Publications

A complete list of publications by Dr. Haibe-Kains can be reviewed on Google Scholar and PubMed.

 

Publication Highlights:

2017

Nature

Defining the biological basis of radiomic phenotypes in lung cancer.
Grossmann P, Stringfield O, El-Hachem N, Bui MM, Rios Velazquez E, Parmar C, Leijenaar RT, Haibe-Kains B,Lambin P, Gillies R, Aerts HJ.
Elife. 2017 Jul 21;6. pii: e23421. doi: 10.7554/eLife.23421.
PMID: 28731408


Nature

Gene isoforms as expression-based biomarkers predictive of drug response in vitro.
Safikhani Z, Smirnov P, Thu KL, Silvester J, Lupien M, Mak TW, Cescon D, Haibe-Kains B, .
BioRxiv 2017 July. doi: 10.1101/160937.




Nature

Software for the integration of multi-omics experiments in Bioconductor.
Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L. Cancer Res 2017 August.



Nature

Tissue specificity of in vitro drug sensitivity.
Yao F, Tonekaboni SAM, Safikhani Z, Smirnov P, El-Hachem N, Freeman M, Manem VSK, Haibe-Kains B. J Am Med Inform Assoc. 2017 July.




Nature

Consensus on Molecular Subtypes of Ovarian Cancer.
Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L. BioRxiv 2017 July. doi: 10.1101/162685




Nature

Genomic biomarkers for precision radiation medicine.
Bratman SV, Milosevic MF, Liu FF, Haibe-Kains B.
Lancet Oncol. 2017 May;18(5):e238.
PMID: 28495284


Nature

Integrative cancer pharmacogenomics to infer large-scale drug taxonomy.
El-Hachem N, Gendoo DM, Soltan Ghoraie L, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader G, Goldenberg A, Haibe-Kains B.
Cancer Res. 2017 Mar 17. pii: canres.0096.2017. doi: 10.1158/0008-5472.CAN-17-0096.
PMID: 28314784


Nature

Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes.
Uwimana N, Collin P, Jeronimo C, Haibe-Kains B, Robert F.
Nucleic Acids Res. 2017 Apr 5.
PMID: 28383698


Nature

Transcriptome Analysis of Human Reninomas as an Approach to Understanding Juxtaglomerular Cell Biology.
Martini AG, Xa LK, Lacombe MJ,Blanchet-Cohen A, Mercure C, Haibe-Kains B, Friesema EC, van den Meiracker AH, Gross KW, Azizi M, Corvol P, Nguyen G, Reudelhuber TL, Danser AH.
Hypertension. 2017 Apr 10.
PMID: 28396539


bib

A review of connectivity map and computational approaches in pharmacogenomics.
Musa A, Ghoraie LS, Zhang SD, Galzko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F.
Brief Bioinform. 2017 Jan 9. pii: bbw112. doi: 10.1093/bib/bbw112.
PMID: 28069634


2016

Nature

Consistency in large pharmacogenomic studies: reply.
Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J,Haibe-Kains B.
Nature. 2016 Nov 30;540(7631):E2-E4. doi: 10.1038/nature19839.
PMID: 27905430


Nature

Drug response consistency in CCLE and CGP: reply.
Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B.
Nature. 2016 Nov 30;540(7631):E11-E12. doi: 10.1038/nature20581.
PMID: 27905423


Nature

Consistency in drug response profiling: reply.
Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B.
Nature. 2016 Nov 30;540(7631):E6-E8. doi: 10.1038/nature20172.
PMID: 27905416


Bib

Predictive approaches for drug combination discovery in cancer
Madani Tonekaboni SA, Soltan Ghoraie L, Manem VS, Haibe-Kains B.
Brief Bioinform. 2016 Nov 22. pii: bbw104.
PMID: 27881431


BioRxiv

Tissue specificity of in vitro drug sensitivity.
Fupan Yao, Seyed Ali Madani Tonekaboni, Zhaleh Safikhani, Petr Smirnov, Nehme El-Hachem, Mark Freeman, Venkata Satya Kumar Manem, Benjamin Haibe-Kains.
BioRxiv 2016, doi: http://dx.doi.org/10.1101/085357



BioRxiv

Integrative pharmacogenomics to infer large-scale drug taxonomy.
Nehme El-Hachem, Deena M.A. Gendoo, Laleh Soltan Ghoraie, Zhaleh Safikhani, Petr Smirnov, Ruth Isserlin, Gary D. Bader, Anna Goldenberg, Benjamin Haibe-Kains.
BioRxiv 2016, doi: http://dx.doi.org/10.1101/046219



F1000Research

Revisiting inconsistency in large pharmacogenomic studies.
Zhaleh Safikhani, Mark Freeman, Petr Smirnov, Nehme El-Hachem, Adrian She, Rene Quevedo, Anna Goldenberg, Nicolai Juul Birkbak, Leming Shi, Andrew H Beck, Hugo JWL Aerts, John Quackenbush,Benjamin Haibe-Kains.
F1000Research 2016, 5:2333, doi: 10.12688/f1000research.9611.1.



