Smirnov; Benjamin Haibe-Kains; Anna Goldenberg (CoRR, 2019)

Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer. - 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; et al. (PLoS Comput. Biol., 2019)

Learning across label confidence distributions using Filtered Transfer Learning. - Seyed Ali Madani Tonekaboni; Andrew E. Brereton; Zhaleh Safikhani; Andreas Windemuth; Benjamin Haibe-Kains; Stephen MacKinnon (ICMLA, 2020)

Hidden Risks of Machine Learning Applied to Healthcare: Unintended Feedback Loops Between Models and Future Data Causing Model Degradation. - George-Alexandru Adam; Chun-Hao Kingsley Chang; Benjamin Haibe-Kains; Anna Goldenberg (MLHC, 2020)

CovidCTNet: An Open-Source Deep Learning Approach to Identify Covid-19 Using CT Image. - 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; et al. (CoRR, 2020)

ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets. - 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 (Nucleic Acids Res., 2020)

SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology. - Heewon Seo; Denis Tkachuk; Chantal Ho; Anthony Mammoliti; Aria Rezaie; Seyed Ali Madani Tonekaboni; Benjamin Haibe-Kains (Nucleic Acids Res., 2020)

Deep-CR MTLR: a Multi-Modal Approach for Cancer Survival Prediction with Competing Risks. - Sejin Kim; Michal Kazmierski; Benjamin Haibe-Kains (SPACA, 2021)

Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models. - Hossein Sharifi-Noghabi; Soheil Jahangiri-Tazehkand; Petr Smirnov; Casey Hon; Anthony Mammoliti; Sisira Kadambat Nair; Arvind Singh Mer; Martin Ester; Benjamin Haibe-Kains (Briefings Bioinform., 2021)

The impact of the variation of imaging parameters on the robustness of Computed Tomography radiomic features: A review. - 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 (Comput. Biol. Medicine, 2021)

A Machine Learning Challenge for Prognostic Modelling in Head and Neck Cancer Using Multi-modal Data. - 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; et al. (CoRR, 2021)

Lymph Node Graph Neural Networks for Cancer Metastasis Prediction. - Michal Kazmierski; Benjamin Haibe-Kains (CoRR, 2021)

CovidCTNet: an open-source deep learning approach to diagnose covid-19 using small cohort of CT images. - 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; et al. (npj Digit. Medicine, 2021)

Error Amplification When Updating Deployed Machine Learning Models. - George-Alexandru Adam; Chun-Hao Kingsley Chang; Benjamin Haibe-Kains; Anna Goldenberg (MLHC, 2022)

Evaluation of statistical approaches for association testing in noisy drug screening data. - 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 (BMC Bioinform., 2022)

FastCPH: Efficient Survival Analysis for Neural Networks. - Xuelin Yang; Louis Abraham; Sejin Kim; Petr Smirnov; Feng Ruan; Benjamin Haibe-Kains; Robert Tibshirani (CoRR, 2022)

PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis. - 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; et al. (Nucleic Acids Res., 2022)

Privacy-Preserving Dashboard for F.A.I.R Head and Neck Cancer data supporting multi-centered collaborations. - Varsha Gouthamchand; Ananya Choudhury; Frank Hoebers; Frederik Wesseling; Mattea Welch; Sejin Kim; Benjamin Haibe-Kains; Joanna Kazmierska; Andre Dekker; Johan van Soest; Leonard Wee (SWAT4HCLS, 2023)

Maintaining Stability and Plasticity for Predictive Churn Reduction. - George Adam; Benjamin Haibe-Kains; Anna Goldenberg (CoRR, 2023)

Reusability report: Evaluating reproducibility and reusability of a fine-tuned model to predict drug response in cancer patient samples. - Emily So; Fengqing Yu; Bo Wang 044; Benjamin Haibe-Kains (Nat. Mac. Intell., 2023)

Radiomic-based prediction of lesion-specific systemic treatment response in metastatic disease. - Caryn Geady; Farnoosh Abbas Aghababazadeh; Andres Kohan; Scott Schuetze; David Shultz; Benjamin Haibe-Kains (Comput. Medical Imaging Graph., 2024)

Integrate Any Omics: Towards genome-wide data integration for patient stratification. - Shihao Ma; Andy G. X. Zeng; Benjamin Haibe-Kains; Anna Goldenberg; John E. Dick; Bo Wang 044 (CoRR, 2024)

MorphoDiff: Cellular Morphology Painting with Diffusion Models. - Zeinab Navidi; Jun Ma 016; Esteban Miglietta; Le Liu; Anne E. Carpenter; Beth A. Cimini; Benjamin Haibe-Kains; Bo Wang 044 (ICLR, 2025)

Moving towards genome-wide data integration for patient stratification with Integrate Any Omics. - Shihao Ma; Andy G. X. Zeng; Benjamin Haibe-Kains; Anna Goldenberg; John E. Dick; Bo Wang 044 (Nat. Mac. Intell., 2025)