Author

Benjamin Haibe-Kains

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 3 Cancer Biology· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Assay:bulk RNA-seq· 3 Organism:human· 3 Research Focus:drug response / drug discovery· 2 Research Focus:gene regulatory network inference· 2 Research Focus:benchmarking· 1 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:clustering· 1

Frequent Co-Authors

Anna GoldenbergiD· 3 shared Rene QuevedoiD· 3 shared Zhaleh SafikhaniiD· 3 shared Christos Hatzis· 2 shared Hugo JWL Aerts· 2 shared John Quackenbush· 2 shared Leming Shi· 2 shared Nehme El-Hachem· 2 shared

Activity by Year

2015-2018 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Anna GoldenbergORCID

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Author profile →

5 papers

Recent·Most cited

Genome analysis and data sharing informs timing of molecular events in pancreatic neuroendocrine tumour

Rene Quevedo, Anna Spreafico, Jeff Bruce, Arnavaz Danesh, Amanda Giesler, Youstina Hanna, Cherry Have, Tiantian Li, S.Y. Cindy Yang, Tong Zhang, Sylvia L. Asa, Benjamin Haibe-Kains, Suzanne Kamel-Reid, Monika Krzyzanowska, Adam Smith, , Trevor J. Pugh

The paper analyzes genomic data from pancreatic neuroendocrine tumors to identify a widespread copy neutral loss-of-heterozygosity pattern linked to tumor progression and potential therapeutic targets.

bioRxiv · Jan 23, 2018 · PreprintCancer Biology

Revisiting inconsistency in large pharmacogenomic studies

Zhaleh Safikhani, Mark Freeman, Petr Smirnov, Nehme El-Hachem, Adrian She, Rene Quevedo, Anna Goldenberg, Nicolai Juul Birkbak, Christos Hatzis, Leming Shi, Andrew H Beck, Hugo JWL Aerts, John Quackenbush, Benjamin Haibe-Kains

This paper reanalyzes pharmacogenomic data from GDSC and CCLE, finding continued inconsistency in drug sensitivity measures despite improved statistical methods and expanded datasets.

F1000Research · Aug 11, 2017Peer-reviewedBioinformatics

Assessment of pharmacogenomic agreement

Zhaleh Safikhani, Nehme El-Hachem, Rene Quevedo, Petr Smirnov, Anna Goldenberg, Nicolai Juul Birkbak, Christopher E Mason, Christos Hatzis, Leming Shi, Hugo JWL Aerts, John Quackenbush, Benjamin Haibe-Kains

The paper reanalyzes pharmacogenomic data from GDSC and CCLE, finding continued inconsistency in drug response measures despite claims of agreement.

F1000Research · May 9, 2016Peer-reviewedBioinformatics

Using Cell line and Patient samples to improve Drug Response Prediction

Cheng Zhao, Ying Li, Zhaleh Safikhani, Benjamin Haibe-Kains, Anna Goldenberg

The paper compares drug response prediction models using cell lines, patients, and integrated data, finding that integrative models outperform cell line-only models and require fewer patients.

bioRxiv · Sep 15, 2015 · PreprintBioinformatics

Avoiding test set bias with rank-based prediction

Prasad Patil, Peirre-Olivier Bachant-Winner, Benjamin Haibe-Kains, Jeffrey T Leek

The paper introduces a rank-based prediction framework to avoid test set bias by eliminating the need for cross-sample normalization, demonstrating its effectiveness with a breast cancer gene signature.

Bioinformatics · Mar 18, 2015Peer-reviewedGenomics