Genome_Biology

DNA replication stress: a source of APOBEC3B expression in breast cancer.
Cescon DW, Haibe-Kains B.
Genome Biol. 2016 Sep 30;17(1):202 10.1186/s13059-016-1069-y.
PMID: 27069505


Genome_Biology

BatchQC: interactive software for evaluating sample and batch effects in genomic data.
Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE.
Bioinformatics. 2016 Aug 18. pii: btw538.
PMID: 27540268


pharmacogenomic

Assessment of pharmacogenomic agreement..
Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B.
F1000Res. 2016 May 9;5:825. doi: 10.12688/f1000research.8705.1.
PMID: 27408686


Biomed_Central

MM2S: personalized diagnosis of medulloblastoma patients and model systems.
Deena DM, Haibe-Kains B.
Source Code Biol Med. 2016 Apr 11;11:6. doi: 10.1186/s13029-016-0053-y. eCollection 2016.
PMID: 27716362


2015

Bioinformatics

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.
Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo DM, Grossmann P, Beck AH, Aerts HJ, Lupien M, Goldenberg A, Haibe-Kains B.
Bioinformatics. 2015 Dec 9. pii: btv723.
PMID: 26656004


Bioinformatics

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.
Gendoo DM, Ratanasirigulchai N, Schröder MS, Paré L, Parker JS, Prat A, Haibe-Kains B.
Bioinformatics. 2015 Nov 24. pii: btv693..
PMID: 26607490


Genomics Data

Using shRNA experiments to validate gene regulatory networks.
Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B.
Genom Data. 2015 Apr 1;4:123-6. doi: 10.1016/j.gdata.2015.03.011.
PMID: 26484195


Brief Bioinformatics

Public data and open source tools for multi-assay genomic investigation of disease.
Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B. Waldron L.
Brief Bioinform. 2015 Oct 12. pii: bbv080.
PMID: 26463000

Scientific Reports

Radiomic feature clusters and prognostic signatures specific for Lung and Head & Neck cancer.
Parmar C, Leijenaar RT, Grossmann P, Rios Velazquez E, Bussink J, Rietveld D, Rietbergen MM, Haibe-Kains B, Lambin P, Aerts HJ.
Sci Rep. 2015 Jun 5;5:11044. doi: 10.1038/srep11044.
PMID: 26251068

EHP

Characterization of Conserved Toxicogenomic Responses in Chemically Exposed Hepatocytes across Species and Platforms.
El-Hachem N, Grossmann P, Blanchet-Cohen A, Bateman AR, Bouchard N, Archambault J, Aerts HJ, Haibe-Kains B.
Environ Health Perspect. 2015 Jul 14.
PMID: 26173225

Bioinformatics

ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.
Bailey SD, Virtanen C, Haibe-Kains B, Lupien M.
Bioinformatics. 2015 Sep 15;31(18):3057-9. doi: 10.1093/bioinformatics/btv321.
PMID: 25995231


Genomics

Personalized diagnosis of medulloblastoma subtypes across patients and model systems.
Gendoo DM, Smirnov P, Lupien M, Haibe-Kains B.
Genomics. 2015 Aug;106(2):96-106. doi: 10.1016/j.ygeno.2015.05.002.
PMID: 25979459


BMC Bioinformatics

A network model for angiogenesis in ovarian cancer.
Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC.
BMC Bioinformatics. 2015 Apr 11;16(1):115.
PMID: 25888305


Bioinformatics

Test set bias affects reproducibility of gene signatures.
Patil P, Bachant-Winner PO, Haibe-Kains B, Leek JT.
Bioinformatics. 2015 Mar 18. pii: btv157.
PMID: 25788628


Nature Communications

CT-based radiomic signature predicts distant metastasis in lung adenocarcinoma.
Coroller TP, Grossmann P, Hou Y, Rios Velazquez E, Leijenaar RT, Hermann G, Lambin P, Haibe-Kains B, Mak RH, Aerts HJ.
Radiother Oncol. 2015 Mar;114(3):345-50. doi: 10.1016/j.radonc.2015.02.015.
PMID: 25746350

Proceedings of the National Academy of Sciences of the United States of America

APOBEC3B expression in breast cancer reflects cellular proliferation while a deletion polymorphism is associated with immune activation.
David W. Cescon, Benjamin Haibe-Kains and Tak W. Mak
Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2841-6. doi: 10.1073/pnas.1424869112,
PMID: 25730878

Nature Communications

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters.
Bailey SD, Zhang X, Desai K, Aid M, Corradin O, Cowper-Sal Lari R, Akhtar-Zaidi B, Scacheri PC, Haibe-Kains B, Lupien M.
Nat Commun. 2015 Feb 3;2:6186.
PMID: 25645053

2014

BMC Genomics

Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology.
Fumagalli D, Blanchet-Cohen A, Brown D, Desmedt C, Gacquer D, Michiels S, Rothé F, Majjaj S, Salgado R, Larsimont D, Ignatiadis M, Maetens M,Piccart M,Detours V, Sotiriou C,Haibe-Kains B.
BMC Genomics. 2014 Nov 21;15(1):1008.
PMID: 25412710

