Benjamin Haibe-Kains

Seyed Ali Madani Tonekaboni, Zhaleh Safikhani, Benjamin Haibe-Kains, 2020, 2020 19th IEEE International Conference on Machine Learning and Applications (ICMLA).

CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

Benjamin Haibe-Kains, Venkata Sk Manem, George Adam, 2017, bioRxiv.

Data-driven validation of gene regulatory networks using knock-down data

Benjamin Haibe-Kains, Gianluca Bontempi, Catharina Olsen, 2013 .

mRMRe: an R package for parallelized mRMR ensemble feature selection

Benjamin Haibe-Kains, Gianluca Bontempi, Catharina Olsen, 2013, Bioinform..

ToxicoGx: R package for analysis of Large Scale Toxicogenomics Datasets

Benjamin Haibe-Kains, Sisira Kadambat Nair, Esther Yoo, 2020 .

Test set bias affects reproducibility of gene signatures

Prasad Patil, Benjamin Haibe-Kains, Jeffrey T. Leek, 2015, Bioinform..

Analysis of Array Data and Clinical Validation of Array-Based Assays

Benjamin Haibe-Kains, John Quackenbush, John Quackenbush, 2012 .

Study of Meta-analysis Strategies for Network Inference Using Information-Theoretic Approaches

Benjamin Haibe-Kains, Gianluca Bontempi, Patrick E. Meyer, 2016, DEXA Workshops.

Reducing Adversarial Example Transferability Using Gradient Regularization pdf

George Adam, Petr Smirnov, Benjamin Haibe-Kains, 2019, ArXiv.

Feature selection methods for mining bioinformatics data

Benjamin Haibe-Kains, Gianluca Bontempi, Gianluca Bontempi, 2005 .

BatchQC: interactive software for evaluating sample and batch effects in genomic data

Benjamin Haibe-Kains, John Quackenbush, Jeffrey T. Leek, 2016, Bioinform..

Multiple-input multiple-output causal strategies for gene selection

Benjamin Haibe-Kains, John Quackenbush, Gianluca Bontempi, 2011, BMC Bioinformatics.

Machine learning approaches to drug response prediction: challenges and recent progress

Benjamin Haibe-Kains, Zhaleh Safikhani, George Adam, 2020, npj Precision Oncology.

CovidCTNet: An Open-Source Deep Learning Approach to Identify Covid-19 Using CT Image pdf

Fatemeh Homayounieh, Mannudeep K. Kalra, Mehdi Hosseinzadeh, 2020, ArXiv.

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response

Søren Brunak, Benjamin Haibe-Kains, Zoltan Szallasi, 2011, BMC Bioinformatics.

The importance of transparency and reproducibility in artificial intelligence research

Trevor Hastie, Joelle Pineau, Robert Tibshirani, 2020, 2003.00898.

A network model for angiogenesis in ovarian cancer

Benjamin Haibe-Kains, John Quackenbush, Guo-Cheng Yuan, 2015, BMC Bioinformatics.

CREAM: new feature selection approach for epigenomic profiles of cells

Seyed Ali Madani Tonekaboni, Benjamin Haibe-Kains, Parisa Mazrooei, 2018, RECOMB 2018.

ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments

Benjamin Haibe-Kains, Mathieu Lupien, Swneke D. Bailey, 2015, Bioinform..

RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface

Aedín C. Culhane, Benjamin Haibe-Kains, John Quackenbush, 2013, Bioinform..

A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?

Benjamin Haibe-Kains, Gianluca Bontempi, Christine Desmedt, 2008, Bioinform..

Stochastic Combinatorial Ensembles for Defending Against Adversarial Examples pdf

Petr Smirnov, Benjamin Haibe-Kains, David Duvenaud, 2018, ArXiv.

Creating reproducible pharmacogenomic analysis pipelines

Zhaleh Safikhani, Petr Smirnov, Benjamin Haibe-Kains, 2019, Scientific Data.

Predictive approaches for drug combination discovery in cancer

Laleh Soltan Ghoraie, Seyed Ali Madani Tonekaboni, Benjamin Haibe-Kains, 2018, Briefings Bioinform..

