Benjamin Haibe-Kains

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Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer

Deena M A Gendoo, Robert E Denroche, Amy Zhang, 2017, bioRxiv.

Modeling cellular response in large-scale radiogenomic databases to advance precision radiotherapy

Benjamin Haibe-Kains, Victor Kofia, Mark Freeman, 2018, bioRxiv.

Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy.

Laleh Soltan Ghoraie, Benjamin Haibe-Kains, Gary D Bader, 2017, Cancer research.

Automatic classification of dental artifact status for efficient image veracity checks: effects of image resolution and convolutional neural network depth

Alberto Traverso, Benjamin Haibe-Kains, David A Jaffray, 2020, Physics in medicine and biology.

Safikhani et al. reply

Benjamin Haibe-Kains, Andrew H. Beck, Petr Smirnov, 2016, Nature.

Why imaging data alone is not enough: AI-based integration of imaging, omics, and clinical data

Benjamin Haibe-Kains, Igor Jurisica, Andreas Holzinger, 2019, European Journal of Nuclear Medicine and Molecular Imaging.

CrosstalkNet: A Visualization Tool for Differential Co-expression Networks and Communities.

Benjamin Haibe-Kains, Mathieu Gigoux, Nicholas Bertos, 2018, Cancer research.

AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study.

Benjamin Haibe-Kains, Nehme El-Hachem, Firas H Kobeissy, 2017, Methods in molecular biology.

External validation and transfer learning of convolutional neural networks for computed tomography dental artifact classification

Alberto Traverso, Benjamin Haibe-Kains, David A Jaffray, 2019, Physics in medicine and biology.

Using shRNA experiments to validate gene regulatory networks

Benjamin Haibe-Kains, John Quackenbush, Gianluca Bontempi, 2015, Genomics data.

Inconsistency in large pharmacogenomic studies

Benjamin Haibe-Kains, Andrew H. Beck, Nehme El-Hachem, 2013, Nature.

Software for the integration of multi-omics experiments in Bioconductor

Benjamin Haibe-Kains, David Gomez-Cabrero, Angela Re, 2017, bioRxiv.

The impact of the variation of imaging parameters on the robustness of Computed Tomography radiomic features: A review

Benjamin Haibe-Kains, Reza Reiazi, Tony Tadic, 2021, Comput. Biol. Medicine.

Prediction of Human Papillomavirus (HPV) Association of Oropharyngeal Cancer (OPC) Using Radiomics: The Impact of the Variation of CT Scanner

Benjamin Haibe-Kains, Reza Reiazi, Scott V. Bratman, 2021, Cancers.

Automated detection of dental artifacts for large-scale radiomic analysis in radiation oncology

Benjamin Haibe-Kains, Reza Reiazi, Scott V. Bratman, 2021, Physics and imaging in radiation oncology.

Revisiting inconsistency in large pharmacogenomic studies

Benjamin Haibe-Kains, Andrew H. Beck, Leming Shi, 2015, bioRxiv.

Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials.

Benjamin Haibe-Kains, Zoltan Szallasi, Charles Swanton, 2010, The Lancet. Oncology.

Network-based approach to identify principal isoforms among four cancer types.

Jun Ma, Laleh Soltan Ghoraie, Xin Men, 2019, Molecular omics.

Assessment of pharmacogenomic agreement

Benjamin Haibe-Kains, Leming Shi, Petr Smirnov, 2016, bioRxiv.

Assessment of modelling strategies for drug response prediction in cell lines and xenografts

Benjamin Haibe-Kains, Benedikt Brors, Benjamin Haibe-Kains, 2020, Scientific Reports.

Minimising Immunohistochemical False Negative ER Classification Using a Complementary 23 Gene Expression Signature of ER Status

Benjamin Haibe-Kains, Zoltan Szallasi, Christopher T. Workman, 2010, PloS one.

Angiogenic mRNA and microRNA Gene Expression Signature Predicts a Novel Subtype of Serous Ovarian Cancer

Benjamin Haibe-Kains, John Quackenbush, Renee Rubio, 2012, PloS one.

MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature

Benjamin Haibe-Kains, Levi Waldron, Natchar Ratanasirigulchai, 2016, Scientific Reports.

Enhancing reproducibility in cancer drug screening: how do we move forward?

Robert Clarke, Benjamin Haibe-Kains, Andrew H. Beck, 2014, Cancer research.

Radiomic feature clusters and Prognostic Signatures specific for Lung and Head & Neck cancer

Benjamin Haibe-Kains, Chintan Parmar, Philippe Lambin, 2015, Scientific Reports.

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer

Benjamin Haibe-Kains, Andrew H. Beck, Sindhu Ghanta, 2015, Genome Biology.

An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Benjamin Haibe-Kains, John Quackenbush, Andrew D. Kelly, 2017, Journal of Hematology & Oncology.

DNA methylation profiling reveals a predominant immune component in breast cancers

Benjamin Haibe-Kains, Stefan Michiels, Matthieu Defrance, 2011, EMBO molecular medicine.

Characterization of Conserved Toxicogenomic Responses in Chemically Exposed Hepatocytes across Species and Platforms

Benjamin Haibe-Kains, Nehme El-Hachem, Hugo J.W.L. Aerts, 2015, Environmental health perspectives.

CD4⁺ follicular helper T cell infiltration predicts breast cancer survival.

Benjamin Haibe-Kains, Stefan Michiels, Christine Desmedt, 2013, The Journal of clinical investigation.

A fuzzy gene expression-based computational approach improves breast cancer prognostication

Benjamin Haibe-Kains, Gianluca Bontempi, Christine Desmedt, 2010, Genome Biology.

The molecular basis of breast cancer pathological phenotypes

Benjamin Haibe-Kains, Andrew H. Beck, David A Gutman, 2017, The Journal of pathology.

PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor–positive breast cancer

Paul Ellis, Terence P. Speed, Benjamin Haibe-Kains, 2010, Proceedings of the National Academy of Sciences.

CD 4 + follicular helper T cell infiltration predicts breast cancer survival

Benjamin Haibe-Kains, Stefan Michiels, Christine Desmedt, 2013 .

Radiomic Biomarkers to Refine Risk Models for Distant Metastasis in HPV-related Oropharyngeal Carcinoma.

Benjamin Haibe-Kains, John Cho, Andrea McNiven, 2018, International journal of radiation oncology, biology, physics.