Frontiers in Genetics

Untangling statistical and biological models to understand network inference: the need for a genomics network ontology.
Emmert-Streib F, Dehmer M, Haibe-Kains B
Front Genet. 2014 Aug 29;5:299. doi: 10.3389/fgene.2014.00299. eCollection 2014. Review.
PMID: 25221572

Frontiers in Cell and Developmental Biology

Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks.
Emmert-Streib F, Dehmer M, Haibe-Kains B
Front Cell Dev Biol. 2014 Aug 19;2:38. doi: 10.3389/fcell.2014.00038 eCollection 2014 Review
PMID: 25364745

Cancer Research

Enhancing Reproducibility in Cancer Drug Screening: How Do We Move Forward?
Hatzis C, Bedard PL, Juul-Birkbak N, Beck AH, Aerts HJWL, Stern DF, Shi L, Clarke R, Quackenbush J, Haibe-Kains B
Cancer Res 2014 August 1; 74(15):4016-4023. Epub 2014 July 11. Review.
PMID: 25015668


Frontiers in Genetics

Quantitative assessment and validation of network inference methods in bioinformatics.
Haibe-Kains B, Emmert-Streib F.
Front Genet. 2014 July 26; 5:221. doi: 10.3389/fgene.2014.00221. eCollection 2014.
PMID: 25076966


Frontiers in Genetics

Relevance of different prior knowledge sources for inferring gene interaction networks
Olsen C, Bontempi G, Emmert-Streib F, Quackenbush J, Haibe-Kains B
Front Genet. 2014 June 24; 5:177. doi: 10.3389/fgene.2014.00177.
PMID: 25009552


Nature Communications

Decoding the tumor phenotype by non-invasive imaging using a quantitative radionics approach
Aerts HJ, Velazquez ER, Leijenaar R, Parmar C, Grossmann P, Cavalho S, Bussink J, Monshouwer R, Haibe-Kains B, Rietveld D, Hoebers F, Rietbergen M, Leemans M, Dekker A, Quackenbush J, Gillies R, Lambin P
Nat Commun. 2014 June 3; 5:4006. doi: 10.1038/ncomms5006.
PMID: 24892406

Journal of the National Cancer Institute

Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer
Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G
J Natl Cancer Inst. 2014 Apr 3; 106(5). pii: dju049. doi: 10.1093/jnci/dju049.Review.
PMID: 24700801

Nature Methods

Similarity network fusion for aggregating data types on a genomic scale
Wang B, Mezlini AM, Demir F, Fiume M, Tu Z, Brudno M, Haibe-Kains B, Goldenberg A
Nat Methods. 2014 Mar; 11(3):333-7. doi: 10.1038/nmeth.2810. Epub 2014 Jan 26.
PMID: 24464287


Genomics

Inference and validation of predictive gene networks from biomedical literature and gene expression data
Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Haibe-Kains B, Quackenbush J
Genomics. 2014 Mar 29. pii: S0888-7543(14)00033-0. doi: 10.1016/j.ygeno.2014.03.004.
[Epub ahead of print]
PMID: 24691108

Scientific Reports

Importance of collection in gene set enrichment analysis of drug response in cancer cell lines
Bateman AR, El-Hachem N, Beck AH, Aerts HJ, Haibe-Kains B
Sci Rep. 2014 Feb 13;4:4092. doi: 10.1038/srep04092.
PMID: 24522610

2013

Nature

Inconsistency in large pharmacogenomic studies
Haibe-Kains B, El-Hachem N, Birkbak NJ, Jin AC, Beck AH, Aerts HJ, Quackenbush J
Nature. 2013 Dec 19; 504(7480):389-93. doi: 10.1038/nature12831. Epub 2013 Nov 27.
PMID: 24284626


Bioinformatics

mRMRe: an R package for parallelized mRMR ensemble feature selection
De Jay N, Papillon-Cavanagh S, Olsen C, El-Hachem N, Bontempi G, Haibe-Kains B
Bioinformatics. 2013 Sep 15;29(18):2365-8. doi: 10.1093/bioinformatics/btt383. Epub 2013 Jul 3.
PMID: 23825369


PLOS Computational Biology - www.ploscompbiol.org

Significance analysis of prognostic signatures
Beck AH, Knoblauch NW, Hefti MM, Kaplan J, Schnitt SJ, Culhane AC, Schroeder MS, Risch T, Quackenbush J, Haibe-Kains B
PLoS Comput Biol. 2013; 9(1):e1002875. doi: 10.1371/journal.pcbi.1002875. Epub 2013 Jan 24.
PMID: 23365551

J. Am. Med. Inform. Assoc.

Comparison and validation of genomic predictors for anticancer drug sensitivity
Papillon-Cavanagh S, De Jay N, Hachem N, Olsen C, Bontempi G, Aerts HJ, Quackenbush J, Haibe-Kains B
J Am Med Inform Assoc. 2013 Jul-Aug; 20(4):597-602. doi: 10.1136/amiajnl-2012-001442. Epub 2013 Jan 26.
PMID: 23355484