Microarray Data Generation and Analysis : Class Discovery and Class Prediction from Human Cancer Microarray Datasets

Benjamin Haibe-Kains, Gianluca Bontempi, Christos Sotiriou, 2006 .

Untangling statistical and biological models to understand network inference: the need for a genomics network ontology

Benjamin Haibe-Kains, Matthias Dehmer, Frank Emmert-Streib, 2014, Front. Genet..

Avoiding test set bias with rank-based prediction

Prasad Patil, Benjamin Haibe-Kains, Jeffrey T. Leek, 2014, bioRxiv.

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

Aedín C. Culhane, Benjamin Haibe-Kains, John Quackenbush, 2011, Nucleic Acids Res..

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome

Benjamin Haibe-Kains, Giovanni Parmigiani, Curtis Huttenhower, 2013, Database J. Biol. Databases Curation.

Public data and open source tools for multi-assay genomic investigation of disease

Aedín C. Culhane, David Gomez-Cabrero, Zhaleh Safikhani, 2015, Briefings Bioinform..

Applications of Computational Systems Biology in Cancer Signaling Pathways

Benjamin Haibe-Kains, Arvind Singh Mer, Venkata Satya Kumar Manem, 2019, Unravelling Cancer Signaling Pathways: A Multidisciplinary Approach.

Deep-CR MTLR: a Multi-Modal Approach for Cancer Survival Prediction with Competing Risks pdf

Benjamin Haibe-Kains, Michal Kazmierski, Sejin Kim, 2020, SPACA.

PharmacoGx: an R package for analysis of large pharmacogenomic datasets

Andrew H. Beck, Zhaleh Safikhani, Benjamin Haibe-Kains, 2015, Bioinform..

Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity

Benjamin Haibe-Kains, John Quackenbush, Gianluca Bontempi, 2013, J. Am. Medical Informatics Assoc..

Study of Meta-analysis strategies for network inference using information-theoretic approaches

Benjamin Haibe-Kains, Gianluca Bontempi, Patrick E. Meyer, 2016, 2016 27th International Workshop on Database and Expert Systems Applications (DEXA).

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks

Benjamin Haibe-Kains, John Quackenbush, Gianluca Bontempi, 2011, Nucleic Acids Res..

Dr.VAE: improving drug response prediction via modeling of drug perturbation effects

Benjamin Haibe-Kains, Anna Goldenberg, Petr Smirnov, 2019, Bioinform..

Relevance of different prior knowledge sources for inferring gene interaction networks

Benjamin Haibe-Kains, John Quackenbush, Gianluca Bontempi, 2014, Front. Genet..

Quantitative Assessment and Validation of Network

Benjamin Haibe-Kains, Frank Emmert-Streib, B. Haibe-Kains, 2015 .

Hidden Risks of Machine Learning Applied to Healthcare: Unintended Feedback Loops Between Models and Future Data Causing Model Degradation

Benjamin Haibe-Kains, Anna Goldenberg, George Alexandru Adam, 2020, MLHC.

Functional and genetic analysis of the colon cancer network

Andreas Holzinger, Benjamin Haibe-Kains, Matthias Dehmer, 2014, BMC Bioinformatics.

Software for the integration of multi-omics experiments in Bioconductor

Aedín C. Culhane, David Gomez-Cabrero, Benjamin Haibe-Kains, 2017 .

Machine Learning for Biomarker Discovery in Cancer Pharmacogenomics Data

Benjamin Haibe-Kains, Petr Smirnov, Arvind Singh Mer, 2019, BCB.

On the Integration of Prior Knowledge in the Inference of Regulatory Networks.

Benjamin Haibe-Kains, John Quackenbush, Gianluca Bontempi, 2013 .

predictionet: Inference for predictive networks designed for (but not limited to) genomic data: R/Bioconductor

Benjamin Haibe-Kains, John Quackenbush, Gianluca Bontempi, 2012 .

A review of connectivity map and computational approaches in pharmacogenomics

Laleh Soltan Ghoraie, Benjamin Haibe-Kains, Matthias Dehmer, 2017, Briefings Bioinform..